PaVESy - User Guide
Contents
1. we search for an accession which starts with EG To define wild cards for the following letters we use the percent sign The results of the search will be displayed in the lower pop up part of the dialog 12 search for Compound Le Accession C Entry ID Attribute Accession EC Picture 19 images the compound search and result For every result it is possible to show defined attributes by selecting the attribute name via the combo box For adding the enzymes to the subset select them in the list and press the OK button and approve the following question with Yes The same can be done for the genes by entering At in the Accession field of the Search for Compound dialog seen in Picture 18 13 Pathway creation Before starting the pathway creation a subset for the pathways must be generated because the Pathway builder needs a subset for storing the constructed pathway Subset and folder creation can be found in the Creating folders and subsets part Creating pathways is possible via the Pathway builder displayed in Picture 20 from the Pathway menu of the main window Picture 5 Starting the Pathway builder delivers different options for creation The options will be explained in the following part Pathway Builder Muni target search Reaction pool start compound oo Target compound Ea Gin oti NE Path complexity restriction a Ignore path compound subset Oe EN Restrict search depth Shortest path on2. G importing tool is available via the Tools submenu mport Picture 9 located in the database menu Before using this function a database destination must be selected by using the Connect option ETAS ama Bess Pathway About Ta connect eee Sade ech Create Tables the Seer cae N Esonitate hudtatase Kar l SC Fr p F q 4 r Export AVLOY PavESy DB content Picture 9 represents the import KEGG menu item Before importing KEGG data it is necessary to define the path to the KEGG Ligand compound reaction and enzyme file The files are available on the KEGG ftp server and are packed into the ligand weekly last tar Z file Defining the paths to the files can be done by using the import dialog displayed in Picture 10 After defining the paths the import function can be started by clicking the Ok button The white panel contains all steps of importing which are finished Importing KEGG data into Pa ESy Define KEGG compound data path Cowwvork Wdatabase keg compound Define KEGG reaction data path C work Watabasetkeqqyeaction Define KEGG enzyme data path Cworkidatabaseikeogienzyme Remark Open input file Ci work datahase kegg pdb out riting database lt ni Status Importing KEGG data finished Picture 10 displays the import KEGG data dialog after importation Exporting database content The exporting tool is available via the database submenu Tools Picture 11 Before using this fun
3. PaVESy User Guide PaVESy USer GUIdE TTT 1 Starting the application 2 2002240022n0nennenennenennenennnnennnnennnnennnnennnnennnnennnnennnnennnnennnnennnnennnnenennennn 3 Working with Pav ERV see eee 3 Creating databasettablesa 2 2 2228 220 ee 6 IMDOrUNg Araye HAr ME dala eerren 7 Mporng KEGG HGand Cate arar fc ta e a a a es hw ee 8 Exporing database Comence a ER 9 MHO datapase Cone NE enon e Ree 10 reaungllolders and SUB else 11 UW eL e cp ersaceutect cis ee ureccum seats E N A E E E E aici A E 14 Starting the application The easiest way to work with PaVESy is to use Javaltm Web Start Version 1 2 In this case you will work always with the latest software release of PaVESy Details about the system requirements and installation instructions for Javaltm Web Start can be found at Installation Guide Java tm Web Start Starting our application via the Javaltm Web Start link in our download page the software requirements will be tested automatically Another way to work with PaVESy is to download the jar file Windows and Mac OS X allow starting Java applications packed in jar files by double clicking If double clicking will not work follow the Linux instructions The Linux instructions have to be accomplished inside a shell Switch to the path where the PaVESy jar file is stored and follow the instructions To start the application type user linux gt java Xmx256m jar PaVESy jar If Java 1 4 or a higher versi
4. bsets Compound and reaction subsets simplify the pathway creation The creation will be explained later In our example we create compound subsets to separate enzymes and genes into different subsets At first we create an enzymes and genes compound subset by using the Create new compound subset button next to the Create new folder button The subsets should be stored in the Compound folder seen in Picture 16 After creation and opening the Compound folder by expanding the tree the new subsets will be imaged Pathway Database jdbc odbe pavesy le E E 3 Database Edit View Tools Search Export Hee OSR RGA AH x te d S I Pathway Database accession A Attributes ri ee El E Compounds S A Attributes replication ict df enzymes F Ban da genes A Attribute Definitions Saving committed Picture 17 shows the expanded explorer after subset creation Adding all enzymes of the database to the enzymes subset a database search is required The blue plus in the button bar allows adding of database entries This button opens a type depending database search dialog shown in Picture 18 In the case of the enzymes subset only compounds are allowed to add search for Compound Le Accession FP Entry ID Gans Be nv Picture 18 represents the compound search dialog The Search for Compound dialog allows to search for defined entry accessions entry ids or defined attributes In the case of adding enzymes to the subset
