| CEBS Release Notes |
| For more information about CEBS, visit the homepage or review the FAQs on the CEBS Development Forum. For questions or comments, please send an email to the CEBS Help Desk. |
Release Date: June 8, 2007
Enhancements
- BioCarta Diagrams: Implemented an enhancement that will allow SVG diagrams to be displayed in web browsers other than Microsoft Internet Explorer. Other browsers (e.g., Firefox 2.x) will attempt to natively render the SVG. However, in non-IE browsers the BioCarta diagrams may look different. For example, a different font may be displayed and the elements on the pathway diagram may lack the "three-dimensional" quality (i.e., lack of shading, no drop shadows). The Adobe SVG Viewer is still required by users of IE.
- Genome Browser: Added the ability to forward results to the UCSC Genome Browser. This feature is available on the "Gene Info Page", which is accessible after the "Differentially Expressed Genes" page that is associated with Microarray Analysis and Annotations (AKA "My Favorite Gene") workflows.
- PDQ_MED: Completed the initial (beta) release of the integration with InPharmix PDQ_MED. This allows a user to send results from CEBS to PDQ_MED, which searches and analyzes the abstracts that are available in MEDLINE. In CEBS, the user is able to select genes of interest for processing by PDQ_MED. When enabled, the feature is accessible on the "Gene Annotation Report", which is associated with the Microarray Analysis and Annotations (AKA "My Favorite Gene") workflows.
- Annotations: If a user searches on a gene using different accession numbers, only one gene will appear on the Annotation report. Handling multiple hits of the same gene has not been implemented.
- BioCarta Pathways: The BioCarta pathway diagrams "blink" as the user scrolls down the page. The issue is with the Adobe SVG viewer. The workaround is to right-click the diagram and select "click to activate".
- Search Results: Selecting checkboxes causes the page to redraw. This is more apparent to users of Internet Explorer than Firefox. When user clicks the checkbox, the browser sends a request to the server and updates the "selected" attribute of the tree node. The "selected" attribute is used for tracking if a tree node is checked or not. Each time, when a new request is sent, a response from the server will send a new page back to the browser. The browser will repaint the page with the new content. Since the Firefox and IE use different technologies to repaint the window, it seems that Firefox has done a more graceful job on repainting window (in that IE takes longer to repaint the window). Therefore, IE seems to "blink" each time user checks a box, but Firefox doesn't seem to "blink" at all (even though the window is repainted as well).
- Filtering: Searching and then filtering once produces the correct results. Using filter again (or using the browser's back button) may result in incorrect results. Moreover, using the browser's back button may return the user to a page that was overridden by a subsequent action. Therefore, selecting a checkbox may produce an error condition that returns an exception report (i.e., HTTP Status 500).
CEBS 2.0.9 Release Summary
Release Date: January 16, 2007
Bug fixes
- Search Results: Selecting a value in the search pages (e.g., "Glycogen depletion" the "Main Diagnosis" field in the "Pathology" section on the "Search by Subject Characteristics" page) may return search results that have no subjects in the comparator groups. Previously, if groups were displayed and the "Show Comparators" check box was selected, the comparator group name was labeled "ShortNameNotSet". The issue is resolved by displaying the comparator group name (e.g., Rat Control 6h) in regular (non-italics) typeface.
- Microarray: The Subject ID column accurately shows all subjects associated with a pool. This issue was apparent when retrieving the individual hybridizations associated with subjects in a comparator/vehicle group.
- Annotations: The Annotations "Enter Gene IDs" box or text-file upload supports additional delimiters: space character, tab character, new-line character, carriage-return character, and the form-feed character.
- Pathology Results: If duplicate records for pathology data are loaded to CEBS, the browser will attempt to prevent apparent duplicates from being displayed.
- General: Implemented improvements to the data loading utilities. Added check to ensure that the data loader will not add a new study with an existing accession number.
- BioCarta Pathways: The pathways are generated from SVGs. CEBS implements the Adobe SVG Viewer, which is not compatible with Mozilla Firefox.
CEBS 2.0.8 Release Summary
Release Date: November 20, 2006
Bug fixes
- Timeline: When no protocols are available for a study, the protocol link on the Timeline page displays "No protocols available."
- General: Implemented improvements to the data loading utilities.
CEBS 2.0.7 Release Summary
Release Date: August 17, 2006
Bug fixes
- General: Implemented a workaround to a bug in the presentation framework, which was causing errors to be generated under concurrency conditions induced during load/stress testing. Implemented method to make actions thread safe.
- Annotations: Pathways listed in the "Pathway Names" column are now valid hyperlinks on the BioCarta Annotation Report page.
- General: Modified content of homepage and left menu. Removed Register link.
- General: Adjusted the session timeout value. When a user exceeds this limit, the browser redirects to a "Session Timeout" page.
- Search Results: Implemented a call back to the TreeManager from the new Node factories that allowed TreeManager to maintain a hash lookup of dependent nodes, removing the need to search the tree for Nodes.
- Microarray: Removed tissue drop-down list.
- Proteomics: Changed connection pool parameters to test connection to the database. Modified parameters to optimize performance.
