User's Guide
Contents
1. Clock Im Clock Mc Clock Muse Clock Ref Clock 2167 Clock Tools Clock Tools provides information on and links to applications used by chronobiologists for processing and analysing data Currently available tools include applications for analysis visualization imaging and modelling Viewing Tool Sets Groups of chronobiology tools may by a logged user from any page by clicking on the Clock Tools sidebar link Viewing Tool Details Information on specific tools may be accessed by selecting a particular tool set e g analysis geared tools from the main page of Clock Tools then select the name of the tool to view information on it Currently the tool details page lists information on operating system compatibility licensing and contact information of the individual s who developed the tool Introd Use Q 1 Cloc a Clock Experi Clock Family 1 Q Cloc Clock Clock Clock Refere cl2. GeneViews Relevant gene information can be viewed at different levels of detail with GeneViews a simple toolbar based selector The default view contains the following information Transcript length Protein length Annotations 1 Gene abbreviation 2 Full name s 3 Synonyms 4 Cross references to external databases 5 Exons 6 7 8 You may shift from one view to another by toggling the GeneViews toolbar which appears on top of every page showing gene Details Contents per view are summarized on the next page Gene Views Summary Clock CI Clock Experi The following table summarizes the content of each view Clock Fam Not available for all entries Summary FASTA Images XML Default Abbreviatio n Full name s v v v v v Synonyms al Location Transcript x structure Transcript v v length Links to v v x sites Exons Structure Protein Length Annotation v v x x x SNPs x formatted sequence XML x x x x x Viewing SNPs SNPs for every gene may be accessed through either the SNPs view or Details view With the exception of the flanks all information on SNPs can be viewed on the page To view the flanks click on the View Flanks link for a
3. To view the details pertaining to a model click on its name from the list of models page see Viewing Searching Models This redirects you to a page containing the following information on the model Description A brief description of the model with accompanying diagrams in PDF format Scale Possible Values Single or Multiscale Cites the organism level or detail the model is describing Is it in the cellular molecular level Or is it dealing with whole organ such as the SCN Scope Answers the following questions 15 the paper presenting models for specific organism or does it talk about the model in a general sense If modeling specific organism which organism Size Shows the number of nodes or reactions the number of pathways and the number of biological components such as proteins Type Determines whether the model is ultradian circadian or evolutionary eIndicates the structure in terms of the number of loops or feedbacks Biological Aspects Indicates the biological aspects present in the model Examples are phosphorylation transcription translation Method Quantitative or Qualitative Discrete or Continuous Stochastic or Deterministic Also includes the actual method used such as Michalis Menten BST Mass Action etc Introd User A Clocks Clock Clock Experi Clock Family Clock In Clock Clock Muse Clock Cloc Tools Names the tools used for simulating
4. 1 Actogram with single data set 2 Actogram with multiple data sets 3 Non actogram A double plot image is automatically generated for the first two formats No double plot image will be generated for non actograms For the first two formats you need to supply information to specify how the double plot image will be generated Please refer to Double Plot Generation Double Plot Generation The following are SOPs in uploading data files for which double plots will be generated 1 The SOP Type field value should have no spaces when it is entered type in LD12 12 not LD 12 12 2 The following should be indicated in minutes a First time of stimulus light heat application under field First time that the stimulus light heat is applied b First time of stimulus removal under field First time that the stimulus light heat ceases Values for these fields are the time points when the stimulus of light or heat is turned on and turned off within a 24 hour day If light heat was applied at the onset of an experiment the value for the first time of stimulus removal will be the first time the stimulus light heat is stopped and the value for the first time of stimulus application will be the time light heat will be applied again within the day For instance for the SOP Type LD8 16 first time of stimulus application has a value of 1440 and the first time of stimulus removal has a value of 480 introduction Clock
5. Clock Restricted function User level requirement patriarch Approval Rejection of Submitted Chronobiologist Entries To approve an entry submitted by a registered user go to the first page of Clock Family Trees and click the link at end of the page A listing of entries waiting for approval will be shown Click on any of the names in the listing A page displaying the details of that specific entry will be shown To approve or reject click on either the Approve or Reject button Q Q ve Clock Expel Clock Fan ii Q Clock li Clock Clock Clock Refe Cloc en The clock genes module provides fast access an integrated view of information on circadian genes of several model organisms commonly used in chronobiology research It is based on a concept similar to that of the MitoP2 database http www mitop de which contains information pertaining to mitochondrial proteins MitoP2 is a manually annotated database which consolidates protein data molecular functions and associated diseases and distinguishes between confirmed reference proteins and candidates based on preliminary experiments or homology analysis The current release has information on clock genes and associated proteins from Neurospora crassa Synechococcus aureus Arabidopsis thaliana Drosophila melanogaster Mus musculus and Homo sapiens Viewing General Clock Gene Information
6. Clock Family Clock Museum Clock References Clock Tools If the experiment began in the absence of light heat stimulation the value for the first time of stimulus application is the first time that this is applied while the value for first time of stimulus removal is the time light heat will be withdrawn within the day For SOP Type DL8 16 first time of stimulus application has a value of 480 and the first time of stimulus removal has a value of 1440 3 The sampling time interval must be entered as integer minutes The experiment duration must be entered as integer days 5 For the data file format actograms with multiple data sets additional information will be required these pertain to the contents of the actual data file to be uploaded A detailed description is as follows a Ignore Columns refers to the number of columns from the start of the file which should not be regarded as activity data b Ignore Rows refers to the number of rows from the start of the file which should not be regarded as activity data c Total DataSets pertains to the number of columns of activity data in the file excluding the ignored columns and rows d Delimiter Name describes the delimiter character separating the columns in the file you are about to upload P Deleting Data Files On the experiment details page click on the data file that you wish to delete then click delete A delete confirmation dialog will be shown to confirm delete c