5. ction a database destination must be selected by using the Connect option Bess Pathway About Ta Connect K Remove FH Create Tables Picture 11 shows the export menu item In the export dialog displayed in Picture 12 the user has to choose the path where the gzip text files which contain the table data should be stored Defining the path can be done by pressing the Path button in the dialog After defining the path the export function can be started by clicking the Ok button The white panel contains all steps of exporting which are finished Exporting PaVESy database Define data path LC tmpiexpoart Remark Exporting from PDB ENTRY into file entr Exporting from PDR IDENTTABLE into file Exporting from PDB SUBSETS into file av Exporting from PDB TEMPLATES into file Exporting database content finished in lees TN L Exporting Hav ESY data finished Picture 12 illustrates the export dialog after exportation Importing database content Importing data needs the same connection conditions as exporting Furthermore files are needed which contains the data to import To start the import tool selecting the Import submenu item seen in Picture 11 is necessary In this submenu three import options are available First data import from AraCyc flat files Second importing data from KEGG Ligand files and last but not least the PaVESy database content import For importing PaVESy database data it is possible to use the gzip t
6. e database contains object classes like compounds reactions pathways subsets and so on Importing AraCyc flat file data The AraCyc importing tool is available via the Tools submenu Import Picture 7 located in the database menu Before using this function a database destination must be selected by using the Connect option PaVESy Bes Pathway About Ta Connect Au en oe Remove Sy Create Tables l amp Export Fr l PavEsy DB content Picture 7 shows the import AraCyc menu item Before importing AraCyc data it is necessary to define the path to the AraCyc compound and dump file The aracyc_compounds and aracyc_dump file can be downloaded from the TAIR ftp server Defining the paths to the files can be done by using the import dialog displayed in Picture 8 After defining the paths the import function can be started by clicking the Ok button The white panel contains all steps of importing which are finished Importing Aralyr data into PaYEsy Define Aralyc compound data path database laracyclaracyc_compounds 06162004 Define Aralyc dump data path ork idatahbas elaracyclaracyc_dump 20040520 txt Remark Open input file Ci work database aracye pdb oo titing database se Data upload into database finished Importing data finished in 93245 ma lt iili Status Importing Aralyc data finished Picture 8 images the import AraCyc data dialog after importation Importing KEGG Ligand data The KEG
7. ext files from our download side After selecting PaVESy DB content option the import dialog presented in Picture 13 opens Importing PaYEsy database content Define data path LC tmpiexpoart Path Remark Importing from file entry txt into table PDR A Importing from file ident txt into table PDB Importing from file subsets txt into table PL Importing from file templates txt into table Importing data finished in Sle ms ka lt gt Status Importing data finished Exit Picture 13 displays the import dialog after importation The import dialog consists of two parts First part where to define the path of the files which contains the data to import Second the display part where the import status is indicated After defining the data source path the Ok button is activated and the import can be started A precondition for importing data is an empty database instance with all needed tables Defining these tables can be done by the Create tables option in the Tools submenu 10 Creating folders and subsets After importing data the database explorer shows no database entries like compounds reactions or pathways Pathway Database jdbc odbc pavesy BE ce E Database Edit View Tools Search Export H GR A AX t FF d EI Pathway Databaze A Attributes accession A Attribute Definitions Pathway Database replication ict wi PDB_Top a D u Picture 14 represents the da
8. ly Max steps Extra steps Max generality Picture 20 shows the Pathway builder The Start Target search The user is able to define a start compound by clicking the question mark left of the Start compound text field displayed in Picture 20 It is the same procedure as defining compounds for a subset Defining a target compound and ignore compound subset is optional Declaring a target the builder search for path between the source and target compound but is restricted by the maximum number of steps This number defines the number of reactions which are placed between these two compounds Choosing the Ignore path compound subset option defines compounds which should be ignored by pathway creation This would be interesting for compounds like ADP or H2O or compounds which not interesting for later work These restrictions are available for most of the building options Multi target search It works like the start target search but more then one target has to be defined The target compounds must be stored in a subset which is predefined in the database 14 Compound pool In this option selecting a compound subset is necessary The builder tries to complete the paths between the compounds of the subset Reaction pool The reaction pool option is abutted on the compound pool option but in this case a reaction subset has to be selected and the path between these reactions where completed After starting the creation by pre