- Timeline: When no protocols are available for a study, if user clicks the protocol link on the Timeline page, the UI should display "No protocols available." This has been fixed for Disposition. The next release will include the fix for the other protocols as well.
CEBS 2.0.6 (beta) Release Summary
Release Date: July 6, 2006
Bug fixes
- Search Studies/Subjects: Corrected JavaScript function on the "Show Advanced Search" links on both search pages.
- Search Studies: Corrected problem that occurred when only one specific study was selected as a search criteria. If the study was part of a multi-study investigation, the search results would return all the studies that belong to its investigation.
- Search Results: Search pages may contain values from private data. When a user without sufficient privileges uses these values to query the private data in CEBS, the search results page displays a message stating "We're sorry, but you selected a study that contains private data". This message about private data will only display if the search returns no results due to private data restrictions. If the user selects criteria resulting in a combination of public and private data, then the private data will be silently removed from the results.
- Show Search Criteria: This page was updated to ensure all query criteria are properly displayed.
- Observations: Saving the report as a CSV file no longer saves the file with a .do extension.
- Annotations: Corrected problem of duplicate rows being displayed (pathway and species) for the KEGG pathways.
- Annotations: Corrected problem retrieving KEGG pathways.
- Annotations: Corrected displaytag logic issue that was discovered for one of the links for "Total Genes" on the KEGG annotations report.
- Annotations: Added pagination to annotation reports .
- Annotations: Added an intermediate "please wait" page to the GO annotation report.
- Annotations: Added "Export to Excel" to BioCarta Pathway, KEGG Pathway, GO Annotations report.
- Annotations: Improved sorting.
- Annotations and Microarray: On the Gene Info page, the links under the BioCarta Pathway section are now working.
- Microarray: QC data is now available for all Affymetrix and Agilent microarray experiments. (Note: QC data for GenePix and ArraySuite are unavailable.)
- Microarray: Corrected data issue associated with certain Affymetrix arrays with factors "dose" and "time".
- Microarray: Corrected misaligned display of sample information on microarray visualization and sample group selection pages for CEBS Two Channel experiments.
- Search Studies/Subjects: Added relative hyperlinks to the search criteria sections on the search pages.
- Search Studies: Removed "Acetaminophen" from chemical name field in the "Chemical Stressors" section. The term "Acetaminophen (APAP)" remains.
- Search Subjects: Units have now been added to the test criteria for Clinical Chemistry, Hematology, and Observations During Timeline Of Study.
- Search Subjects: A "Show species and strains" pop-up window has now been added to the In vivo search criteria section. This provides the species-strain listing for which toxicogenomics data is currently available within CEBS.
- Search Results: The "Available Data" column on the search results page now has a tool tip when a user hovers over each of the icons. The tool tip indicates that the appropriate links are at the bottom of the screen.
- Search Results: The radio button "All Groups" in the "Display Options" section now says (in parenthesis) that when this option is selected, the comparator groups are not shown; however, even though the are not shown, they are automatically selected if the group is selected.
- Search Results: The text at the top of this page now defines the difference between an investigation and a study.
- Search Results: Changed text to: View Selected Microarray Data by Studies/Experiments or Individual Hybridizations
- Timeline: When no disposition protocols are available for a study, if user clicks the protocol link for Disposition, the UI displays "No disposition protocols available."
- Clinical Results/Pathology Results: Improved performance of bottleneck that could occur if a user attempted to retrieve very large amounts of test results spanning multiple studies.
- Observations: Added description to explain how the sort order is originally set for the columns (investigation, study, group, subject ID, and protocol name). The table can be re-sorted by clicking on one of the column headers, at which time the table will be sorted by the column that was selected.
- Help: On-line is now available for all pages of the CEBS application.
- Get an Accession Number: Updated the content on this page.
- Links: Updated links.
- Download Center: Added the CEBS Download Center, which contains additional information about the CEBS object models (SysBio-OM and SysTox-OM). This feature provides users with access to the XMI and Rational Rose MDL files.
- Data: Two issues were reported for the University of Tennessee study (accession number 003-00001-0011-000-6 , experiment ID 1060246001): (1) The "Available Data" column on the Search Results page does not displaying the MA icon, and (2) factor values are missing from the hybridization report.
- Microarray: The drop-down list on microarray experiment search page correctly displays data retrieved from the database. However, there are some values in drop-down lists (i.e., in the "Investigator Name" field) that may not retrieve any data.
CEBS 2.0.5 (beta) Release Summary
Release Date: May 9, 2006
Bug fixes
- Group Information: The subjects for each group are sorted by alphanumeric order.
- Observation Data: The table is sorted in the following order: Investigation, Study, Protocol Name, Group, and Subject ID.
- Microarray: QC data is now available for all Affymetrix and Agilent microarray experiments. (Note: QC data for GenePix and ArraySuite are unavailable.)
- Annotation: Annotation (AKA My Favorite Gene) is a new feature in this release of CEBS. This feature allows a user to search on any gene (or list of genes) by either its GenBank Accession Number, Affymetrix Probe ID, Agilent Probe ID, Locus Link/EntrezGene, or Gene Symbol and receive a simple annotation report or reports from other sources such as BioCarta, KEGG and GO reports. Currently only the human, mouse, and rat species are available for annotation. CEBS Annotation is powered by caBIO.