7. General information about the clock gene catalogue can be viewed by users from any page prior to login To access this information click on the Clock Genes link on the sidebar Viewing Organisms The view of the list of organisms for which clock genes are available can be accessed by logged users from any page by clicking the Clock Genes sidebar link Access to this functionality and all succeeding functionalities requires that a user is at least a registered user Viewing Genes Genes associated with an organism can be accessed by logged users through the Clock Genes page where a list of organisms with records in the database is displayed To view an organism s genes click on the organism name This redirects you to a page showing either the current known gene regulatory network for that organism or a table of clock genes Each gene in the network can be used to view Gene Details Introd User A Clocks Clock Clock Experi Clock Family Clo Clock In Clock Clock Muse Clock Cloc Viewing Gene Details Information such as the chromosomal location transcript structure exons protein structure and single nucleotide polymorphisms SNPs are available in EUCLIS for each clock gene To view these details for a specific gene click on its name in the gene map or on the gene table to access these see Viewing Genes Different information on genes may be displayed separately see Gene Views
8. User will generally be unable to download these Registered users may not upload material in EUCLIS User Level 2 Apart from viewing data restricted users are allowed to download data There are also some material that are visible to restricted but not to registered users Restricted users however do not have upload privileges User Level 3 A project investigator has similar access capabilities as restricted users but with the additional capability of editing project details including data on members involved gene links and bibliographic entry links Users with this access level may edit the sets of data within the module for which they have level 3 access User Level 4 In addition to the basic functions of viewing data and downloading material users with this access level can create and delete sets project lead investigator annotate genes lead annotator add entries to the library collection coordinator or manage class material class coordinator They can also edit details in existing data sets where applicable This role is granted to a list of pre approved users only All users with this access level have file upload privileges and are allowed to create delete and manage sets of data within the module for which they have level 4 access They can also manage the members to which the data within a set are visible User Level 5 Administrators have similar access privileges as restricted users Apart from this the a
9. operation introduction Clock Experiments Clock Family Clock Genes Clock Images Clock Models Clock Museum Clock References Clock Tools Restricted functions User level requirement lead annotator Changing the default view An annotator may change the default view of the clock genes page for their organism by clicking on the Change Default View button that appears below the gene network or the gene table The default view is currently set to the network view A The gene table view is currently available for Homo sapiens only Managing Annotation Staff Adding an annotator From the page displaying the gene network map of an organism click on the Manage annotation staff button then select assign a new annotator You will be redirected to a page that lists all registered EUCLIS users Select the add as annotator link that appears beside the name of the user you wish to add to the annotation staff To view changes made to the annotator list click on the return to annotators page for your organism button Removing an annotator From the manage annotation staff page click on the remove button that appears beside the name of an annotator Introdt User Clo Clock Cle Clock Experi Clock Family Clo Clock Clock Clock Mt Clock Refer Cloc Clock Images The Clock Images module serves as a repository for images with their associated metadata for and from the users of
10. the model Computational Properties States the standards used such as SBML and MIRIAM Experimental Evidence Includes experimental evidences for the model Downloading Model Description Click on the hyperlink for the description from the model details page to open a new browser window where the document contents will be loaded To save the data to your local drive use the save function of your browser File gt Save As File gt Save Page As Editing Model Entries Restricted functions User level requirement model coordinators From the model details page click on the edit button Enter the changes in the details form and then click Update Deleting Model Entries From the model details page click on the Delete button to delete the model entry from the list A delete confirmation dialog will be shown to confirm delete click OK Adding Model Entries To add a model entry go to the main page of Clock Models where the taxonomy diagram is displayed and scroll down to the end of the page Click on the hyperlink Add New Model Enter the information in the details form and then click Add Model introduction Clocks R Us Clock Clock Experiments Clock Family Trees Clock Ge m Clock Ii Clock Mus Clock References Clock Museum Clock Museum provides users with a way to create collections for restricted or general viewing by other users in EUCLIS Collections are g
11. CLIS users on the collection A list of associated slideshows and a preview of one of these Introd User A Clocks Clock Clock Experi Clock Family Clock Ge Clock In Clock Clock M Clock Cloc slideshows are also shown Preview a Collection Slideshow To preview the images making up a slideshow in a collection click on any of the slideshow titles listed in the collection details page see Viewing a Collection This displays the preview of the slideshow selected by the user Viewing a Linked Image To preview an image linked to the collection one may click on any of the image name or description under the Images list of the Related Links table in the collection details page This displays the actual image and information related to it Viewing a Linked Reference To preview a reference linked to the collection one may click on any of the reference titles under the References list of the Related Links table in the collection details page This displays the information about the literature linked to the collection Creating a new Collection A user may create a new collection by clicking on the Create New link beside the header of the type of collection standard public or private one wishes to create The user needs to specify the title of the collection a description for it keywords related to the collection and the category to which it belongs Clicking on the Create Collect
12. EUCLIS Information System Version 2 5 User s Guide About EUCLIS The EUCLOCK Information System EUCLIS is a comprehensive web based information system that aims to serve as a venue for chronobiologists for efficient networking and collaboration It provides support for the organization of experimental data through facilities for results storage systematic annotation and data visualization It also houses a digital library which contains organized bibliographic references of the various researchers as well as repository of course materials EUCLIS can be accessed at http www bioinfo mpg de euclis EUCLIS Architecture The general architecture of EUCLIS integrates a database for circadian systems biology containing modules for experimental data Clock Experiments and models Clock Models with a digital library Clock KnowledgeBase for the research community Figure 1 This architecture will provide a more flexible framework for the evolving information needs of the chronobiology community than current access mining and data warehouse approaches in other information systems This architecture will also allow easier integration with other systems in the future i Reg User Services Database for Systems Biology gt Eils et al EASE E ER ee ae E ES Digital Library Figure 1 EUCLIS architecture Intro User A Clocl KS Clock C Clock Exp
