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1. Figure 7 4 3 3 The Edge size slider 7 5 Arrow Head Options Similar to nodes and edges arrowheads also have the ability to be coloured Osprey only allows for User Defined colouring of Arrow Heads and as such provides no additional annotation data to the Arrows themselves Users can manipulate the colour of the arrowheads in order to manipulate the current network Note Each of these options will continue to apply to all new edges with arrowheads that get added to the screen after the option has changed Osprey 7 21 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization 7 5 1 User Defined Arrow Head Colour There are two ways to manipulate the user defined arrowhead colours It can be done in one of the following ways e Toolbar Arrow Head Colour Button O O Select all the edges whose arrow head colours you want changed Click on the arrow head colour selection button on the Toolbar as shown in figure 7 5 1 1 From the resulting colour choosing window you can now choose the colour to reflect on the User Defined arrowheads For more information on the colour choosing window see section 7 3 3 Colour Choosing Window User defined arrowhead colours will immediately be reflected in the selected edges in the Network Display Area Format Filters Layout Help i Modes d F m rai Edges Brows Colour Text p
2. New Ctri h Oper I Ctri 5 Save Os Save Colour Index P Save Sektings I 8 Print Ctrl P SUperin pose b Export work Offline Exit Osprey Figure 3 2 1 Save To save a file under another name e Click on the File Menu bar e Click on Save As e Type an appropriate name for the file and click the Save button BE dOsprey Untitled File Never File Edit View Insert Format 4 Mew Ctrl fon Open Save Colour Index Save Settings 28 Print SUPerimpose Export Work OFfline Exit Osprey Osprey 3 15 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 3 Opening and Saving Files Figure 3 2 2 Save As 3 3 Exporting Osprey offers the option of exporting osprey networks to image files This feature allows users to manipulate the images and use them in presentations and publications 3 3 1 Image Types Osprey networks can be exported as images There are currently three formats that Osprey can export to 1 JPEG for details see section 3 3 1 1 JPEG 2 PNG for details see section 3 3 1 2 PNG 3 SVG for details see section 3 3 1 3 SVG 3 3 1 1 JPEG JPEG Joint Photographic Experts Group is an ISO IEC group of experts that develops and maintains standards for a suite of compression algorithms for computer image files http searchwebservices techtarget com sDefinition 0 sid26_gc1212425 00 html PNG pronounced ping as in ping
3. ccc cece cece ETARA 3 4 3 1 2 4 Custom File Variation 4 ccc ccc cece cece eee e eee eeeeneees 3 5 5 ie Us e E ee re reer ee ee EN rec eno ee Pee ee 3 7 9 lor Gene LISV arialon 7 leeres roari nEn EEE ENTS 3 7 Sol 3 2 Gene List V anato 72 ere ertr r E EE 3 8 Se Openin DatasclS taaa A A A aa 3 9 3 1 4 1 Downloading new datasets 0 cece cece cece cece eeeneee e 3 10 3 14 2 Adding personak datasets score vc ae EE EEI A 3 12 3 1 5 SUPCTIMPOSING Dalasels 5c ccs acute nadie sleasidiedametabeeidneeates 3 13 3 2 Saving to Osprey Files OSp ccc cece cc cceeeeennsneeeeeeeeeeeues 3 14 S EPO a Cone Se tT er eee ee a 3 16 Sek MACS Typos vwice cco scacsianetaudevacudooriwiwseieesseasnwsedeuaaeanwsentan 3 16 Bey Naa eel Taa A E oesect eters seis A E ES 3 16 T N ener er ea er 3 16 3 3 1 3 SVG Scalable Vector Graphics 00 ccc ccc eee e eee eee eee 3 17 Fo MI IIG saro stele a E tyra wtae A A oad Canale AA 3 17 Roo HOWO EXPO eener E diet cautaaateetaivatsncetemasebinaus 3 17 A Basic IN rOGUCHON cccciscsercectecensheaesecocawcteniesigctnabearacesetadetsupctentes 4 1 Aa TOSWLEY Lay OW eero Start sin ace navieoedanesn Se tantsan ace nevieoedandas 4 A gt OSDICV INI COUS 3535s saeaeasemaa E E 4 2 a cl ahs a e eR EEE ane ee 4 3 A Dic De MAIN NCTA iere a a ea ash acest lc T 4 7 BO dee NEN 5 01 En eT Oe ee ee oe eT Oe ee 4 9 B23 MeMo eeri sawn engine a EE EEEE cian ou ad EE Enae 4 14 AS TOn MON r
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5. Figure 4 2 3 5 The Drawing Options Submenu e Dragging Options An Osprey network is in dragging mode whenever a single node or a group of nodes are being dragged about the network display area There are four options under this menu o Nodes By clicking this option you can specify whether or nodes are displayed while in dragging mode o Edges By clicking this option you can specify whether or edges are displayed while in dragging mode o Labels By clicking this option you can specify whether or labels are displayed while in dragging mode o Always By clicking this option you can specify whether the above three options are drawn for all nodes or for only the ones currently being dragged View Insert Format Filters Layout L Colour Indexes Toolbars d Drawing Options d Dragging Options fv Nodes _ Network Statisies F7 Edges Selected Mode Report I Labels View All Comments p always Figure 4 2 3 6 The Dragging Options Submenu e Network Statistics This option will show several statistics about the currently displayed network Osprey 4 12 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 F g Statistics xj Total of vertices fio49 of Visible vertices jio4g Total of Edges 1395 of Visible Edges fi395 Average Edgesi Mode 1 32 Figure 4 2 3 7 Network Statistics selected nodes Rag all Selected Genes Regula
6. KE dOsprey Untitled File Never Been Saved File Edit View Insert Format Filters Layout Debs apa de Gene Info Get Mew Interactions Screen Name BBP change Add Comment Description Trevobved in rdtotie cell cycle and melosis Go Component spindle pole body Go Process ruocrotubule rucleation Figure 4 5 1 1 Orf Info Area The gene info area is used to display additional information about a selected orf in the Network Display Area In addition to this it also provides a button that allows for the incorporation of new interactions into the already established graph To get this process started simply highlight a node on the graph and click the GET NEW INTERACTIONS button on the Gene Info Area When this button is clicked a window with a listing of new interactions is launched Osprey 4 46 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction E Published Interactions for PL255W HLOOQE LR MLOG4_ MLOG2C Add Selected Interactions Add All Interactions Figure 4 5 1 2 An example listing of additional interactions for a selected orf in a network This listing of interactions has several key areas crucial to deciding which interactions you want to add to the existing network e A ORF This field shows the orf name of any other orfs interacting with the selected node e B Gene This field shows some of
7. GO Process Bar ed Turn Off Filters Connection Filters hinir arri H 4 ofl 38 43 Loner Nodes YES Draw V Nodes V Edges V Labels V Arrow C Source D GO Process PA Figure 5 1 1 4 Network in Colour by Source mode In this section we ll take you through an example of the features available to you when filtering a network by source Since all three of the network filters work in a similar fashion this should give you a brief overview of how all the network filters work After selecting the filter by source option in Osprey you will be confronted with a window similar to figure 5 1 2 1 1 that has the following features e The top list box titled Existing Sources contains the main list of all the sources that are currently connecting nodes e The bottom list box titled Visible Sources is a list of all nodes that are allowed to be shown on the screen by this filter Osprey Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters e By default all experimental Systems are in the Visible list Egrilter by Source o x r Figure 5 1 2 1 1 Filter by source window e To filter out one or more items click on an item in the Visible list to highlight it Osprey 5 6 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters 10 x Existing Sources Add Add All Group Selected Remove Remove All V
8. Layout Help i Auto Relaxation P SansSerif h Circular b Dual Ring b Spokes b Global 2 38 2 Spoked Dual Ring Spoked Dual Ring Options Figure 4 2 7 6 The Global Submenu 4 2 8 Help Menu Help Help Manual Ctrl H Check For Updates About Figure 4 2 8 1 The Osprey Help Menu e Help Manual This option calls the help manual that you are currently reading e Check for Updates This option goes to the osprey web site and checks to see if the version of Osprey you are using is the latest one or not e About Use this option to view information about Osprey including Osprey developers and version information Osprey 4 21 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction RID Untitled File Never Been Saved mak Filters Database Layout Help fioo Change Database O east GRID C Mouse GRID Fly GRID Human GRID Worn GRID C S Pombe GRID Rat GRID Zebra Fish GRID Figure 4 2 9 1 The Osprey Database Menu e Change Database This option allows you to change the database Osprey is connected too see section 7 10 Changing Databases for details Osprey 4 22 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction In this section we will examine a simple Osprey network and some of the options that accompany them Eg Osprey U
9. 1 1 1 Conventions used in this manual This manual uses the following Typographical Conventions Links Represents Links either to external pages or to other pages inside this reference manual HEADINGS Denotes the start of a new section or subsection in this manual Osprey 1 2 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 1 General Information 1 2 What is Osprey Osprey is a tool for graphically representing biological interactions It can be used in one of two ways 1 Asa freely distributed standalone version available at http biodata mshri on ca osprey 2 Asan add on interaction visualization system for use with online interaction databases see section 1 5 Osprey Licensing for more details For all of the latest information concerning Osprey please visit the Osprey web page at http biodata mshri on ca osprey 1 2 1 The Main Features of Osprey The following list describes some of the important characteristics of the Osprey Network Visualization System e Portability cross platform availability o Osprey is available on almost all Platforms that support the latest Java Plugin e Tools for Biological Analysis o Osprey provides many features such as network filters connectivity filters advanced layouts and dataset superimposing which are extremely useful to biologists who are interested in analyzing their data e Powerful Support Database o Integrated with Osprey is a power
10. File Edit view Insert Format Filters Layout Help New Ctri h Open b Ey Save Ctrl 5 Save As Save Colour Index b Save Settings Adyvanced Settings Eh Print Ctrl P Colour Settings Superimpose I Export work Offline Exit Osprey Figure 7 8 1 1 1 The advanced settings save option 7 8 1 2 Saving Colour Settings Colour settings are all the colour index settings in the Go Process index Experimental Colour index and Source index as discussed in section 7 3 2 User Defined Node Colours and section 7 4 2 User Defined Edge Colours These are the colour specific settings for exactly how to colour each and every annotation that is displayed on an edge or a node in Osprey Follow these steps to save the colour settings Osprey 7 35 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization e Click on the File from the menu bar e Click on the Save Settings submenu e Click on save Colour Settings Note By changing colour settings you will affect only the colours on the network when colouring the graph by user defined colours mode see section 7 1 Graph Colouring When colouring by default or by Osprey File Colours these colour settings will not apply E Osprey Untitled File Never Been Saved File Edit view Insert Format Filters Layout Help Cy New Ctrl loa gt C st h Open I Ey Save Ctrl 5 Save os Save Colour Index b Save Se
11. Turn Off Fitters Connection Filters Minirurn iterative Minirnurm Depth Turn Off Connectivity Figure 6 5 1 1 Network demonstrating the Spoked Dual Ring layout Osprey 6 21 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts 6 5 1 1 Accessing Spoked Dual Ring Layout There are currently two ways in which the user can access Spoked Dual Ring Layout Option 1 The Layout option in the Menu Bar o Click on the Layout overhead menu o Click on the Global submenu o Click on Spoked Dual Ring Layout Help i Auto Relaxation P SansSerif h2 i Circular b Dual Ring Spokes b Global Figure 6 5 1 1 1 Accessing the spoked dual ring via the main menu 2 Right Click Menu o Right click in an empty area of the graph o Click on Spoked Dual Ring Osprey 6 22 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts AVE Insert All Interactions for Selected i Insert Only Interactions within Selected x a Se aT z Frida nie p 5 Bey E Fy mi One Girdle Layout Concentric Gircdes Layout Greate Default spokes d Greate Forced Spokes ME oked Dual Ring Layout S Lock Wodes aa Unlock Modes eS Remove Nodes e Remove Edges 1 i Figure 6 5 1 1 2 Accessing the spoked dual ring via the right click menu 6 5 2 Spoked Dual Ring Options Using the Spoked Dual
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13. 4 2 3 View Menu The View Menu provides a variety of options for changing the look and feel of the currently displayed graph The following is a listing of each of the options available in the view menu with a brief description of what service the option provides View Insert Format Filters i Colour Indexes a Toolbars Loner Modes Drawing Options b Dragging Options d Network Statistics Selected Node Report View All Comments Figure 4 2 3 1 The Osprey View Menu e Colour Indexes The Colour indexes submenu contains options for viewing each of the colour sets used for annotation on nodes and edges in Osprey There are three options under this menu Osprey 4 9 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction o Experimental Systems Choosing this colour index will show a listing of colours used to describe experimental system annotation on edges It also provides the ability to manipulate these colours o Sources Choosing this colour index will show a listing of colours used to describe source annotation on edges It also provides the ability to manipulate these colours o GO Process Choosing this colour index will show a listing of colours used to describe GO Process annotation on nodes It also provides the ability to manipulate these colours View Insert Format Filters Layout Help i Colour Indexes Experimental Systems Toolbar
14. s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization Mode Colour x fH 239 4 cs BO eB f 1004 Be R 102 Gj 102 By 255 m E Sample Text Sample Text i E Sample Text Sample Text Figure 7 3 3 2 1 The Osprey HSB Tab of the Colour Chooser RGB red green and blue refers to a system for representing the colors to be used on a computer display Red green and blue can be combined in various proportions to obtain any color in the visible spectrum Levels of R G and B can each range from 0 to 100 percent of full intensity Each level is represented by the range of decimal numbers from 0 to 255 256 levels for each color http whatis techtarget com definition 0 sid9_gc1212900 00 html The RGB tab of the Colour chooser allows for greater flexibility when selecting the perfect colour for displaying in Osprey Osprey 7 13 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization x Red er ar O 170 259 Green a a a n om GA E E J 10 74 T 1 0 255 Blue pourrtyourerypuedest 755 T oo 1 70 2595 B E Sample Text Sample Text i C Sample Text Sample Text Figure 7 3 3 2 1 The Osprey RGB Tab of the Colour Chooser In addition to changing colours of nodes Osprey also provides the ability to manipulate the physical size of nodes on the
15. About Osprey REGISTRATION Thank You For Registering An Email has been sent to the address that you provided Once you recieve the email click below to download Osprey DOWNLOAD OSPREY Contact Us Osprey Community Terms and Conditions Copyright 2002 2003 Mount Sinai Hospital All Rights Reserved D G OY EJ amp Done Figure 2 1 2 4 The resulting page after a successful registration Once you have registered and you have received an email from Osprey containing your account name and password you are now ready to download Osprey If for some reason you have successfully registered but did not receive an email containing you password please contact us see section 1 4 Contact Information Before downloading you must first login to the downloads area using your newly acquired Osprey password Osprey 2 7 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation E Osprey Network isualization System Download Login Mozilla Rate ie at Oj x File Edit View Go Bookmarks Tools Window Help Search Support Forums http biodata mshri on cafosprey servlet Login product 2 amp 5ubmit DOWNLOAD OSPREY Downloads Screenshots Documentation Partners Tutorials Support Forums About Osprey DOWNLOAD OSPREY Although Osprey is available without a purchased license to academics and not for profit organizations we
16. Advanced Settings o Look for the Spoke Settings tab and click it Format Filters Layout Help Modes Edges b APRONS p Text d Background Colour Advanced Settings Figure 6 4 3 1 2 Accessing the spokes options via the main menus advanced settings under the Format menu Osprey 6 20 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts By global we mean that these layouts will be applied to all visible unfiltered nodes These layouts will ignore any locks that are currently on nodes and it does not matter what nodes are currently selected these algorithms are applied to all nodes The current graph size will also be adjusted to best fit the nodes This function places the most highly connected spokes customizable minimum in the inner spoked ring It places the less highly connected spokes customizable minimum in the outer spoked ring and it relaxes all nodes that are shared between two or more nodes to the center of mass position where all shared spoke centers are an equal distance away see figure 6 5 1 1 There are two ways to call this function see section 6 5 1 1 Accessing Spoked Dual Ring Layout for details Eg Osprey C Documents and Settings hosam My Documents showSpokes osp modified File Edit View Insert Format Filters Layout Help De SQ Q fox Ol ab omc AmE wz 8 fors P aah aA Gene Edge Info Select a single vertex edge LN e Lt bayt
17. Background Colour Advanced Settings Figure 4 2 5 4 The Arrows Submenu e Text The edges submenu has options that affect labels specifically colour font and visibility o Colour This options provides the ability to change the selected labels colour o Font This options provides the ability to change the selected labels font size and style Show When this is clicked it makes selected labels visible Hide When this is clicked it makes selected labels not visible Format Filters Layout Help i Nodes pot g Edges b rrowS b Text Colour Background Colour Font j Advanced Settings Show Hide Figure 4 2 5 5 The Text Submenu e Background Colour This provides the ability to change the graph s background colour e Advanced Settings This has all other options and settings that were not mentioned above such as layout settings and colouring modes Osprey 4 16 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction 4 2 6 Filters Menu The filters menu has the same functionality as the buttons in the bottom left hand corner window It offers access to the Network filters which filter the graph depending on network features such as Source or Experimental System and Connection filters which filter the graph depending on number of connections each node has Filters Layout Help 7 Network Filters 7 Connection Filters P Figure 4 2 6 1 The
18. Figure 2 3 7 Osprey Network Visualization System User Agreement 8 On the next screen you will be asked about the installation folder for Osprey By default Osprey uses home Osprey as an installation directory If you would like to install in a different directory select the new directory from this page If you are happy with the default installation folder click NEXT to continue Osprey 2 27 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation Yaa Choose Install Folder Where Would You Like to Install fhome stark osprey 1 0 0 Restore Default Folder Choose Pre nstallavidin Sanary maj __ Installi Figure 2 3 8 The Osprey Installation Choose Install Folder page 9 On the following screen you will be presented with several options for installing Osprey shortcuts By defaults Osprey will install shortcuts into your home folder for you to access If you would rather have the shortcuts installed elsewhere such as usr bin you can customize these options to suit your preferences When you have made your shortcut choice click NEXT to continue Osprey 2 28 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Ej introduction a Choose Install Fo nee setae ery hs ears Bilis Osprey Installation Choose Link Folder Where would you like to create links In your home folder Do
19. MODIFIED VERSIONS OR UPDATES COLLECTIVELY Previous Cancel Figure 2 2 4 Osprey Network Visualization System User Agreement 4 On the next screen you will be asked about the installation folder for Osprey By default Osprey uses C Program Files osprey_1 0 0 as an installation directory If you would like to install in a different directory select the new folder from this page If you are happy with the default installation folder click NEXT to continue Osprey 2 17 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation wI Osprey 1 0 0 Choose Install Folder EJ Introduction a Y Important Information a D Choose Install Folder oe O Chagee Shartni Poder i Bresnetal ation suri Where Would You Like to Install Frosa Files osprey 1 0 0 Restore Default Folder Choose Cancel Previous Figure 2 2 5 The Osprey Installation Choose Install Folder page 5 On the following screen you will be presented with several options for installing Osprey shortcuts By defaults Osprey will install shortcuts into the start menu program group for you to access If you would rather have the shortcuts installed elsewhere you can customize these options to suit your preferences When you have made your shortcut choice click NEXT to continue Osprey 2 18 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Ch
20. Mus musculus 4 Fly Drosophila melanogaster 5 S Pombe Schizosaccharomyces pombe 6 Worm C Elegans 7 Rat Rattus norvegicus 8 Zebra Fish Danio rerio All of the above databases are maintained by the GRID which receives their information from several different sources including SGD NCBI and Locus Link Osprey 7 37 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization Note This option allows the more ambitious Osprey user to create a MySQL database to maintain a private version of interaction data For more information on this option please contact the Osprey administrators for more details ospreyadmin mshri on ca There are currently 3 ways in which you can change the database in which Osprey will connect to for interaction and annotaion information 1 On Start up New to version 1 2 0 is the ability to change the database during the inialization stage of Osprey If it is the first time that you have run Osprey you ll be promted with the screen shown in figure 7 10 1 Here you ll have the ability to set the following a Select the database you would like Osprey to connect to b Make the selection the default database in the future c Decide whether or not you want this screen to show up the next time you load Osprey KE dDatabase Connection Settings E x select which database you would like to be connected with Mou
21. Uninstall osprey Figure 2 7 3 2 Unistall osprey program located in the UnistallerData folder 2 8 Version Checking Osprey offers a version checking feature that goes to the osprey web site and finds out whether or not you are currently running the most recent version of Osprey For best results it is a good idea to do this check periodically and download the most up to date version of Osprey as we will constantly be implementing new features that you will want to take advantage of For more information on Osprey patches and updates see appendix C Future Updates and Obtaining Patches There are two major ways to check your version of Osprey e Via the Version Checking Option in the Menu bar o Click on the Help Menu in the Menu bar o Goto Check for Updates see figure 2 8 1 o The resulting dialog will update you about the version you are running see figure 2 8 2 Osprey 2 48 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada hair Chapter 2 Osprey Installation Help Help Manual Ctri H Check For Updates Figure 2 8 1 The Check for Updates option in the Help Menu This Yersion of Osprey is Up to Date lt i Osprey has detected that your version is up to date Your version 0 9 5 Latest version 0 9 5 There is no reason For you to upgrade ak this tine Please be sure to run this Feature often as new versions are constantly available Figure 2 8 2 An example r
22. tis strongly recommended that you quit all programs before continuing with this installation You may cancel this installation at any time by clicking the Tancel O button Cancel Previous Figure 2 2 3 Osprey installation introduction Osprey 2 16 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation 3 Next you will be presented with the Osprey Network Visualization System User Agreement Please read this carefully By clicking NEXT you will agree to these terms and conditions If you do not agree to the terms and conditions simply click CANCEL at any time to abort the Osprey installation If you agree click the NEXT button to continue 2 Osprey 1 0 0 Important Information Introduction a Important Information gt Choose liete Folder l Grocse Shortent Puer Srresnetallation SUT aly PR installing Please Read Before Continuing Copyright Notice Copyright 2002 Mount inai Hospital Toronto Canada All Rights Reserved Warning This system bay be monitored by system or Security personnel License Agreement for the Usprey Network Visualization System and all documentation THIS AGREEMENT SETS OUT THE TERMS AND CONDITIONS FOR DOWNLOADING COPYING INSTALLING OR USING OSPREY NETWORK VISUALIZATION SYSTEM SOFTWARE AND ASSOCTATED MATERIAL AND DOCUMENTATION INCLUDING ANY
23. you encounter an error and wish to apprise the Osprey team of the problem please send Osprey Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Appendix A Known Problems and Common Errors us this log file For more information see section A 3 Reporting Errors to the Osprey Team A 3 Reporting Errors to the Osprey Team If you encounter an error we would like to know about it Writing a good bug report takes patience but doing it right the first time saves time for us and for you A good bug report containing a step by step procedure for duplicating the bug will make it very likely that we will fix it in the next release This section will help you write your report correctly so that you don t waste your time doing things that may not help us much or at all We encourage everyone who encounters an error be it small or large to report the bug to us as soon as possible All bug reports should contain the following key pieces of information to help us best isolate the cause of the problem e the time and date that the bug occurred e astep by step procedure for duplicating the error 1 e do this then this then that and the program will crash e acopy of the error log see section A 2 The Osprey Error Log Note The normal place to report bugs and problems is ospreyadmin mshri on ca If you are not running the latest copy of Osprey we highly recommend upgrading to the latest version and trying the problem
24. 1 Osprey File 2 Custom Gene Network for details see section 3 1 2 Custom File 3 Gene List for details see section 3 1 3 Gene List 3 1 1 Osprey File The Osprey file format is a tab delimited text file that contains all the necessary information to reinitialize a saved network The text file is saved with a osp extension to set it apart from all the other text files Any manipulation of this file will cause serious problems with your network and could ultimately result in an unrecoverable file So it is in your best interest to leave this file alone and manipulate your graph only through the Osprey program 3 1 2 Custom File The Custom file format is a tab delimited text file that allows the user to load personal interaction data Osprey recognizes both txt extensions as well as ocg Osprey Custom Graph file extensions With this format the user can quickly import their data into Osprey and use the interactions available from any of the other three file formats available to Osprey as well as the published interactions found in The GRID Osprey can currently recognize four different variations of custom files Direction is implicitly defined to go from GeneA to GeneB Osprey represents the direction by placing an arrow at one end of the edge to represent the direction A double headed arrow indicates the interaction was shown both ways For example in Figure 3 2 3 1 1 row 2 shows CDC28 interacting with CLN1 and row 7 shows
25. 1 contains the headers GeneA GeneB GeneA Screen Name GeneB Screen Name Experimental System Source and PubMed Osprey 3 5 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 3 Opening and Saving Files ID of the seven columns that must exist in this variation of a custom interaction file This variation of the custom interaction file contains all the previous variations of the custom interaction files See sections 3 1 2 2 Custom File Variation 2 and 3 1 2 3 Custom File Variation 3 for information of the different variations of the custom interaction files Figure 3 1 2 4 2 demonstrates what the network would look like after opening it up in Osprey Note The rows and columns in red are necessary The rows and columns in gray are optional You can choose to only change the grey rows that need changing GeneA Screen GeneB Screen Experimental Gene GeneB DETG DETG System Source PubMed ID YMR199W Ga Ga Ga CLN1 11805826 CLN CLN2 11805826 CDC7 11805826 CLNI CDC53 11805826 MET10 11805826 Figure 3 1 2 4 1 Custom File Variation 4 CDCS3 CLN1 CLN2 _ gt 5 Figure 3 1 2 4 2 Result of loading custom file variation 4 into Osprey Osprey 3 6 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 3 Opening and Saving Files 3 1 3 Gene List The Gene List format is a tab delimited text file that allows the user to load lists of
26. 2 7 4 The Dual Ring Submenu e Spokes This submenu gives the user two methods of bringing all the nodes connected to a selected nodes into a spoke layout o Default This option makes sure that the spoke does not disturb the current look of the graph it only brings in nodes that are not currently in the center of a spoke layout or in between two or more spoke layouts o Forced This forces all nodes that are connected to the selected nodes to come in to the spoke layout o Spoke Options This offers the user a way of adjusting how many nodes go into each ring and how large each ring of the spoke layout is Layout Help Auto Relaxation SansSerif Circular Dual Ring Spokes Default Global Forced Spoke Options Figure 4 2 7 5 The Spokes Submenu e Global This submenu has algorithms that act on the entire graph disregarding whether or not nodes are selected or locked o Spoked Dual Ring This is a global layout that attempts to place a large number of nodes into two rings of spokes layouts with the most highly concentrated spokes on the inside ring and the least concentrated spokes layouts in the outer ring o Spoked Dual Ring Options This option allows the user to adjust the parameters that the spoked dual ring layout uses to determine which hubs go in which ring and how large every hub is Osprey 4 20 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction
27. 21 O52 SpOked DUR eccone AEN TEN RR EAE 6 21 6 5 1 1 Accessing Spoked Dual Ring Layout cee 6 22 6 5 2 Spoked Dual Ring Options ssssssisiseressdesorivisirisarericiresidassr 6 23 6 5 2 1 Accessing Spoked Dual Ring Layout Option settings 6 25 6 0 FumcnonaliC sterni ea bee mea datete a G 6 26 6 6 1 Accessing Functional Clustering options cccee eee e wees 6 27 00 2 iGO Process Order ianitih cv gericiaraew A aes 6 27 OOS CUr GID OZE e ne ee eee 6 31 6 6 4 Turning Functional Clustering On Off 00 ccc cece eeee 6 33 6 6 5 Degree of GO Process COlOUIING sacsciusnccneend arenes eee es 6 34 7 Osprey Preferences and CustoOmization ccccccccccccccccccccccccccseess 7 1 Tol SAP MC oloun arr a tin tthe E deena Duncan ee areas ae 7 1 LEL Accessing Graph Colouring cece cece cece cece E 7 2 7 2 Drawing Dragging Graph Options 00 c cece cece cece cece eeeeeeneeees 7 3 7 2 1 Accessing Drawing Dragging graph options cca ee 7 4 Ty Node OPONS errean eA N EATE EAA 7 7 7 3 1 Choosing Method of Colouring Nodes ccc cece cece eens 7 7 T2 User Detined Node Colour sectas aea 7 9 Osprey iV Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Table of Contents 7 3 0 Colour Choosing W ImdOw 4scvscenedeas seer ees e veered eee 7 11 FDS OW DE TAD aie ocacee sai aie utan tsi teteaad EA 7 11 Tis CAO agi
28. 3 Opening and Saving Files 4 My Pictures hy Webs Desktop pr My Documents 1 File nare O Save M My Metyvork TileE of type Matrix bt Cancel Matrix tt _ JPEG Graphic jpg ped Portable Metwork Graphic C prg 1 Scalable Vector Graphic t svq Figure 3 3 3 2 Save File dialog demonstrating the four different file formats available for exporting images Osprey 3 19 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada 4 Basic Introduction This section provides an introduction to Osprey showing the overall layout of the application as well as how to do many simple tasks This section assumes that you already have Osprey installed on your computer and it is available for you to use If this is not the case please refer to section 2 Osprey Installation This section also assumes that you are able to launch the Osprey Network Visualization System and that you are familiar with procedures for opening Osprey files If you are unfamiliar with these procedures please see section 3 Opening and Saving Files 4 1 Osprey Layout The following 1s a description of the major sections comprising the Osprey layout e A ToolBar The toolbar places the most commonly used options in osprey at the users fingertips Options such as saving zooming and changing item colour and size are all available via the toolbar e B Gene Edge Info This area of the layout d
29. After 30 Days you will need to purchase an Osprey license http biodata mshri on ca osprey servlet CommercialRegistration to continue using Osprey All academic users are free to download our fully functioning and free Osprey academic version for all major platforms Osprey 2 3 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation E Osprey Network Yisualization System Downloads Microsoft Internet Explorer File J Back fx fat A Search G Favorites EMedia ca Ehr T a Address E bttp biodata mshri on ca osprey servlet Downloads z P E Google Search Web Q Search Site D Gy PageRank p Ezra blocked fe Autor il Woptions fey gt al Edit View Favorites Tools Help ee aay Osprey Search Support Forums Downloads Screenshots Documentation Partners Tutorials Support Forums Commercial Applications About Osprey DOWNLOADS The software from Osprey that you can download from the pages listed below comes In two different varieties The academic version is a fully functioning version of Osprey and is intended for use by non profit academic organizations The 30 Day trial version is intended for use by For Profit commercial organizations and is fully functional for 30 days as a test period before purchasing an Osprey license Both are provided as is and is are without any warranty You need to purchas