9. nection as working connection the Pathway menu is activated and you can use the database explorer pathway builder and search or visualization tool Before connecting to a database is allowed a database destination must be defined viathe Add Dialog Picture 3 of the database submenu Tools displayed in Picture 2 BEERA Pathway About Ta connect g aa zu m oa Remove SH Create Tables E Export Aral yc Bm soma KE PavESy DB content Picture 2 displays the menu to define database settings aVEOY Add database Select database type Insert database name Select database file work Wdatahbasevdernd mdb Path Picture 3 represents the database connection properties dialog Picture 3 shows the settings for aMS Access data source The user has to define aname and the path to the MS Access file Adding a SAP DB needs the URL where the database is located If these settings are confirmed it is possible to choose this data source via the Connect dialog Picture 4 Database resources for connections can be deleted by calling the Remove dialog over the Remove entry in the Database menu Enter user name pO Enter password Picture 4 shows the database selecting dialog After validation of selection the Pathway menu seen in Picture 5 is enabled and the mentioned functions are available Database Pathway f amp Explorer Be Pathway Builder i Search 5 Reaction Finder 701 SQL Query Vi
10. on is installed and the JAVA_HOME and PATH variable is defined everything will work automatically If an error occurs the JAVA_HOME must be defined to the path where it is installed in our case usr java j2sdk1 4 0 Under Linux for example user linux gt export JAVA_HOME usr java j2sdk1 4 0 user linux gt export PATH JAVA_HOME bin PATH user linux gt java version Windows user use a semicolon instead of the colon If a declaration like java version 1 4 follows everything is OK and you can start PaVESy again Working with PaVESy After starting the application the main window Picture 1 offers the possible functions of PaVESy Database Pathway About ernnikate Audratsss re Sis ad aia R Be Eee i A ae r T Ba Z Bi REE pali NIE BaN EST ecohitate hydratase RENE Gai z F 17 Y E n SE aa scoritate hydiatase b fa te KLD a Pr t a en anf ns nn D lan T y eT ee LTH A Li fea en S B OY Picture 1 shows the main window of the application In this window you have the possibilities t0 choose between two menus The database menu which contains a submenu called Tools to define database connections delete these connections creating tables in empty database instances and if you are connected to a database the import and export functions for complete databases The second option is the About menu to get information about PaVESy If a database connection is defined and you selected this con
11. ssing the blue arrow the builder starts Increasing the maximum number of steps means rising up the time of creation If the creation is finished a window opens where the user has to select the pathway subset in which the pathway should be stored After defining a name for the pathway pressing the store button is necessary Subsequently closing the Pathway builder and switching to the Database explorer is possible Selecting the created pathway in the tree of the explorer on the right side the elements of the pathway where listed The pathway can be visualized in the integrated Visualizer by clicking Open the Visualizer button In this window different layout functions are included Moving the edges get detailed information or adding and deleting of reactions is possible For critics wishes or proposals please contact us 15
12. sualisation i J T ga pi P mmi m L v a i Picture 5 pictures the menu to access the PaVESy main functions Creating database tables Storing and editing data for PaVESy needs a database connection to a defined database source In this source the data must be stored in a defined table organization To simplify the table creation the Create Tables menu item is include in the application Choosing this menu item calls the Create PaVESy database tables dialog displayed in Picture 6 Create Pa ESy database tables Select a database type Define the target hatance Select database file C w orkidatabasewderno rdh Path User informations User pO Password pO Kind of creation With table initialisation For data importing Create pathway database at url jdbciodbc pavesy created Picture 6 displays the Create PaVESy database tables dialog For table creation different information is needed At the moment two database types are supported the SAP DB or MS Access Using MS Access PaVESy has to run under Microsoft Windows because PaVESy uses the standard ODBC driver Further particular is the name of the instance Using MS Access the path to the data file is also essential In the case of using SAP DB the URL to the database instance must be defined At last the user can choose between an empty or initialized database For data importing the database has to be empty Initialized means that th
13. tabase explorer after importing data To display these entries it is necessary to create folders and subsets which contain the database elements These folders allow structuring the database content in a user driven way A folder could contain subfolders and subsets A subset holds compounds reactions or pathways A mixture of compounds reactions or pathways in a subset is not possible For creating a folder pressing the yellow folder button in the button bar is essential The last step before creating the folder is to define the name in the dialog Create Folder ACCESSS1001 Picture 15 displays the folder creation dialog To create subfolders selecting the parent folder is inevitable because the new folder will be added into the selected layer If no layer is selected the folder will be created in the top level layer After folder creation a refresh of the explorer is essential to show the new folders This can be done by the View menu or the Refresh button Pathway Database jdbc odbc pavesy le EB EJ Database Edit wiew Tools Search Export HO os ARX t F EI Pathway Database A Attributes EY Compounds A Attribute Definitions accession Y Compounds Saving committed Picture 16 displays the refreshed explorer after folder creation 11 Subsets allow displaying the elements of the database in the explorer Different types of subsets are available Compound reaction and pathway su
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