13. EUCLIS In this module users may upload download search images that may be closely coupled with other modules in EUCLIS such as Clock Experiments It also serves as the image source for Clock Family Trees and Clock Museum Restricted functions User level requirement registered or restricted users Viewing Searching Clock Images Images in the repository may be viewed by a logged user from any page by clicking on the Clock Images sidebar link All images hosted in the module will be displayed as thumbnails Clock Images makes use of the concept of image sets where the creator may allow each image in the set to be generally accessible or public or may choose to restrict access to other images to members of the set If the image is set as open to public or if the user is a member of an image set to which an image belongs it will have a link to the image itself and to the image set details an image is designated as private only its thumbnail be viewed The user may search the clock images module by specifying the image path name the image set title or the creator or by specifying a keyword in the module search field Results are grouped in two sets these are comprised all the hits within image sets and all the hits within images Viewing Image Details Image details contain information on the image set membership creator date of upload and miscellaneous comments To view details pertaining to an image click on its caption
14. ad To select these files from a local folder click on the Browse button to specify its location your hard drive For each image a user may set the visibility to public or private by using the dropdown menu that appears below each image file path Alternately users may add images to an existing image set Select the edit button on the image set details page see Viewing Image Set Details then select Add More Images Each image file uploaded to EUCLIS must not be larger than 20 MB Editing Images Select the edit button from the image set details page This redirects the user to a page where comments may be entered and where image accessibility may be changed To save changes click the Submit button Users are only allowed to edit images that they have uploaded Deleting Images To delete images from an image set view the image set to which it belongs see View Image Set Details select the checkbox that appears under the Introdu User Cloc Clock CI Clock Experime Clock Family Clock Ge Cloc Clock M Clock Mu Clock Refer Cloc thumbnail s of the image s that you want to delete then click the Delete button A user may also select an image see View Image Details then click on the Delete button Users are only allowed to delete images that they have uploaded Editing Image Sets From the image set details page select the edit button This redirects the user to a page where image set at
15. ck Images and Clock References Clock Experiments stores and manages sets of experiments which are comprised of integrated experimental results and links to relevant components from the KnowledgeBase mainly genes and references These will eventually include modelling and simulation results from Clock Models Clock Experiments also provides facilities for managing resources involved per experiment and for managing links to Clock Genes and Clock References It also provides a tool for graphic visualization of experiment data files containing activity time series double plots Each experiment set has its own users that may have different privileges Clock Genes provides an integrated view of information regarding the circadian genes of model organisms of interest in chronobiology The current release contains gene catalogues for Neurospora crassa Synechococcus aureus Homo sapiens Arabidopsis thaliana Drosophila melanogaster and Mus musculus Clocks RUs Clock Cla Clock Experiments Clock Family Tees Clock Clock Images Clock Models Clock Museum Clock References Clock Tools Clock Models contains a taxonomy of existing models of chronobiological data this taxonomy classifies models based on information such as the methods used for creating the model the scale and scope of the model as well as the organism or organisms for which the model was developed Entries in clock models has links to the references from
16. dministrator is responsible for granting requests for user accounts as well as for granting primary user roles user level 4 in the system Administrator functions are not discussed in this manual References to user roles will be made in each module for purposes of clarity Introd User Clocks x Clock Clock Experi Clock Family Clock Ge Clock In Clock Clock Muse Clock Cloc introduction Clock Cle Clocks R US Clock Experiments Clock Family Trees Clock Ge The Clocks Registered User Clocks R US module provides the accessibility and Clock Images user account management interfaces for the system Clocks R Us also provides a general search facility that will allow users to find information within EUCLIS Clock Models through a keyword search Clock Museum Clock References Requesting for a User Account Clock Tools An unregistered user may request for an account to access the EUCLIS modules From the main page go to Home and select the request button This redirects you to a page through which you must specify your login details and contact information Fill out all required fields then press request to submit If your request is approved your account will be activated within 24 hours of receipt Account details will be sent via e Mail Logging in to EUCLIS All users with existing accounts can access EUCLIS resources by logging in to the system From the main
17. e Edit button or the Edit Collection buttons edit mode a user may modify the contents and the visibility of a note Click on the Save Changes button to apply the modifications Deleting a Collection A user may delete a collection by clicking on the Delete button on the rightmost part of the collection entry see Viewing List of Collections This option is generally available for Lead Curators and Curators other users may only delete collections s he created Deleting a Collection Slideshow A user may delete a collection slideshow by clicking on the Delete button beside the slideshow title that appears in the slideshow list on the collection details page Deleting a Collection Image A user may delete a collection image by clicking on the Delete button beside the image name or description in the image list that appears in the Related Clock Clock Family Clock Ge Clock Images co cos sil Clock Referer Links table in the collection details page Deleting a Collection Reference A user may delete a collection reference by clicking on the Delete button beside the reference title listed in the reference list within the Related Links table in the collection details page Deleting a Collection Note A user may delete a collection note by clicking on the Delete button beside the note that appears in the table of notes within the collection details page 2 22 Clock classes Clock Experiments Clock Fa
18. e allowed to delete classes that they have created cot introduction Clock Experiments The clock experiments module contains experiment sets which allow the modularized management of biological information in EUCLIS Each experiment set may contain links to the following data Experiments which correspond to actual laboratory experiments and contains a description associated data files and accessibility details Data files which contains experiment details including the organism on which it was performed when it was performed and SOP details It also contains the link to the double plot when applicable Experiment sets may be accessed by members at least a registered user specified by its creator Details of the access privileges in Clock Experiments are as follows User Experiment Privileges Level Access Level View Download Upload Edit Assign Create or Experiments Data Files Data Files Experiment Membership Delete Set Details inan Experiment Experiment Sets Set 2 Accessible to Project Lead Investigator 3 Accessible to Project Investigator 4 Accessible to Restricted User 5 Accessible to x x Registered User This is at the discretion of the owner of the experiment set who may or may not make data files available to registered users Viewing Experiments Sets Experiment sets may be accessed by a logged user from any page by clicki