30. Area Command Menu LPL Zo Insert All Interactions For Selected Insert Only Interactions within Selected i One Circle Layout Concentric Circles Layout Create Default Spokes Create Forced Spokes Spoked Dual Ring Layout Lock Modes Unlock Modes Remove Nodes Remove Edges Figure 4 3 3 1 Image of all the possible options on the Network Display Area Command Menu The Network Display Area Command Menu can be launched by right clicking anywhere in the Network Display Area Depending on whether nodes or edges have been selected the options available on the command menu may vary Each of these options is outlined as follows e Insert All Interactions for Selected This option will query The GRID and bring in all nodes that have an edge with currently selected Nodes e Insert Only Interactions within Selected This option will query The GRID and bring in all edges that can currently go between selected nodes e One Circle Layout This will place all selected nodes into a circle e Concentric Circle Layout This will place all selected nodes into concentric circles e Create Default Spoke This option will bring all nodes that are connected to currently selected nodes into spoke layouts without disturbing the graph it will leave nodes that are in the center of other spokes layouts and spokes that are shared between two or more spoke layouts untouched Osprey 4 35 Operator s Manual Copyright 2002 Mount
31. CRID oerien ieee re EEE EEO EEEE 8 1 A Known Problems and Common ETrors cccccccccccscccscccccccesceess A 1 A l What to do if you Encounter an Error 0 ccc cece eee e ence cece cence ees A 1 AL Phe Osprey Ett Ord O eeren a eae A 1 A 3 Reporting Errors to the Osprey Team 0 cece cece cece ness A 2 Ae Kanowa PFODICMS vnc dssnscmnarcareespenmastanatsseneeatiedss Menmadaxatsheaweatans A 2 SS A OMMIMON ENO eE T EE E A E E NE A 3 A 5 1 Unable to Install Osprey under a Windows 2000 NT or XP A 3 A 5 2 Unable to Add Interactions 0 cece cece ccc c cece eeeaeeeennes A 3 Osprey v Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Table of Contents B Credits 2 ican scaiwsasscarwiasiavinnscesnudansscacdvactvatudsucteataareeneahentuadsueiehans B 1 B 1 The Osprey Team B 1 B 2 The Osprey Contributors B 1 B 3 The Osprey Supporters B 2 C Future Updates and Obtaining Patches sscssssscccccccccsscccsssees C 1 D Osprey Change HIStory 2 sacicdcascctcocccasaicn N Ee D 1 E Purchasing Osprey Licenses for Commercial Organizations E 1 E 1 Commercial Applications cece cece cece e eee e cece eeennneeeeeees E 1 Osprey vi Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada 1 General Information The Osprey Network Visualization System Copyright 2002 Mount Sinai Hospital is a tool for vi
32. Canada Chapter 5 Filters F drilter by Source Existing Sources Group Selected Remove Remove All Apply to Graph Close Figure 5 1 2 3 4 Filter by source window demonstrating how to add all the items from the existing list to the visible list by selecting the Add All button e To see the changes on the screen click the Apply to Graph button e Use this feature if you want to see only interactions of a group of items For example only interactions mentioned in source A source B and source C e To adda group of items to the Visible list choose two or more items in the Existing list by holding the Ctrl button while clicking on the items e Then click on the Group Selected button You will see the selected items together on one line separated by amp amp Osprey 5 14 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters e The logic behind this is that every line is a separate condition so for a node to be on the graph it has to satisfy line 1 or line 2 or line 3 etc e Items on the same line must all occur to satisfy a condition So for a node to satisfy the condition on line 1 it must satisfy the conditions for item on line 1 and item 2 on line 1 and item 3 on line 1 etc E drilter by Source Ioj x Existing Sources ITO ET AL GAVIN ET AL UETZ ET amp L Add Add All Ji Remove Remove All Visible Sources ITO ET AL Se GAIN ET AL me
33. Complete All items were successfully uninstalled aes EE Eaa TIT s aruy M il AA mit ne sae aaeeensnsseeens sees snes sens sesesseees sneee eenes aeren naar nesses sess esses esses epep e PS PE PP Pr Pe Pe Pe Gancel Previous eter te Figure 2 7 3 Osprey Uninstall Complete Dialog In Linux the Osprey installation will provide an uninstall script in Osprey s install directory that can be used to completely remove Osprey from your system The unistall program for the Mac OS X has the same steps as the Windows version see section 2 7 1 Uninstalling Osprey on Microsoft Windows Systems ME XP 2000 98 95 NT for details The only difference is the unistall program is located in a folder called UninstallerData located in the default location in which Osprey was loaded see figure 2 7 3 1 Inside this folder you ll find the unistaller program Unistall osprey see Osprey 2 46 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation figure 2 7 3 2 osprey_1 2 0 11 items 15 24 GB available JAR osprey jar Preferences UninstallerData User_Agreement Figure 2 7 3 1 Default Osprey folder with the UnistallerData folder circled Osprey 2 47 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation UninstallerData 1 item 15 24 GB available
34. KI a2 Go Function si A 4 ine Wore ow Mae Fate J RS x Ne ANN ATS nae We SAN ON She a mK S 4 Go Special RNA processing ribosome biogenesis transcription LA AN Xx PES zl SBS Se ANE N phic metabolism cell orgaruzation and biogenesis cell growth andor maintenance Network Filters X Hifa gt e31 mm 169 Loner Nodes YES Draw v IV Nodes Edges I7 Labels IX Arrows mm Exp System GOProcess sll Figure 4 3 2 1 1 Network with a single node selected When a single node is clicked on in the Network Display Area that node becomes highlighted 1 e A in Figure 4 3 2 1 1 A selected node will have additional database information displayed about it as soon as it is clicked This information will be Osprey 4 25 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction shown in the Gene Edge info area on the left hand side of Osprey The following describes briefly the information shown in the Gene Edge Info area for a selected node Osprey B Specific Gene Info At the top of the area specific information about the gene is displayed In the table on the left hand side ORF names and Gene Alias Names are displayed On the right hand side a zoomed in image of the node itself is displayed This zoomed in node will show the colours it currently represents C Get New Interactions Button Clicking this button will
35. Microsoft Windows Systems ME XE 2000 98 995 NI Jiao EENE E EEEN 2 3 Standard Installation Procedure for Red Hat Linux Systems versions TO OAOT aa ats eoemoraianeesneeuaeeaene ees 2 4 Standard Installation Procedure for Mac OS X versions 10 2 or HDCT Reet T E I EE AEEA EATE ROAT 2I POSE INSTA AU on sereia n turns eE a E EEEE E EE ARES 2 5 1 Running Osprey on Microsoft Windows Systems ME XP DOO IS NT neea a a A N 2 5 2 Running Osprey on Red Hat Linux Systems versions 7 3 or 2 5 3 Running Osprey on Mac OS X versions 10 2 or Higher 2 6 Common Installation Issues acaccsssceccessisc Mepnnetua red nnaddacdanctaadaeanck 2 7 Umata lE OS rey aiaee ane aA E AEE aban AE 2 7 1 Uninstalling Osprey on Microsoft Windows Systems ME XP 2000798 SIN rerea E T Ea 2 7 2 Uninstalling Osprey on Red Hat Linux Systems versions 7 3 or 2 7 3 Uninstalling Osprey on Mac OS X versions 10 2 or Higher 28 Neon C he KO ena e EA Osprey Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Table of Contents 3 Opening and Savin Pues ss ssisecsesecsccvisvcwasaessesacvsings save vicwcsenaesouseuisisis 3 1 3 1 Types of Files Opened by Osprey ccc cece eee eeeeeeeeeeeeeeeeees 3 1 Solel MOSPECY T eaer an OS 3 1 A CSO PE aena E AO 3 1 3 1 2 1 Custom File Variation 1 0 cece cece cece E E 3 2 Jl y2 2 Custom File V anianon eee e ra a i 3 3 3 1 2 3 Custom File Variation 3
36. Opening and Saving Files FJ Osprey powered by Yeast GRID Untitled File Never Been Saved ie a E e _ e EA File Edit View Insert Format Filters Database Layout Help C New Crin fons gt Re E oe ba Sansserit Ah E pz fis Ge Standard Crito Ee save Cr Download New Datasets Save 4s Fly Networks b Save Colour Index b worm Metworks b Save Settings Yeast Networks Affinity Chromatography asp Affinity Precipitation osp d Print f Bassler _et_al osp superimpose Biochemical Assay osp Export Dosage_Lethality osp Work Offline Fatica et_al osp Exit Osprey Gavin_et_alosp Harnpicharnchai_et_al osp Ho_et_al osp Tho_et_al osp Purified Complex osp Reconstituked Complex osp Synthetic Lethality osp Synthetic _Rescue osp Tong_et_al osp Two Hybrid osp Uetz et_alosp Network Filters Experimental System Source E m co i du 4 0 0 m 0 0 Loner Modes YES Draw IY Modes V Edges V Labels V Arrows m Exp Systern Figure 3 1 4 1 Open Dataset 3 1 4 1 Downloading new datasets New to Osprey 1 2 0 is the ability to connect to the web and download any datasets supported by the GRID Visit http biodata mshri on ca grid servlet Downloads to check out all the datasets available for download or select the Download New Datasets option under the File menu see figure 3 1 4 1 1 After selecting this option you ll be presented with the web page
37. Organizations This appendix outlines the basic procedure for purchasing Osprey Licenses for Commercial Organizations You are required to purchase an Osprey license if e Ifyou plan to distribute Osprey with another application of any kind e If your organization is non academic or for profit e If you wish to support further Osprey development If you fall into any of the above categories please follow the following steps for purchasing Osprey In order to purchase a license you must first visit the Osprey commercial licenses webpage http biodata mshri on ca osprey servlet CommercialRegistration From this page see figure E 1 1 you can fill out our simple form to contact us about your interest in licensing Osprey Osprey E 1 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Appendix E Osprey Licenses for Commercial Organizations E Osprey Network Yisualization System Commercial License Registration Microsoft Internet Explorer File Edit View Favorites Tools Help Back p fe fat EA Search Favorites ehMedia ca Ey EA T B E Address A ttp if biodata mshri on ca osprewtservleti Commercial Registration Google Research Web Q Search Site a d E paenan ghh Eherablocked YE AutoFill eJoptions fey 2 PD secich WT Ospr ey Search Support Forums Downloads Screenshots Documentation Partners Tutorials Support Forums Commerctal A
38. Osprey 1 The Menu Bar o Click on the Filters overhead menu o Click on the Network Filters submenu o Chose the appropriate filter name Filters Layout Help 1 Network Filters Experimental System z Connection Filters P Source Go Process Turn off Filters Figure 5 1 1 1 Accessing the network filters via the main menu 2 Bottom Left hand Frame o Click on the button for the desired filter located under the Network Filters heading in bottom left hand frame menu Osprey 5 2 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters Experimental system SOUrCE GO Process Torn OTT Filters Connection Filters halirirea irri E 4 r i m 0 Loner Nodes YES Draw M Modes W Ede Figure 5 1 1 2 Accessing the network filters via the bottom left hand frame Note You can only access the network filters under the following circumstances e Filter by Experimental System only works when the Colour by Experimental System mode is selected see figure 5 1 1 3 To find out how to change the node colouring mode see section 7 3 Node Options Also the filter by Source method only works when the Colour by Source mode is selected see figure 5 1 1 4 e Similarly filter by Go Process only works when Colour Nodes by Go Process mode is selected To find out how to change the edge colouring mode see section 7 4 Edge Options e If User Defined mode is chosen for ed
39. Osprey visit the Osprey web site at http biodata mshri on ca osprey As patches become available this section will outline the upgrades that each of the patches provide If a patch is available and you are not currently running the latest version please install the latest version to ensure that you are not affected by bugs that may be repaired by a patch For information on how to check your version of Osprey see section 2 7 Version Checking Osprey C 1 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada ID Osprey Change History This appendix lists the changes from version to version in the Osprey distribution Note that we tend to update the manual at the same time we make changes to Osprey so the Manual is as dynamic as the application itself Make sure that you are always using the latest Osprey manual to ensure that the procedures described are up to date e Changes made from Version 1 0 1 to Version 1 2 0 O O Osprey WebStart capable for online viewing of interactions Support for Multiple Organisms such as Yeast Fly Human Mouse and most recently Worm C elegans S Pombe Schizosaccharomyces pombe Rat Rattus norvegicus and Zebra Fish Danio rerio Access to thousands of new interactions stored in The GRID http biodata mshri on ca grid Yeast GRID contains 19039 unique interactions 14114 physical and 4925 genetic Fly GRID contains 26596 unique interactions 2050
40. Save As Use this option to save files that have not been previously saved or you wish to save as an alternative name e Save Colour Index Can be used to save the current set of colours used to extenuate annotation within Osprey to SVG PNG or JPG images see section 4 6 Saving Colour Indices There are two options under this menu o Only visible This saves an image of the colours currently used by osprey It will only save visible colours so colours that have been filtered will not be saved o Both Visible and Invisible This saves an image of the colour index that includes both visible and invisible colours used in annotation on the current graph Osprey 4 4 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction E dOsprey powered by feast GRID Untitled File Never Bee Fie Edit View Insert Format Filters Database Layout He Mew Open mi SAYE Save os Save Colour Index Only Visible Save Settings b Both visible and Invisible 8 Print Ctrl P SUperimpose I Export Work Offline Exit Osprey Figure 4 2 1 4 The Save Colour Index submenu options e Save Settings This option can be used to save options customized by the user for automatic initialization each time that the application is run There are two options under this menu o Advanced Settings Advanced Settings include all the settings in the Advanced Settings Menu as well as all user defined n
41. Settings O x cr Reenter akglagout Settings Drawing Graph Dragging Graph Backsround Colouring Graph Spoked Dual Ring Colour Edges By C User Defined C By Experimental System By Source Figure 7 2 1 3 The Colour Nodes By Option in the Advanced Settings Menu 7 3 2 User Defined Node Colours User defined colours do not reflect any annotation stored in Osprey or The GRID This option is used to manually colour nodes at the users discretion Osprey is in User Defined mode whenever GO Process colours are not being used to colour nodes Osprey 7 9 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization Note To view nodes in User Defined Colours user defined mode has to be selected as described in section 7 3 1 Choosing Method of Colouring Nodes When in user defined mode node colours can be changed in the following two ways Osprey O O O Toolbar Node Colour Button Select all the nodes whose colours you want changed Click on the Node Colour selection button on the Toolbar as shown in figure 7 3 2 1 From the resulting node colour choosing window you can now choose the colour to reflect on the nodes For more information on the colour choosing window see section 7 3 3 Colour Choosing Window User defined node colours will immediately be reflected on the selected nodes in the Network Display Area Se eet te man dh A
42. Size Background Colour Advanced Settings Figure 7 5 1 1 The Colour setting of the Arrows submenu e Via the Menu bar O O O O Osprey Select all the edges whose arrow head colours you want changed Click on the Format menu from the Menu bar Click on the arrows submenu Choose the Colour option to change the User Defined arrow head colours see figure 7 4 2 2 From the resulting arrowhead colour choosing window you can now choose the colour to reflect on the User Defined arrowheads For more information on the colour choosing window see section 7 3 3 Colour Choosing Window User defined arrowhead colours will immediately be reflected in the selected edges in the Network Display Area 7 22 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization Ea NO iitrscs Format Filters Layout Help Nodes d F w rai Edges b Arrows Colour Text b Size Background Colour Advanced Settings Figure 7 5 1 2 The arrow head Colour Option of the Format Menu on the Menu bar 7 5 2 Arrow Head Size In addition to changing colours of arrowheads Osprey also provides the ability to manipulate the physical size of an arrowhead in proportion to the size of the edge it resides on To accomplish this we have two major methods of accessing the arrowhead S1Ze Note Arrow Heads will change size proportionally to edge sizes e Arrow
43. Toronto Canada Chapter 5 Filters F drilter by Source HO ET AL S GAVIN ET AL amp amp UETZ ET AL Figure 5 1 4 2 Filter Settings to remove all nodes with sources other than MIPS or all three Ho Et Al and Gavin Et Al and Uetz Et Al Osprey 5 20 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters FARA Od olT 4 a AP A dig 33 STE12 551 Pa Figure 5 1 4 3 Filtered Network 5 1 5 GO Process The GO Process filter only keeps nodes that are related by the chosen GO Process See section 5 1 1 Accessing Network Filters and 5 1 2 Using the Network filtering windows to learn how to access and use the filter window The following images display an example of how to take advantage of the GO Process filter e Figure 5 1 5 1 show the network before performing the filter e Figure 5 1 5 2 shows the filter settings to only colour nodes that have a GO Process of Cell Cycle or Metabolism or unknown e Figure 5 1 5 3 show the actual filtered network Osprey 5 21 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters La em Process Colours Index a Change Colour 2 Change Colour ae Change Colour 9 Change Colour amp Change Colour amp Change Colour oO OPA MSEC Change Colour dig LILP 1 Change Colour on Change Colour o Change Colour o Change Colour Change Colour D Change Colo
44. again to see if we have already fixed the problem A 4 Known Problems The following section describes some problems known to the Osprey development team These problems are not errors but they are issues you should be aware of when using the application Really long screen names may exceed the size of the graph area e When changing the visible screen name of a gene in Osprey names consisting of too many characters may cause the screen name to exceed the bounds of the graph If this occurs simply reduce the size of the name so that it will fit inside the graph area Colour index jpg and png files not working under Mac OS X Osprey A 2 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Appendix A Known Problems and Common Errors e When saving the index using the Mac OS X version of Osprey do not choose the Jpg or png file types This option currently only works using the svg file types We are working with Mac to figure the problem out please check for updates Progress Bars using the Mac OS X version of Osprey currently not working e When using the Mac OS X version of Osprey the progress bars are not working properly We have submitted a bug report to the Mac developers and expect to fix the problem shortly A 5 Common Errors This section lists some errors that users frequently get You will find descriptions of the errors and how to solve the problem here A 5 1 Unable to Install Osprey under
45. and Insert INTC T ante oo Panam netn Silanes a aa ans a 4 48 4 5 2 1 Adding all interactions to selected vertices 2 008 4 48 4 5 2 2 Adding only interactions within Selected Vertices 4 51 AO COUT nd OS a E 4 54 40E Go Process Indek sice seriresicuno s eria a rea air E EEO 4 55 4 6 2 Experimental Systems Index 0 cece cece cece cece cece eeeeenes 4 56 BGO DOUCES Mie K oi rh sec edad ale Sack sawed ade oa eda see aaa 4 56 4 6 4 Saving Colour Indices cece cece eens eeeeeeeeeeeeeeeeeeeees 4 57 4T Multiple Organismi SUP POR eierniie EEEE TEET 4 60 S FIE S nn E E 5 1 SL Neiwork FEN erene ea e e 5 1 SFA Accessing NetWork Filters crecen seent er a te A heeee ee 5 2 5 1 2 Using the Network filtering windows ccceeeee cece ees 5 5 5 1 2 1 Overview of the network filtering window 0008 5 5 Dold Filterine nodes OUlnaonn senas T 5 6 Dil 2 AGING nodes DAC Kesgerro checcndsesaaseaseotaes TAO E 5 10 Dole QGP AE MENS eren E E weed goinaea be case 5 14 5il Experimental S VSteimssnic 5cte se saesuetaeawaue o a E TA 5 16 Dl DOUCE Sire ESTEE EE EEEN 5 18 Dik AO POCE S S ra E E EENE 5 21 Oe KO OE O S a a ee E E E 5 24 S2 COMME CTIVILY FIETS oerein n E AEAEE EEA REA 5 25 5 2 Accessing Connection FIETS crnesessrsirscesrererooni eisien Vukan 5 25 322 Minimu ss cde ce e an E AEE 5 26 3A APSA VS Mini sesanan EEE EEEE 5 27 Osprey Operator s Manu
46. andor role in cell cycle START protein kinase raitotic cell cycle ralntenarce regulator reentry into mitotic mating sensu cell cycle after saccharoryces pheromone arrest Interacts with cyclin dependent kinase PHOS to form kinase complex with G1 penoche activity involved in cell cycle cycln dependent cyclin dependent cell cycle protein kinase protein kinase cell growth andor holoenzyme regulator maintenance progression Figure 4 4 3 2 Selected Nodes Report Window Note This table can be copied and pasted into a spread sheet program using the ctrl c and ctrl v hotkeys but this option is not endorsed by this program Osprey 4 43 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction This option will connect to the GRID database and may change the annotation of your layout to the latest annotations available Follow these steps to call this function e Click on the Edit Menu in the Menu Bar e Click on Update Node Annotation Fd Osprey Untitled File Never Been Saved File Edit View Insert Format Filters Layout Help C Select All Ctrl z _ st Invert Selected Nodes ji F Crop White Space is Fit To Screen DE E zoom In Ctrlt Seli T zoom Out Ckrl Minus Lack Modes Unlock Modes Remove Modes Remove Edges ith Find Ctrl F Update Node Annotation Figure 4 4 4 1 Update Node Annotation e A warning message will app
47. button e To add one or more items to the visible list click on the item you want to add Osprey 5 10 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters Le Ges by Source MIPS HO ET AL ITO ET AL Figure 5 1 2 3 1 Filter by source window demonstrating how to highlight something in the existing list e To select more than one at the same time hold the Ctrl key and click on more from the Existing list Osprey 5 11 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters E drilter by Source Ioj x Existing Sources MIPS HO ET AL ITO ET AL GAVIN ET AL WET ET AL Add Add All Group Selected Remove Remove All Visible Sources Apply to Graph Close Figure 5 1 2 3 2 Filter by source window demonstrating how to highlight multiple items in the existing list e Then click the add button you will see them added to the Visible list Osprey 5 12 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters Le Ges by Source MIPS HO ET AL ITO ET AL GAVvIN ET AL UETZ ET AL Figure 5 1 2 3 3 Filter by source window demonstrating how to add the highlight items to the visible list by selecting the Add button e The Add all button adds all items from the Existing list to the Visible list Osprey 5 13 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto
48. developers at Appl Downloads and after two months of compatibility enhancement work we are happy to announce that Osprey For RedHat Linux full support for Osprey on OS X The Osprey Network will be incorporated into the weve aign oul is upcoming 1 0 0 release Mac OS X Microsoft Windows RedHat Linux Osprey For Mac OS X Osprey For Windows a The Osprey Network wa The Osprey Network misuallzalion redial isualization System Microsoft is now available for All WINDOW Os x Download Here gt Osprey 1 0 0 Beta Testing Begi July 3rd 2003 16 12 58 Today the beta version of the newest release of Osprey began Testing will proceed for roughly a 1 month period after which version 1 0 0 will be released to w KI n RA IO D t OY EJ A Done a Platforms Download Here Download Here Figure 2 1 2 1 The location of the Download link on the Osprey homepage There are two versions of Osprey available for download The academic version and our 30 Day trial version see figure 2 1 2 1b You must download the 30 Day trial version if you fall into any of the following 3 categories e Ifyou plan to distribute Osprey with any other application e If your organization is non academic or for profit e Ifyou wish to support further Osprey development The 30 Day trial version 1s a fully functioning version of Osprey for testing use by Commercial organizations
49. do require that you register and login before downloading our software to help make it easier for us to relay important information about updates to Osprey Email Address jyouremail address com Cid Password ecco Don t have a Password Lost Yours Simply Click Below Its Free and Easy Register To Download Contact Us Osprey Community Terms and Conditions Copyright 2002 2003 Mount Sinai Hospital All Rights Reserved D amp 4 OF B amp Done Figure 2 1 3 1 The Osprey download login page After login you will be prompted with the copyright notice that you must agree with before proceeding to the downloads page See section 1 3 Copyright Notice for more details Osprey 2 8 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation H Osprey Download Terms and Conditions Mozilla File Edit View Go Bookmarks Tools Window Help 09 9Y I http biodata mshri on cafosprey servlet TermsAndConditions product 2 Gsm o fil a Seach Search Support Forums vZ Osprey Downloads Screenshots Documentation Partners Tutorials Support Forums About Osprey TERMS AND CONDITIONS i Hl Copyright Notice Copyright 2002 Mount Sinai Hospital Toronto Canada All Rights Reserved Warning This system may be monitored by system or security personnel License Agreement for the Osprey Netwo
50. genes into Osprey Osprey recognizes both txt extensions as well as gl Gene List file extensions With this format the user can quickly import their genes of interest into Osprey and use the interactions available from any of the other three file formats available to Osprey as well as the published interactions found in The GRID Osprey can currently recognize two different variations of gene list files Osprey will accept any string placed in the columns except blanks Sections 3 1 3 1 Gene List Variation 1 and 3 1 3 2 Gene List Variation 2 demonstrate the different variations in the custom interaction format that Osprey currently accepts The first row in figure 3 1 3 1 1 contains the header Gene that must exist in this variation of the gene list file Figure 3 1 3 1 2 demonstrates what the network would look like after opening the gene list in Osprey Note The rows and columns in red are necessary The rows and columns in gray are optional You can choose to only change the grey rows that need changing Gene CDC28 CLNI1 CLN2 CLN3 CCT6 DCP NPI46 Figure 3 1 3 1 1 Gene List Variation 1 Osprey 3 7 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 3 Opening and Saving Files Der CDC28 kh d eae CLNI CLN3 a CLN2 g Figure 3 1 3 1 2 Result of loading gene list from figure 3 1 3 1 1 into Osprey The first row in figure 3 1 3 2 1 contains the headers Gene and Screen
51. installer has launched you will be asked a series of questions about your installation Firstly you are presented with an introduction to the install procedure see figure 3 Please read this carefully and click NEXT to proceed Osprey 2 33 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation Osprey 1 0 0 m Introduction ir a InstallAnywhere will guide you through the installation of BT immortant informene osprey_1 0 0 It is strongly recommended that you quit all programs before continuing with this installation Click the Next button to proceed to the next screen If you want to change something on a previous screen click the Previous button You may cancel this installation at any time by clicking the Cancel button Cancel Figure 3 Osprey installation introduction 3 Next you will be presented with the Osprey Network Visualization System User Agreement see figure 4 Please read this carefully By clicking NEXT you will agree to these terms and conditions If you do not agree to the terms and conditions simply click CANCEL at any time to abort the osprey installation If you agree click the NEXT button to continue Osprey 2 34 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 3 Introduction J important Information Cancel Osprey Installation Osprey 1 0 0 Important Information P
52. neran dr Oo x d der ao Set Node Colour YPLOI AW 3 a a Figure 7 3 2 1 The Node Colour Selection button on the Osprey Toolbar Via the Menu bar O O O oO Select all the nodes whose colours you want changed Click on the Format menu from the Menu bar Click on the Nodes submenu Choose the Colour option to change the User Defined Node Colours see figure 7 3 2 2 From the resulting node colour choosing window you can now choose the colour to reflect on the User Defined nodes For more information on the colour choosing window see section 7 3 3 Colour Choosing Window User defined node colours will immediately be reflected in the selected nodes in the Network Display Area Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization Format Filters Layout Help Edges Size Arrows Text Background Colour Advanced Settings Figure 7 3 2 2 The Node Colour Option of the Format Menu on the Menu bar 7 3 3 Colour Choosing Window Whenever you change colours of anything in Osprey you are presented with the Osprey colour chooser This colour chooser has several key areas that allow for the most flexibility when customizing colour settings These sections are as follows e Swatches Tab e HSB Tab e RGB Tab 7 3 3 1 Swatches tab The Swatches tab has a standard set of basic colours that can be picked as the colour of c
53. nodes on the screen regardless of the number of interactions stemming from them o Hide When this option 1s selected it will turn the Loner Nodes filter on which will hide nodes on the screen with zero interactions stemming from them View Insert Format Filters Layout Colour Indexes b C Toolbars b l Loner Modes fe Show Drawing Options Fi Hide Dragging Options I Metwork Statistics Selected Node Report View All Comments Figure 4 2 3 4 The Loner Nodes Submenu e Drawing Options An Osprey network is in drawing mode when the graph is stationary and no nodes are currently being moved around the screen There are four options under this menu o Nodes By clicking this option you can specify whether or nodes are displayed while in Drawing mode o Edges By clicking this option you can specify whether or edges are displayed while in Drawing mode o Labels By clicking this option you can specify whether or labels are displayed while in Drawing mode o Arrows By clicking this option you can specify whether or arrows are displayed while in Drawing mode Osprey 4 11 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction View Insert Format Filters Layout i Colour Indexes b Toolbars q Loner Modes ranny oms GINE i Dragging Options d 7 Edges Metwork Statistics Labels Selected Mode Report Arrows View All Comments
54. of the options available in the edit menu with a brief description of what service the option provides Osprey 4 7 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction Ed Osprey powered by feast GRID Untitled File Never Been Saved File Edit View Insert Format Filters Database Layout Help Z i C Topy Screen Names SansSerif Copy Node Info Copy Edge Info er Py cag Copy Neighboring Edges Info of selected Modes E Select All Chrl 2 Invert Selected Nodes Select All Baits ir Crop White Space is Fit To Screen E zoom In Ctrl Sy zoom Cut Ctrl Minus Lock Modes Unlock Nodes Remove Nodes Remove Edges ith Find Ctrl F Update Mode Annotation Figure 4 2 2 1 The Osprey Edit Menu e Copy Screen Names Click on this option to copy all the currently selected screen names to the systems clip board e Copy Node Info Selecting this menu item will copy all the annotation information for the selected genes to the systems clip board e Copy Edge Info This option will copy all the edge info for all the selected edges to the systems clip board e Copy Neighboring Edges Info of selected Nodes When clicked this will copy any Edge info of the selected node s to the systems clip board e Select All Click on this option to select all of the vertices and edges currently visible on the network e Invert Selected Nodes Selecting this menu item will select
55. option to change the label size see figure 7 6 1 2 From the resulting font options dialog you have the ability to manipulate the size as well as most other label options described in this section see figure 7 6 1 3 Format Filters Layout Help O O O i Nodes al ar Bi Edges b Arrows b Text Colour Background Colour Advanced Settings Show Hide F Figure 7 6 1 2 The Text submenu in the Format menu Osprey 7 26 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization Font Options a X Fonts SansSerif Figure 7 6 1 3 The font options dialog 1 6 2 Label Font Osprey offers two methods for manipulating the font of a label Before attempting to change the font of a label ensure that you have at least one node selected in the Network Display Area The following describes the two major methods of accessing the label font e Label Font Selection Box o Select all labels whose font is to be changed o Select the desired font in the Osprey font selection box see figure 7 6 2 1 o Changes to label font are immediately reflected on the Network displayed in the Network Display Area SE U lol x aie A l sanssent Eo I E 7 e lae e g SimSun STOMP Almonte Woo STOMP _Angostura STOMP Blue Highway STOMP Blue Highway STOMP Bullpen STOMP Coolvetica e Figure 7 6 2 1 The Osprey Label Font Sele
56. prior written arrangement of the copyright holder For commercial licensing opportunities contact ospreyadmin mshri on ca or visit http biodata mshri on ca osprey servlet CommercialRegistration for more details Termination This Agreement and your license to use the Software will continue so long as you remain in compliance with the terms and conditions of this Agreement Your license will terminate automatically without notice from Mount Sinai Hospital if you breach any of your obligations hereunder Upon termination you shall cease using the Software and shall destroy all copies of the Software and associated materials and documentation in any form All disclaimers of warranties and limitations of liability shall survive any termination of this Agreement Disclaimers IN NO EVENT SHALL MOUNT SINAI HOSPITAL BE LIABLE TO ANY PARTY FOR DIRECT INDIRECT SPECIAL INCIDENTAL OR CONSEQUENTIAL DAMAGES INCLUDING LOST PROFITS ARISING OUT OF THE USE OR INABILITY TO USE THIS SOFTWARE AND ITS DOCUMENTATION EVEN IF MOUNT SINAI HOSPITAL HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE THE SOFTWARE AND ACCOMPANYING DOCUMENTATION IF ANY PROVIDED HEREUNDER IS PROVIDED AS IS MOUNT SINAI HOSPITAL SPECIFICALLY DISCLAIMS ANY IMPLIED WARRANTIES OF ANY KIND INCLUDING BUT NOT LIMITED TO WARRANTIES OF MERCHANTABILITY NONFRINGEMENT AND FITNESS FOR A PARTICULAR PURPOSE MOUNT SINAI HOSPITAL HAS NO OBLIGATION TO PROVIDE MAINTENANCE SUPPORT UPDATE
57. screen To accomplish this we have two major methods of accessing the node size e Node Size Selection Box o Select all nodes whose size needs to be changed o Select the desired size from the node size selection box see figure 7 3 4 l o Node size changes are reflected immediately on the Network Display Area Osprey 7 14 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization eM DOROSHC AA PER Figure 7 3 4 1 The Node Size Selection Box e Node Size Configuration Dialog Select all nodes whose size needs to be changed Click on the Format menu in the Menu bar Click on the Nodes submenu Click on Size see figure 7 3 4 2 Use the node size slider to increase or decrease the size of a node see figure 7 3 4 3 o Node size changes are reflected immediately on the Network Display Area Format Filters Layouk Help i Modes Colour Size O O O O O Edges Aros b Text b Background Colour Advanced Settings Figure 7 3 4 2 The Nodes submenu in the Format menu Osprey 7 15 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization 5 15 25 35 45 55 65 75 85 5 Close Figure 7 3 4 3 The Node size slider 7 4 Edge Options Similar to nodes edges also have the ability to be coloured by annotation Osprey provides three major methods of colourin
58. shown in figure 3 1 4 1 2 From here you ll select the organism of choose and download the desired datasets After the datasets are downloaded you ll need to place them in the desired organism folder located at OSPREY HOME Datasets OSPREY HOME is the location in which Osprey was installed For example if you downloaded the Two Hybrid osp dataset for Yeast you would then place the file in the following path OSPREY HOME Datasets Yeast T wo Hybrid osp Osprey 3 10 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 3 Opening and Saving Files Note If the Download New Datasets link does not work from Osprey you can visit http biodata mshri on ca grid servlet Downloads manually in any web browser E dOsprey powered by Yeast GRID Untitled File Never Been Saved File Edit View Insert Format Filters Database Layout Help Ci New ctn foo QB 4 oC df Sansserit fo gt E B zle hs Fl s f Open d Ga Standard Chrl o ley Save Ctri 5 Download New Datasets Save 4s Fly Networks b Save Colour Index b MY FILES b Save Settings Worm Networks E Print Ctrl P Yeast Networks SUperimpose b Export Work OFFline Exit Osprey Network Filters Experimental System SOURCE j oft i a o m 0 0 Loner Nodes YES Draw I Nodes JV Edges IV Labels IM Arrows Exp System GO Proc Figure 3 1 4 1 Download New Datasets Osprey 3 11 Operator s Manual C
59. the common gene names and aliases for other genes that interact with the selected node e C System This field shows the experimental system that was used to derive the particular interaction e JD Source This field shows the source that reported this interaction within the support database Osprey 4 47 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction You can select any of the interactions listed on this screen by clicking on them with the left mouse button To select multiple interactions simple click and hold the left mouse button and drag through the list to select as many interactions as desired Once you have selected interactions you can add them by clicking on the Add Selected Interactions button pictured as E in Figure 4 5 1 2 This will take these new interactions and incorporate them into the network currently stored in the Network display area If at any time you simply want to add all interactions available in the listing click the Add All Interactions button pictured as F in Figure 4 5 1 2 4 5 2 From the Network Display Area Command Menu and Insert Menu The Network Display Area Command Menu and the edit menu offers two easy methods for incorporating new interactions into a network 1 Adding all interactions to selected vertices section 4 5 2 1 Adding all interactions to selected vertices 2 Adding only interactions within Selected Vert
60. 02 Mount Sinai Hospital Toronto Canada Appendix E Osprey Licenses for Commercial Organizations Successful Osprey Commercial Registration Microsoft Internet Explorer File Back p fat Search G Favorites gP Media ca E5 a Ei l E Address e http biodata mshri on calospreylservleti Commercial Registration Go Google Search Web iSearch Site a do asmak p Ebzro blocked fe Autorill WalOptions 7 l Edit wiew Favorites Tools Help E Seach Search Support Forums Downloads Screenshots Documentation Partners Tutorials Support Forums Commercial Applications About Osprey REGISTRATION Thank You For Registering An Email has been sent to the address that you provided and an Osprey representative will contact you concerning your request Contact Us Osprey Community Terms and Conditions Best viewed at 1024x768 resolution with all modern web browsers Copyright 2001 2003 Mount Sinai Hospital AI Rights Reserved Le ype litter Figure E 2 2 Upon successful registration an email is sent to the Osprey team informing us of your interest Osprey E 3 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada
61. 2 1 2 Figure 4 5 2 1 1 after Insert All Interactions for Selected has been applied to the selected nodes 2 Using The Insert Menu o Select the desired nodes for more info on selecting nodes see section 4 3 2 1 Selecting Nodes o Click on the Insert menu from the Menu bar Osprey 4 50 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction o Click on All Interactions for Selected Nodes as shown in Figure 4 5 2 2 3 tled File Never Been Saved Insert Format Filters Layout Help 3 All Interactions For Selected Nodes shift 4 ShiFE O Only Interactions within Selected Modes E New Node Ctrl ShiFt N eee hen Interaction Chrl ShiFE I au Figure 4 5 2 2 3 Insert Menu 4 5 2 2 Adding only interactions within Selected Vertices This is one of the most popular options for retrieving new interactions and one that is rarely seen in other network display systems With this option one can retrieve interactions that exist ONLY within a set of nodes in a network There are 2 ways to access this feature 1 Using The Network Display Area Command Menu Right click menu o Select the desired nodes for more info on selecting nodes see section 4 3 2 1 Selecting Nodes Right click on an empty area of the screen Click on Insert Only Interactions within as shown in Figure 4 5 2 2 1 Osprey 4 5 Operator s Manual Copyright 2002 Mount Sinai Ho
62. 6 6 1 Concentric Circles with Functional Clustering turned on Osprey 6 26 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts 6 6 1 Accessing Functional Clustering options Functional Clustering can be turned on or off under the Functional Clustering heading in Advanced Settings Follow these steps to find out exactly how to do so The Advanced settings options in the Menu Bar e Click on the Format overhead menu e Click on Advanced Settings e Look for the Functional Clustering tab and click it Format Filters Layout Help i Nodes at Edges b ArrOWS p Text p Background Colour Advanced Settings OR as Figure 6 6 1 1 Accessing Functional Clustering options via the main menu bar under the Format menu 6 6 2 GO Process Order The GO Processes can be ordered in terms of importance so that if a node 1s classified under several GO Processes it will be clustered with the most important one After accessing the Functional Clustering menu described in section 6 6 1 Accessing Functional Clustering options the next few steps will explain how the ordering is done 1 Moving a GO Process down the list e Click on the desired GO Process e Either drag it down to the desired order e Orclick the down arrow moves down one step at a time Osprey 6 27 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts Bd Advanced Settin
63. 9 physical 6087 genetic Worm GRID contains 4453 unique physical interactions Increased memory to java vm in order to handle the large scale networks see section 7 11 Memory Setting in the user manual on how to adjust the allocation of memory Improved functionality to organizing and adding new datasets see section 3 1 4 Opening Datasets in the user manual Fixes to a number of small bugs found in 1 0 1 Updated User Manuals sections e 2 1 2 Registering minor update on how to register and download Osprey e 2 5 3 Running Osprey on Mac OS X versions 10 2 or Higher update to how Osprey is opened on the Mac OS X e 2 7 3 Uninstalling Osprey on Mac OS X versions 10 2 or Higher update to how Osprey is unistalled on the Mac OS X e 3 1 4 Opening Datasets updated to indicated changes in the datasets available with Osprey and the ability to download new datasets e 4 2 1 File Menu and 4 2 2 Edit Menu updated to show changes to both the datasets and the change database menu items e 7 10 Changing Database section added to help explain the various databases Osprey can connect too e 7 11 Memory Setting sections added to allow users to increase the amount of memory allocated to Osprey Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Appendix A Known Problems and Common Errors e Appendix E Purchasing Osprey Licenses for Commercial Organizations added e Changes made from Version 1 0 0 to V
64. A EN EAS 4 14 AZO Fiter Men srasni r ae EE OT E ROEE 4 17 A ASAY OU MEDU jcchsbrotcadeanast a E a 4 18 a cs A e O O 4 21 Wo Pard BASS Me Mese a a e eT 4 22 A NOWO orare E NE E ote be oie eee 4 23 LL Network Display Aredia ae a E A 4 24 4 3 2 Manipulating the Network ccccc cece eee e eee e eee e cece eee ees 4 25 Me als DEICCHIS INCU CS arian cust cur actigunaii swears a ten 4 25 A ie SCICCHNG POC E E E E T 4 27 4 3 2 3 Moving Individual Nodes 0 cece cece cece eee eeneeeees 4 28 4 3 2 4 Selecting Multiple NOdES cciats saciciwndacesctevebsiats sautshandacs 4 28 Osprey ll Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Table of Contents 4 32 Movima Multiple NOOCS iccias4 ncrse detente canst EET 4 29 432 Removing Nodes roroesan eenaialese ies ENO 4 29 A 2l REMOVNE ELIES aara EAN 4 31 A 2o SHOWING ONE NOJ ES osese p anar E N 4 33 4 3 3 Network Display Area Command Menu 0000e ees 4 35 AA ene BOGS INOA a erise re a 4 36 AAN Ahane mne Screen NaNe ereer raa 4 37 A42 Adda CONMMCINS erea EE EEE 4 39 4 4 3 Viewing Selected Node Report cccccc cece cece cece cece eens 4 42 aoe Upda Annota eene TE TTEN 4 44 AAS Edge Tni Oss casanecasaceeinakektuatesann ner sntervaaeuent wae sdaneeriaeee es 4 45 AD Odie IMteraChOns nennen rE mudeceeentedadie cauteedeseec ee 4 45 Aak chrom the OOA decana a 4 46 4 5 2 From the Network Display Area Command Menu
65. BA Wg en Pe ak RC EXITS EAV h Ie y EA A fay r Mo TA E Se ea Sources System C AFFINITY PRECIPITATION oe ET AL SYNTHETIC LETHALITY f MIPS aa D J i F u gb f 7 d 5 T i X ST PATE i T N X RK ORR f A AALS Ee gm ter AA 7 x WW NSA TT r Yi l rh aoe See Fia He A i x WESTA AAH PT Ay Network Filters FE m 169 Loner Nodes YES a V Nodes MV Edges IV Labels V Arrows m Exp System GO Process Y 2 zji J Figure 4 3 2 2 1 Network with a single edge selected When a single edge is clicked on in the Network Display Area that edge becomes highlighted ie A in Figure 4 3 2 2 1 A selected edge will have additional database information displayed about it as soon as it is clicked This information will be shown in the Gene Edge info area on the left hand side of Osprey The following describes briefly the information shown in the Gene Edge Info area for a selected edge e B Interacting Genes At the top of the Gene Edge Info area when an edge is selected information about genes participating in an interaction will be shown Information such as the ORF names and Gene Alias names will be displayed e C Experimental System Sources This table shows the various experimental systems and sources that correspond to the selected edge Although the edges will Osprey 4 27 Operator s Manual Copyright 2002 Mount Sinai Hospital Toro
66. Been Saved Eg Osprey Untitled File Never Been Saved File Edit View Insert Format Filters Layout Help File Edit View Insert Format Filters Layout Help ON De BOO hor MH D el amp amp posd t A lfe Gene Info or ons Gene Info Get Wew Interactions Screen Name CLN2 Change Add Comment Description role in cell cycle START Go Component Go Process Get Mew Interachions LNs Change Add Comment user defined node NONE regulation of CDE actraty LS transition of reatotic cell HOHE cycle reentry into mitotic cell cycle after pheromone arrest emere ele Tj F m zj z z z HOHE Go Special UNENOWN Go Function cyclin dependent protein kinase regulator Go Special cell cycle cell growth anclior maintenance mating sensu Saccharomyces 4 4 5 0 Loner Nodes YES Draw M Modes e 5 D Loner Modes YES Draw IY Nodes R Figure 4 4 1 Gene Info for CLN2 Figure 4 4 2 Gene Info for CLN5 unknown To change the name of a selected node on your graph follow these steps e Click on the desired node e Click on the text box under the Screen Name label shown below in Figure 4 4 1 1 Osprey 4 37 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction Fd Osprey Untitled File Never Been Saved File Edit View Insert Format Fi
67. CLN1 also interacts with CDC28 Figure 3 1 2 1 2 show the resulting double headed arrow on the edge connecting CLN1 and CDC28 Osprey 3 1 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 3 Opening and Saving Files Osprey will accept any string placed into the columns Blanks are not accepted in any columns indicated with the colour red Sections 3 1 2 1 to 3 1 2 4 demonstrate the different variations in the custom interaction format that Osprey currently accepts 3 1 2 1 Custom File Variation 1 The first row in figure 3 1 2 1 1 contains the headers GeneA and GeneB of the two columns that must exist in this variation of a custom interaction file The two columns represent the different interacting pairs that will be loaded into Osprey Figure 3 1 2 1 2 demonstrates what the network would look like after opening it up in Osprey Note The rows and columns in red are necessary where as the rows and columns in gray are optional wened GeneB CDC28 CLNI CDC28 CLN3 CDC28 CLB2 CDC26 CDC CDC26 MET10 CLNI CDC26 CLNI CLN2 CLNI CDCS3 Figure 3 1 2 1 1 Custom File Variation 1 Osprey 3 2 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 3 Opening and Saving Files DC53 ELNI CLN2 s gt LB Figure 3 1 2 1 2 Result of loading custom file variation 1 into Osprey 3 1 2 2 Custom File Variation 2 The first row in figure 3 1 2 2 1 contains th
68. Filters Menu e Network Filters These filters filter the nodes on the graph depending on network features such as Experimental System Source and Go Process Note Only the Currently viable filters will be enabled To change the available filters change the colouring mode see section 5 Filters for more detail o Experimental System Select this option to invoke the Experimental System Filter Source Select this option to invoke the Source Filter Go Process Select this option to invoke the Gene Ontology Process Filter Turn off Filters This option turns off a network filter 1f one of them is turned on Filters Layout Help ji Network Filters Experimental System Connection Filters P SOUrCE 0 Process Turn ath Filters Figure 4 2 6 2 The Network Filters Submenu e Connection Filters These filters filter the nodes on the graph depending on the number of connections they have with each other o Minimum Select this option to invoke the connection minimum filter it will only keep nodes with a chosen minimum amount of connections before any nodes are removed Osprey 4 17 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction o Iterative Minimum Select this option to invoke the iterative connection minimum filter it is similar to the above filter except it only keeps nodes with a chosen minimum amount of nodes after all nodes are removed o Depth Select this option to invoke
69. Head Size Selection Box o Select all edges whose arrow head size needs to be changed o Select the desired size from the arrow head size selection box see figure 7 5 2 1 o Arrow head size changes are reflected immediately on the Network Display Area Osprey 7 23 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization zk da Edo ah amp th Bees Bea MScy Figure 7 5 2 1 The Arrow Head Size Selection Box e Edge Size Configuration Dialog o Select all Edges whose arrow head size needs to be changed Click on the Format menu in the Menu bar Click on the Arrows submenu Click on Size see figure 7 5 2 2 Use the arrow head size slider to increase or decrease the size of an arrow head see figure 7 5 2 3 o Arrow head size changes are reflected immediately on the Network Display Area Format Filters Layout Help i Nodes dE om gh San Edges b Arrows Colour Text d Background Colour O O O Advanced Settings ia Figure 7 5 2 2 The Arrows submenu in the Format menu Osprey 7 24 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization Arrow Size Figure 7 5 2 3 The Arrow Head size slider 7 6 Label Options In addition to manipulating the size of nodes and edges in Osprey we also provide the ability to ma
70. IV Nodes M Edges Labels Arrows m User Defined v User Defined ali Figure 6 4 1 1 Default Spoke Models Osprey 6 14 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts 6 4 1 1 Accessing the default spoke model There are currently two ways in which the user can access the default spoke model 1 The Menu Bar o Select all nodes that you want to be in the centers of default spokes Click on the Layout overhead menu Click on the Spokes submenu Click on Default Layout Hep 0 Layout Help j uto Relaxation F SansSerif ansSerif Circular Dual Ring b Spokes Default Global 7 ee Figure 6 4 1 1 1 Accessing the default spokes layout via the main menu 2 Right Click Menu o Select all nodes that you want to be in the centers of default spokes Right click in an empty area of the graph Click on Create Default Spokes Osprey 6 15 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts Insert All Interactions For Selected Insert Only Interactions within Selected One Circle Layout Concentric Circles Layout Create Default Spokes Create Forced Spokes Spoked Dual Ring Layout Lock Nodes Unlock Modes Remove Modes Remove Edges Figure 6 4 1 1 2 Accessing the default spokes layout via the Right Click menu 6 4 2 Forced Spokes Forced spokes bring in all nodes that are connected to the select
71. Insert Format Filters Layout Help E Deeds H A sanssenit Ahe Ae Bz eh ae Ale b NO Gene Edge Info Select a single vertex edge Network Filters Experimental Syste GO Process Turn Off Fitters Connection Filters Minirnurn erative Minimu Depth Turn Off Connectivity 4 Menus Osprey is a menu driven application By accessing the collection of options stored under the different menu headings Osprey provides the tools necessary for manipulation and analysis of the networks All options available to the user can be accessed via the Osprey menus even though some options may have methods of access outside of the Menu bar The following sections will outline briefly the options available in each of Osprey s menus Ed Osprey powered by feast GRID Untitled File Never Been Saved File Edit View Insert Format Filters Database Layout Help rh ee ee il a ee ee TT Figure 4 2 1 This is an isolated view of the menus available in Osprey Osprey 4 2 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction 4 2 1 File Menu The Osprey File Menu contains many of the options for writing to files as well as opening from files The following is a listing of each of the options available in the file menu with a brief description of what service the option provides E dOsprey Untitled File Neve File Edit wiew Insert Format 4 Mew Ct
72. Name that must exist in this variation of the gene list file The screen name allows the user to change the name viewed on the network Figure 3 1 3 2 2 demonstrates what the network would look like after opening the gene list in Osprey Note The rows and columns in red are necessary The rows and columns in gray are optional You can choose to only change the grey rows that need changing Gene Screen Name CDC28 CDC28 CLNI CLN2 CLN3 CCTS DCP2 NPI46 Osprey 3 8 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 3 Opening and Saving Files Figure 3 1 3 2 1 Gene List Variation 2 are CDC kaai koa MPI46 CLAY CLAS ad Ld CLA s Figure 3 1 3 2 2 Result of loading gene list from figure 3 1 3 2 1 into Osprey 3 1 4 Opening Datasets Osprey comes with a set of well known datasets already built in for quick access These datasets are derived from both experimental systems and sources currently stored in the GRID The datasets have been grouped into different menu items based on the organisms they belong to As of Osprey 1 2 0 the number of organisms containing interaction data in the grid include Yeast Fly and Worm The datasets can be opened from the Menu bar see figure 3 1 4 1 e Click on the File Menu bar e Click on Open submenu e Select the organism menu and dataset you want to open Osprey 3 9 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 3
73. Osprey 5 25 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters Turn Ott Fitters Connection Filters arth 4 335 m 43 Loner Modes MO Draw I Figure 5 2 1 2 Accessing the connection filters via bottom left hand frame 5 2 2 Minimum The minimum filter only keeps nodes that have at least the minimum selected number of edges connected to them 1 e Nodes will be removed based on an initial count of how many edges each node has See section 5 2 1 Accessing Connection Filters for details on how to access the minimum filter The following four steps demonstrates how to use the minimum filter e Click on the text box shown in figure 5 2 2 1 and type the minimum number of edges that each node must have before you invoke this function to remain on the screen e Click on Filter button shown in figure 5 2 2 1 to perform the algorithm e Click on Clear button shown in figure 5 2 2 1 to clear the text box e Click on Close button shown in figure 5 2 2 1 to close the text box Connection Minimum a x Removes nodes with less than the Following number of connections fi Clear Close Figure 5 2 2 1 Minimum connection filter window Osprey 5 26 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters 5 2 3 Iterative Minimum The iterative minimum connection filter only keeps nodes that have at least the minimum selected number o
74. Osprey Network Visualization System Reference Manual for Version 1 2 0 oy Osprey kersion didi Network Visualization System e User Guide and Tutorial Osprey Network Visualization System Reference Manual for Version 1 2 0 kersion didi Network Visualization System Written by Chris Stark Bobby Joe Breitkreutz COPYRIGHT 2002 No part of this Guide may be reproduced stored in a retrieval system or transmitted in any form or by any means electronic mechanical photocopying microfilming recording or otherwise without written permission from Mount Sinai Hospital Toronto Canada For Technical Assistance If you need help to resolve a problem there are several ways to contact the Osprey team World Wide Web http biodata mshri on ca osprey E mail ospreyadmin mshri on ca Copyright Notice Copyright 2002 Mount Sinai Hospital Toronto Canada All Rights Reserved Warning This system may be monitored by system or security personnel License Agreement for the Osprey Network Visualization System and all documentation THIS AGREEMENT SETS OUT THE TERMS AND CONDITIONS FOR DOWNLOADING COPYING INSTALLING OR USING OSPREY NETWORK VISUALIZATION SYSTEM SOFTWARE AND ASSOCIATED MATERIAL AND DOCUMENTATION INCLUDING ANY MODIFIED VERSIONS OR UPDATES COLLECTIVELY SOFTWARE READ THE TERMS OF THIS AGREEMENT AND ANY PROVIDED SUPPLEMENTAL LICENSE TERMS COLLECTIVELY AGREEMENT CA
75. R PURPOSE MOUNT SINAI HOSPITAL HAS NO OBLIGATION TO PROVIDE MAINTENANCE SUPPORT UPDATES ENHANCEMENTS OR MODIFICATIONS MOUNT SINAI HOSPITAL DOES NOT WARRANT OR ASSUME RESPONSIBILITY FOR THE ACCURACY OR COMPLETENESS OF ANY INFORMATION TEXT GRAPHICS LINKS OR OTHER ITEMS CONTAINED WITHIN THE SOFTWARE Published research assisted by this software should cite Breitkreutz BJ Stark C Tyers M Osprey A Network Visualization System Genome Biology 2003 4 3 R22 Table of Contents 1 General Information ssscccceccccccocosccccesosssccccccceccccoososcccececcccoooe HL PNOOUE TIS Mnman EANA 1 1 1 Convections Used in the Manual ccc ccccce eee e eee eees LZ WG ISS OSPE y cae gist seas neeaseaui ates amen gas meee vega A E 1 2 1 The Main Features of Osprey ies soscid ockceatesivassiediouidectseans L Copy OMEN OTC Ce aerer EEA LA Contact hnormaHo eps r O WD Osprey LICEnSIN O ersesiern reha EE AEE EAER 1 6 Joining the Osprey Mailing acts 2 5 anc cenennntesd oeintycasataeeeeeeaeesae 2 Osprey Mstalatiom eisen a O E E EEEa 21 Obame OSPY ssccaccvnsannmssraiaanuihs E EE EE LEL TE Osprey Home pi rererere EErEE E ND REE e E E E DES ADO TO ACUI ory oeoa N a A ye eee 2 1 3 1 Downloading for WindowWS cc e AE AREE 21 3 2 Downloading for Red Hats ccccescccaverexetavstevacssereseaeverees 2 1 3 3 Downloading for Mac OS X ccc cece eee cece ee ee ees 2 2 Standard Installation Procedure for
76. REFULLY BEFORE OPENING THE SOFTWARE PACKAGE BY OPENING THE SOFTWARE PACKAGE YOU AGREE TO THE TERMS OF THIS AGREEMENT AND THAT IT IS ENFORCEABLE LIKE ANY WRITTEN NEGOTIATED AGREEMENT SIGNED BY YOU INDICATE YOUR ACCEPTANCE OF THESE TERMS BY SELECTING THE ACCEPT BUTTON AT THE END OF THIS AGREEMENT IF YOU DO NOT AGREE TO ALL OF THESE TERMS SELECT THE DISAGREE BUTTON AT THE END OF THIS AGREEMENT AND THE SOFTWARE DOWNLOAD WILL NOT CONTINUE Restrictions All downloads and use of the Osprey Network Visualization System are subject to the following terms As long as you comply with the terms of this Agreement you are granted a non exclusive license to install and use the Software on a single computer for educational research and not for profit purposes without fee Except as expressly permitted in this Agreement you may not use copy decompile reverse engineer disassemble modify rent lease loan sublicense distribute or create derivative works based upon the Software in whole or part or transmit the Software over a network You shall not remove any copyright notices or other proprietary notices from the Software Except as expressly stated herein this Agreement does not grant you any intellectual property rights in the Software and all rights not expressly granted herein are reserved by Mount Sinai Hospital The right to download copy install use and distribute this software and its documentation by companies or other for pr
77. Ring Options found in the Advanced Settings window under the tab labeled Spoked Dual Ring Figure 6 5 2 1 label 1 it is possible to adjust the following settings 1 Min Edges for spokes in INNER ring Figure 6 5 2 1 label 2 e This sets the minimum cutoff for the number of connected free nodes required for a spoke to be in the INNER ring e Anything less than this cutoff will be in the outer ring 2 Min Edges for spokes in OUTER ring Figure 6 5 2 1 label 3 e This sets the minimum cutoff for the number of connected free nodes required for a spoke to be in the OUTER ring e Anything less than this cutoff will not make it to either ring It will relaxed somewhere on the screen 3 Size of smallest spoke ring Figure 6 5 2 1 label 4 e This adjusts the radius of the smallest ring as a percentage of the largest ring Osprey 6 23 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts e The distance between every ring larger than the smallest is divided equally 4 Capacity of smallest spoke ring Figure 6 5 2 1 label 5 e This adjusts the capacity of the smallest ring as a percentage of all nodes currently selected e The remaining percentage of nodes 1s divided in an increasing manner so that the larger the ring the higher the percentage of nodes There are two ways to access the Spoked Dual Ring Options see section 6 5 2 1 Accessing Spoked Dual Ring Layout Option settings tg Advan
78. S Draw IV Nodes V Edges Labels V Arrows mm Exp System CO Process a Figure 6 6 5 2 Network with a degree of GO Process colouring of 1 Osprey 6 35 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts EJ Osprey powered by Yeast GRID Untitled File Never Been Saved 5 x File Edit View Insert Format Filters Layout Help hoos ll A soncser ho ew zlehe dla fo de Gene Edge Info oe lect a single vertexedge SPA2 MDS PLOW 44 CTR g 0 Network Filters Experimental System SOUFCE 4 fe le 27 0 ma 33 0 Loner Modes YES Draw M Modes V Edges I Labels M Arrows m Exp System GOProcess IERIE Figure 6 6 5 2 Network with a degree of GO Process colouring of 3 Osprey 6 36 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada 7 Osprey Preferences and Customization This section will describe several options that are available for customization within Osprey These options include the following e Ability to change sizes and colours of most Osprey objects such as edges nodes labels and arrowheads e Ability to change background colours 7 1 Graph Colouring The graph can be coloured by three different methods These methods change the colours used by Osprey to colour a network A graph can be coloured by one of the following methods e Default Colours Colouring by defau
79. S ENHANCEMENTS OR MODIFICATIONS MOUNT SINAI HOSPITAL DOES NOT WARRANT OR ASSUME RESPONSIBILITY FOR THE ACCURACY OR COMPLETENESS OF ANY INFORMATION TEXT GRAPHICS LINKS OR OTHER ITEMS CONTAINED WITHIN THE SOFTWARE Published research assisted by this software should cite Breitkreutz BJ Stark C Tyers M Osprey A Network Visualization System Genome Biology 2003 4 3 R22 Osprey 1 5 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 1 General Information 1 4 Contact Information For commercial licensing opportunities suggestions corrections bug reports more information or for joining our mailing list contact The Osprey Administrator E mail ospreyadmin mshri on ca 1 5 Osprey Licensing Please see section E Purchasing Osprey Licenses for Commercial Organizations for full details of Osprey licensing policy 1 6 Joining the Osprey Mailing List To be kept up to date on all the latest bug fixes version releases and other information about the Osprey Network Visualization System please subscribe to the Osprey mailing list by sending an email to The Osprey Administrator E mail ospreyadmin mshri on ca Or visit the Osprey web site at http biodata mshri on ca Osprey Osprey 1 6 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada 2 Osprey Installation This section describes how to obtain and install Osprey on supported operating systems The follo
80. Sinai Hospital Toronto Canada Chapter 4 Basic Introduction Create Default Spoke This option will bring all nodes that are connected to currently selected nodes into spoke layouts disregarding where these nodes were before Spoked Dual Ring Layout This is a global layout that will attempt to place a large amount of nodes into an easily manageable layout Lock Nodes This option will lock any selected genes in place so that they will not be affected by any layout algorithm except the global ones Unlock Nodes This option will unlock any locked selected genes allowing their position to be manipulated by all layout algorithms Remove Nodes This option will permanently remove any selected nodes from the network See section 4 3 2 6 Removing Nodes for more details Remove Edges This option will permanently remove any selected edges from the network See section 4 3 2 7 Removing Edges from more detail 4 4 Gene Edge Info The Gene Info Area displays information about the selected node This information is obtained from the Grid database Osprey If the gene is known as the one in figure 4 4 1 all the data about this gene will be displayed in this section If the data is not know or if the added gene is a custom gene this area will not display much information as in figure 4 4 2 4 36 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction E dOsprey Untitled File Never
81. Spoked Dual Ring Concentric Circles Spoke layout Settings Drawing Graph Dragging Graph BackGraund Functional Clustering Visible GO Process Order Carbohydrate Metabolisr Cell Organization and Biogenesis Cell Shape and cell size control A DNA metabolism Default Order DNA Damage Response DMA Repair V DAS recombination a Y DMA Replication ap size between clusters Degree of GO Process colouring fi Functional Clustering Figure 6 6 3 1 Choosing Gap size Osprey 6 31 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Layouts Chapter 6 EgOsprey C Documents and Settings hosam My Documents showSpokes osp modified File Edit view Insert Format Filters Layout Help O S S amp fhs O HM aA Sansseri Bre E szie fsals k e Ng Gene Edge Info eee es e aeveng t Select a single vertex edge s patt we S ees s a Po Sas m s t a s ete as oe o 02 9 PFET E aaa PH E 6 a eo e a in aE E a E Pa ss 4t 2 Ps EEA e e i r E r E E ets ts prt tr E 4 0 E E es e s ec tf 2 o 02 Pag Me te eg HH oa ot tg 0 getty 2 at o a b es e tet 7 E a4 s to B B e s2 oo t 6 s gt o p r 270 Sa ste Pte tea g otto eve oH eee O d 4 G r s a r E t gt
82. The Change Default Background Button in Advanced Settings 7 8 Saving Preferences Osprey provides the ability to save network preferences so that they are maintained each time the application is launched With this users can fully customize the look and feel of their networks including all settings described in section 7 Osprey Preferences and Customization and ensure that each time they launch Osprey these settings will be maintained 7 8 1 Saving settings Osprey provides two different options for saving settings These options allow the user to customize certain aspects of the application so that they may be maintained with each initialization of the application The types of settings that can be saved within Osprey are e Advanced Settings e Colour Settings Osprey 7 34 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization 7 8 1 1 Saving Advanced Settings Advanced Settings include all the settings in the Advanced Settings Menu as well as all user defined node edge label and arrow sizes and colours Follow these steps to save the advanced settings e Click on File from the menu bar e Click on the Save Settings submenu e Click on save Advanced Settings option Note This option will take all of your settings described above and will initialize Osprey with these settings each time the application is run E dOsprey Untitled File Never Been Saved