19. ened where you can select the organism from which the gene to be linked originates Select on the organism name to display its gene network map Select the gene which you wish to link to view its details On the same page select add link to project to link the gene or back to view other genes Introd User Ac Cloc Clock Clock Expe Clock Family Clock Ge Clock In Clock Clock Mus Clock Refer Cloc Adding references To add a reference link click on the add link beside the references table header In the new browser a list of available references is displayed You may browse through the list or use the keyword search facility to find a specific reference Select the title that you wish to add to display its details Click on link this reference or back to select another reference Removing links From the form page select the checkbox es of experiment s gene s or reference s that you wish to delete from the project then click on remove link Viewing members and editing membership To view the list of users who can access an experiment set select the view members link A table of users is displayed To add a member click on the add member link and select a name from the list of users To remove a member s select the checkbox es beside the name of the member s you wish to remove from the project and click remove member To change the roles of members select the new role from the dro
20. ented in the system to manage information accessibility Each user role is associated with certain functionalities these are assigned to persons eligible for registration by the EUCLOCK project management team The following table summarizes the roles that have been defined per module Clocks R Clock Classes Clock Clock Images Clock Us Experiments i Models Administrator Class Project Lead Patriarch Lead Image Set Model Lead Coordinator Investigator Annotator Coordinator Coordinator Curator Contributor Project Annotator Image Set Curator Investigator Contributor Restricted Restricted User Restricted User User Registered User Unregistered User Each user role is assigned independently per module i e one can be a contributor under Clock Library and a restricted user under Clock Classes with each user level having approximately similar access permissions across modules These are as follows User Level 0 Unregistered users may view the general information about each EUCLIS module but will not be able to access any data In order to acquire access rights unregistered users may request for an account see Requesting for a User Account User Level 1 In addition to general information access registered users will be able to view material with general visibility in the module in which s he is registered but Clock Experiments Clock Family 1 References Collection Coordinator Contributor Restricted
21. eri Clock Family Clock Ge Clock In Clock Clock Muse Clock Cloc The current release of EUCLIS has a new module Clock Models alongside enhanced versions of modules from previous releases Clock Classes Clock Experiments Clock Family Trees Clock Genes Clock Images Clock Museum Clock References and Clock Tools EUCLIS Modules Clock Family Trees allows users to document and trace their ancestry in the chronobiology research community It also serves as a virtual dictionary of chronobiologists where fields of specialization and dissertation information are indicated Clock Images serves as a repository of image files and associated information from EUCLIS users It provides facilities for image viewing sharing and organization Clock References provides researchers access to a central reference repository with integrated tools for bibliographic information sharing This module also contains a special section for dissertations in chronobiology A separate module Clock Classes serves as a repository of materials for chronobiology related courses including selected presentations from summer schools Clock Museum provides a venue for organizing images and references into collections containing information on relevant events in chronobiology history It also allows the users to generate slideshows using these material and to make annotations to such collections This module makes use of existing entries in Clo
22. form for where you can enter the details for a publication Fill up the form and click submit The PhD collection will be updated and will show the newly created entry in the list of available theses Uploading a PhD thesis Once a bibliographic entry for a dissertation has been created see previous item one may now upload the PhD thesis Click on the thesis title from the list of theses then click on the Manage Document button You will be redirected to a page from which one can upload the document Specify the path of the document that you wish to upload then click the Upload button Downloading a Thesis To download a thesis click its title from the list of theses then select Download Document Modifying files associate with a Thesis To change the file associated with a bibliographic entry select the title of the thesis from the theses list then click the Manage Document button Click on the Browse button to specify the file path of the replacement file then select Upload To delete the file currently associated with the thesis select the title of the thesis from the theses list click Manage Document then select Delete Associated Document Removing a Thesis To remove a thesis click on the thesis title and select Manage Document The details of the document will be displayed Click the delete button and confirm the delete action Introdu User Clocks Clock C Clock Experi Clock Family 7 Clock G
23. formation on the class then click submit Users will only be allowed to edit classes that they have created Managing a class Adding participants to a class Select the name of the class to which you wish to add members then select the manage class participants link On the page that appears click on the add participants button You will be redirected to a page containing a list of all registered users of EUCLIS Click on the checkboxes beside the names of the users you wish to add then select the appropriate class role that you wish to assign to them from the dropdown menu Click submit to save the changes Editing participant roles From the manage class participants page of a class click on the name of the participant whose role you wish to alter This redirects you to a page containing the information about the participant Click the edit button select the new participant role from the dropdown list then click submit to save changes Removing participants from a class From the manage class participants page of a class select the delete link beside the participant that you wish to remove then select yes to confirm Introdu User Cloc Cloc Clock Experir Clock Family Clock Ge Clock In Clock Clock Mus Clock Refer Cloc Deleting a class Select the delete link beside the name of a class that you wish to delete from a class set then click yes to confirm deletion Users will only b
24. ged user from any page by clicking on the Clock Classes sidebar link Viewing Course Materials Course materials available for each class may be viewed by clicking the title of a course on the main Clock Classes page Information on course materials will be displayed if these are available Downloading Course Materials Restricted function User level requirement restricted user Course materials may be downloaded by users designated as participants in a class by the class coordinator To download course material click on its filename the file will be opened in a new browser window Restricted function User level requirement class contributor Uploading Course Materials To upload course material select the name of the course from the Clock Classes page Specify the location of the file you wish to upload and click the upload button Introdu Clocks Clock Clock Experiments Clock Family Trees Clock Genes Clock Images Clock M Clock M Clock Refe Cloc Restricted function User level requirement class coordinator Adding a class Select the Clock Classes link from the sidebar then select the link to the class set to which you wish to add a class Click on the Add new class button that appears enter the information about the class you wish to add then click submit Editing a class Select the edit link for the class whose information you wish to change Enter the new in