83. Toronto Canada Chapter 4 Basic Introduction hy Documents Save in Recent Desktop a pr My Documents ks a I Us ee a es JPEG Graphic jpg jpedi Portable Wetwork Graphic i png 3 File name Scalable Vector Graphic svq o opn Files of type Cancel My Computer My Network Scalable Vector Graphic svq Figure 4 6 4 2 The File Chooser for saving a color index e Choose a destination to save the file and type a name for the index and click save to create the index For an example of a colour index for an arbitrary network see the following figure figure 4 6 4 3 Osprey 4 58 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Osprey Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Vertices Cell Growth and or maintenance Cy Mating sensu Saccharomyces ceicycte unknown gt Budding Cell Organization and Biogenesis Signal transduction Protein transport Transport metabolism DNA Repair gt DNA metabolism DNA Replication Protein metabolism and modification Protein amino acid phosphorylation cell Shape and cell size control Sporulation Protein biosynthesis Stress Response Protein Degradation Carbohydrate Metabolism DNA recombination B Transcription amp RNA processing B Ribosome Biogenesis Experimental Systems OS SYNTHETIC LETHALITY E
84. UETZ ET AL Apply to Graph Close Figure 5 1 2 4 1 Filter by source window demonstrating how to group the selected items in the existing list to the visible list by selecting the Group Selected buttons Osprey 5 15 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters 5 1 3 Experimental System The experimental systems filter helps the user to display nodes that are related by the chosen experimental systems See sections 5 1 1 Accessing Network Filters and 5 1 2 Using the Network filtering windows to learn how to access and use the filter window The following images display an example of how to take advantage of the experimental systems filter Figure 5 1 3 1 is the original unfiltered graph coloured using Experimental System Colours Figure 5 1 3 2 is the settings to filter away the Affinity Precipitation and Dual Hybrid Experimental Systems and keep only the Synthetic Lethality Experimental System e Figure 5 1 3 3 is the filtered graph Al Change Colour B tio Hyver Change Colour D AFFINITY PRECIPITATION Change Colour D SYNTHETIC LETHALITY YMRS ADY Figure 5 1 3 1 The original unfiltered graph coloured using Experimental System Colours Osprey Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters F drilter by Experimental System SYATHETIC LETHALITY AFFINITY PRECIPITATION TiO HYBRID SYATHETIC LETHALITY Figur
85. UR ACCEPTANCE OF THESE TERMS BY SELECTING THE ACCEPT BUTTON AT THE END OF THIS AGREEMENT IF YOU DO NOT AGREE TO ALL OF THESE TERMS SELECT THE DISAGREE BUTTON AT THE END OF THIS AGREEMENT AND THE SOFTWARE DOWNLOAD WILL NOT CONTINUE Restrictions All downloads and use of the Osprey Network Visualization System are subject to the following terms As long as you comply with the terms of this Agreement you are granted a non exclusive license to install and use the Software on a single computer for educational research and not for profit purposes without fee Except as expressly permitted in this Agreement you may not use copy decompile reverse engineer disassemble modify rent lease loan sublicense distribute or create derivative works based upon the Software in whole or part or transmit the Software over a network You shall not remove any copyright notices or other proprietary notices from the Software Except as expressly stated herein this Agreement does not grant you any intellectual property rights in the Software and all rights not expressly granted herein are reserved by Mount Sinai Hospital Osprey 1 4 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 1 General Information The right to download copy install use and distribute this software and its documentation by companies or other for profit organizations or in conjunction with for profit activities are not granted except by
86. a Windows 2000 NT or XP In order to install Osprey you must be using an account that has Administrative rights so that the installer will be able to write to the Windows registry If you are unsure whether your account has these privileges contact your system administrator who will be able to advise you on your account status A 5 2 Unable to Add Interactions If you are unable to add interactions to your network by querying The GRID the most likely problem is that you do not have an active connection to the Internet Close Osprey make sure that your Internet connection 1s active and try running Osprey again to see if you can establish a connection to The GRID Osprey A 3 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada B Credits This appendix lists the developers contributors and supporters that have helped to make the Osprey Network Visualization System what it is today B 1 The Osprey Team These are the developers that are or have been on the Osprey project and have contributed to the project in one form or another They are listed roughly in the order they were involved in the project Above each of the members is small description of their contribution to the project All team members are still actively involved in support of Osprey Developed and Designed by Bobby Joe Breitkreutz Chris Stark Principal Investigator Mike Tyers Contributors Hosam Abdulrrazek Testing Team Rob
87. action Ctrl ShiFE I Figure 4 5 2 2 3 Insert Menu Only interactions within Selected Nodes 4 6 Colour Indices Colour indices show a mapping of colours used in a network to their meaning There are three major colour indices used by Osprey when displaying a network e Go Process Index Shows colours for each of the GO Process categories currently displayed on the Network and used to colour the individual nodes on the graph e Experimental Systems Index Shows colours for each of the Experimental Systems currently displayed by Osprey and used to colour the edge segments when the graph is in Colour By Experimental System Mode see section 7 1 Graph Colouring for more details e Sources Index Shows colours for each of the Sources currently displayed by Osprey and used to colour the edge segments when the graph is in Colour By Source Mode see section 7 1 Graph Colouring for more details To access the various colour indices please refer to the windows menu see section 4 2 5 Windows Menu Osprey 4 54 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction 4 6 1 Go Process Index EgGo Process Colours Index ie B x Change Colour A Cell Cycle Change Colour Cell Growth and or maintenance Change Colour Mating sensu Saccharormyce Change Colour Transcription Change Colour Metabolism Change Colour Budding Change Colour amp Cell Organization and Bio
88. advanced Settings gee 2 0 x Colour WodesfEdges By Spoked Dual Ring Concentric Circles Spoke layout Settings Dragging Graph BackGround Draw the selected items IY Nodes fw Edges Labels Arrows Figure 7 2 1 3 The Drawing Graph tab of the Advanced Settings Dialog Osprey 7 6 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization g Advanced Settings O x Colour WodesfEdges By Colouring Graph Concentric Circles Spoke layout Settings Drawing Graph Dragging Graph aii BackGround Draw the selected items while dragging the graph JY Nodes fw Edges Labels Always Figure 7 2 1 4 The Dragging Graph tab of the Advanced Settings Dialog 7 3 Node Options Nodes can be coloured by their biological process as defined by standardized Gene Ontology GO annotations Nodes that have been assigned more than one GO process are represented as multicolored pie charts Osprey currently recognizes 29 biological processes derived from the categories maintained by the GO Consortium Users have the option of displaying nodes by these colours or by their own set of user defined colours By choosing GO Process nodes will be coloured based on the appropriate GO annotation category Note Each of these options will continue to apply to all new nodes that get added to the screen after the option has changed 7 3 1 Choosing Me
89. al Copyright 2002 Mount Sinai Hospital Toronto Canada ili Table of Contents Dee MC Meher recente teste kare eter rete kas eo nae 5 27 2 5 MAON CONNEC e e e E E dese oune eset 5 28 6 WGAy OWES aer E E NE E N E Ga 6 1 Gol Auto R laxo E E A E A AE 6 1 6 1 1 Accessing the auto relaxation from the main menu 6 1 62 C odlar Way OWS esna a nee ceseiva an RE eam iadansanueens 6 3 OZ ORCS Ole arccusnms cient arse cctsnnuei ses E teeta EE 6 3 6 2 1 1 Accessing the one circle layout 0 0 ccc cece cece e ees 6 4 O22 Conecte Circles cerren er a a a ee 6 6 6 2 2 1 Accessing the concentric circles layout ccc cece ee 6 7 6 2 3 Concentric Circles Options cen diseies coetedeswaine dpsed awassoedes teens 6 8 6 2 3 1 Accessing the Concentric Circles Options 0008 6 10 6 3 Dual Rng Way OUtS versace ccatadad teens E dena nawekeases te 6 11 oe PORO ee ee ee ee eee ne een eer ne oe 6 13 Oe TOC rAUICS POKE Siac setters ccs ets reeds ee eels Secs as cn anne 6 14 6 4 1 1 Accessing the default spoke model cc cee eens 6 15 C42 WOCE SPOK S areira EE EOE TEREE 6 16 6 4 2 1 Accessing the forced spoke model ccc cece eee e ee eens 6 17 G43 SPOKS OPlOiSesic once one aioneyiiewadedsne A a 6 18 6 4 3 1 Accessing the spoke Options cc cece cece eee eeeneeeeees 6 20 6 5 Global TA OUIS arenes can doieeasgtaarsoniGinens thee henglaermumatendlactcades 6
90. all the nodes that are not currently selected and unselect all the currently selected nodes e Crop White Space This option will get rid of all excess white space around the graph and will move the graph to the upper left to save the most space on the Network Display Area Osprey 4 8 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction e Fit to Screen When clicked this will adjust the zoom percentage between 25 125 to best fit the network completely on your current screen e Zoom In This will make the network appear larger on the screen increased by 1 e Zoom Out This will make the network appear smaller on the screen decreased by 1 e Lock Nodes This option will take all of the selected nodes on the graph and will lock them in place so that they are unaffected by automatic layout procedures such as Automatic Relax e Unlock Nodes Use this feature to take any nodes that have been locked in place and allow them to be moved by automatic layout procedures e Remove Nodes This will take any nodes currently highlighted in the network and permanently remove them e Remove Edges This will take any edges currently highlighted in the network and permanently remove them e Find This will search for a node by its gene name orf name or screen name e Update Node Annotation This will connect to the GRID and download the latest Node Annotations see section 4 4 4 Update Annotation
91. apter 2 Osprey Installation wI Osprey 1 0 0 Choose Shortcut Folder TJ Introduction gi J Important Information H Choose Install Folder a 4 SJ choose Shortcut Folder be Erednetalletimnie ciprini bri na ag las oe Onthe Desktop J Instal Earla Inthe Quick Launch Bar a E Other Choose 1 i Dont create icons Where would you like to create product icons In a new Frogram Group osprey 0 0 O nan existing Program rove Osprey 1 0 0 of Inthe Start Menu i p i ae E Create loons for All Users Cancel Previous Figure 2 2 6 Osprey Installation Choose Shortcut Folder page 6 The next page will outline the options you have selected in a pre installation summary Please review the information and ensure that everything is correct and click NEXT to continue Osprey 2 19 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation wI Osprey 1 0 0 Pre Installation Summary EJ introduction Please Review the Following Before Continuing A important information Product Name iv Choose Install Folder pas osprey 1 0 0 Choose Shortcut Folder z Fre Installation Summary i B lrrsteillinie m fj a sill Gormglaiz Shortcut Folder CADocuments and Settingsihobbyjoestart Witt MenusProgramssosprey_ 1 0 0 i Install Folder LProgram Files Osprey 1 0 0 Disk Space Information f
92. ar Dual Ring Spokes b Global Figure 4 2 7 2 The Auto Relaxation Submenu e Circular This submenu has the circular layouts you can choose from o One Circle This option places all the selected nodes in a circle whose size is proportionate to the size of the selection box o Concentric Circles This option places all the selected options in concentric circles o Concentric Circle Options This option gives the user the ability to change the number of rings as well as the capacity of rings to achieve the best fit Layout Help Auto Relaxation P B TT 77 lesneferif B Ih a Circular D One circle Dual Ring b 2 Concentric Circles Spokes le Global Concentric Circles Options d Figure 4 2 7 3 The Circular Submenu e Dual Ring The following two layouts split the nodes into two groups highly connected nodes in and highly connected nodes out o Highly Connected In This option places all the highly connected nodes in the inner circle and all other nodes in the outer circle o Highly Connected Out This option places all the highly connected nodes in the outer circle and all other nodes in the inner circle Osprey 4 19 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction Layout Help j uto Relaxation SansSerif hz Circular Dual Ring Highly Connected In Spokes C Highly Connected Gut Global z Figure 4
93. artners Tutorials Support Forums About Osprey DOWNLOAD OSPREY Osprey Network Visualization System Academic Version linux gt Release Version 1 0 0 Osprey is a software platform for visualization and manipulation F of complex interaction networks Osprey builds data rich Osprey graphical representations that are color coded for gene function l ES and experimental interaction data Mouse over functions allow Network Visualization rapid elaboration and organization of network diagrams in a System spoke model format Osprey also allows for user defined large scale datasets to be readily combined for comparison of diferent methods In addition to this Osprey is linked to the GRID and comes rich with annotation and interaction data for many commonly studied organisms such as Yeast Mouse Human and Drosophila Minimum System Requirements gt Pentium Il 450 Mhz CPU gt 126 MB of Memory gt 70 MB of Harddrive Space Problems Downloading or Installing Click Here Contact Us Osprey Community Terms and Conditions Copyright 2002 2003 Mount Sinai Hospital All Rights Reserved D t Sf E GH Dore Osprey 2 12 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation Figure 2 1 3 2 1 The Linux Osprey Download Page There are three major sections to the download page for Linux Each of these 1s necessary for downloading the Osprey Network Visualization Syst
94. ation method attempts to place the nodes in the graph at a pre defined distance from each other without intersecting any lines This iterated relaxation results in a more easily viewable graph The auto relaxation method is an extension of the Java Sun graphing algorithm version 1 8 98 10 28 which can be found at http java sun com Note When Start Relax is called it will continue relaxing the nodes until Stop Relax is called Section 6 1 1 Accessing the auto relaxation from the main menu demonstrates the ways in which to activate the auto relaxation method 6 1 1 Accessing the auto relaxation from the main menu There are currently two ways in which the user can access the auto relaxation method 1 The Menu Bar Select all nodes that need to be relaxed Click on the Layout overhead menu Click on the Auto Relaxation submenu Click on Start Relax see figure 6 1 1 1 To Stop the relaxation process follow the same steps as above and click on Stop Relax O O O O O Osprey 6 1 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts Layout Help Suto Relaxation Start Relax Ctri R Circular Dual Ring Spokes Global Kr F F F Figure 6 1 1 1 Accessing the relaxation method via the main menu Note The other way to stop is to click the small stop button at the bottom right hand corner of the screen this button is only active when the graph is being relaxed see
95. ave Osprey running you ll have to re start it in order to recognize any new datasets that have been added Osprey 3 12 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 3 Opening and Saving Files Bd Osprey powered by feast GRID Untitled File Never Been Saved ee k O x File Edit View Insert Format Filters Database Layout Help Onen cei fons O at AA sanccen aE e 78 fs al ta Standard Ctra ey Save Ctrl 5 Download New Datasets Save s Fly Networks p Save Colour Index MY FILES F My Osprey File 1 0sp Save Settings b worm Metworks b My Osprey File 2 05p E Print Ctrl P Yeast Networks SUperimpose d Export Work OFFline Exit Osprey Network Filters ee ee 1 HE e O 0 m O c0 Loner Modes YES Draw IY Nodes I Edges If Labels I Arrows Exp System 7 Figure 3 1 4 2 1 Adding Personal Datasets 3 1 5 Superimposing Datasets Osprey offers you the option of superimposing or adding two or more datasets on top of each other This feature can be very helpful for comparing data created by different sources or using different experimental systems Osprey can superimpose all three of the accepted file formats including the built in datasets See section 3 1 Types of Files Opened by Osprey for a description of the types of files that can be superimposed Follow these steps to superimpose datasets e Click on the File Menu bar e Click the Sup
96. being dragged o Turn any of these on or off by clicking the appropriate checkbox see figure 7 2 1 1 Osprey 7 4 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization EJ Osprey Untitled File Never Been Saved E O x File Edit view Insert Formak Filters Layout Help D amp E S Q froox el A eser ie E ez lee lse e QQ Gene Edge Info ee lect a single vertex edge Selected Node Report Eo DIG ULP1 CO Turn Off Fiters TEN Y Connection Filters s SRP 1D PEP1 Minitriven D rae YMRS ADYS erative Miniriurn Depth Turn ati connectivity F 4 a PE mm 43 Loner Nodes Draw Nodes Edges IM Labels Arrows Leiource GOProcess sol x Figure 7 2 1 1 The Drawing Dragging options area in the Osprey Status Bar e Via the Menu bar o Click on Format in the Menu bar o Click on Advanced Settings o Click on Drawing Graph as shown in Figure 7 2 1 3 or Dragging Graph as shown in Figure 7 2 1 4 o Turn any of these on or off by clicking the appropriate checkbox Osprey 7 5 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization Format Filters Layout Help 1 Nodes Edges b A Arrows p Text d Background Colour Advanced Settings Figure 7 2 1 2 The advanced settings option in the Format Eg
97. ced Settings Concentric Circles Spoke layout Settings Drawing Graph Colour NodeslEdges By Colouring Sraph Spoked Dual Ring 2l Min edges For INMEF ring in spoke layouts F Min edges For OUTER ring in spoke layouts ho Capacity of smallest ring of spoke layouts m 4 Size of smallest ring of spoke layouts Apply to ALL nodes Figure 6 5 2 1 Spoked dual ring layout settings advanced options tag Osprey 6 24 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts 6 5 2 1 Accessing Spoked Dual Ring Layout Option settings There are currently two ways in which the user can access Spoked Dual Ring Layout Option settings 1 The Layout option in the Menu Bar o Click on the Layout overhead menu o Click on the Global submenu o Click on Spoked Dual Ring Options Layout Help j Auto Relaxation P SansSerit a a Circular b Dual Ring b Spokes b Global i Figure 6 5 2 1 1 Accessing the spoked dual ring layout options via the main menu bar under the Layout menu 2 The Advanced settings options in the Menu Bar o Click on the Format overhead menu o Click on Advanced Settings o Look for the Spoked Dual Ring tab and click it Format Filters Layout Help Nodes at Edges b ArrOWS p Text p Background Colour Advanced Settings oS as Osprey 6 25 Operator s Manual Copyright 2002 Mount Sina
98. creen click the Previous button You may cancel this installation at anytime by clicking the Cancel button Prewious Figure 2 3 6 The Osprey Installer Introduction 7 Next you will be presented with the Osprey Network Visualization System User Agreement Please read this carefully By clicking NEXT you will agree to these terms and conditions If you do not agree to the terms and conditions simply click CANCEL at any time to abort the osprey installation If you agree click the NEXT button to continue Osprey 2 26 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation wI Osprey 1 0 0 Important Information Introduction important Information Choose Install Folden Choose Shortlutrelder e Erez Please Read Before Continuing Copyright Notice Copyright 2002 Mount Sinai Canada All Rights Reserved Hospital Toronto Stel AU Ghh SU tiiiiiety jai security personnel Warning This system may be monitored by system or i License Agreement for the Usprey Network 7 Visualization System and all documentation THIS AGREEMENT SETS OUT THE TERMS AND CONDITIONS FOR DOWNLOADING COPYING INSTALLING OR USING OSPREY NETWORK VISUALIZATION SYSTEM SOFTWARE AND ASSOCTATED MATERIAL AND DOCUMENTATION INCLUDING ANY MODIFIED VERSIONS OR UPDATES COLLECTIVELY Previous
99. ction Box Osprey 7 27 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization e Via the Menu bar o Select all the nodes whose label font you want changed Click on the Format menu from the Menu bar Click on the Text submenu Choose the font option to change the label font see figure 7 6 1 2 From the resulting font options dialog you have the ability to manipulate the font as well as most other label options described in this section see figure 7 6 2 2 O O O Font Options ags E x Fonts Sanset v Sans serif SimSun STOMP Almonte Woodgrain STOMP _Angoastura STOMP Blue Highway STOMP Blue Highway Condensed Figure 7 6 2 2 The Font Options Dialog 7 6 3 Label Style Osprey offers two methods for manipulating the style of a label Before attempting to change the style of a label ensure that you have at least one node selected in the Network Display Area The following describes the two major methods of accessing the label style e Label Style Selection Buttons o Select all labels whose style is to be changed o Click the desired style button Bold Italic or Both in the Osprey toolbar see figure 7 6 3 1 o Changes to label style are immediately reflected on the Network displayed in the Network Display Area Osprey 7 28 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences an
100. d Customization Figure 7 6 3 1 The Osprey Label Style Selection Buttons e Via the Menu bar Select all the nodes whose label style you want changed Click on the Format menu from the Menu bar Click on the Text submenu Choose the Font option to change the label style see figure 7 6 1 2 From the resulting font options dialog you have the ability to manipulate the font style as well as most other label options described in this section see figure 7 6 3 2 O O O O 0 F Font Options a x Fonts SansSerif Sizes Styles PLAIN ITAI bir Figure 7 6 3 2 The Font Options Dialog 7 6 4 Label Colour Osprey offers two methods for manipulating the colour of the text in a label Before attempting to change the colour of a label ensure that you have at least one node selected in the Network Display Area The following describes the two major methods of accessing the label colour e Label Colour Selection Box o Select all labels whose font colour is to be changed Osprey 7 29 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization o Select the desired color in the from the resulting colour choosing window see section 7 3 3 Colour Choosing Window o Changes to label colour are immediately reflected on the Network displayed in the Network Display Area 5 x Pe CLA CKS1 AEAN e Via the Menu bar o Select all the nodes
101. d prompt see figure 2 3 3 File Edit View Terminal Go Help Figure 2 3 3 Modifying the permissions of the Osprey bin file to allow it to be executed 4 Once you have modified the permissions on the file you can now execute the osprey installer by typing osprey_1_ 0 0 bin at the command prompt Osprey 2294 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation File Edit View Terminal Go Help osprey tar gz Desktop osprey tar osprey tar Figure 2 3 4 Osprey Installation File and the command line option to run it 5 The Osprey installer will now launch and the installation application will initialize oai File Edit View Terminal Go Help Figure 2 3 5 The Osprey installer initialization Osprey 2 25 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation 6 Once the Osprey installer has launched you will be asked a series of questions about your installation Firstly you are presented with an introduction to the install procedure fig 2 3 6 Please read this carefully and click NEXT to proceed JRE Introduction InstallAanywhere will guide wou through the installation of osprey 1 0 0 It is strongly recommended that you quit all programs before continuing with this installation Click the Wext button to proceed to the next screen If you wart to change something on a previous s
102. date Comment Remove Comment Close Figure 4 4 2 4 View Comment Window e To modify the comment type in the desired modifications then click on the Update Comment button e To remove the comment completely click on the Remove Comment button e To close the comment without making changes click the close button 4 4 3 Viewing Selected Node Report You can view the gene info for two or more genes in a report like table Follow these steps to find out how e Select the desired nodes e From the Main Menu bar select the Selected Node Report menu item under the view menu Osprey 4 42 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction File Edit View Insert Format Filters Layout He O ce p Colour Indexes i Toolbars Cene loner Modes Drawing Options b p 3 decia Dragging Options Network Statistics ted Mode Report view All Comments Figure 4 4 3 1 Selected Node Report menu item e Click on it and a report window will appear Egal Selected Genes user defined node HOHE HOHE HOHE UHEHOWH o n PELA YOLI2TW ae role in cell cycle START cyclin dependent l reg Pea cell cycle cellar component actrity z protein kinase n cell growth andlor unknowt GLS transition of regulator te Traintenarice mitotic cell cycle regulation of CDE actrity cell eyele cyclin dependent GLS transition of cell growth
103. disk Installation Sui nman Macintosh HD a Alias Folder Desktop in the folder bobbyjoe on the disk Macintosh HD Disk Space Information for Installation Target Required 23 399 370 bytes Available 18 652 421 632 bytes Cancel Previous Install Figure 7 Osprey Pre Installation Summary 7 The Osprey install will now copy all of the files needed to run Osprey see figure 8 Osprey 2 38 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation Tener ee 0 0 2 PP install Complete CEE Cm itis kis Sis Installing section2 3image4 png Figure 8 Osprey install progress copying files to your computer 8 Now the Osprey installation is complete see figure 9 Click on the DONE button to finish the install and close the Osprey installer Osprey 2 39 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation Osprey 1 0 0 a Install Complete Congratulations osprey_1 0 0 has been successfully installed to Applications osprey_1 0 0 Choose Alias Folder Prass Done to quit the Installer E Pre installation Summary Figure 9 Osprey Install Complete This section assumes that you have previously installed Osprey on your computer If you have not installed Osprey see section 2 2 Standard Installation Procedure for Microsoft Windows Systems ME XP 2000 98 95 NT or sec
104. divided equally 2 Capacity of smallest ring Figure 6 4 3 1 label 3 e This adjusts the capacity of the smallest ring as a percentage of all nodes currently selected e The remaining percentage of nodes 1s divided in an increasing manner so that the larger the ring the higher the percentage of nodes There are two ways to access the concentric circles options see section 6 4 3 1 Accessing the spoke options eae _ o x l ing Graph Spoked Dual Ring Drawing Graph Dragging Graph BackGround Advanced Settings Colour NodestEdoes By Concentric Circles Spoke Layout settings Capacity of smallest ring of spoke layouts f 0 Size of smallest ring of spoke layouts 26 Figure 6 4 3 1 Spoke layout settings advanced options tag Osprey 6 19 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts 6 4 3 1 Accessing the spoke options There are currently two ways in which the user can access the spoke options 1 The Layout option in the Menu Bar o Click on the Layout overhead menu o Click on the Spokes submenu o Click on Spoke Options Layout Help Suto Relaxation P SansSerif a Circular Dual Ring b Spokes Default Global b Forced Spoke Options Figure 6 4 3 1 1 Accessing the spokes options via the main menu 2 The Advanced settings options in the Menu Bar o Click on the Format overhead menu o Click on
105. e 5 1 3 2 Filter settings to remove everything but Synthetic Lethality Osprey 5 17 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters Figure 5 1 3 3 Filtered Network 5 1 4 Source The sources filter only keeps nodes that are related by the chosen source See section 5 1 1 Accessing Network Filters and 5 1 2 Using the Network filtering windows to learn how to access and use the filter window The following images display an example of how to take advantage of the source filter e Figure 5 1 4 1 is the original unfiltered graph coloured using Source colours e Figure 5 1 4 2 shows the Source Filter settings that remove all nodes with sources other than MIPS or Ho Et Al and Gavin Et Al and Uetz Et Al e Figure 5 1 4 3 shows the filtered network Note the edge between CLLN1 and CDC28 with 4 colours arrow is the edge with all three Ho Et Al and Gavin Et Al and Uetz Et Al as sources Osprey 5 18 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters b Sa age k ah i F g Sources Colour Index Ioj Change Colour B verz er av Change Colour D mips Change Colour ITO ET AL Change Colour B Ho ET aL Change Colour Fe GAWIN ET AL al rf Figure 5 1 4 1 Original unfiltered graph with edges coloured by source The source colours are defined in the bottom right Osprey 5 19 Operator s Manual Copyright 2002 Mount Sinai Hospital
106. e GRID The General Repository of Interaction Datasets Important Reports of any errors often called bugs as well as questions and comments should be sent to ospreyadmin mshri on ca For more information on contacting us please see section 1 4 Contact Information Osprey 1 1 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 1 General Information 1 1 About this Manual This is the Osprey Network Visualization System manual Being a reference manual it does not provide any general information on the actual development involved in the product No documentation of source code or tools 1s provided within as Osprey is under constant development this manual is also updated frequently The most recent version of the manual is available at http biodata mshri on ca osprey in various formats If you have any suggestions concerning additions or corrections to this manual please send them to the documentation team at ospreyadmin mshri on ca This manual was initially written by Bobby Joe Breitkreutz Chris Stark and Hosam Abdultrrazek It is currently maintained by the Osprey development team at Mount Sinai Hospital For other contributors please see section B Credits The copyright 2002 to this manual is owned by Mount Sinai Hospital in Toronto Ontario See section 1 3 Copyright Notice This manual is best viewed with Microsoft Internet Explorer version 6 0 or Netscape Mozilla version 1 1
107. e an Osprey License e Ifyou distribute Osprey with another application of any kind if your organization is non academic e Ifyou wish to Support further Osprey development If you fall into any of the above categories click here to purchase Osprey licenses Osprey Network Visualization System Osprey Academic Applications Osprey 1 0 1 for Windows Latest Release ACADEMICS ONLY Osprey 1 0 1 for Mac OS X Latest Release ACADEMICS ONLY e Osprey 1 0 1 for Linux Latest Release ACADEMICS ONLY Osprey Commercial Applications Osprey 1 0 1 30 Day Trial for Windows Latest Release Osprey 1 0 1 30 Day Trial for Mac OS X Latest Release e Osprey 1 0 1 30 Day Trial for Linux Latest Release Confused Or Having Trouble Downloading Or Installing he Download And Installation Sections Of The Osprey User Manual Have Information That May Get You Going Again Contact Us Osprey Community Terms and Conditions Best viewed at 10242768 resolution wih all modern web browsers Copyright 2001 2003 Mount Sinai Hospital Sil Rights Reserved xl BOO OO O O ne Figure 2 1 2 1b The Osprey download page with all versions both Academic and Commercial available for download Choose the version that is appropriate for you academic or commercial and the platform you will be running Osprey on Mac OS X Windows or Linux by clicking the link associated with that version This will take you to the Osprey download login page I
108. e headers GeneA GeneB GeneA Screen Name and GeneB Screen Name of the four columns that must exist in this variation of a custom interaction file The first two columns represent the different interacting pairs that will be loaded into Osprey The third and fourth columns represent the names that will be displayed on the screen Figure 3 1 2 2 2 demonstrates what the network would look like after opening it up in Osprey Note The rows and columns in red are necessary The rows and columns in gray are optional You can choose to only change the gray rows that need changing Osprey 3 3 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 3 Opening and Saving Files sene GeneB reneA Screen Name sene B Screen Name CDC28 YMR199W CLNI CDC28 CLN3 CDC28 CLB2 CLB2 CDC28 CDC7 CDC28 MET10 YMR199 CDC28 YMR199 CLN2 YMRI199_CDCS53 Figure 3 1 2 2 1 Custom File Variation 2 0S3 CLA CLA ea Lg Figure 3 1 2 2 2 Result of loading custom file variation 2 into Osprey 3 1 2 3 Custom File Variation 3 The first row in figure 3 1 2 3 1 contains the headers GeneA GeneB Experimental System Source and PubMed ID of the five columns that must exist in this variation of a custom interaction file The first two columns represent the different interacting pairs that will be loaded into Osprey The last three columns contain details about the interactions The third column contains the E
109. ear asking you if you are sure you want to do this it may take a long time if you have a slow internet connection Update Annotation Option a i xX to the latest annotation available Are vou sure you want to do this Cancel AN This option will connect to The GRID and may change the annotation of your layout Osprey 4 44 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction Figure 4 4 4 2 Update Note Annotation Warning e Ifyou click Update Osprey will connect to The GRID and update your annotation 4 4 5 Edge Info If you click on an edge the Gene Edge Info area will show you the edge info It will display the node s given Gene and ORF names as well as Experimental System Source info and any PubMed links 4 5 Adding Interactions The ability to incorporate new interactions into an already existing network is one of the most powerful features that Osprey has to offer Interactions can be added to the graph from a large selection available in Ospreys underlying support database see section 8 The GRID The General Repository of Interaction Datasets There are three major areas of Osprey that can be used to add new interactions Namely e The Orf Info Area e The Network Display Area Command Menu Right click menu e The Edit Menu Osprey 4 45 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction
110. ed Edge Colours To view User Defined Coloured Edges the user defined mode has to be chosen for edges as described in section 7 4 1 Choosing Method of Colouring Edges There are two ways to manipulate user defined colours It can be done in one of the following ways e Toolbar Edge Colour Button o Select all the edges whose colours you want changed o Click on the edge Colour selection button on the Toolbar as shown in figure 7 3 2 1 o From the resulting edge colour choosing window you can now choose the colour to reflect on the User Defined edges For more information on the colour choosing window see section 7 3 3 Colour Choosing Window User defined edge colours will immediately be reflected in the selected edges in the Network Display Area Set Edge Colour TEM P Figure 7 4 2 1 The Edge Colour Selection button on the Osprey Toolbar e Via the Menu bar Select all the edges whose colours you want changed Click on the Format menu from the Menu bar Click on the edges submenu Choose the Colour option to change the User Defined Edge Colours see figure 7 4 2 2 o From the resulting edge colour choosing window you can now choose the colour to reflect on the User Defined edges For more information on the colour choosing window see section 7 3 3 Colour Choosing Window O O O Osprey 7 19 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization U
111. ed node into a spoke model By comparing the blue and purple nodes in figures 6 4 2 1 and 6 4 1 1 you can see the difference between the default and forced spokes method The nodes coloured purple represent nodes that share interactions with more than one spoke model in the default spoke method these nodes would not get circled up into on of the three possible rings But in the forced spoked model all interactions are treated the same and therefore the purple ones get added to the rings of the blue spoke model seen in figure 6 4 2 1 There are two ways to call the forced spokes function see section 6 4 2 1 Accessing the forced spoke model for details Osprey 6 16 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts Bg Osprey C Documents and Settings hosam My Documents showSpokes osp modified iol xj File Edit view Insert Format Filters Layout Help D amp MS QQ ps H dh sancsenit Ah AE e zle h ae az Al Gene Edge Info Select a single vertex edge Turn Off Fitters Connection Filters Minirnurn erative Minimurn Depth Turn Off Gonnectivity le 262 284 Loner Nodes YES Draw IV Nodes M Edges Labels Arrows m User Defined User Defined KA Figure 6 4 2 1 Forced Spoked Models There are currently two ways in which the user can access the default spoke model 1 The Menu Bar o Select all nodes that you want
112. elected nodes in 2 Size of rings Figure 6 2 3 1 label 3 e This adjusts the radius of the smallest ring as a percentage of the largest ring e The distance between every ring larger than the smallest is divided equally 3 Capacity of rings Figure 6 2 3 1 label 4 Osprey 6 8 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts e This adjusts the capacity of the smallest ring as a percentage of all nodes currently selected e The remaining percentage of nodes 1s divided in an increasing manner so that the larger the ring the higher the percentage of nodes Note if the percentage is too high to be able to place the remaining nodes in the selected number of rings the largest possible percentage will be applied to the graph Any changes made to the concentric circles options can be applied to the selected nodes by pressing the Apply to selected nodes button seen in figure 6 2 3 1 label 5 There are two ways to access the concentric circles options see section 6 2 3 Concentric Circles Options Fg Advanced Settings ee o x CEE Colour No Illes Ey Colouring Graph spoked Dual Ring Spoke layout Settings Drawing Graph Dragging Graph BackGround gt Concentric Circles Humber of rings Size of smallest ring percentage of screen 20 Capacity of smallest ring percentage of total nodes E Apply to selected nodes Fi
113. els Arrows User Defined GOProcess al Figure 6 6 3 3 Concentric Circles with large gap After accessing the Functional Clustering menu described in section 6 6 1 Accessing Functional Clustering options follow these steps e Click on the drop down box shown below to turn it on or off e Note you will have to perform the layout again to see a change Osprey 6 33 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts Bd Advanced Settings one Dl x Colour Hodes Edges By Colouring Graph Spoked Dual Ring Concentric Circles Spoke layout Settings Drawing Graph Dragging Graph BackGraund Functional Clustering Visible GO Process Order Carbohydrate Metabolisrn Cell Organization and Biogenesis Cell Shape and cell size control DNA metabolism Al Default Order DMA Damage Response DMA Repair V DAA recombination DMA Replication escent zl Y Degree of GO Process colouring fi Gap size between clusters Functional Clustering Figure 6 6 1 2 Turning Functional Clustering on off 6 6 5 Degree of GO Process colouring The Degree of GO Process colouring option allows the user to determine how many colours they want to see in Osprey For example 1f you only want to see one colour for each gene based on the GO Process order then you will want to select a degree of 1 If you wanted to see
114. em The following is a listing of the three sections shown in figure 2 1 3 1 1 Osprey Section This section contains your operating system specific download of Osprey Click on the link to download the Osprey installer Section 2 This section contains links for downloading instructions for installing Osprey You can download the installation instructions in the following format o Adobe PDF Portable Document Format This is a file format that has captured all the elements of a printed document as an electronic image that you can view navigate print or forward to someone else PDF files are created using Adobe Acrobat Acrobat Capture or similar products To view and use the files you need the free Acrobat Reader which you can easily download o Text File txt This format provides the installation documentation in a plain text format that can easily be viewed in applications such as GEdit XEmacs Emacs NEdit VI or Pico This format is limited in that it does not support the use of screen shots o HTML This format provides the installation documentation in a properly formatted HTML web page You must have a web browser available to view this document 1 e Netscape Mozilla Konqueror Opera Galeon etc Section 3 These are the system requirements for Osprey Please be sure to read these carefully before downloading and installing Osprey On the left hand side are the minimum requirements Any computer running with requir
115. ements less than these should not attempt to install Osprey On the right hand side are the recommended requirements For maximum performance we highly recommend using a computer that maintains these requirements 2 13 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation 2 1 3 3 Downloading for Mac OS X 3 Osprey DOWNLOAD Osprey Network Yisualization System Academic ersion Mozilla ie Ioj x File Edit View Go Bookmarks Tools Window Help G9 V9 Ol o m po Search Search Support Forums http biodata mshri on ca osprey servlet DownloadProduct Submit 4GREE amp product 2 Downloads Screenshots Documentation Partners Tutorials Support Forums About Osprey DOWNLOAD OSPREY Osprey Network Visualization System Academic Version macintosh gt Release Version 1 0 0 Osprey is a software platform for visualization and manipulation of T complex interaction networks Osprey builds data rich graphical Osprey representations that are color coded for gene function and experimental interaction data Mouse over functions allow rapid elaboration and organization of network diagrams in a spoke model format Osprey also allows for user defined large scale datasets to be readily combined for comparison of diferent methods In addition to this Osprey is linked to the GRID and comes rich with annotation and interaction data for many commonly studied
116. emove Edges 3 Blk o A A CTRA Figure 4 3 2 7 2 Remove Edges Right click menu 4 3 2 8 Showing Loner Nodes Loner nodes are nodes that do not have any edges coming out of them or into them They can either be left visible or removed from the graph and set to invisible There are currently two ways of changing the visibility option of loner nodes 1 The Menu Bar o Click on the View menu in the Menu Bar o Click on the Loner Nodes submenu o Select either the Show or Hide radial button Osprey 4 33 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Y Untitled File Never Been Saved View Insert Format Filters Layout Colour Indexes IE _ Toolbars p _ Al Loner Nodes f Show Drawing Options Fi Hide Dragging Options P Network Statistics if view All Comments Pah mar Figure 4 3 2 8 1 Loner Nodes Submenu 2 The Status Bar button Basic Introduction o Ifthe button says Loner Nodes Yes it means they are visible o Ifthe button says Loner Nodes No it means they are invisible o Click on the button to change its status 20 Process i Torn Ott Filters Connection Filters flier rri c 2T me 5 Figure 4 3 2 8 2 Loner Nodes button Osprey Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Y 4 Loner Modes YES iir aw Y v 4 34 Chapter 4 Basic Introduction 4 3 3 Network Display
117. ented with the ability to download Osprey for the operating system you selected at the begriming of the installation procedure Osprey 2 9 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation Osprey DOWNLOAD Osprey Network isualization System Academic ersion Mozilla File Edit View Go Bookmarks Tools Window Help B99 OI http biodata mshri on cafosprey servlet DownloadProduct Submit AGREE amp product 2 po Search Search Support Forums Downloads Screenshots Documentation Partners Tutorials Support Forums About Osprey DOWNLOAD OSPREY Osprey Network Visualization System Academic Version macintosh gt Release Version 1 0 0 Osprey is a software platform for visualization and manipulation of T complex interaction networks Osprey builds data rich graphical Osprey representations that are color coded for gene function and experimental interaction data Mouse over functions allow rapid elaboration and organization of network diagrams in a spoke model format Osprey also allows for user defined large scale datasets to be readily combined for comparison of different methods In addition to this Osprey is linked to the GRID and comes rich with annotation and interaction data for many commonly studied organisms such as Yeast Mouse Human and Drosophila Network Visualization System Minimum System Requirements gt App
118. eracting partners and lays them out in a circular fashion up to three rings deep The Spokes name comes from the resemblance of the spokes in a wheel Osprey currently supports two different types of Spoked layouts 1 Default Spokes section 6 4 1 Default Spokes 2 Forced Spokes section 6 4 2 Forced Spokes Osprey 6 13 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts Default spokes circles up all nodes that are connected except nodes that are centers of other spokes and nodes that are shared between two spoke models Figure 6 4 1 1 demonstrates 5 default spoke models separated by the colours red green grey blue and yellow The nodes coloured in purple are those that are connected to two or more spoke models and thus have not been placed in one of the rings of a spoke to allow the user to easily see highly connected nodes There are two ways to call the default spokes function see section 6 4 1 1 Accessing the default spoke model Eg Osprey C Documents and Settings hosam My Documents showSpokes osp modified File Edit View Insert Format Filters Layout Help D SESA Aps iQ A easset oor E ez e fsai b aae aAl O x Get New Interactions Screen Name CLN3 Change Add Comment Turn Off Filters Connection Filters Minirnurn erative Minimurn Depth Turn Off Connectivity MEE le 262 284 Loner Nodes YES Draw
119. erences and Customization 7 11 Memory Settings Due to the increasing size of networks being published Osprey may need to have its memory settings changed to be able to handle the thousands of objects being manipulated Some signs that may point to a memory problem include 1 Osprey hangs while trying to open save or export a file 2 Osprey takes and extremely long time to draw the network By default as of Osprey 1 2 0 128Mb of memory has been allocated to the java virtual machine that powers Osprey This is generally enough memory to handle networks containing 5000 nodes and 10 000 edges Once your network start getting larger than this you ll notice a hit in performance while manipulating the network There are two ways in which you can increase the amount of memory to Osprey 1 For users that have the currently release of Java installed you can launch Opsrey via the command line as follows java jar Xmx256m Osprey jar Osprey jar will be located in the folder in which you installed Osprey The Xmx256m sets the maximum heap size for Java in this case it is set to 256MB Adjust this number to the appropriate size based on the amount of memory you currently have available In practice you should never increase this number more than half of your total memory For example if you have 1024MB of memory than you should never go larger than 512MB This technique will work for all the operating systems that Osprey has been tested fo
120. erimpose submenu e Click Standard to select your own saved file or Click the Dataset submenu and choose one of the datasets provided see section 3 1 4 for details Osprey 3 13 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 3 Opening and Saving Files E dOsprey powered by Yeast GRID Untitled File Never Been File Edit View Insert Format Filters Database Layout Help New Ctrl Open b ey Save Ctril 5 Save s Save Colour Index p Save Settings I 8 Print Ctrl F Superimpose ae Standard Ctrl I Export Fly Networks Work OfFline worm Metworks Exit Osprey Yeast Networks Figure 3 1 5 1 Superimpose dataset 3 2 Saving to Osprey Files osp Any opened Osprey file can be saved as a tab delimited text file with the osp file extension When saved the next time the file 1s opened it will remember the location and formatting of all the visible nodes To save an Osprey file follow these steps e Click on the File Menu bar e Click on Save e Type an appropriate name for the file and click the Save button Note Filtering information and currently invisible nodes will not be saved to the osp file only the visible nodes and interactions will be saved Osprey 3 14 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 3 Opening and Saving Files E dOsprey Untitled File Never Been 5 File Edit View Insert Format Filters
121. ersion 1 0 1 o Support for proxies and accessing The GRID through a web proxy o Fix fora Mac font issue that prevents Osprey initialization in some cases on OS X Substantial speedup of Gene List and Custom Osprey file load times Automated detection of Osprey version upgrades and new messaging system for informing Osprey users o Fix for a bug in the latest Java update on the Mac that prevented Osprey from loading o Moved the Change Database option to its own menu called Database for easier access e Changes made from Version 0 9 10 to Version 1 0 0 Functional clustering added to the network layouts Provide annotation for multiple organisms Fully Mac OS X compatible Greatly improved data retrieval speeds A matrix output format for clustering Graphics improvements Several small bug fixes Ability to add and search for multiple nodes Ability to copy both node and edge annotation to the systems clip board for pasting into text editors O O O O O O O a e Changes made from Version 0 9 9 to Version 0 9 10 o Fixed small problem with Edges not returning after a get all interactions call to the GRID o Updated many links inside of the user manual that were non existant or broken o Fixed problem with Get All Interactions button on the Gene Info Display Area not properly enabling disabling during normal operati Osprey D 2 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Appendix E Osprey Licenses for Commercial
122. ert Lucas Lorne Flagel Jeffery Higgins Lorrie Boucher Theresa Reguly Rob Ingham Neil Warner Kara Dolinski Marc Sohrmann Clark Wells Jose Morales Daisy Anderson Jason Moffat B 2 The Osprey Contributors While Osprey was developed in the Tyers Lab which owns all copyrights to the Osprey Network Visualization System and the Osprey manual we wish to recognize those who have made contributions of one kind or another to the Osprey distribution Contributors are listed here in somewhat random order Osprey B 1 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Appendix B Credits MySQL AB and the MySQL database http www mysql com Sun Microsystems and the Java Standard Development Kit http java sun com B 3 The Osprey Supporters While Osprey was developed in the Tyers Lab which owns all copyrights to the Osprey Network Visualization System and the Osprey manual we wish to recognize those that have supported us Our definition of support spans from space in which to physically reside with our computers to financial contributions to the project Osprey supporters are listed here in a Somewhat random order Canadian Institutes of Health Research Development of Osprey was funded by a grant from the Canadian Institutes of Health Research Osprey B 2 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada For more information about updates and patches to the current version of
123. es are being dragged about the network display area When in either of these modes several preferences can be set that determine what Osprey will display to the screen When in drawing mode users have the option of displaying any combination of Nodes Labels Edges and Arrows When in dragging mode users Osprey 7 3 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization have the option of displaying Nodes Edges and Labels In addition to this when in dragging mode the user has the ability to determine whether or not these options will be reflected on all nodes in the graph or only on nodes directly connected to the set that is being dragged by clicking the always option By clicking the checkbox that corresponds to any of these settings Osprey will switch between displaying or not displaying the given option 7 2 1 Accessing Drawing Dragging graph options Dragging and Drawing options can be accessed via two methods in Osprey e Status Bar Options o Click on the status bar button on the bottom of the screen o The drop down menu displays Draw when the graph is stationary and Drag when the graph is being dragged o When the drop down menu says Draw the four checkboxes beside it show what is being displayed to the graph when it is stationary o When the drop down menu says Drag the four checkboxes beside it show what is being displayed to the graph when it is
124. esult of running the Check for Updates option e Via Comparison of your Version and the Latest Version for Download Click on the Help Menu in the Menu bar Go to the About option see figure 2 8 3 From the resulting about page check the Osprey version number that you are currently running see figure 2 8 4 o Compare this version to the latest version available at our web site http biodata mshri on ca Osprey If the version available online is greater than your current version then you should consider upgrading the Osprey software you are running see figure 2 8 5 Help Help Manual Cbrl H Check For Updates Figure 2 8 3 The About option in the Help Menu Osprey 2 49 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation The Usprey Network Visualization System was developed in the Tyers Lab at the Samuel Lunenfeld Research Institute in Toronto Untaria The following ia a list of all the people involved in the project Figure 2 8 4 The Osprey about page with the Version Number highlighted Osprey 2 50 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation Osprey Network isualization System Downloads Mozilla oj x File Edit View Go Bookmarks Tools Window Help Q Q Q Q http biodata mshri on ca osprey servlet Downloads Se A Po Search Ospr ey Search Support Forums Download
125. ey Installation After you have installed Osprey onto your Mac OS X you can run the program one of two ways 1 By executing the osprey_1 2 0 app file or the osprey jar file located where the Osprey program was installed by default this would be located on the disk inside osprey 1 2 0 in the folder Applications see figure 2 5 3 1 2 osprey_1 2 0 JAR osprey jar Preferences UninstallerData User_Agreement Figure 2 5 3 1 Default Osprey Location 2 If you created an alias for Osprey then you can execute the alias to the file Osprey _1 2 0 app by default this should have been placed on the desktop see figure 2 5 3 2 Egs osprey_1 2 0 app Alias Figure 2 5 3 2 Default Alias Icon Osprey 2 42 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation The following are common errors that may occur during an Osprey installation If you notice any errors that are not listed here please contact us see section 1 4 Contact Information to let us know about the problem 1 Problem with no Admin rights o Ifyou are unable to install Osprey due to permissions you do not have refer to appendix A 5 1 Unable to Install Osprey under Windows 2000 NT or XP for possible solutions If you no longer want to have Osprey installed on your computer you can quickly uninstall it by choosing the Uninstall Osprey shortcut Simply follow the instructions in the Ospre
126. f you already have an account you can simply login here to proceed with the download If you do not have an account simply click the large red button entitled CLICK HERE TO REGISTER to proceed with Osprey download registration Osprey 2 4 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation Osprey Network Visualization System Download Login Mozilla aoe lol x File Edit View Go Bookmarks Tools Window Help pO Search Search Support Forums DOWNLOAD OSPREY Although Osprey is available without a purchased license to academics and not for profit organizations we do require that you register and login before downloading our software to help make it easier for us to relay important information about updates to Osprey Email Address Password attirare a Password Lo IES imply Click Below Its Free and Easy Register To Download Contact Us Osprey Community Terms and Condition Copyright 2002 2003 Mount Sinai Hospital All Rights Reserved D ed OF E Done 1 E T Figure 2 1 2 2 The Download Login page with the registration link shown Fill in all of the fields and click the register button to register with Osprey Please ensure that you have used an email address that is valid because all Osprey correspondence including obtaining passwords will be done via this account Osprey 2 5 Operator s Manual Copyri
127. f edges connected to them after removing all nodes with less than the minimum amount of edges 1 e if the removal of a node caused another node to have less than the minimum selected number it will be removed also See section 5 2 1 Accessing Connection Filters for details on how to access the iterative minimum filter The following four steps demonstrates how to use the iterative minimum filter e Click on the text box shown in figure 5 2 3 1 and type the number of edges that each node must have after invoking this function to remain on the screen e Click on Filter button shown in figure 5 2 3 1 to perform the algorithm e Click on Clear button shown in figure 5 2 3 1to clear the text box e Click on Close button shown in figure 5 2 3 1 to close the text box E glterative Connection Minimum Be Remove nodes until all remaining nodes have the Following number of connections fi Clear Close Figure 5 2 3 1 Iterative Minimum connection filter window The depth filter works on selected nodes by only keeping nodes that have at most the selected number of node connections away from the selected nodes See section 5 2 1 Accessing Connection Filters for details on how to access the iterative minimum filter The following four steps demonstrates how to use the depth filter e Click on the text box shown in figure 5 2 4 1 and type the maximum number of connections deep that a node must be away from a selected node to stay on the gra
128. figure 6 1 1 2 E i Figure 6 1 1 2 Stop relaxation button 2 Hot Key ctrl R Select all nodes that need to be relaxed Click the ctrl R buttons together on your keyboard to start relaxation o Click the ctrl R buttons again to stop relaxation Osprey 6 2 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts o The other way to stop is to click the small stop button at the bottom right hand corner of the screen see Figure 6 1 1 1 6 2 Circular Layouts The circular layouts place the selected nodes in either a single circle or concentric circles The concentric circles function can be adjusted in advanced settings to achieve the best look for each situation Note The radii of the circles depend on the size of the selection box created with the mouse before calling these functions If all the Nodes on the screen are selected this gets overridden and the radii become as large as possible in the current graph size If the function call is repeated the diameter will increase until the maximum graph width and height are reached 6 2 1 One Circle This layout is used to position the selected nodes in one circle There are 2 ways to call this function see section 6 2 1 1 Accessing the one circle layout for details Osprey 6 3 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts EK gOsprey Untitled File Never Been Saved File Edit Yiew In
129. filters have been developed that allow the user to query the network For example an interaction network can be parsed for interactions derived from a particular experimental method Current Osprey filters include two major types of filters 1 Network Filters see section 5 1 Network Filters Network filters deal with filtering out biological information that is supplied to Osprey either by the user or the Grid Currently the network filters consist of e Experimental System e Source e GO Process 2 Connectivity filters see section 5 2 Connection Filters Connectivity filters deal with filtering out nodes based on its connectivity levels Currently Osprey has three connectivity filters e Minimum e Iterative Minimum e Depth 5 1 Network Filters The network filters work by removing nodes that do not belong to a certain network based on the biological information retrieved from the user or the Grid Currently Osprey contains three major types of network filters 1 Experimental system 2 Source 3 GO Process Osprey 5 1 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters Network filters can be accessed in two convenient ways Either by choosing the desired filter from the overhead menu or by clicking the corresponding button from the button in the bottom left hand frame 5 1 1 Accessing Network Filters There are currently two different ways to access the network filters in
130. for adding additional information such as interactions and nodes to a currently displayed network The following 1s a listing of each of the options available in the insert menu with a brief description of what service the option provides Insert Format Filters Layout Help 3 All Interactions For Selected Modes ShiFt 44 Only Interactions within Selected Modes Shift 0 e GB New Node Chrl Shift N eee New Interaction Ctrl ShiFk 1 Figure 4 2 4 1 The Osprey Insert Menu e All Interactions for Selected Nodes This option will query The GRID and retrieve all interactions stored for the currently selected nodes e Only Interactions within Selected Nodes This option will query The GRID and retrieve all interactions stored that are contained only within the selected set of nodes e New Node This option provides the ability to add individual nodes manually by name e New Interaction This option allows for manual addition of interactions between nodes currently in the network 4 2 5 Format Menu The format menu provides several options for adding additional information such as interactions and nodes to a currently displayed network The following 1s a listing of each of the options available in the insert menu with a brief description of what service the option provides Format Filters Layout i Modes b Edges AP FAIS Text d Background Colour Advanced Settings Osprey 4 14 Operator s Manual Cop
131. ful database of interactions and annotation see section 8 The GRID The General Repository of Interaction Datasets e Fase of use o Osprey provides an extremely user friendly interface for working with interaction data e Online Database Add on Ability o Osprey can be incorporated as a standard visualization tool with online databases such as The GRID http biodata mshri on ca grid e Support for figures o Osprey networks can be saved in SVG PNG and JPG format so they can be used with image programs Osprey 1 3 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 1 General Information 1 3 Copyright Notice Copyright 2002 Mount Sinai Hospital Toronto Canada All Rights Reserved Warning This system may be monitored by system or security personnel License Agreement for the Osprey Network Visualization System and all documentation THIS AGREEMENT SETS OUT THE TERMS AND CONDITIONS FOR DOWNLOADING COPYING INSTALLING OR USING OSPREY NETWORK VISUALIZATION SYSTEM SOFTWARE AND ASSOCIATED MATERIAL AND DOCUMENTATION INCLUDING ANY MODIFIED VERSIONS OR UPDATES COLLECTIVELY SOFTWARE READ THE TERMS OF THIS AGREEMENT AND ANY PROVIDED SUPPLEMENTAL LICENSE TERMS COLLECTIVELY AGREEMENT CAREFULLY BEFORE OPENING THE SOFTWARE PACKAGE BY OPENING THE SOFTWARE PACKAGE YOU AGREE TO THE TERMS OF THIS AGREEMENT AND THAT IT IS ENFORCEABLE LIKE ANY WRITTEN NEGOTIATED AGREEMENT SIGNED BY YOU INDICATE YO
132. g edges They are as follows e User Defined This option allows for individual customization of edge colouring When set to user defined Osprey will display colours chosen by the user to represent the individual edges In this mode edges cannot be segmented into multiply coloured pieces e Experimental System When activated edges in Osprey will be coloured according to the experimental systems that are reflected by the interaction Edges can be segmented into multiple pieces with this method where each segment represents a different experimental system e Sources When this option is activated edges in Osprey will be coloured according to the sources that reported the interaction Edges can be segmented into multiple pieces with this method where each segment represents a different source from which we have obtained this interaction Note Each of these options will continue to apply to all new edges that get added to the screen after the option has changed 7 4 1 Choosing Method of Colouring Edges There are two methods of switching the edge colouring setting that Osprey uses to colour edges in the Network Display Area To view a listing of colours used when in either experimental system mode or source mode view the respective colour index see section 4 6 Colour Indices The following describes these methods of access e Via the Status Bar Osprey 7 16 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Cha
133. ge AA Ie 34 f at Y ji MT Le z a A as Dasi y AWN Ds BA Ws AAT oO J h e e CN ANA TTEA Turn Off Fitters Connection Filters Minimnurn terative Minimum Depth Turn Off Connectivity Fa b MEK 330 mm 370 Loner Nodes YES Draw T I Nodes V Edges I Labels I Arrows mm Source GO Process 7 afi Figure 6 3 3 Dual Ring layout with the highly connected nodes in the inner ring Osprey 6 12 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts Eg Osprey Untitled File Never Been Saved Eigi xi Fie Edit Yiew Insert Format Filters Layout Help O S el S QQ fps FM Ah sansseri Bho E ezie fsals bk ale b O Gene Edge Info Select a single vertex edge Pasa Ne ere T j H Ye REL us J I a t i ste a it Beat i ih ii rh atin ar cat NO EET p MASSY Ll hte ami Lill Awe Sc a SS Cy Gi rae Wt MYA j ti Sin We A bn nI ry i ea ra w TIA Turn Off Fitters Tp ian ee aS Poe pe Vy i ra R S eS PP ie LAs Connection Filters s A a VE Minimum erative Minirurn Depth Turn Off Connectivity gt MEK e330 mm 370 Loner Nodes YES Draw IV Nodes Edges I Labels I Arrows mm Source GO Process El al Figure 6 3 4 Dual Ring layout with the highly connected nodes in the outer ring The Spokes layout attempts to take a selected node int
134. genes that are involved in multiple GO Processes then you can adjust the degree value accordingly To change the degree of GO Process colouring click on the drop down box shown in figure 6 6 5 1 and select the desired degree See figure 6 6 5 2 for an example of a degree of and figure 6 6 5 3 for an example of a network representing a degree of 3 Osprey 6 34 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts Fg Advanced Settings Z a Colour Hodes Edges By Colouring Graph Spoked Dual Ring Concentric Circles Spoke layout Settings Drawing Graph Dragging Graph BackGround Functional Clustering Visible GO Process Order Carbohydrate Metabolizrn Cell Organization and Biogenesis Cell Shape and cell size control A DNA metabolism Default Order DMA Damage Response DMA Repair DMA recombination Gap size between clusters Medium Degree of SO Procg Functional Clustering DN of Figure 6 6 5 1 Degree of GO Process colouring Eg Osprey powered by Yeast GRID Untitled File Never Been Saved oj x File Edit View Insert Format Filters Layout Help D S HAA fos I tM ab fanse Aa IE e z e Se Po ah A Gene Edge Info GM2 Select a single vertex edge SPA2 YPLO1 4 CTRG CDC3 PCK2 ee FAR1 SAP190 me G0 Ps Pi 0 Network Filters Experimental System Source als F gt le 27 0 33 0 Loner Nodes YE
135. genesis Change Colour Signal transduction Change Colour UNENCA Change Colour Protein Degradation Change Colour Protein metabolism and modification Change Colour eo Cell Shape and cell size control Change Colour Transport Change Colour Carbohydrate Metabolism Figure 4 6 1 1 An example of a GO Process Index for a given network The GO Process Index describes the various colours used on the individual nodes to represent Special GO Process categories These colours are completely customizable and can be changed simply by clicking on the Change Colour button behind any particular Go Process category Osprey 4 55 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction 4 6 2 Experimental Systems Index F d Experimental Systems Colours Inde a Change Colour D AFFINITY PRECIPITATION Change Colour B tio Hyer Figure 4 6 1 1 An example of an Experimental Systems Index for a given network The Experimental Systems Index describes the various colours used on the individual edge segments used to represent the different experimental systems These colours are completely customizable and can be changed simply by clicking on the Change Colour button behind any particular experimental system in the index 4 6 3 Sources Index Fd Sources Colour Index a oe ioli Change Colour QM Ho er av Change Colour P mrs Change Colour ITO ET AL Change Co