25. his feature is at the discretion of the owner of an experiment set a Clock Clock Family Clock Museum Clock References cot Restricted functions User level requirement project lead investigator project investigator Editing Experiment Sets Access the experiment set that you wish to edit see Viewing Experiment Sets On the experiment set page select edit A form appears wherein you can perform any of the following functions Modify project details Add experiments Add links to genes Add links to references Remove links to genes and or references Viewing members and editing membership or Each function will be discussed in the succeeding subsections Modifying project details To change the experiment set title or description type the modifications in the appropriate fields on the form and click save details Adding experiments To add an experiment click on the add link beside the experiments table header This opens a new browser window where you can specify the experiment name the experiment details and experiment accessibility If you wish your experiment to be accessible to Registered Users you have the option of making the data file content downloadable by ticking the Make Data Files Accessible checkbox After entering the details select add experiment Adding genes To link a gene to an experiment click on the add link beside the genes table header A new browser window is op
26. ion button will add the new collection to the system Adding a Collection Slideshow A user may add new slideshow for a collection by clicking on the Add link beside the slideshows header in the collection details page This directs the user to a page prompting for the title and description of the slideshow that s he wishes to add Clicking on the Add Slideshow button redirects the user to the page for adding images which displays the image sets and the corresponding list of images per set that can be used for the slideshow To select an image to add to a slideshow the user should click on the checkbox below the image s Click on the Include Selected Images button to create the show introduction Clock Experiments Clock Family Trees Adding a Collection Image A user may link a new image to the collection by clicking on the Add link beside the images header in the collection details page This redirects the user to the add image page where the image sets available to the user and the list of images under it are displayed To link the image click on the checkbox below it then click on the Include Selected Images button To link multiple images at the same time click on the checkboxes below the images to be included and click on the Include Selected Images button In the event that a user is adding a collection slideshow or adding a collection image and is unable to find the image that s he wants to include s he may click o
27. lead curator may edit a collection by clicking on the Edit button beside a specific collection in the collection list page or by clicking the Edit Collection button that appears at the bottom of the collection details page For registered users collection editing is restricted to the A collections which s he created consequently the Edit or the Edit collection button may not be available at all times in all collections Once user is in edit mode information about the collection i e title description keywords and category may be updated Click on the Save Changes button to save modifications Under this mode a user may also delete slideshows created for the collection as well as images references and notes associated with it A user may likewise edit slideshows and notes created for the collection in this mode Click on the Done button at the bottom of the page to save changes Editing a Collection Slideshow A lead curator a curator or the creator of a collection may edit a slideshow by clicking the Edit button that appears beside each slideshow title in the collection details page In Edit Mode a user may modify information about the slideshow remove an image or images from it add images to the slideshow or change the sequence of the images in the slideshow Detailed instructions for performing these tasks are provided within this section Click on the Save Changes button to finish editing the slideshow Removing Image
28. lick OK Restricted functions User level requirement project lead investigator Creating Experiment Sets From the main page Clock Experiments select create new project Indicate the project name and description on the form page then click add project To build the experiment set see Editing Experiment Sets Deleting Experiment Sets From the main page Clock Experiments select the name of experiment set that you want to delete then click delete Clock Clock Family Clock Ge Clock Images co a Clock Museum Clock Clock Family Trees Clock Family Trees is a repository of chronobiologists scientific genealogy It allows chronobiologists to create links to their PhD advisors the chronoparents their PhD advisees the chronochildren and to enter other related information Links to their PhD theses in Clock References as well as to available images in Clock Images are provided Any registered user can access Family Trees Viewing Searching Clock Family Trees Chronobiologists Information on chronobiologists may be viewed by a logged user from any page by clicking on the Clock Family Trees sidebar link The user can view the listing of chronobiologists in Family Trees by either one of two options a browsing by clicking the first letter of the last name or b searching by any of the fields like last name first name middle name university degree year
29. link Select the edit link of the class that you wish to edit change the user set information then click submit Primary users of each module will only be allowed to edit classes that you have created Adding members to a user set From the sidebar select the manage user set link then select the link to the class to which you wish to add members Click on the add members button then select the users that you wish to add to the set from the list Click submit to add the members Introd User A cl Cloc T Clock Experim Clock Family K Clock Clock Clock Clock Muse Clock Referei Clock T Deleting members from a user set From the sidebar select the manage user set link then select the link to the class from which you wish to remove members Select the delete link that appears beside the name of each member of a user set then select yes to confirm user set deletion Deleting user sets From the sidebar select the manage user set link then select the delete link of the user set you wish to remove Click yes to confirm deletion Primary users of each module will only be allowed to delete classes that you have created Clock Expel Clock Family Cloc Clock In Clock M Clock Classes contain lecture materials including lecture notes posters and slide presentations from courses offered by EUCLOCK researchers Viewing Classes Courses offered may be viewed by a log
30. mily Trees Clock Images condo Clock References Clock References is repository of bibliographic entries of journal articles old manuscripts books and PhD Theses in EUCLIS Efficient file sharing is facilitated through the availability of functions for file and link uploading as well as for link viewing The default accessibility requirement for use of the library is for a registered user Viewing Searching Bibliographic Entries Bibliographic Entries may be viewed by a logged user from any page by clicking on the Clock References sidebar link Alternately the user may search the database using keywords or the author s name title or the year a reference was released Viewing Bibliographic Details To view bibliographic details click on the title of the reference entry from the table of references page see Viewing Bibliographic Entries This redirects you to a page containing information on the publication Restricted functions User level requirement restricted user Exporting Entries to EndNoteXML Files Use the checkboxes in the rightmost column of the table of references to select entries to be exported to select all entries click on the topmost checkbox then click export to generate the EndNoteXML file Download the generated file by clicking on the link provided The user can then have a local copy of the entries by importing from the downloaded file using his her EndNote application When