136. ges then the network filters Source and Experimental System cannot be applied e Similarly if User Defined mode is chosen for nodes the network filter Go Process cannot be applied Osprey 5 3 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters o x Eg Osprey Untitled File Never Been Saved File Edit view Insert Format Filters Layout Help EHAA foo Network Filters h2 m E BZ B fis a f JQ Connection Filters gt Source Go Process Gene Edge Info Tarmon Filters NM ee A SPA2 Select a single vertex edge 3 6ck2 YPLO1 4N SC DIG ULP1 i C01 BBP1 FUS a SN1 KSS1 i STE12 Network Filters TEM1 036 x SRP D PEP1 SOUTCE go Turn Off Fitters Connection Filters Minirruiarn z 4 033 mm 43 Loner Nodes YES Draw x V Nodes V Edges IV Labels V Arrows Comm Exp System GO Process PAIRI Figure 5 1 1 3 Network in Colour by Experimental System mode 5 4 Osprey Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters Eg Osprey Untitled File Never Been Saved File Edit view Insert Format Filters Layout Help FO momo D APE e err eA Go Process Gene Edge Info Turn off Filters y Mi NM C1 4 SPA2 Select a single vertex edge ae h CK2 YPLO14 V cDC5 Py K BBF1 y e SN1 STE12 Network Filters TEM1 RO36 Experimental System eZ Bs DIG R 6 p ULP1
137. ght 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation Osprey Network isualization System Download Registration Mozilla ESE a E a ioj x Fie Edit View Go Bookmarks Tools Window Help Q 6 Q R http biodata mshri on cafosprey servlet Registration product 2 amp Submit Register To Download Search Support Forums Downloads Screenshots Documentation Partners Tutorials Support Forums About Osprey REGISTRATION Although Osprey is available without a purchased license to academics and not for profit organizations we do require that you register and login before downloading our software to help make it easier for us to relay important information about updates to Osprey REGISTER FirstName Institute od LastName Email _ Contact Us Osprey Community Terms and Conditions Copyright 2002 2003 Mount Sinai Hospital All Rights Reserved D tI OF E amp Done Figure 2 1 2 3 An Osprey registration form Osprey 2 6 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation Y Successful Osprey Registration Mozilla ane loj x File Edit View Go Bookmarks Tools Window Help Q S Q http biodata mshri on cafosprey servlet Registration SS Search Support Forums Downloads Screenshots Documentation Partners Tutorials Support Forums
138. gs Carbohydrate Metabolisrn Cell Organization and Biogenesis Cell Shape and cell size control DNA metabolism DNA Damage Response DMA Repair DNA recombination DAA Replication Figure 6 6 2 1 Move down the list e Note to move all the way down click the bottom button Osprey 6 28 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts FJ Advanced Settings ee O x Colour Modes Edges By Colouring Graph Spoked Dual Ring Concentric Circles Spoke layout Settings Drawing Graph Dragging Graph BackGround Functional Clustering Visible GO Process Order Carbohydrate Metabolisrn Cell Organization and Biogenesis DNA metabolism DMA Damage Response DMA Repair DAS recombination Detaut Order lt lt gt gt Mating ile nea Dia sei Gap size between clusters Medium Degree of SO Process colouring fi Functional Clustering DN te Figure 6 6 2 2 Move to the bottom of the list 2 Moving a GO Process up the list e Click on the desired GO Process e Either drag it up to the desired order e Or click the up arrow moves down one step at a time Osprey 6 29 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts FJ Advanced Settings ee O x Colour Hodes Edges By Colouring Graph Spoked Dual Ring Concentric Circles Spoke layout Settings Drawing Graph Dragging Graph BackGraund Functional Cl
139. gure 6 2 3 1 Concentric Circles advanced options tag Osprey 6 9 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts 6 2 3 1 Accessing the Concentric Circles Options There are currently two ways in which the user can access the concentric circle options 1 The Menu Bar o Click on the Layout overhead menu o Click on the Circular submenu o Click on Concentric Circles Options Layout Help Auto Relaxation P amp osnecerit Circular D One circle Dual Ring b fon Concentric Circles Spokes p P d Global Figure 6 2 3 1 Accessing the concentric circles options via the main menu 2 Right Click Menu o Click on the Format overhead menu o Click on Advanced Settings o Look for the Concentric Circles tab and click on it Format Filters Layout Help Nodes at Edges ArrOWS p Text p Background Colour Advanced Settings Figure 6 2 3 2 Accessing the concentric circles options via the Right Click Menu Osprey 6 10 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts 6 3 Dual Ring Layouts The dual ring layouts pick out the most highly connected nodes and place them in one ring either in the inner ring or the outer ring depending on your selection and place all the other nodes in the other ring Note The radii of the circles depend on the size of the selection box created with the mo
140. here are currently two ways in which the user can access the concentric circle layout 1 The Menu Bar o Select all nodes that you want in concentric circles o Click on the Layout overhead menu o Click on the Circular submenu o Click on Concentric Circles Layout Help Auto Relaxation Circular Dual Ring b Spokes b alobal Danc Sarit T D One circle S Concentric Circles Figure 6 2 2 1 Accessing the concentric circles layout via the main menu 2 Right Click Menu o Select all nodes that you want in a circle o Right click in an empty area of the graph o Click on Concentric Circles Layout Osprey 6 7 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts t77 Insert All Interactions For Selected S y Insert Only Interactions within Selected One Circle Layout Concentric Circles Layout Create Default Spokes Create Forced Spokes Spoked Dual Ring Layout Lock Modes Unlock Modes Remove Nodes Remove Edges Figure 6 2 2 2 Accessing the concentric circles layout via the Right Click Menu 6 2 3 Concentric Circles Options Using the concentric circles options found in the Advanced Settings window under the tab labeled Concentric Circles Figure 6 2 3 1 label 1 it is possible to adjust the following settings 1 Number of rings Figure 6 2 3 1 label 2 This adjusts the total number of concentric circles you want to place your s
141. hoice To pick a colour from the Swatches tab simply click on it the colour will appear at the bottom of the screen then click OK to actually apply the colour change Osprey Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization x Peete eee Recent Fil E el z E E l ee ae ae eae tt SS Cee Cee Lae ee a eee eae ERR eae a ae ee B E Sample Text Sample Text L C Sample Text Sample Text Figure 7 3 3 1 1 The Osprey Colour Chooser with the Swatches Tab Selected 7 3 3 2 HSB tab Hue saturation and brightness are aspects of color in the red green and blue RGB scheme These terms are most often used in reference to the color of each pixel in a cathode ray tube CRT display All possible colors can be specified according to hue saturation and brightness also called brilliance just as colors can be represented in terms of the R G and B components http whatis techtarget com definition 0 sid9_gc1212262 00 html To pick a colour from this tab you must first move the vertical chooser to determine the desired Colour hue After the hue is chosen you can click on the colour window to change the Saturation and Brightness of the colour When the desired colour is chosen click on OK to apply the colour to the Osprey Network Display Area Osprey 7 12 Operator
142. i Hospital Toronto Canada Chapter 6 Layouts Figure 6 5 2 1 2 Accessing the spoked dual ring layout options via the main menu bar under the Format menu Osprey has the ability to cluster genes by their GO Process When any of the layouts discussed above except the Dual ring layouts are invoked nodes that have a common Go Process will be grouped together When nodes have multiple Go Processes they are put in the group with the highest order GO Process This GO Process Order can be adjusted in Advanced Settings which is discussed is section 6 6 2 GO Process Ordering below To make clusters easier to see there are empty gaps between them The gap size can be adjusted or taken out completely how to do this is discussed below in section 6 6 3 Cluster Gap Size Bg Osprey C Documents and Settings hosam My Documents showSpokes osp modified Oj x File Edit View Insert Format Filters Layout Help TIERA ELET AAO Gene Edge Info poveeee eee evoes poveret orvons peer eeeee rons Select a single vertex edge gt po vere eeroes 7 8 00h PP POO reg 9 He a TTT ELE ELT tee tee t eevee oon ey ts KATTEET T Me gt pevtetros e Network Filters Experimental Syster GO Process Turn Off Filters Connection Filters hinir arr zi 4 1049 1395 Loner Nodes YES Draw V Nodes Edges Labels Arrows User Defined GO Process 7 al Figure
143. ices Section 4 5 2 2 Adding only interactions within Selected Vertices 4 5 2 1 Adding all interactions to selected vertices You can add ALL interactions to a single node or several nodes in two different ways 1 Using The Network Display Area Command Menu Right click menu o Select the desired nodes for more info on selecting nodes see section 4 3 2 1 Selecting Nodes o Right click in an empty area of the graph to bring up The Network Display Command Menu o Click on Insert All Interactions for Selected as shown below in Figure 4 5 2 1 1 Osprey 4 48 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction Insert All Interactions For Selected Insert Only Interactions within Selected One Circle Layout Concentric Circles Layout Create Default Spokes Create Forced Spokes Spoked Dual Ring Layout Lock Modes Unlock Modes Remove Nodes Remove Edges P a Figure 4 5 2 1 1 A set of selected nodes with the Network Display Area Command Menu open By clicking on the Insert All Interactions for Selected option all interactions stored in the underlying database for ALL ofthe selected vertices will be added to the network Osprey 4 49 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction PA Dd TMADS FAR MOS a SIT4 BEKA YPLOI 4 Pidie CTR9 capi SAP BUD2 Figure 4 5
144. ich you can easily download o Text File txt This format provides the installation documentation in a plain text format that can easily be viewed in applications such as GEdit XEmacs Emacs NEdit VI or Pico This format is limited in that it does not support the use of screenshots o HTML This format provides the installation documentation in a properly formatted HTML web page You must have a web browser available to view this document 1 e Netscape Mozilla Konqueror Opera Galeon etc e Section 3 These are the system requirements for Osprey Please be sure to read these carefully before downloading and installing Osprey On the left hand side are the minimum requirements Any computer running with requirements less than these should not attempt to install Osprey On the right hand side are the recommended requirements For maximum performance we highly recommend using a computer that maintains these requirements 2 2 Standard Installation Procedure for Microsoft Windows Systems ME XP 2000 98 95 NT In order to proceed with the Osprey installation for Windows you must first download a copy of Osprey If you have not yet obtained a copy see section 2 1 Obtaining Osprey for more details Once you have a copy of the Osprey installer osprey exe you are ready to continue The Osprey installation is very simple and easy Installation is completely free and will take less than 5 minutes to complete To proceed
145. ight 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation Install Complete fe v Introduction s i i The installation of osprey_1 0 0 is finished but some warnings fe Choose Install Fo iF occurred during the install Please see the installation log for details Prewious Figure 2 3 12 Osprey Install Complete In order to proceed with the Osprey installation for Mac OS X you must first download a copy of Osprey and have java 1 4 1 working Please run the software update to check if you need to install the latest java for your Mac If you have not yet obtained a copy see section 2 1 Obtaining Osprey for more details Once you have a copy of the Osprey zip file osprey zip you are ready to continue The Osprey installation is very simple and easy Installation is completely free To proceed with installation follow these steps 1 To begin the installation start by executing the osprey zip file see figure 1 and wait while Stuffit unzips the Osprey installer program see figure 2 to continue execute this file Note you will need to have already installed stuffit onto your computer see http www stuffit com expander for more info Osprey 2 32 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation OSPREY 1P Figure 1 The Osprey zip Icon osprey_1 0 0 Figure 2 Stuffit unzips the osprey installer program 2 Once the osprey
146. ing will proceed for roughly a 1 month period after which version 1 0 0 will be released to w gt KI f ESE D amp OY E A Done Figure 2 1 1 1 The main page of the Osprey homepage In order to download Osprey you must first register and obtain a password Registration is easy and completely free Simply click on the Download link of the operating system you are using to begin the process Osprey 2 2 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation OSPREY Network Visualization System Mozilla La on File Edit View Go Bookmarks Tools Window Help EON SST Aol f AYJ T ey Search Support Forums FOTON Downloads zreenshots Documentation Partners Tutorials Support Forums About Osprey Osprey Updates gt Osprey Version 1 0 0 Released August 7th 2003 16 22 09 Today the latest release of Osprey version 1 0 0 was opened to the public with compatibility for Mac OS X Red Hat Linux and all versions of Microsoft Windows Follow the download link on the navigation bar to download your copy today T Osprey f Network Visualization gt Osprey 1 0 0 To Support OS X S VS fe th July 7th 2003 16 15 39 Due to limitations of the platform for a long time we were unable tg bring Osprey to Macintosh OS X systems Recently we have had the opportunity to work hand in hand with the
147. interactions removed or added to Osprey are displayed in this area The NDA provides many options for working with networks By left clicking on a node or an edge using a mouse the node or edge will be selected Selected nodes can be 4 24 Osprey Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction dragged and placed anywhere within the Network Display Area For more information on manipulating networks see section 4 3 2 Manipulating the Network NA oh AAT atina 4 r Pee e y a f JuUlc Ee There are many ways that a network can be manipulated using Osprey This includes basic things such as moving individual nodes and selecting and moving groups of nodes to options like removing nodes and edges Bg Osprey Untitled File Never Been Saved oj x File Edit wiew Insert Format Filters Layout Help SHS QQ pss H A sanssent am AE e zle er e op 5 DOCI _MAKS AK21 CDC23 wo e r g Se LAS z ms APC FYVv14 vy ra Saa ESA SES AG sr aN u A 1K sone SF X Y ee 4S SN The RS Re a Sk Get New Interactions K C Screen Name a ii N OP4 Change ji ALF as Fe H Add Comment R AEA Ad a Se i Sea UAV Description F RNA recognition Ay A RVZ SEN NY N SKN Go Component ps ND WR Ky SA s x G ASK AY N INES ng PR Go Process H Ag a K ak eau
148. irst download a copy of Osprey If you have not yet obtained a copy see section 2 1 Obtaining Osprey for more details Once you have a copy of the Osprey installer osprey tar gz you are ready to continue The Osprey installation is very simple and easy Installation is completely free To proceed with installation follow these steps 1 Once you have downloaded Osprey to your local file system you will have a file called osprey tar gz This is the compressed file containing the Osprey installer You will need to extract it before proceeding which we will cover in the next few steps Osprey 2 22 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation File Edit Wiew Terminal Go Help osprey tar gz Desktop Figure 2 3 1 Command Line with the Osprey gzip d file showing 2 To extract Osprey first gunzip the file by executing the command gunzip osprey tar gz and then untar the file by executing the command tar xvf osprey tar see figure 2 3 2 File Edit View Terminal Go Help osprey tar gz Desktop Osprey 2 23 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation Figure 2 3 2 Extracting the Osprey installer and installation manuals from the compressed Osprey file 3 In order to execute the Osprey installer you will have to set its permissions To do this type chmod 777 osprey_1_ 0 0 bin at the comman
149. isible Sources Apply to Graph Close Figure 5 1 2 2 1 Filter by source window demonstrating how to highlight something in the visible list e To select more than one item at the same time hold the Ctrl key and click on more items Osprey 5 7 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters Filter by Source Sei x Existing Sources Add Add All Group Selected Remove Remove All Visible Sources HOET AL ITO ET AL GAVIN ET AL UETZ ET Ab Apply to Graph Close Figure 5 1 2 2 2 Filter by source window demonstrating how to highlight multiple items in the visible list e Then click the remove button you will see the items removed from the Visible list Osprey 5 8 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters F drilter by Source Figure 5 1 2 2 3 Filter by source window demonstrating how to remove the highlight items from the visible list e The Remove all button removes all items from the Visible list Osprey 5 9 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters Add Add All Group Selected Remove Visible Sources Apply to Graph Close Figure 5 1 2 2 4 Filter by source window demonstrating how to remove all the items from the visible list e When you are ready to see the changes on the screen click the Apply to Graph
150. isplays information queried from The GRID see section 8 The GRID The General Repository of Interaction Datasets about a selected node or edge in the network For a description of what is in this area see section 4 4 Gene Edge Info Area e C Network Filters These buttons are used to invoke any one of the network filters available to the user see section 5 1 Filtering Networks e D Connectivity Filters These buttons are used to invoke any one of the connectivity filters available to the user see section Connectivity Filters 5 2 e E Osprey Menus All options available in Osprey can be accessed via these menus For more information on the specific options available in each menu see section 4 2 Osprey Menus e F Show Loner Nodes Option By setting this option to YES nodes without interactions stemming from them will be shown on the screen By setting this option to NO nodes with no interactions will be hidden from view e G Network Display Area This is the area where user defined networks are manipulated When loading a graph from a file or loading from a database all nodes and interactions will be displayed here see section 4 3 Networks e H Status Bar This area has buttons and statistics that change as the status of the graph changes Osprey 4 1 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction Bg Osprey Untitled File Never Been Saved File Edit view
151. ith several options for installing osprey shortcuts see figure 6 By default Osprey will install shortcuts on the desktop for you to access If you would rather have the shortcuts installed elsewhere you can customize these options to suit your preferences When you have made your shortcut choice click NEXT to continue Osprey 2 36 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation sprey 1 0 0 ign Choose Alias Folder B Introduction Where would you like to create aliases DJ Choose Aliasifolder Ere Installations Surrirriary In your home folder On the Desktop T r lash le S BB install Compere EAH ld other Choose Don t create aliases Figure 6 Osprey Installation Choose Shortcut Folder page 6 The next page will outline the options you have selected in a pre installation summary see figure 7 Please review the information and ensure that everything is correct and click NEXT to continue Osprey 2 37 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation Osprey 1 0 0 3 Pre Installation Summary Ed Introduction Please Review the Following Before Continuing E important Information Product Name 2 lo Eas osprey_1 0 0 Choose Install Folder FJ Choose Alias Fold Install Folder EA aoo i Ba asprey_1 0 0 in the folder Applications on the
152. j eee SiS af APCS J OX INR Se a Po oii SR vers Ss a DC Ay i vere IDA aS a Saas aw aN i ER LAN ARA WA AA PAOR SAS KV ee af MN EASON Ra Sen TIFG NINAN AG Di be ee ay ORS Ns ae ag Va ae J N xe RA X H TSA ATN ANN W K YA s a a 3 _ Tater oe Ale hA a WMA aN TA APC11 A K RIL Ln E N n z ag hy KS p lt lt Was Sk ANAIA LESE gf b Fr 2 ee a ne a rally 4 f al me oa AS sa PPR es Ys Vy LORE Vi a ie ol SA 044 Sy RI a RTE PO Pe a M Fat sate a i 3 SES ag 2 Figure 4 3 1 1 The Network Display Area The Network Display Area NDA is the most powerful section of the Osprey application The NDA is used to display all information regarding nodes and interactions Here nodes are represented by colourful circles and interactions edges are represented by colourful lines Interactions can be shown using user defined experimental system or sources to determine colouring see section 7 Osprey Preferences and Customization Nodes can be shown using user defined or Gene Ontology Process categories to determine colouring see section 7 Osprey Preferences and Customization Any
153. lating a network and you encounter a problem try to duplicate exactly what you were doing to see if the error occurs again If you can duplicate the error record the steps required to reproduce the error and send a bug report to the Osprey development team see section 1 4 Contact Information By apprising us of errors you encounter you help us to troubleshoot problems and help to make Osprey a better application The following is a listing of the minimum PC hardware required for running Osprey e Does your computer meet The Osprey Network Visualization Systems minimum system requirements o Osprey requires the following system hardware as a minimum for running the application Pentium HI 600 Mhz CPU or equivalent 128 MB of RAM Memory 50 MB of Available Hard drive space A Broadband cable ADSL internet connection Does your computer seem to run the Osprey Network Visualization System slowly o Although Osprey will run with the above hardware configuration this system 1s not recommended For optimal performance of Osprey use a computer that meets the following system requirements Pentium III 1000 Mhz CPU or equivalent 256 MB of RAM Memory 50 MB of Available Hard drive space ATI or Greater Internet Connection A 2 The Osprey Error Log Osprey maintains a running log of errors that occur while running the application This log is contained inside the directory Logs inside the Osprey installation directory If
154. le PowerG3 at 450 Mhz CPU gt 125 MB of Memory gt 70 MB of Harddrive Space Problems Downloading or Installing Click Here Contact Us Osprey Community Terms and Conditions Copyright 2002 2003 Mount Sinai Hospital All Rights Reserved D i OF p A Done a e Figure 2 1 3 3 The downloads page Osprey 2 10 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation 2 1 3 1 Downloading for Windows Osprey DOWNLOAD Osprey Network Visualization System Academic ersion Mozilla Bayes Oj x File Edit View Go Bookmarks Tools Window Help G 90 9 OL WT Ospr ey Search Support Forums Downloads Screenshots Documentation Partners Tutorials Support Forums About Osprey DOWNLOAD OSPREY http biodata mshri on cafosprey servlet DownloadProduct Submit 4GREE amp product 1 Osprey Network Visualization System Academic Version windows gt Release Version 1 0 0 Osprey is a software platform for visualization and manipulation of T complex interaction networks Osprey builds data rich graphical Osprey representations that are color coded for gene function and Network Visualization experimental interaction data Mouse over functions allow rapid f Vv Gotu elaboration and organization of network diagrams in a spoke model ww format Osprey also allows for user defined large scale datasets to be readily combined for compari
155. lease Read Before Continuing E Copyright Notice f Copyright 2002 Mount Sinai Hospital Toronto Canada ALL Rights Reserved Warning This system may be monitored by system or security personnel License Agreement for the Osprey Network Visualization System and all documentation THIS AGREEMENT SETS OUT THE TERMS AND CONDITIONS FOR DOWNLOADING COPYING INSTALLING OR USING OSPREY NETWORK VISUALIZATION SYSTEM SOFTWARE AND ASSOCIATED MATERIAL AND DOCUMENTATION INCLUDING ANY MODIFIED VERSIONS OR UPDATES CCOLLECTIVELY SOFTWARE Previous Figure 4 Osprey Network Visualization System User Agreement 4 On the next screen you will be asked about the installation folder for Osprey see figure 5 By default this would be located on the disk inside osprey_ 1 0 0 in the folder Applications as an installation directory If you would like to install in a different directory select the new folder from this page If you are happy with the default installation folder click NEXT to continue Osprey 2 35 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation Osprey 1 0 0 Choose Install Folder Where Would You Like to Install inside osprey_1 0 0 in the folder Applications on the disk Macintosh HD Restore Default Folder Wie Figure 5 The Osprey Installation Choose Install Folder page 5 On the following screen you will be presented w
156. les Layout Create Default Spokes Create Forced Spokes Spoked Dual Ring Layout Lock Modes Unlock Modes Remove Nodes Remove Edges Figure 6 2 1 2 Accessing the one circle layout via the Right Click Menu Osprey 6 5 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts This layout is used to position the selected nodes in a customizable number of concentric circles Figure 6 2 2 1 demonstrates a network layout using the concentric circles layout with 6 rings For details on the options available for customizing the concentric circles see section 6 2 3 Concentric Circles Options There are 2 ways to call this function see section 6 2 2 1 Accessing the Concentric Circles Layout for details Eg Osprey Untitled File Never Been Saved fel X File Edit view Insert Format Filters Layout Help Dae S QQHM TH MM fassen da dE B zlep da Aa lO Gene Edge Info z Select a single vertex edge ae Turn Off Fitters Connection Filters Minirnurn terative Minimum Depth Turn Off Connectivity Z E ofl MEK 0330 mm 370 Loner Nodes YES Draw v Nodes V Edges I Labels I Arrows mm Source GO Process PARAI Figure 6 2 2 1 Example of the concentric circles layouts with 6 rings Osprey 6 6 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts 6 2 2 1 Accessing the concentric circles layout T
157. lour B verzer av Figure 4 6 1 1 An example of a Sources Index for a given network The Sources Index describes the various colours used on the individual edge segments used to represent the different sources of interactions These colours are completely customizable and can be changed simply by clicking on the Change Colour button behind any particular source in the index Osprey 4 56 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction 4 6 4 Saving Colour Indices These three colour indices can also be saved as either a JPG PNG or SVG images so that they may be incorporated into figures or other projects outside of Osprey itself Follow these steps to save the Colour Indices e Click on the Osprey File Menu e Click on the Save Colour Index submenu e Choose either to save Only Visible colours or Both Visible and Invisible Colours E dOsprey Untitled File Never Been Saved File Edit wiew Insert Format Filters Layout Help New Ctrl M Open b Ly Save Ctril 5 Save s Save Colour Index Only visible Save Settings Both Visible and Invisible e Print Ctrl P Superimpose I Export Work Offline Exit Osprey PRI Figure 4 6 4 1 The Save Color Index Menu e This option will then ask you for a location and format for which to save the index see figure 4 6 4 2 Osprey 4 57 Operator s Manual Copyright 2002 Mount Sinai Hospital
158. lt colours will change the network colours including colours for experimental systems sources and the background to the default colour as defined by Osprey Use this option if you want to view the colours as defined originally by the application developers e User Defined Colours Colouring by user defined colours will colour the displayed network via the colours customized from within the application itself These are the colours that are manipulated within the Osprey application and are saved to the preferences file e Osprey File Colours Osprey File Colours are the colours stored within an Osprey save file If Osprey is set to colour by file the current network will be coloured to reflect the colours stored within the currently opened Osprey file Note By selecting the Always default to colouring by Osprey File checkbox Osprey will colour opened networks by the colours stored within the file by default If this option is not selected Osprey will default to colouring based on user defined colours Osprey 7 1 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization Eg Advanced Settings loj x Concentric Circles Spoke layout Settinas n Dragging Graph Backsround Colour Modes Edges By Colouring Graph Spoked Dual Ring Colour Graph According to Default Colours User Defined Colours C Osprey File Colo
159. lters Layout Help D Hagel a how role in cell cycle START nvobred m G sub 1 size control Go Component nnn lans Figure 4 4 1 1 Screen Name e Type in the desired name e Then Click on Change e The change will be reflected on the graph but nothing in the database or the gene info will change shown below in Figure 4 4 1 2 Osprey 4 38 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction BE gOsprey Untitled File Never Been Saved File Edit View Insert Format Filters Layout Help OSHS QQ foe x Get Mew Interactions Screen Name Cool ene Change Add Comment Description role in cell cycle START nevobved in G sub 1 size control Go Component Figure 4 4 1 2 Change Screen Name Osprey offers the option of adding comments to selected genes that can be viewed and updated as needed Follow these steps to add a comment e Click on the desired gene e Click on the Add Comment button Osprey 4 39 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction EB dOsprey Untitled File Never Been Saved File Edit View Insert Format Filters Layout Help D a BW S fxs MA Fans Gene Info jorr YDLIZTW PCL GENE cow a Get Mew Interactions Screen Name ICLN4 Add Comment Description Change Interacts with cyclin de
160. monero D AFFINITY PRECIPITATION E Purre compex E AFFINITY CHROMATOGRAPHY Sources TONGETAL E mps D GAVINETAL E ITOETAL E poeta E overzetar Basic Introduction Figure 4 6 4 3 An example Colour Index for an Arbitrary Network 4 59 Chapter 4 Basic Introduction 4 7 Multiple Organism Support New to Osprey version 1 0 0 is the ability access different databases containing annotation information from several different organisms As of Feb 2004 Osprey supports the following organisms 1 Yeast Saccharomyces cerevisiae 2 Human Homo sapiens 3 Mouse Mus musculus 4 Fly Drosophila melanogaster 5 S Pombe Schizosaccharomyces pombe 6 Worm C Elegans 7 Rat Rattus norvegicus 8 Zebra Fish Danio rerio All of the above databases are maintained by the GRID which receives their information from several different sources including SGD NCBI and Locus Link See http biodata mshri on ca grid for more information See section 7 10 Changing Databases for information on the various ways to change the database Osprey connects to Note This option allows the more ambitious Osprey user to create a MySQL database to maintain a private version of interaction data For more information on this option please contact the Osprey administrators for more details ospreyadmin mshri on ca Osprey 4 60 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada 5 Filters Various
161. n 4 THC ie aw ig ee Nt JAD T iterative Minirnurn ia P Depth C aes gt 4 31 169 Loner Nodes YES Draw x I Nodes V Edges V Labels IV Arrows Exp System GO Process a y Turn Off Connectivity Figure 4 3 2 4 1 Our tutorial network with a box being dragged to select multiple nodes Osprey 4 28 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction Osprey also allows for selecting of multiple nodes in the network This is done by encompassing the nodes in a selection rectangle To encompass the nodes in a selection rectangle simply left click and hold the mouse button in an unoccupied area of the Network Display Area ie One with no nodes or edges and drag the resulting rectangle until the nodes you want selected are all inside the rectangle ie A in the above figure 4 3 2 4 When you release the mouse button all of the nodes inside the rectangle will be selected Note The other way to select nodes is to hold the ctrl button on your keyboard while clicking on the nodes you would like to select 4 3 2 5 Moving Multiple Nodes With multiple nodes selected see section 4 3 2 4 Selecting Multiple Nodes simply left click and hold the mouse button on any one of the selected nodes While holding the mouse you can drag the entire group of selected nodes and place them anywhere in the Network Display Area 4 3 2 6 Removing N
162. n retains E E 7 12 Toe oO RTESOUA Dearest ed ase ratenn asa E eceen a aeaunneee aes 7 13 To NOI 1c OT Oe ee eee ee en renee a nee eer ae 7 14 TA Edge OPUS oisin a eA o EAE 7 16 7 4 1 Choosing Method of Colouring Edges ccc cece eee e eee eens 7 16 TAZ User Defined Edge Colours asses cacnesverescis oat EEA 7 19 Teas E e E e A E T T EE E 7 20 Lo Anow Head OPHONS cesa aT A Aa 7 21 7 5 1 User Defined Arrow Head Colour nnsnnsnnnnsunsesensnnenn 7 22 o2 AOW Had DIZE esarri nr E T OE 7 23 To Labe FODOS 7 25 LON TaD SIZE errre erne EE EAEE 7 25 FOZ LabolFon erer E E E A eres 7 27 TOS LADES es EEEO 7 28 TO MGA COOU eee a Maes Gane oo 7 29 PO MANE WAC Erer a eee entero e 7 30 Tat ack Sround C OlOUE ii ceriieceri dedeaainseveeucasiesacevedddonteaiorsesaianeanene 7 31 7 7 1 Accessing Background Colour ccccccc eens eee e eee eeeans 7 31 TO AVN PUCIChCNCES eaaa 7 34 TOG Savine SCUINGS csiack ednw chorea a aa aG 7 34 7 8 1 1 Saving Advanced SettingS ccccccccceeeeeeeeeeeeeeeeees 7 35 18 12 Saving Colour Sunes eeren aE EAEE sheeantoens xeds 7 35 PO PLOXY SGINE Sasa EE AO EEEE 7 36 TWO C hans ime Database Sarera E E E EAI 7 37 Toll Memory SCUINGS wcsita swcananuisdarduanpaacslasicananumdda men dapimestasrrcnanon ates 7 43 8 The GRID The General Repository of Interaction Datasets 8 1 SL del gen em nnd bale Gil D Deen e nee A weer Cer rarer ea see 8 1 6 2 Osprey and The
163. n t create links Figure 2 3 9 Osprey Installation Choose Shortcut Folder page 10 The next page will outline the options you have selected in a pre installation summary Please review the information and ensure that everything is correct and click NEXT to continue Osprey 2 29 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation Pre Installation Summary B Introduction Please Review the Following Before Continuing Eg Choose Install F Product Name ad osprey 1 0 0 Install Folder fhome stark osprey 1 0 0 Link Folder fhame s stark Disk Space Information for Installation Target Required 79 125 476 bytes Avallable 106 036 464 992 bytes Prewiolls Install Figure 2 3 10 Osprey Pre Installation Summary 11 The Osprey install will now copy all of the files needed to run Osprey This process will take only a few minutes to run Osprey 2 30 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation Installing asprey_ 1 0 0 Fd introcucti a Ae E Choose Install Fold EJ Choose Link Folder Pre Installation SUMMA installing osprew jar ca Figure 2 3 11 Osprey install progress copying files to your computer 12 Now the Osprey installation is complete Click on the DONE button to finish the install and close the Osprey installer Osprey 2 31 Operator s Manual Copyr
164. nd side frame turns off all Network Filters and in the overhead menu It only becomes clickable when a Network Filter has been applied Osprey 5 24 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters 5 2 Connection Filters The connection filters work by checking the connections edges of nodes and removing the ones that do not follow the specific connection criteria Currently Osprey contains three major types of connection filters 1 Minimum see section 5 2 2 Minimum 2 Iterative Minimum see section 5 2 3 Iterative Minimum 3 Depth see section 5 2 4 Depth The connection filters can be accessed 1n two convenient ways Either by choosing the desired filter from the overhead menu or by clicking the corresponding button from the button in the bottom left hand frame 5 2 1 Accessing Connection Filters There are currently two different ways to access the connections filters in Osprey 1 The Menu Bar o Click on the Filters overhead menu o Click on the Connection Filters submenu o Chose the appropriate filter name Filters Layout Help 1 Network Filters P F me cantarit Connection Filters Minimum Iterative Minimum Depth Turn obh Gonnectiwit a Figure 5 2 1 1 Accessing the connection filters via the main menu 2 Bottom Left hand Frame o Click on the button for the desired filter located under the Connection Filters heading in bottom left hand frame menu
165. ne applet version of the Osprey Network Visualization System for visualizing interactions graphically For more information on The GRID and its interactions visit The GRID web page http biodata mshri on ca grid Osprey uses The GRID as its underlying support database of annotation and interactions All interaction and annotation data displayed both in the standalone application version of Osprey and the applet version of Osprey have been derived from the The GRID database Currently The GRID maintains its annotation from the Saccharomyces Genome Database http genome www stanford edu Saccharomyces and the Gene Ontology Consortium http www geneontology org For more information on ways of adding interactions from The GRID into Osprey see sections 4 5 3 1 Add All Selected Vertices Interactions and section 4 5 3 2 Add All Interactions Contained within Selected Vertices Osprey 8 1 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada A Known Problems and Common Errors This chapter lists some common problems and error messages that users have run into You will learn how to figure out what the problem is and what to do to solve it You will also find proper solutions to some common problems A 1 What to do if you Encounter an Error When you run into problems the first thing you should do is try to figure out exactly which feature of Osprey is causing the problem For example 1f you are manipu
166. ngs s i x select which database you would like to be connected with Mouse GRID Fly GRID Human GRID Worm GRID S Pombe GRID C Rat GRID C Zebra Fish GRID Figure 7 10 4 Changing database options Note By default Osprey will connect to the yeast database if you want Osprey to default to a different database you can simple connect to the database of interest and save your settings The title at the very top of the Osprey application will let you know what database you are currently connected to without having to go the Database menu see figure 7 10 5 and 7 10 6 for examples Osprey 7 41 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization F dOsprey powered by Yeast GRID Untith 1 File Never Been Saved File Edit Format Insert View Gene Edere Info oelect a single vertex edge Figure 7 10 5 Osprey currently connected to the Yeast GRID which contains the yeast database E dOsprey powered by Fly GRID Untitled File Ne r Been Sayed File Edit Layout Help F dh SansSerif View Insert Format Filters SeA A fiom ene Edge Info oelect a single vertex edge Figure 7 10 6 Osprey currently connected to the Fly GRID which contains the fly database Osprey 7 42 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Pref
167. nipulate the text that comprises the label screen name of a node The following lists the major label options that are provided e Manipulating Label Font Size e Manipulating Label Font e Manipulating Label Style e Manipulating Label Colour Each of these options is readily available via the Osprey toolbar as well as via the Osprey Menu bar Note Each of these options will continue to apply to all new labels that get added to the screen after the option has changed 7 6 1 Label Size Osprey offers two methods for manipulating the size of a label Before attempting to change the size of a label ensure that you have at least one node selected in the Network Display Area The following describes the two major methods of accessing the label size e Label Size Selection Box o Select all labels whose size is to be changed o Select the desired size in the Osprey size selection box see figure 7 6 1 1 o Changes to font label size are immediately reflected on the Network displayed in the Network Display Area Osprey 7 25 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization Mt nlx e efesF ek 10 2 Poh2 CLA CKS1 ie as i f i Figure 7 6 1 1 The Osprey Label Size Selection Box e Via the Menu bar o Select all the nodes whose label size you want changed Click on the Format menu from the Menu bar Click on the Text submenu Choose the font
168. ntitled File Never Been Saved M x File Edit View Insert Format Filters Layout Help O S E g amp Q ps d O sansserit zh E e zle h ae er gO op 5 DOCI _MAK5 CD C23 Simge an EANN POST PA n E YVI ORR eee Wee rh gt s4 a ee m a BOR SREL N A A a r AE OTN aP TA PANA NS S Get New Interactions F aA L IRRI O EAN es S Ta ee p ie a Ws A Pec NOP2 Change yi4 MOD ENO hy XI i rs Ay AS Add Comment AEAT k BY Was AP b r PEA Ree TA ANIAN HAAA N a PLAN BIN ANAS Description ia y Ay LD A X D 4 f May participate in nucleolar aid X AANA j function during the transition NN IRIN from stationary phase to rapid Vi yi Ya wi oh s Ke W AORA INA DY RAY Network Filters X x AS Z raS Ki ae A A ee Experimental Systern z A T T ae Source LX 4 GO Process LES Turn Off Filters Connection Filters Minirnurn tterative Minirnurn Depth Turn Off Connectivity oi 4 le 31 169 Loner Nodes YES Draw IV Nodes V Edges IV Labels IV Arrows Exp System GO Process jeli Figure 4 3 1 A Simple Example Network Osprey 4 23 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction 4 3 1 Network Display Area MAKS Nops DOCI CDC r y
169. nto Canada Chapter 4 Basic Introduction not be coloured by both simultaneously see section 7 1 Graph Colouring this table will still reflect both sets of information e D PubMed ID A link to any PubMed listing on a given interaction Note Selecting multiple edges can be done by holding the ctrl button and clicking on all the desired edges 4 3 2 3 Moving Individual Nodes By clicking and holding the left mouse button on a single node you can drag a node to different places on the screen This may take a little practice as it requires a little bit of coordination This technique is ideal for placing nodes in a format that makes networks suitable for use as published figures 4 3 2 4 Selecting Multiple Nodes Eg Osprey Untitled File Never Been Saved Oj x File Edit wiew Insert Format Filters Layout Help De ES Qo pss A sansserit zh E szle fpo alse alz b Al Gene Edge Info Nop15 DOCI MAKS CDC23 Seg a ian ee g i NNS s z RIS aR L A oe Tis en em ONS SAV SRR AMSAT SKY SW TN LIK EA fee NTA fie a PENNAU RD TaN i A i ADS AY Select a single vertex edge SGN AY WN MAAN qt P 4 NY A T Network Filters OF VY to NBR i y p q Experimental System Source GO Process IA 4 Turn Off Fitters wi A S vA w jp a e i e Connection Filters Sle PLO ot Se by aN y ne NP Eri gt Sy ae TERY a a z Ba 7 ini WAY BASLER eee ee aes Minirnur
170. ode edge labels arrow sizes and colours This option will take all these settings and will initialize Osprey with them each time the application is run o Colour Settings Colour Settings are all the colour index settings in the Go Process index Experimental Colour index and Source index By changing colour settings you will affect only the colours on the network when colouring the graph by user defined colours mode see section 7 1 Graph Colouring When colouring by default or by Osprey File Colours these colour settings will not apply Osprey 4 5 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction E dOsprey powered by Yeast GRID Untitled File Never Been File Edit wiew Insert Format Filters Database Layout Help 9 Mew Open mj Save Save Os Save Colour Index Save Settings Adyanced Settings E Print Ctrl P Colour Settings Superimpose b Export Work Offline Exit Osprey Figure 4 2 1 5 The Save Settings submenu options e Print This option will take the graph currently displayed in the Network Display Area and print the graph to a printer attached to your computer e Superimpose To lay or place something on or over something else http www dictionary com search q Superimpose The superimpose option will allow for overlaying additional files onto an existing network in Osprey There are two options under this menu o Standard Su
171. odes Follow these steps to remove a node and all its edges There are currently two ways of doing this 1 The Menu Bar o Select a node or several nodes as described above in section 4 3 2 4 Selecting Multiple Nodes o Click on the Edit Osprey Menu o Click on Remove Nodes Osprey 4 29 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction E dOsprey Untitled File Never Been Saved File Ol GE Get Edit View Insert Format Filters Layout Select All Chrl 2 Inverk Selected Nodes F Crop White Space is Fit To Screen E Zoom In Ctrl D zoom Out Ctrl Minus i Lock Modes Unlock Modes Remove Modes Remove Edges ith Find Ctrl F er Update Node Annotation Go Component Figure 4 3 2 6 1 Remove Nodes on Edit Menu Bar 2 Right Click Menu o Select a node or several nodes as described above in section 4 3 2 4 Selecting Multiple Nodes Right click on an empty area of the Graph Click on Remove Node Osprey 4 30 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction Insert All Interactions For Selected Insert Only Interactions within Selected One Circle Layout Concentric Circles Layout Create Default Spokes PRI Create Forced Spokes Spoked Dual Ring Layout Lock Nodes Unlock Nodes Remove Nodes Remove Edges Figure 4 3 2 6 2 Remove Nodes Righ
172. ofit organizations or in conjunction with for profit activities are not granted except by prior written arrangement of the copyright holder For commercial licensing opportunities contact ospreyadmin mshri on ca or visit http biodata mshri on ca osprey servlet CommercialRegistration for more details Termination This Agreement and your license to use the Software will continue so long as you remain in compliance with the terms and conditions of this Agreement Your license will terminate automatically without notice from Mount Sinai Hospital if you breach any of your obligations hereunder Upon termination you shall cease using the Software and shall destroy all copies of the Software and associated materials and documentation in any form All disclaimers of warranties and limitations of liability shall survive any termination of this Agreement Disclaimers IN NO EVENT SHALL MOUNT SINAI HOSPITAL BE LIABLE TO ANY PARTY FOR DIRECT INDIRECT SPECIAL INCIDENTAL OR CONSEQUENTIAL DAMAGES INCLUDING LOST PROFITS ARISING OUT OF THE USE OR INABILITY TO USE THIS SOFTWARE AND ITS DOCUMENTATION EVEN IF MOUNT SINAI HOSPITAL HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE THE SOFTWARE AND ACCOMPANYING DOCUMENTATION IF ANY PROVIDED HEREUNDER IS PROVIDED AS IS MOUNT SINAI HOSPITAL SPECIFICALLY DISCLAIMS ANY IMPLIED WARRANTIES OF ANY KIND INCLUDING BUT NOT LIMITED TO WARRANTIES OF MERCHANTABILITY NONFRINGEMENT AND FITNESS FOR A PARTICULA
173. opyright 2002 Mount Sinai Hospital Toronto Canada Chapter 3 Opening and Saving Files 4 The GRID Download Portal Microsoft Internet Explorer pn 5 x File Edit wiew Favorites Tools Help dm Back mp fa 2 Google esearch Web Search Site a Pat gt gt 5 s a S gF p 4 gf Tia l E D r z i i F F Yeast Grid Fly Grid Worm Grid Downloads Support Forums DOWNLOADS PORTAL Click the appropriate GRID database for interaction datasets and Osprey Network Visualization System data files available for download Best viewed at 10242768 resolution with all modern web browsers Copyright amp 2001 2003 Mount Sinai Hospital Al Rights Reserved E j http biodata mshri omn catgridiserwleti Index ka a F Internet F Figure 3 1 4 1 2 Dataset website In addition to downloading new datasets you can also add personal datasets to the organism folders located at OSPREY HOME Datasets OSPREY HOME 1s the location in which Osprey was installed as well as create your own folder to add the datasets For example if you wanted to add a folder to contain some personal dataset you could create a folder called MY FILES in the Datasets folder and add your files to it see figure 3 1 4 2 1 take note of the additional menu option MY FILES that has appeared Note the name of the menu item will be the same as the name of the folder you created Also if you h
174. or Installation Target Required 62 007 526 bytes Available 63 710 076 926 bytes Cancel Previous W Figure 2 2 7 Osprey Pre Installation Summary 7 The Osprey install will now copy all of the files needed to run Osprey This process will take only a few minutes to run Osprey 2 20 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation wI Osprey 1 0 0 Aa ie ee a Introduction i i Irnportant Information 3 Choose Install Folder Choose Shortcut Folder P tallati n Sum il a ae Ving gt retell Garris Installing Java Runtime Emaronment Cancel Figure 2 2 8 Osprey install progress copying files to your computer 8 Now the Osprey installation is complete Click on the DONE button to finish the install and close the Osprey installer Osprey 2 21 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation YI Osprey 1 0 0 Install Complete BA Introduction Congratulations osprey_1 0 0 has been successfully installed to o EJ important information v Choose Install Folde z CAProgram Files Osprey 1 0 0 i Choose Shortcut Folder nstallation Summa Press Done to quit the installer EEE enacts a el ey ee E Cancel Previous Figure 2 2 9 Osprey Install Complete In order to proceed with the Osprey installation for Linux you must f
175. organisms such as Yeast Mouse Human and Drosophila Network Visualization System Minimum System Requirements gt Apple PowerG3 at 450 Mhz CPU gt 126 MB of Memory gt 70 MB of Harddrive Space Problems Downloading or Installing Click Here Contact Us Osprey Community Terms and Conditions Copyright 2002 2003 Mount Sinai Hospital All Rights Reserved D bd OF E A Done fp Figure 2 1 3 3 1 The Mac OS X Osprey Download Page There are three major sections to the download page for Mac OS X Each of these is necessary for downloading the Osprey Network Visualization System The following is a listing of the three sections shown in figure 2 1 3 3 1 e Section 1 This section contains your operating system specific download of Osprey Click on the link to download the Osprey installer e Section 2 This section contains links for downloading instructions for installing Osprey You can download the installation instructions in the following format o Adobe PDF Portable Document Format This is a file format that has captured all the elements of a printed document as an electronic image that you can view navigate print or forward to someone else PDF files are created using Adobe Acrobat Acrobat Capture or similar products To Osprey 2 14 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation view and use the files you need the free Acrobat Reader wh
176. ou have the option of simple changing the database or setting the selected database as the default If you where to select the Change Database option you would be presented with the window shown in figure 7 10 4 where you ll be asked to select the database you would like to Osprey 7 39 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization connect with Note if you are in offline mode then any changes you make to the database settings will not take affect until you restore the network connection Fd Advanced Settings it S Eo iol x Concentric Circles Sonke lawout Setinis Colour Nodes Edges By Colouring Graph spoked Dual Ring C Drawing Graph Dragging Graph BackGround Functional Clustering Proxies Database Settings Database Settings EES Currently Connected to Human GRID Change Database Set as Defaut Database NOTE If you are currently in offline mode then you must restore your internet connection before any changes can take affect Once the internet connection is restored you can then switch back into online mode one of two ways 1 Restarting Osprey 2 Select the following menu item File gt Work Online Figure 7 10 3 Changing database from Advanced Settings Osprey 7 40 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization F Database Connection Setti
177. pendent kinase PHOS gt to form kinase H complex with G 1 periodic actraty neolved im cell cycle progression Go Component Figure 4 4 2 1 Add Comment Button e A window will pop up for you to type your comment in E gadd Comment for CLN4 ae Be X I like this gene Add Comment Close Figure 4 4 2 2 Add Comment window Osprey 4 40 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction e After adding your comment click on the Add Comment button e To close the comment window without making any changes click on close e The original Add Comment button on the Gene Edge Info area will change to View Comment to reflect the fact that there is a comment saved now E dOsprey Untitled File Never Been Saved File Edit View Insert Format Filters Layout Help Dee amp amp fos e mm ORF YDLIZTW PCL GENE ha coe a Get Mew Interactions Screen Name ICLN4 WIE Comment Description Change Interacts with cyclin dependent kinase PHOSS to form kinase e complex with G1 periochic actraty irvoed im cell cycle progression Figure 4 4 2 3 View Comment Button e To view edit or remove the comment click on the View Comment button Osprey 4 4 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction Fd Comments for CLN4 ae x Ir like this gene Up
178. perimposes any one of the three recognized file formats See section 3 1 Types of Files Opened by Osprey for details o Dataset Superimposes one of the pre made datasets included with Osprey see figure 4 2 1 3 see section 3 1 5 for details Osprey 4 6 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction F dOsprey powered by feast GRID Untitled File Never Been Saved File Edit View Insert Format Filters Database Layout Help C Mew Crin Joos i i or cet dh Sane Open a Ey Save Ctrl 5 Save Os Save Colour Index Save Settings b F Print Ctrl F SUperimpose a Standard Ctrl I Export Fly Nekworks Work offline Worm Networks Exit Osprey Yeast Networks b Figure 4 2 1 6 The Superimpose submenu e Export Use this option to take the current network displayed by Osprey and save it to an image for incorporation into figures or for viewing and manipulation in other applications such as Adobe Photoshop or Macromedia Fireworks Osprey can currently export to SVG JPG or PNG images e Work Offline This option is available for those users who do not have a readily available connection to the internet Note working offline will limit your options within Osprey e Exit Osprey This menu option will exit the application 4 2 2 Edit Menu The Osprey edit menu contains many options for manipulating a currently displayed graph The following is a listing of each
179. ph e Click on Filter button shown in figure 5 2 4 1 to perform the algorithm e Click on Clear button shown in figure 5 2 4 1 to clear the text box e Click on Close button shown in figure 5 2 4 1 to close the text box Osprey 5 27 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters F g Remove By Depth a o x Remove nodes more than the Following away From selected nodes fi Clear Close Figure 5 2 4 1 Depth filter window 5 2 5 Turn Off Connectivity This button is located under the Connections Filters heading on the bottom left hand side frame and in the overhead menu It turns off all Connection Filters Osprey 5 28 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada 6 Layouts As network complexity increases graphical representations become cluttered and difficult to interpret Osprey simplifies network layouts through user implemented node relaxation which disperses nodes and edges according to any one of a number of layout options Any given node or set of nodes can be locked into place in order to anchor the network Osprey also provides several default network layouts including One Circle section 6 2 1 One Circle Concentric section 6 2 2 Concentric Circles Dual Ring section 6 3 Dual Ring Layouts Spokes section 6 4 Spokes Spoked Dual Ring section 6 5 1 Spoked Dual Ring oo ae ae ea 6 1 Auto Relaxation The auto relax
180. pong for Portable Network Graphics is a file format for image compression that in time is expected to replace the Graphics Interchange Format GIF that is widely used on today s Internet Owned by Unisys the GIF format and its usage in image handling software involve licensing or other legal considerations Web users can make view and send GIF files freely but they can t develop software that builds them without an arrangement with Unisys The PNG format on the other hand was developed by an Internet committee expressly to be patent free It provides a number of improvements over the GIF format http searchwebservices techtarget com sDefinition 0 sid26_gc1214307 00 html Osprey 3 16 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 3 Opening and Saving Files 3 3 1 3 SVG Scalable Vector Graphics Scalable Vector Graphics SVG 1s the description of an image as an application of the Extensible Markup Language XML Any program such as a Web browser that recognizes XML can display the image using the information provided in the SVG format vector graphics is the expression of an image using mathematical statements rather than a bit pattern description Scalable emphasizes that vector graphic images can easily be made scalable whereas an image specified in raster graphics is a fixed size bitmap Thus the SVG format enables the viewing of an image on a computer display of any size and resolution whe
181. pplications About Osprey COMMERCIAL APPLICATIONS Osprey Licensing Our current Osprey license prices are shown below The Osprey application license is a per computer license Osprey installed on a single computer There are no restrictions on the number of CPUs amount of memory or hard drive space available on the installed machine Price Per Copy N ber of Li umber of Licenses caD usD EUR GBP Osprey Licenses 2200 00 1890 00 1520 00 1070 00 E Each Additional License 1000 00 F5o 00 610 00 430 00 Not Sure To Try our Free 30 Day Evaluation Click Here Flease accurately complete the following form This information will be used to contact you about Osprey licensing and commercial opportunities INQUIRE NOO O LastName eal ciy C phones Province State O S License Range 1 5Licenses Country PostalCodeiZipCode o o Questions Comments Suggestions or Problems Let us Know gt Contact Us Osprey Community Terms and Conditions A Figure E 1 1 The Osprey commercial application webpage your first stop for inquiring about Osprey licensing opportunities Simply fill in all the fields and click register If you have filled in successfully an email will be sent to the Osprey team informing us of your interest We will then contact you within 48 hours to proceed with the Osprey licensing procedure Osprey E 2 Operator s Manual Copyright 20
182. pter 7 Osprey Preferences and Customization o The status bar button will either say Exp System Source or User Defined reflecting the chosen mode of colouring see figure 7 4 1 1 To change it click on the button and pick the method of choice The change will be reflected immediately on the graph ef Pi E KSS Figure 7 4 1 1 The Edge Colouring option on the Status Bar e Via the Menu Bar o Click on the Format overhead menu o Click on Advanced Settings option see figure 7 4 1 2 Osprey 7 17 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization o Click on the Colour Nodes Edges by tab to access the edge colouring options see figure 7 4 1 3 Format Filters Layout Help Nodes 4t mc Edges b i Arrows Text b Background Colour Advanced Settings Figure 7 4 1 2 The advanced settings option in the Format Fd Advanced Settings 10 x T Concepjjjg siusvmmamminalg layout Settings Drawing Graph Dragging Graph BackGround Colouring Graph Spoked Dual Ring Colour Nodes By C User Defined f By Go Process Colour Edges By C User Defined 0 By Experimental System By Source Figure 7 4 1 3 The Colour Edges By Option in the Advanced Settings Menu Osprey 7 18 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization 7 4 2 User Defin
183. query the database and retrieve a list of interactions involving the selected node that are not currently displayed in the Network Display Area See section 4 5 Adding Interactions for more information about adding interactions D Ability to change the current screen name E Allows the user to add comments to any selected gene F Description This section displays a plain text description of the currently selected node This description will be retrieved from the underlying database G H I Gene Ontology Information These three sections display the three major categories used by the Gene Ontology Consortium Namely Go Component Go Process and Go Function respectively The specific categories corresponding to the selected node are shown in this area J Gene Ontology Special This section of the Gene Edge Info area shows the Gene Ontology Special categories used for this gene GO Special categories are the ones used for colouring of nodes 4 26 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction Eg Osprey Untitled File Never Been Saved oj x File Edit wiew Insert Format Filters Layout Help eS AQ pss i MM sanser fis I E B zle dae daek Al Edge Info NoP15 ROCI PAS IN See nteracting Genes w ZAS we te ORF YLR127C YHR166C aot ef SIN AY Sa 4 eS a Fas E as L X n IN PS ARS SUZ AA AN ND BERS R
184. r and have a working updated version of Java Osprey 1 2 0 was compiled using the 1 4 2 03 compiler 2 Windows users Only To increase the memory to Osprey using Windows find the file osprey 1 2 0 lax located in the default location that Osprey was installed Open the file and find the line starting with lax nl java option java heap size max The number that follows indicates the memory allocated to the Java Virtual machine in bits So if you want to increase the memory to 256MB 268435456bits you would replace the line with lax nl java option java heap size max 268435456 and save the file NOTE Mac OSX users can use the command line option above because java should come pre installed with the operating system If you do not have java installed simple run your software update and download the latest java Osprey 7 43 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada The GRID General Repository of Interaction Datasets is a database of genetic and physical interactions developed in The Tyers Group at the Samuel Lunenfeld Research Institute at Mount Sinai Hospital It contains interaction data from many sources including several genome proteome wide studies the MIPS http mips gsf de database and BIND http www bind ca The GRID can be found at its home page located at http biodata mshri on ca grid Available at the GRID is a text based search of the stored interactions as well as an onli
185. rk Visualization System and all documentation THIS AGREEMENT SETS OUT THE TERMS AND CONDITIONS FOR DOWNLOADING COPYING INSTALLING OR USING OSPREY NETWORK VISUALIZATION SYSTEM SOFTWARE AND ASSOCIATED MATERIAL AND DOCUMENTATION INCLUDING ANY MODIFIED VERSIONS OR UPDATES COLLECTIVELY SOF TWARE READ THE TERMS OF THIS AGREEMENT AND ANY PROVIDED SUPPLEMENTAL LICENSE TERMS COLLECTIVELY AGREEMENT CAREFULLY BEFORE OPENING THE SOFTWARE PACKAGE BY OPENING THE SOFTWARE PACKAGE YOU AGREE TO THE TERMS OF THIS AGREEMENT AND THAT IT IS ENFORCEABLE LIKE ANY WRITTEN NEGOTIATED AGREEMENT SIGNED BY YOU INDICATE YOUR ACCEPTANCE OF THESE TERMS BY SELECTING THE ACCEPT BUTTON AT THE END OF THIS AGREEMENT IF YOU DO NOT AGREE TO ALL OF THESE TERMS SELECT THE DISAGREE BUTTON AT THE END OF THIS AGREEMENT AND THE SOFTWARE DOWNLOAD WILL NOT CONTINUE Restrictions All downloads and use of the Osprey Network Visualization System version 1 0 0 are subject to the following terms As long as you comply with the terms of this Agreement you are granted a non exclusive license to install and use the Software on a single computer for educational research and not for profit purposes without fee Except as expressly permitted in this Aqreemen may no e conv decomnile reverse endineer disassemble modify rent lease loan blicense distribute D a SY B A Dore De Figure 2 1 3 2 The Copyright Page After agreeing to the copyright notice you will be pres
186. rl M Open H Ey Save Ctrl 5 Save s Save Colour Index b Save Sektings b g Print Ctrl F Superimpose b Export Work Offline Exit Osprey Figure 4 2 1 1 The Osprey File Menu e New This option creates a new blank network that can be used to start developing a network from scratch e Open Use this menu to access the options for opening one of the many file types recognized by Osprey For an outline of the files recognized by Osprey see section 3 1 Types of Files Opened by Osprey There are two options under open see figure 4 2 1 2 o Standard opens a file that you have previously saved using Osprey o Dataset opens one of the pre made datasets included with Osprey see figure 4 2 1 3 see secton 3 1 4 for details Osprey 4 3 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction E dOsprey powered by Yeast GRID Untitled File Never Been Saved File Edit View Insert Format Filters Database Layout Help C Mew ctrl o J0 H fh SansSerif E Standard duke el Save Ctrl 5 Download New Datasets Save 45 Fly Networks b Save Colour Index p worm Metworks b Save Settings Yeast Networks b 8 Print SUperimnpose p Ctrl F Export Work Offline Exit Osprey Figure 4 2 1 2 The Options available in the Osprey File Menu e Save This option is used to save files that have been opened by Osprey or have been previously saved e
187. s Screenshots Documentation Partners Tutorials Support Forums About Osprey DOWNLOAD The software available for download below is provided free of charge to Academics Only AS IS and is without any warranty You need to purchase commercial Osprey licenses e f your not either an academic or not for profit institution e lf you want to support further development of Osprey For more information on commercial licensing visit our commercial opportunites page by clicking here Osprey Network Visualization System Osprey for Mac OS Academic Version gt Version 1 0 0 Osprey for Microso gt Version 1 0 0 Osprey for RedHat Nnux version 7 or higher Academic Version gt Version 1 0 0 Wew Featuresefunctional Clustering GO Degrees Mac OS X Support Mouse Human and Fly Annotation DOWNLOAD HERE m E Oy 3 GYA http biodata mshri on ca 80 OspreyNew servlet Index Figure 2 8 5 The Osprey web site with the Osprey latest version of Osprey for download highlighted Osprey 2 51 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada 3 Opening and Saving Files This section assumes that Osprey has been installed already For installation procedures see section 2 Osprey Installation 3 1 Types of Files Opened by Osprey Osprey can load the following three different file formats 1 Osprey File for details see section 3 1
188. s Sources Loner Nodes p 0 Process Drawing Options b Dragging Options d Network Statistics Selected Node Report view All Comments Figure 4 2 3 2 The Colour Indices Submenu e Toolbars The toolbars submenu contains options for viewing the Standard Buttons toolbar and the Status Bar There are two options under this menu o Standard Buttons When this option is checked the toolbar at the top of Osprey will be visible When it is not checked the toolbar will be invisible providing additional room for the Network Display Area o Status Bar When this option is checked the status bar at the bottom of Osprey will be Visible When it is not checked the status bar will be invisible providing additional room for the Network Display Area View Insert Format Filters Layout Help i Colour Indexes i a Toolbars M Standard Buttons Laner Modes R Status Bar Drawing Options b l Dragging Options b Network Statistics Selected Node Report view All Comments Osprey 4 10 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction Figure 4 2 3 3 The Toolbars Submenu e Loner Nodes The loner nodes submenu contains options for turning the loner nodes filter on or off making nodes without edges visible or invisible There are two options under this menu o Show When this option is selected it will turn the Loner Nodes filter off which will show all
189. se GRID Fly GRID Human GRID Worm GRID C S Pombe GRID Rat GRID C Zebra Fish GRID Iv Make this my defaut databaser a Show this Screen next time Figure 7 10 1 Database Setting on Osprey Start up Osprey 7 38 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization NOTE If Osprey can not find an active network connection at start up this screen will not appear 2 Using the Change Database option under the Database menu item EB dOsprey powered by Fly GRID Untitled File Never Been Sayed a i i K joj x File Edit View Insert Format Filters Database Layouk Help hz E pz fis e geo 0 e Hala amp hos l Change Database i east GRIC C Mouse GRID Gene Edge Info Fly GRID C Human GRID elect a single vertexedge Worm GRID C S Pombe GRID C Rat GRID Zebra Fish GRID Network Filters Experimental System SOURCE ol rari Oracess x 4 o m 0 0 Loner Nodes YES Draw z Nodes Edges 7 Labels 7 Arrows Exp System GO Process Figure 7 10 2 Changing database from Database menu item 3 Inside the Database Settings section of the Advanced Settings window From the Advanced Settings window see section 7 1 1 for details on how to access select the Database Settings option and figure 7 10 3 is what you ll be preseneted with In this window y