31. n rename this when your browser prompts you for the local directory to which you want to save a file or after you have downloaded the file Using View Manager The View Manager feature allows a user to view multiple high resolution images in a single page and is accessible from the Clock Images home page and on image set details pages Creating a view From the Clock Images home page or from an image set details page select checkboxes under images that you wish to view simultaneously then click the Include in View button Saving a view To save a view indicate the view name and click the Save View As button on top of the page introduction User access Clocks RUs Clock classes Clock Experiments Clock Family cee co a Clock Museum Clock Retrieving a saved view Previously saved views may be accessed by clicking on the My Saved Views link on the Clock Images home page Deleting a view To delete a view go to My Saved Views select the views that you want to remove then click Delete Adding Images to Image Sets Restricted functions User level requirement contributor Images may be added upon the creation of an image set see Creating Image Sets or to existing image sets Select the image set which you wish to add images to then click the edit button then select add more images You will be redirected to a page where you can indicate the file paths of the images you wish to uplo
32. n the link D provided in the instructions text below the list of images shown in the page This option will only be available to Image Set Coordinators and Image Set Contributors of the image set s he is currently viewing For other users instructions on how to contact ClockHelp will be provided in the page Adding a Collection Reference A user may link a new reference to the collection by clicking on the Add link beside the References header under the collection details page This redirects the user to a page containing the list of reference collections Click on the reference collection title to view the references under that collection then click on the reference titles to view details about a reference Click on the Link this reference button to link a reference to the collection Adding a Collection Note A user may link a new reference to a collection by clicking on the Add link beside the Notes header under the collection details page This redirects the user to a page where s he can input the text of the note and where s he can specify if the note will be publically available or not Click the Add Annotation button to associate the note with the collection Introd User A Clocks Clock Clock Experi Clock Family Clock Ge Clock In Clock Clock M Clock Cloc Restricted functions User level requirement Registered user Curator Lead Curator Editing a Collection A curator or a
33. ng on the Clock Experiments sidebar link A table of experiment sets and their descriptions will be displayed from which a user may select the set that s he is interested in To view its content click on its name Users may view the members of an experiment set through this page Viewing Experiments To view the details and contents of an experiment click on the name of the experiment from the experiment set page see Viewing Experiment Sets This redirects you to a page containing the data files for a particular experiment which you may access Restricted functions User level requirement restricted user Viewing Data Files Data files may be accessed through the experiment details page To view a data file click on its name Additional data file details and links for downloading the data file and viewing the double plot are shown Downloading Data Files From the data file page click on the download data file button This opens a new browser window where the data file contents will be loaded Use your browser s save function to create a local Viewing Double Plots Double plots that show activity time series data and visible light protocol information may be downloaded from the data file page Click on the go button beside the double plot name the image is opened in a separate browser window To save a local copy right click on the image and click Save Target As As with data file download the availability of t
34. ng to a taxonomy presented in a study by Roenneberg and co authors To allow a more efficient present ation of the models to users each entry in the collection is provided with attributes scale scope size type biological aspects tools computational properties experimental evidences and an accompanying portable document format pdf file which contains a summary of the reference from which the model was taken Viewing Searching Models A logged user may view the taxonomy diagram by clicking on the Clock Models sidebar link This module displays biological models categorized according to the following taxonomy Explicit iodelling Conceptual Diagrammatic Disc ete Continuous Dete ministic Discrete Computational Qualitative Quantitative Contextual Computational Qualitative Continuous Dete ministic Quantitative Clock Clock Family Trees coca In the preceding diagram the leaves in red serve as the classification of the models and the user can click on any of these to view all the models belonging to these categories Alternately the user may search the database using keywords for the name scale scope size type biological aspects tools experimental evidence or computational properties of a model Models are subsequently based listed using names which are based on the name of the first author of the source paper Viewing Model Details
35. nted here manual entry addition Endnote Reference Manager file import or external database import Each variant is discussed separately If it is possible we are requesting contributors to follow this A format for authors in bibliographic entries Smith J A Doe J A and Doe J B Introdu User Cloc Clock Clock Experir Clock Family Clock Ge Clock In Clock M Clock Mus Clock Refi Cloc Manual entry addition From the main page select add new reference You will be redirected to a page containing a form where you can enter the details for a publication Fill up the form and click submit Importing an Endnote Reference Manager file To upload an Endnote or Reference Manager file select import references from file Select the file type that you wish to import specify the file location in your local drive then click import Importing from an external database To upload a bibliographic entry from an external database select import references from external database Choose the database from which you want to obtain information type the keywords and click go Retrieved document titles will be displayed Select all checkboxes of documents which you want to save in EUCLIS then click submit Currently only a link to PubMed is available For adding theses a registered user should e mail Clockhelp first about his her intention to upload his her thesis and wait for approval If the reque