190. ser defined edge colours will immediately be reflected in the selected edges in the Network Display Area Figure 7 4 2 2 The Edge Colour Option of the Format Menu on the Menu bar 7 4 3 Edge Size In addition to changing colours of edges Osprey also provides the ability to manipulate the physical size of edges on the screen To accomplish this we have two major methods of accessing the edge size e Edge Size Selection Box o Select all edges whose size needs to be changed o Select the desired size from the edge size selection box see figure 7 4 3 l o Edge size changes are reflected immediately on the Network Display Area a 10 x 3 4 5 G r g m RSE FEF Ca Figure 7 4 3 1 The Edge Size Selection Box e Edge Size Configuration Dialog Select all Edges whose size needs to be changed Click on the Format menu in the Menu bar Click on the Edges submenu Click on Size see figure 7 4 3 2 O O O O Osprey 7 20 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization o Use the edge size slider to increase or decrease the size of a node see figure 7 4 3 3 o Edge size changes are reflected immediately on the Network Display Area Format Filters Layout Help 1 Nodes i w Edges Colour AEOS d Text d Background Colour Advanced Settings Figure 7 4 3 2 The Edges submenu in the Format menu
191. sert Format Filters Layout Help DSHS QQ EE f XM sasse rhe E ezi e foxls f ale b O Gene Edge Info Select a single vertex edge f p i i vi CMU Ta 27 Sf ih ig jae NA js i LETITI UAE tir tates VN i it PET Network Filters Experimental System Source GO Process Turn Off Fitters Connection Filters r inirni rr hal i a 330 370 Loner Nodes YES Draw x IV Nodes V Edges Labels Arrows m Source GO Process v x Figure 6 2 1 1 Network layout out using the one circle method There are currently two ways in which the user can access the one circle layout 1 The Menu Bar Select all nodes that you want in a circle Click on the Layout overhead menu Click on the Circular submenu Click on One Circle O O O O Osprey 6 4 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts Layout Help Auto Relaxation P B 7 leaneferf B Ih z Circular One circle Dual Rin d a Concentric Circles Spokes b Global b Concentric Circles Options Figure 6 2 1 1 Accessing the one circle layout via the main menu 2 Right Click Menu e Select all nodes that you want in a circle e Right click in an empty area of the graph e Click on One Circle Layout Insert All Interactions For Selected Insert Only Interactions within Selected One Circle Layout Concentric Circ
192. son of different methods In addition to this Osprey is linked to the GRID and comes rich with annotation and interaction data for many commonly studied organisms such as Yeast Mouse Human and Drosophila Ee Minimum System Requirements Microsoft gt Pentium Il 450 Mhz CPU WINDOWS gt 126 MB of Memory gt 70 MB of Harddrive Space Problems Downloading or Installing Click Here Contact Us Osprey Community Terms and Conditions Copyright 2002 2003 Mount Sinai Hospital All Rights Reserved D t OF LE GH Done p Figure 2 1 3 1 1 The Windows Osprey Download Page There are three major sections to the download page for windows Each of these 1s necessary for downloading the Osprey Network Visualization System The following is a listing of the three sections shown in figure 2 1 3 1 1 e Section 1 This section contains your operating system specific download of Osprey Click on the link to download the osprey installer e Section 2 This section contains links for downloading instructions for installing Osprey You can download the installation instructions in the following format o Adobe PDF Portable Document Format This is a file format that has captured all the elements of a printed document as an electronic image that you can view navigate print or forward to someone else PDF files are created using Adobe Acrobat Acrobat Capture or similar products To Osprey 2 11 Operator s Manual Copyright 2002 Moun
193. spital Toronto Canada Chapter 4 Osprey Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Insert All Interactions For Selected Insert Only Interactions within Selected One Circle Layout Concentric Circles Layout Create Default Spokes Create Forced Spokes Spoked Dual Ring Layout Lock Nodes Unlock Modes Remove Nodes Remove Edges Figure 4 5 2 2 1 A set of nodes with no interactions shown Basic Introduction 4 52 Chapter 4 Basic Introduction Figure 4 5 2 2 2 same image as 4 5 2 2 1 but with all interactions within the selected nodes inserted Notice how only interactions involving only the selected nodes were added to the network No new nodes are ever added when using this option This can be very powerful for determining connections between a core set of nodes in the network 2 Using The Insert Menu o Select the desired nodes for more info on selecting nodes see section 4 3 2 1 Selecting Nodes o Click on the Insert Menu in the Menu Bar Osprey 4 53 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction o Click on Only interactions within Selected Nodes as shown in Figure 4 5 2 2 3 titled File Never Been Saved 1 Insert Format Filters Layout Help All Interactions For Selected Nodes Shift 4 Only Interactions within Selected Nodes Shift 0 New Node Ctrl eShift h ee New Inter
194. sualization and manipulation of complex interaction networks Osprey builds data rich graphical representations that are color coded for gene function and experimental interaction data Mouse over functions allow rapid elaboration and organization of network diagrams in a spoke model format User defined large scale data sets can be readily combined with Osprey for comparison of different methods The Osprey Network Visualization System is a copyright of the Samuel Lunenfeld Research Institute at Mount Sinai Hospital in Toronto Ontario Canada For all of the latest information about Osprey including latest patches and updates please visit the Osprey web site http biodata mshri on ca osprey The following list describes some sections of particular interest in this manual e For information about the developers and team behind Osprey see appendix B Credits e For information about joining the Osprey mailing list see section 1 6 Joining the Osprey Mailing List e For installation instructions see section 2 Osprey Installation e Fora listing of basic Osprey layouts and descriptions see section 4 Basic Introduction e Fora history of new features and bug fixes see appendix D Osprey Change History e Fora list of currently known bugs and misfeatures see appendix A Known Problems and Common Errors e For future Osprey plans see appendix C Future Updates and Obtaining Patches e For more information about The GRID see section 8 Th
195. t Sinai Hospital Toronto Canada Chapter 2 Osprey Installation view and use the files you need the free Acrobat Reader which you can easily download o Text File txt This format provides the installation documentation in a plain text format that can easily be viewed in applications such as Word Wordpad or Notepad This format is limited in that it does not support the use of screen shots o HTML This format provides the installation documentation in a properly formatted HTML web page You must have a web browser available to view this document 1 e Netscape Internet Explorer Mozilla etc e Section 3 These are the system requirements for Osprey Please be sure to read these carefully before downloading and installing Osprey On the left hand side are the minimum requirements Any computer running with requirements less than these should not attempt to install Osprey On the right hand side are the recommended requirements For maximum performance we highly recommend using a computer that maintains these requirements 2 1 3 2 Downloading for Red Hat H Osprey DOWNLOAD Osprey Network isualization System Academic ersion Mozilla ee loj x File Edit View Go Bookmarks Tools Window Help Q Q Q Q http biodata mshri on ca osprey servlet DownloadProduct Submit AGREE amp product 3 Qy Search SS m M Q search o a Search Search Support Forums Downloads Screenshots Documentation P
196. t click menu 4 3 2 7 Removing Edges Follow these steps to remove an edge There are currently two ways of doing this 1 The Menu Bar o Select an edge or several nodes by holding the ctrl button and clicking on all the desired edges Click on the Edit Osprey Menu Click on Remove Edges Osprey 4 3 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction E dOsprey Untitled File Never Been Saved File Edit View Insert Format Filters Layout Help C Select All Ctrl z n 4t l Invert Selected Modes Fe F Crop White Space is Fit To Screen Zoom In Ctrl 0l S zoom uk Ctrl Minus Lock Modes Unlock Modes Remove Modes Remove Edges ith Find Ctrl F Update Mode Annotation SYHTHETIC LETHALITY MIPS Figure 4 3 2 7 1 Remove Edges on Edit Menu Bar 2 Right Click Menu o Select an edge or several nodes by holding the ctrl button and clicking on all the desired edges Right click on an empty area of the Graph Click on Remove Edges Osprey 4 32 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction CDCs4 ATP Pt fae Insert All Interactions for Selected Cho Insert Only Interactions within Selected One Circle Layout N Concentric Girdes Layout Greate Default spokes Greate Forced spokes Spoked Dual Ring Layout Lock Hades Unlock Modes YD MADS T MMES Remove Hodes R
197. the connectivity depth filter it keeps nodes that are a chosen number of connections deep from the selected nodes o Turn off Filters This option turns off any connection filters if any were turned on Filters Layout Help Network Filters e ah Josnecorit Connection Filters Minimum Iterative Minimum Depth Turn obh Gonnectivity Figure 4 2 6 3 The Connection Filters Submenu 4 2 7 Layout Menu This menu offers all the different ways to layout nodes in an Osprey Network It ranges from the relax algorithm to a simple circular layout to a more advanced Dual Spoked Ring Layout that attempts to display up to 1500 2000 nodes in a easily manageable format See section 6 Layouts for more details on layouts Layout Help Auto Relaxation P Circular Dual Ring Spokes Global Fr F F F Figure 4 2 7 1 The Osprey Layout Menu e Auto Relaxation This submenu has the relaxation algorithm that attempts to relax the graph by separating all the nodes and edges Osprey 4 18 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction o Start Relaxation Use this option to begin automatic relaxation on all of the nodes currently selected in the network o Stop Relaxation When Relaxation is in progress Start Relaxation will be replaced by Stop Relaxation click it to stop the nodes from relaxing Layout Help il Auto Relaxation Stark Relax Ctrl F a Circul
198. ther a tiny LCD screen in a cell phone or a large CRT display in a workstation In addition to ease of size reduction and enlargement SVG allows text within images to be recognized as such so that the text can be located by a search engine and easily translated into other languages http searchwebservices techtarget com sDefinition 0 sid26_ c1342078 00 html 3 3 2 Matrix This option returns a tab delimited text file of all the interacting genes in the network An interaction between two genes is represented by a 1 and those that don t interact by a 0 This file format can be used in several different clustering programs to help get a different perspective of the network 3 3 3 How to Export To export Osprey networks to images follow the 3 easy steps 1 Click on the File Menu bar 2 Click on Export Osprey 3 17 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 3 BE dOsprey Untitled File Never Be File Edit wiew Insert Format F New Ctrl M Open b a Save Ctrl 5 Save Os Save Colour Index b Save Sektings H ZF Print Ctrl P Superimpose Export Work Offline Exit Osprey Opening and Saving Files Figure 3 3 3 1 File Menu demonstrating how to export an Osprey network to an image 3 Choose which of the four formats you want to export your Network to Osprey 3 18 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter
199. thod of Colouring Nodes There are two methods of switching the setting that Osprey uses to colour nodes in the Network display area To view a listing of colours used when in Go Process colouring Osprey 7 7 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization mode view the GO Process colour index see section 4 6 Colour Indices The following describes these methods of access e Via the Status Bar o The status bar button will either say Go Process or User Defined reflecting the chosen mode of colouring o To change it click on the button and pick the method of choice see figure 7 3 1 1 o The change will be reflected immediately on the graph E A afl es User Defined m OUrCe ki GO Process Figure 7 3 1 1 How to switch between colouring by GO Process or user defined via the Status Bar e Via the Menu Bar o Click on the Format menu in the menu bar o Click on Advanced Settings option see figure 7 2 1 2 o Click on the Colour Nodes Edges by tab to access the node colouring options see figure 7 2 1 3 Osprey 7 8 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization Format Filters Layout Help 1 Nodes Edges b A Arrows p Text d Background Colour Advanced Settings Figure 7 2 1 2 The advanced settings option in the Format Eg advanced
200. tion 2 3 Standard Installation Procedure for Red Hat Linux Systems versions 7 3 or Higher or section 2 4 Standard Installation Procedure for Mac OS X versions 10 2 or Higher for installation procedures Once Osprey has been installed on your computer you can now start the application by clicking on the Osprey shortcut If you used the default install options this shortcut will exist in your start menu in Windows see figure 2 5 1 Osprey 2 40 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation x Lava MICrOSOTC UTICE UU Microsoft Office Tools Mozilla Fy Netscape 7 0 m Osprey QuickTime Startup F Uninstall Osprey Winamp WINRAR WinZip ws_FTP Tr Y F F F F F Fie F F F Emacs Acrobat Reader 5 0 Internet Explorer Microsoft Mouse b MSN Messenger 5 0 Figure 2 5 1 The Osprey shortcut in the Windows start menu 2 5 2 Running Osprey on Red Hat Linux Systems versions 7 3 or Higher For Linux users if you have chosen to create shortcuts to Osprey the installer will create a shortcut called runOsprey that you will simply have to invoke in order to launch the application 1 e runOsprey 2 5 3 Running Osprey on Mac OS X versions 10 2 or Higher Osprey 2 41 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Ospr
201. to be in the centers of forced spokes Click on the Layout overhead menu Click on the Spokes submenu Click on Forced Osprey 6 17 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts Layout Help li Auto Relaxation P SansSerf Circular Dual Spokes o Default lt Spoke incl Figure 6 4 2 1 1 Accessing the forced spokes layout via the main menu 2 Right Click Menu o Select all nodes that you want to be in the centers of forced spokes Right click in an empty area of the graph Click on Create Forced Spokes d C E a Insert All Interactions For Selected Insert Only Interactions within Selected One Circle Layout Concentric Circles Layout Create Default Spokes Create Forced Spokes Spoked Dual Ring Layout Lock Nodes Unlock Modes Remove Nodes Remove Edges Figure 6 4 2 1 2 Accessing the forced spokes layout via the right click menu 6 4 3 Spoke Options Using the spoke options found in the Advanced Settings window under the tab labeled Spoke layout Settings Figure 6 4 3 1 label 1 it is possible to adjust the following settings Osprey 6 18 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts 1 Size of smallest ring Figure 6 4 3 1 label 2 e This adjusts the radius of the smallest ring as a percentage of the largest ring e The distance between every ring larger than the smallest is
202. tory Particle Non ATPase homolog of marunalian proteasomal suburit p55 195 proteasome regulatory particle proteasome endopeptidase dbiquitin dependent POCEN protein degradation Probable 265 protease submit and mernber of the CDCAPFASLSECIS family of 4TPases adenosinetriphosphatase proteasome endopeptidase 195 proteasome regulatory particle vbiquitin dependent EF oe protem degradation YTAL Interaction with the 195 remulatory particle of the 265 Mean proteasome detected by 195 proteasome regulatory particle Clase molecular function unknow vane proteolysis and peptidolysis commmunoprecipitation Basic Introduction Selected Node Report This option will display all gene info about the currently protein degradatio protein raetabolisr and modification metabolism cell growth andor rralnitenarice protein degradatio protein metabolism and rmochtication metabolism cell growth andlor ralntenarce protein degradatio protein retabolisrm and rodification metaboalisrri Ei Figure 4 2 3 7 Selected Gene Report on any nodes currently in the Network Display Area Osprey Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada View All Comments This option will display all comments that have been made 4 13 Chapter 4 Basic Introduction 4 2 4 Insert Menu The insert menu provides several options
203. ttings Advanced Settings Ss Print Ctrl F Colour Settings Superimpose b Export work Offline Exit Osprey Figure 7 8 1 2 1 The Colour Settings save option 7 9 Proxy Settings In order to get Osprey to connect to the Internet through a proxy server you must do the following 1 Open the Advanced Settings window by going to the Format gt Advanced Settings menu see figure 7 9 1 2 Check the box Web Proxy HTTP to indicate if you want to us a proxy or not 3 Fill in the Proxy URL Port and User Name and Password if they are required 4 Press Apply Now to apply the changes Osprey 7 36 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization Fg Advanced Settings i i Eo O x Colour Nodes Edges By Colouring Graph Spoked Dual Ring Concentric Circles Spoke layout Settings Drawing Graph Dragging Graph Back sraund Functional Clustering Proxies F Proxy Settings I veb Proxy HTTP Proxy URL lproxy ur Port feoeo User Marne test Password eranan Apply How Figure 7 9 1 Proxy Setting 7 10 Changing Databases New to Osprey version 1 0 0 is the ability access different databases containing annotation information from several different organisms As of Feb 2004 Osprey supports the following organisms 1 Yeast Saccharomyces cerevisiae 2 Human Homo sapiens 3 Mouse
204. u bar o Click on the Advanced Settings option see figure 7 7 1 2 o Click on the Background tab see figure 7 7 1 3 o Click on the Change Default Background button see figure 7 7 1 4 and select the new background colour from the Osprey Colour Chooser see section 7 3 3 Colour Choosing Window Format Filters Layout Help Nodes Edges b Arrows b Text b Background Calour Advanced Settings Figure 7 7 1 2 The Advanced Settings option of the Format menu Osprey 7 32 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization Eg Advanced Settings Ei Mil x Concentric Circles Spoke layout Settings Drawing Graph Dragana Gran BackGroun ai Colour NodesfEdges By Colouring Sraph Spoked Dual Ring Min edges for INNER ring in spoke layouts E Min edges For OUTER ring in spoke layouts fi Capacity of smallest ring of spoke layouts fi 0 Size of smallest ring of spoke layouts 26 Apply to ALL nodes Figure 7 7 1 3 Advanced Settings Dialog Osprey 7 33 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization Eg advanced Settings Ei Mil x Colour WodesfEdges By Colouring Graph Spoked Dual Rina Concentric Circles Spoke layout Settings Drawing Graph Dragging Graph Backoround Change Default Background Colour Figure 7 7 1 4
205. umentation Partners Tutorials Support Forums About Osprey WT Osprey Network Visualization System Osprey Updates Osprey Version 1 0 0 Released August 7th 2003 16 22 09 Today the latest release of Osprey version 1 0 0 was opened to the public with compatibility for Mac OS xX Red Hat Linux and all versions of Microsoft Windows Follow the download link on the navigation bar to download your copy today gt Osprey 1 0 0 To Support OS X July 7th 2003 16 15 39 Due to limitations of the platform for a long time we were unable tq bring Osprey to Macintosh OS X systems Recently we have had the opportunity to work hand in hand with the developers at Appl and after two months of compatibility enhancement work Downloads Mac OS X Microsoft Windows RedHat Linux we ara happy to announce that Osprey For Mac OS X Osprey For Windows Osprey For RedHat Linux full support for Osprey on OS X J The Osprey Network The Osprey Network The Osprey Network will be incorporated into the Visualization System yo isualization System Visualization System is upcoming 1 0 0 release is now available for Microsoft is now available for All now available for RedHat Mac OS X WINDOWS Microsoft Windows Linux gt Osprey 1 0 0 Beta Testing Begi Download Here Platforms Download Here July 3rd 2003 16 12 58 Download Here Today the beta version of the newest release of Osprey began Test
206. ur 3 Change Colour 6 Change Colour amp Change Colour Change Colour Change Colour Change Colour g POM gun CKS Kool Cell Cycle Cell Growth andor maintenance Cell Shape and cell size control Protein transport Transport Protein biosynthesis Metabolism Protein Degradation Cell Organization and Biogenesis UNKNOWN Signal transduction Protein amino acid phozphorylatior Mating sensu Saccharamyce Carbohydrate Metabolism Transcription Budding Sporulation DMA recombination DAA metabolism F Figure 5 1 5 1 Network with node coloured by GO Process before performing the GO Process filter Osprey Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada 5 22 Chapter 5 Filters F drilter by Go Process Cell Cycle Cell Growth andor maintenance Cell Shape and cell size control Protein transport Transport Protein biosynthesis Metabolism Protein Degradation Cell Organization and Biogenesis Figure 5 1 5 2 Filter settings to only keep nodes with a GO Process of Cell Cycle or Metabolism or unknown Osprey 5 23 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 5 Filters Al olf digz LILP 1 0 CKS1 Figure 5 1 5 2 Resulting Network of the GO Process filter described in figure 5 1 5 2 5 1 6 Turn Off Filters This button is located under the Network Filters heading on the bottom left ha
207. urs J Always default to colouring by Osprey File Figure 7 1 1 The Osprey advanced settings menu with the Colouring Graph option highlighted 7 1 1 Accessing Graph Colouring The Graph colouring options can be accessed in two ways Both options provide quick access to the Graph colouring tab of the advanced settings dialog The following describes the methods of access e Via the Menu bar o Click on the Format in the menu bar o Choose the Advanced Settings option see figure 7 1 1 1 o Look for the Graph Colouring tab and click on it as shown in figure 7 1 l Osprey 7 2 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization Format Filters Layout Help Nodes p i d Edges i rEOwS p Text p Background Colour Advanced Settings Figure 7 1 1 1 Accessing the advanced settings menu e By Clicking on the Graph Colouring Button on the Status Bar o Look for the Graph Colouring tab and click on it as shown in figure 7 1 J Figure 7 1 1 2 The Graph Colouring Button on the Status Bar 7 2 Drawing Dragging Graph options An Osprey network can be in one of two modes at any given time e Drawing An Osprey network is in drawing mode when the graph is stationary and no nodes are currently being moved around the screen e Dragging An Osprey network is in dragging mode whenever a single node or a group of nod
208. use before calling these functions If all the Nodes on the screen are selected this gets overridden and the radii become the largest that can fit on the viewable area of your screen Follow the simple steps below to run either the Highly Connected In or Highly Connected Out Dual Ring Layouts Select all nodes that you want in the Dual Ring Layout Click on the Layout overhead menu Click on the Dual Ring submenu Click on Highly Connected In Figure 6 3 1 or the Highly Connected Out Figure 6 3 2 option Layout Help Auto Relaxation SansSerif i O O O Circular Dual Ring f 3 Highly Connected In Spokes alobal CO Highly Connected Out Figure 6 3 1 Main menu location of the highly connected in dual ring layout Osprey 6 11 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts Layout Help i Auto Relaxation P SansSerif vf Highly Connected In Circular b Dual Ring Spokes b alobal Figure 6 3 2 Main menu location of the highly connected out dual ring layout Figure 6 3 3 demonstrates a network with a highly connected in layout and figure 6 3 4 demonstrates a network with a highly connected out layout Eg Osprey Untitled File Never Been Saved a Oj x File Edit view Insert Format Filters Layout Help DSS QQ ps MM sansseri Bho E szie fsals k e Al Gene Edge Info z Select a single vertex ed
209. ustering Visible GO Process Order Carbohydrate Metabolisrn Detaut Order DMA Damage Response DMA Repair DAA recombination Cell Organization and Biogenesis Al DHA metabolism Mating H a Cin eae nim ad Gap size between clusters Medium Degree of SO Process colouring fi Functional Clustering DN t Figure 6 6 2 3 Move up the list e Note to move all the way up click the top button Fj Advanced Settings a panies Ioj x Colour Nodes Edqes By Colouring Graph spoked Dual King Concentric Circles Spoke layout Settings Drawing Graph Dragging Graph BackGround Functional Clustering Visible GO Process Order Carbohydrate Metabolism Cell Organization and Biogenesis DHA metabolic A Default Order DNA Damage Response DHA Repair V DHA recombination Mating Dilan Cin nani Gap size between clusters Medium Degree of GO Process colouring fi Functional Clustering On Figure 6 6 2 4 Move to the top of the list Osprey 6 30 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 6 Layouts After accessing the Functional Clustering menu described in section 6 6 1 Accessing Functional Clustering options follow these steps to create a smaller or larger gap that separates the clusters in a layout e Choose the desired gap size or none for no gap at all Advanced Settings nee 0 x Colour Modes Edges By Colouring Graph
210. whose label colour you want changed Click on the Format menu from the Menu bar Click on the Text submenu Choose the Colour option to change the label colour see figure 7 6 4 2 From the resulting colour choosing window see section 7 3 3 Colour Choosing Window you have the ability to manipulate the colour O O O O Format Filters Layout Help Modes pt et FT Edges b Arrows b Background Colour Font Advanced Settings Show Hide Figure 7 6 4 2 The Text Submenu for changing Colour 7 6 5 Hiding Labels In Osprey you have the ability to manipulate the visibility of individual node labels You can turn the label of any node on and off to help make figures and images This can be accomplished in the following way Osprey 7 30 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization e Via the Menu bar o Select all the nodes whose label you want to Hide or Show o Click on the Format menu from the Menu bar o Click on the Text submenu o Choose Show or Hide depending on whether you want to show or hide the selected labels see figure 7 6 3 1 Format Filters Layout Help Format Filters Layout Help Nodes F F Modes I pf oe dh e Edges e Edges b rrows d Arrows b Text Colour Text Colour Background Colour Font Background Colour Font Advanced Settings Advanced Settings Show a Figure 7 6 5 1 The Te
211. wing lists the operating systems in which Osprey can be installed e Microsoft Windows operating systems 95 98 NT ME 2000 XP e Red Hat Linux systems ver 7 3 or higher e Mac OS X ver 10 2 or higher If you are currently not running one of these operating systems Osprey will not work with your computer We are looking into solutions for other systems such as Solaris so if your system is not currently supported please be sure to check back as we continue to make updates 2 1 Obtaining Osprey Before proceeding with installation you must first obtain a copy of the Osprey installer that is appropriate for your system The following subsections outline where and how to get the installer To obtain Osprey you must be on a computer that is connected to the Internet 2 1 1 The Osprey Homepage To obtain a copy of Osprey you must first visit the Osprey homepage located at http biodata mshri on ca osprey If you are unable to access the Internet in order to visit the Osprey homepage you may request a CD copy of Osprey by contacting us see section 1 4 Contact Information Osprey 2 1 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation F OSPREY Network isualization System Mozilla File Edit View Go Bookmarks Tools Window Help Q O Q QF erem 3 yaaa lt 4 i we Seach Osprey Search Support Forums Downloads Screenshots Doc
212. with installation follow these steps 1 Before installation you must extract using WinZip http www winzip com the executable from the osprey zip file obtained after downloading Osprey To begin the installation start by double clicking the Osprey Installer osprey exe and wait while Osprey initializes some packages required for installation w Osprey exe Figure 2 2 1 The Osprey Installer Icon Osprey 2 15 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation Installanywhere 4m lnstallQny where i preparing to install Extracting Cancel Created with Install4nywhere 1996 2002 ero G Software lnc weww zeroi com Figure 2 2 2 Osprey initializing packages before proceeding with installation 2 Once the Osprey installer has launched you will be asked a series of questions about your installation Firstly you are presented with an introduction to the install procedure Please read this carefully and click NEXT to proceed Introduction 2 Osprey 1 0 0 InstalAnywhere will guide you through the installation of osprey 7 0 0 important Infortetion Baar bb nono finer Folderi a oe sae i Choose Shottitkolder S a eee Bes Click the Wet button to proceed to the next screen Ifyou want to change something on a previous screen click the Previous button J Introduction
213. xperimental System the system used to identify the interaction The fourth column contains the source where the interaction was found The fifth column contains the PubMed ID of any papers that backs this interaction up multiple PubMed ID s are separated with semicolons Figure 3 1 2 3 2 demonstrates what the network would look like after opening it up in Osprey Osprey 3 4 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 3 Opening and Saving Files The variations of the custom files described in sections 3 1 2 1 Custom File Variation 1 and 3 1 2 2 Custom File Variation 2 lack the last three columns describing the specifics of the interactions The lack of these three columns forces Osprey to place the interactions into a CUSTOM mode By supplying Osprey with these additional three columns you will be able to take advantage of the built in network filters described in section 5 1 Network Filters Note The rows and columns in red are necessary The rows and columns in gray are optional You can choose to only change the grey rows that need changing reneA GeneB Experimental System source PubMed ID CDC28 CLINI CDC28 CLN3 CDC28 CLB2 CDC28 CDC CDC28 METI10 CLINI CDC28 CLNI CIM CLN1 ____ CDCS53 Figure 3 1 2 3 1 Custom File Variation 3 COCs CLM s Figure 3 1 2 3 2 Result of loading custom file variation 3 into Osprey 3 1 2 4 Custom File Variation 4 The first row in figure 3 1 2 4
214. xt submenu with the Show and Hide options highlighted 7 7 Background Colour In addition to changing colours and sizes of individual objects on the Network Display Area such as nodes edges and labels Osprey also provides options for changing the entire background of the Network Display Area This option is useful for creating networks that are more colourful and allow for more colours in highlighting specific features of a graph For example labels or nodes that are coloured white may be important in specific circumstances but a background of white would make these invisible Changing the background to black or blue however would make it a lot easier to visualize white colour objects 7 7 1 Accessing Background Colour The background colour can be changed using one of the following two methods e Via the Menu bar o Click on the Format menu from the Menu bar o Click on the Background Colour option o Simply choose the colour you want for the background using the Osprey Colour Chooser see section 7 3 3 Colour Choosing Window Osprey 7 31 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 7 Osprey Preferences and Customization Format Filters Layout Hel i Nodes f Edges b FEDS d Text d Background Colour dvanced Settings Figure 7 7 1 1 The Background Colour option of the Format menu e Via the Advanced Settings Dialog o Click on the Format menu from the Men
215. y uninstaller to completely remove Osprey from your system When you start the uninstaller please read carefully the warning provided and if you are sure you want to continue uninstalling click UNINSTALL Osprey 2 43 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation Er Osprey l lols Uninstall About to uninstall A Introd instalimi Te Osprey a D D AE a EE This will remove features installed by InstallAnyvwhere twill not remove files and folders created after the installation istallanyviere by sern G Cancel Figure 2 7 1 Osprey Uninstall Warning The Uninstaller will completely remove Osprey from your system When the uninstall process completes Osprey will be gone from your computer Osprey 2 44 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation Uninstall Osprey Please wait while Installanywhere s uninstaller removes the Following Features Files Shortcuts LaunchAnywhere Folders Registry pe Sr te eT a ETE so Uninstalling Uninstall Osprey ink TSE annette iy Aone TIITILI TIT ILLii Figure 2 7 2 Osprey uninstalls progress Click DONE to close the Osprey installer Osprey 2 45 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 2 Osprey Installation WZ Osprey E MEE Uninstall
216. yright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction Figure 4 2 5 1 The Osprey Format Menu e Nodes The nodes submenu has options that affect nodes specifically colour and size o Colour This options provides the ability to change the selected nodes colour o Size This options provides the ability to change the selected nodes size Format Filters Layout Help Nodes Colour Edges b Size ArrOus b Text Background Colour Advanced Settings Figure 4 2 5 2 The Nodes Submenu e Edges The edges submenu has options that affect edges specifically colour and size o Colour This options provides the ability to change the selected edges colour o Size This options provides the ability to change the selected edges size Format Filters Layouk Help Nodes i w Edges Colour Ar FOS d Size Text Background Colour Advanced Settings Figure 4 2 5 3 The Edges Submenu e Arrows The edges submenu has options that affect arrows specifically colour and size o Colour This options provides the ability to change the selected arrow heads colour Osprey 4 15 Operator s Manual Copyright 2002 Mount Sinai Hospital Toronto Canada Chapter 4 Basic Introduction o Size This options provides the ability to change the selected arrow heads size RE area ii a ifsc Format Filters Layout Help i Nodes b 4t a z Edges d Arrows Colour Text d Size

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