36. of degree thesis dissertation title or keywords and specialization and clicking on the Submit Query button Viewing Chronobiologist Details To view information about a chronobiologist click on the full name of the chronobiologist in the list of chronobiologists obtained through Viewing Searching Clock Family Trees Chronobiologists This redirects you to a page displaying the following details available on the chronobiologist Full name Photograph University Degree and year degree was obtained Thesis dissertation title Specialization Chronoparent s name university and the year the parent obtained his her degree 8 Chronochild ren s name university and the year each chronochild obtained his her degree Oy UT a Introd User A Clocks Clock Clock Experi Clock Fami Clock Clock Clock Clock Muse Clock Clock T Viewing Chronoparent or Chronochild Details Click on the chronoparent or chronochild link from a page displaying information ona chronobiologist See Viewing Chronobiologist Details Adding a Chronobiogist To add a chronobiologist s entry to EUCLIS go to the main Clock Family Trees page and click the Add chronobiologist button Fill up the form and click the Continue button to create links to the chronobiologist s photograph in Clock Images and or links to a chronobiologist s thesis or dissertation in Clock References as well as links to chr
37. onoparent s Click the Finish button If the submission was made by a registered user the entry has to be approved by a Clock Family Trees patriarch before it is officially added to Family Trees Restricted function User level requirement patriarch or entry creator registered user Editing Chronobiologist Details From the chronobiologist details page click on the Edit button Enter the changes in the form including additional or modified links to chronoparent s thesis and photograph To link images select add link under photograph then select the name of the image to be linked to an entry Click the Link button to save changes To remove or change links to an image select either change link or remove link then proceed as before To link a thesis or dissertation from clock references select add link under thesis dissertation link then select the collection that contains the dissertation Select the title of the thesis or dissertation then select Link this reference An entry creator can edit his her own entry the entry of his her chronoparents and the entries of his her chronochildren Deleting a Chronobiologist From the chronobiologist details page click on the Delete button to delete the chronobiologist A confirmation page will be shown to confirm deletion click OK Introdu User Clocks F Clock Cla Clock Experir Clock Fami Clock Ge ma Clock Ii Clock Clock Mu Clock
38. or its filename in the absence of a caption from the Clock Images home page from search results or from the image set details page Viewing Image Set Details From the Clock Images home page click the View Image Sets link A list of Introd User Clocks Clock Clock Experi Clock Family Clock Clock Clock N Clock Muse Clock Referer Clock T available image sets will be displayed from which a user may select a particular set Alternately image set details may be accessed through Image details see Viewing Image Details where the image set links of an image are displayed Information on image sets include its title creator date of creation and the members who may access it Downloading Images and Image Sets Images may be downloaded individually or may be downloaded as a set provided that a user has the appropriate privileges for these If an image is publicly visible it may be downloaded by registered users Individual image file downloads To download a single image file click on the Download button that appears on the same page as the image Batch download A user may download multiple images to a single zipped file through an image set see Viewing Image Set Details From an image set select the check boxes corresponding to the images that will be downloaded Click on the Download button to save these images By default these will be saved ina file called outfile zip You ca
39. page Home select Login Provide your login details and press login to submit Logging out from the system All logged users will have the option to logout from the system through an additional link in the sidebar that appears upon login Changing account details Editing user information Logged users may edit their profiles by selecting the my profile link and changing the information associated with their account Select the update button to save the changes Changing your password Logged users may change their passwords by selecting the my profile link then the change password link A user must type his her old password as well as his her new password Click update to save changes Requesting for a new password Registered users may request for a new password by sending an e mail to ClockHelp clockhelp rzg mpg de this will be issued within 24 hours of the request User set management Restricted function User level requirement primary user for each module administrator A user set is used to define subsets of users who participate in selected activities within the chronobiology community User set creation From the sidebar select the manage user set link You will then be redirected to a page from which you can create a user set by clicking on the Add new user set button Enter a name and a description for your user set then click submit Editing user sets From the sidebar select the manage user set
40. particular SNP Flanking sequences are displayed in a popup window Downloading SNPs Worksheets containing all information on the SNP tables may be downloaded for each gene from the SNPs view or Details view To start an automatic file download click on the Dowload SNPs link above the SNPs table SNPs may be downloaded by registered users and other users with higher access privileges Restricted functions User level requirement lead annotator or annotator Adding Annotations Annotations can be added from the summary or default view see viewing gene details and gene views To add an annotation click on the add annotation button which appears immediately below the table containing the gene descriptions This redirects you to a page where you can enter your new annotation and add links to it Enter the necessary information and click on submit Editing Annotations Existing annotations may be modified using the edit link under options that appears beside each entry Click on the link corresponding to the annotation you wish to change You will be redirected to a page where you can edit your annotation text change the annotation link or add a link to reference When you have made all the necessary changes click on save details Deleting Annotations To delete a specific annotation click on the delete link under options that appears beside it You will be prompted to confirm deletion Click OK to proceed or cancel to abort the
41. pdown menu beside each member s name and click update roles Editing Experiments To modify the information on an experiment click on the experiment name from the experiment details page You are automatically redirected to a page where you can make changes to the experiment title description and or experiment accessibility Click on the Save Details button to keep changes Editing Data Files On the experiment details page see Viewing Experiment Details for access instructions click on the data file that you wish to edit then click the edit button Enter the changes in the data file information form and click submit Make sure that all required fields are filled If you wish to upload a file to replace the data file see adding data files Clock Clock Family Clock Ge Clock Images co a Clock Museum Clock Adding Data Files This section deals with data file upload and double plot generation To add a data file go to the experiment details page to view this please refer to Viewing Experiment Details and click the edit button then select add A form will be generated to enable the user to specify experiment details Enter the title organism experiment date and remarks pertaining to the data file Indicate the location of the data file that you wish to upload by using the Browse button and indicate its format There are currently three supported data file formats
42. roups of slideshows comprised of photos linked images and linked references from the Clock Images and Clock References modules of EUCLIS A collection may also contain relevant notes contributed by other users There will be standard public and private collections individually described as follows Standard collection The standard collection will contain curated and annotated slideshows images and links This may only be created by a curator but may be accessed by registered users Public collection A public collection contains slideshows images and links that may be created by and accessed by any registered user Private collection A private collection contains images from a single image set in clock images this collection may be created and viewed by members of the particular image set where the material was obtained Viewing List of Collections The list of collections in Clock Museum may be accessed by clicking on the Clock Museum sidebar link A table of collections categorized as Standard Private or Public will be displayed from which a user may select the specific collection that s he wants to view Viewing a Collection To view the details of a collection click on the title of the collection from the collection list page see Viewing List of Collections Collection details include its description creation and update information the list of images and references linked to it and a table of notes contributed by EU
43. s from the Slideshow To remove image s from the slideshow clicking on the checkbox es below the image s to be removed then click on the Remove Image button Introdu User Cloc Clock CI Clock Experime Clock Family Clock Clock Ime Clock Clock Clock Refer Cloc Adding an image or images to a slideshow A user may add image s to an existing slideshow by clicking on the Add link in the edit slideshow page This redirects the user to a page that displays the image sets and the list of images under it from which the user can choose Select an image set then click on the checkbox es below the image s to be added to the slideshow Cicking the Include Selected Images button to save changes See information box on page 34 Changing the image sequence slideshow A user may change the sequence of images in a slideshow by clicking on the Edit Image Sequence link in the edit slideshow page The user is redirected to a page where it is possible to specify the position that an image will take in the slideshow the text box appears beside each of the images listed in the page Click on the Save Changes button to apply changes Editing a Collection Note A user may edit a note within a collection that s he create by clicking the Edit Button associated with it under the list of notes in the collection details page This function can be accessed by Lead Curators and Curators by clicking on th
44. st is approved a new bibliographic entry must be created for the paper before it can be uploaded No paper can be uploaded without an existing bibliographic entry Managing Clock References Collection Users From the main page Clock References scroll to the bottom of the page and select the option for managing Clock References accounts i e You can manage Clock References accounts by clicking here You will be redirected to a page showing a table of users Select the login name of the user whose account you wish to edit From the user s details page select edit Select a new Clock References access level for the user and click submit Introd User A Clocks Clock Clock Experi Clock Family Clock In Clock Clock Muse Clock Re Cloc Euclis PhD Thesis Collection EUCLIS currently has a facility for uploading dissertations on chronobiology research the PhD thesis collection Theses may only be uploaded by users with library contributor privileges Registered users may view and download theses in the collection Accessing the collection You must be logged into EUCLIS to access the collection From the main page click on Clock References then click the PhD thesis collection link Adding a thesis Creating a bibliographic entry It is necessary to create a reference to a PhD thesis before it can be uploaded On the PhD thesis collection page select Add New Reference You will be redirected to a
45. tributes title and description may be altered The same page also allows the coordinator to add and remove images and or members to or from an image set Click the Update button to save changes Restricted functions User level requirement image set coordinator Creating Image Sets From the main page select the Create Image Link that appears on top of the page Enter the image set title and description on the page that appears and click the Create Image Set button Adding Members to Image Sets To add members to an image set view its details see Viewing Image Set Details then select Edit then select Add Member This redirects you to a page displaying the list of all EUCLIS members Indicate the membership type for all members that you wish to include in the image set using the dropdown menu that is available for each name A member may be designate as an image contributor or an image contributor or as a regular image set member Deleting Image Sets To delete an image view its details see View Image Set Details then select the edit button This redirects you to a page where you can select the Delete Image Set to delete the whole set introduction User access Clocks RUs Clock classes Clock Experiments Clock Family cee co a Clock Museum Clock gt Clock Models Clock Models features a collection of circadian models from several published papers in chronobiology Theses are classified accordi
46. using the Import functionality of EndNote specify EndNote generated XML as the Import Option and Unicode UTF 8 as the Text Translation Introd User A Clocks Clock Clock Experi Clock Family Clock Clock Clock Muse Clock Re Cloc Downloading Documents Click on the download document button from the bibliographic details page to open a new browser window where the document contents will be loaded To save the data to your local drive use the save function of your browser File gt Save As File gt Save Page As Uploading Documents Restricted functions User level requirement library contributor Click on the manage document button from the bibliographic details page to open a new browser window to upload document contents Use browse button to find the document to be uploaded and then click upload button to complete the process Editing Bibliographic Entries From the bibliographic details page click on the edit button Enter the changes in the details form and then click submit Deleting Bibliographic Entries From the bibliographic details page click on the delete button to delete the entry on the table A delete confirmation dialog will be shown to confirm delete click OK Adding Bibliographic Entries To add a bibliographic entry go to the main page Clock References and scroll down to the end of the page The options for adding entries are prese
47. which these models were obtained Clock Tools provides descriptions and links to software used by the EUCLOCK community for processing and analysing chronobiology related data The Clock Registered User Services module Clocks R US handles the management of user accounts which can be divided into several levels based on associated privileges Clocks R Us is also used for the management of user sets which provides the additional possibility of having specialized access levels for collections or sets in selected modules How to use the manual The manual is organized according to the different clock modules with the corresponding functionalities for each module listed to approximate typical access flow Functions for more general access are listed before those requiring stricter access conditions Access levels for module features are always indicated before each set of described functionalities Functionalities that require higher access levels are listed towards the end of each section For information on this please refer to User Access section All entries that cross reference other material in the manual or external web pages appear in boldface All page tabs are linked to their corresponding sections in the manual Intros User A Clocks Clock C Clock Experim Clock Family A Clock Clock In Clock Clock Mus Clock Refere Clock User Access A role based authorization scheme was implem
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