- Search Results: When a user selects a study, the comparators will automatically be selected unless manually unselected.
- Search Results: If a user's search for a study for which they do not have the appropriate access to view, CEBS will now provide a proper error message that indicates the user has insufficient rights to view the study.
- Gene Information: Improved the layout of the "gene info" page.
- Microarray: Added buttons to select "all" and "none" on the "Individual Hybridization" page. By default, all hybridizations are selected. The user can select the "none" button to deselect all hybridizations, which then allows the user to select only the hybridizations of interested.
- Microarray: Changed the name of "Generic One Channel" to "CEBS One Channel" and "Generic Two Channel" to "CEBS Two Channel" (Image Processing Software).
- Annotations: The column headers on the Annotation Reports for BioCarta, KEGG, and GO are not sortable.
- Annotations and Microarray: On the Gene Info page, the links under the BioCarta Pathway section are currently not working.
CEBS 2.0.4 (beta) Release Summary
Release Date: March 1, 2006
Bug fixes
- Data: All datasets that were present in earlier releases were reloaded. This excercise resolved previous data-related issues (i.e., comparator groups, stressor information, protocols).
- Group Information: This page now displays the upper and lower boundary limits for age if the individual age of the subject is not available.
- Protocols: Histopathology findings are now displayed, when available, under "Specimen Preparation/Preparation Protocols and Assay Protocols" page.
- Data: Additional investigations/studies were added to CEBS.
- Search by Studies: Added additional search criteria.
- Search Results: Changed default behavior of checkboxes to include/select comparators. Added button (located below the search results table) that allows the user to unselect/deselect comparators if they were selected.
- Security: Modify Account and Change Password now send emails to the user to indicate a change has been made to their account.
CEBS 2.0.3 (beta) Release Summary
Release Date: February 9, 2006
Bug fixes
- Search: Sorted the values in search criteria fields on the search pages.
- Show Search Criteria: If no search criteria were selected, display the message "No search criteria selected."
- Show Search Criteria: Clear values from previous search when a user selects the "Display all Studies" link.
- Protocols: Updated all protocol pages to correctly display data.
- Group Information: The "Age at Start" field correctly displays data and units.
- Microarray: CEBS accession number is properly displayed on the Experiment Information Report.
- Microarray: Added a warning if the user selects arrays from different array designs. This scenario could be present if the user selected studies that were conducted with different array designs and then selected "Individual Hybridizations" as the path to analysis.
- Proteomics: Exporting a table/form correctly shows header instead of HTML code [i.e., Protein Expression Analysis Data (Confirmed Protein IDs only)].
- Search: For fields that do not return data, the field is disabled and shows "No data available". For fields that have not been enabled, the field is disabled and shows "Not enabled".
- Search by Studies: Added the ability to search on advanced study characteristics, chemical and genetic stressor characteristics.
- Clinical Results: Abbreviations and their descriptions are dynamically generated and displayed in pop-up window.
- CEBS Feedback: Added a form that allows the user to provide feedback about CEBS. An email message is sent to cebsfeedback@list.niehs.nih.gov.
- Proteomics: On pages displaying the raw spot and expression data, the spot abundance column has an asterisk and a footnote that summarizes the process of gel visualization and image analysis.
- Security: Encrypted password storage.
- Security: An email is now sent to the user when the user modifies their account or changes their password.
- Security: PIs are required to login to CEBS to approve a user's request to be added to their group.
- Security: Registration process now requires the combination of first name, last name, and email address to be unique.
- Show search criteria: This page may not update and show the correct query information.
- Data: Comparators are not being displayed properly because of issues with certain original data sets (studies 005-00002-0012-000-0, 001-00003-0011-000-6, 004-00004-0011-000-0, 006-00001-0011-000-9, and 004-00002-0011-000-8). Data reload will correct this issue. Data submitted for study 003-00001-0011-000-6 did not identify comparators. The comparators are correct in studies 005-00003-0011-000-9 and 001-00002-0013-000-7.
- Microarray: The stressor name field displays "null" for some experiments (i.e., #839178001) on the Experiment Information Report.
- Microarray: Experiment Information Report does not display Stressor Name(s) and Experiment Description.
CEBS 2.0.2 (beta) Release Summary
Release Date: December 22, 2005
Bug fixes
- Search by Study Characteristics: Fixed problem that prevented a user to be able to search by PI name.
- Search by Study Characteristics: Selecting the "reset" button resets the page instead of displaying an error message.
- Search by Subject Characteristics: If a user filters by subject characteristics on the results from the "Search by Subject Characteristics" but does not select additional criteria, CEBS will redisplay the original search results.
- Search by Subject Characteristics: The default value in the Clinical Signs field now displays "Please choose a clinical sign" instead of "Body Weight-Final".
- Search by Subject Characteristics: Selecting the "reset" button resets the page instead of displaying an error message.
- Search by Subject Characteristics: If the user submits a search request but does not select any search criteria, CEBS will display all studies.
- Search by Subject Characteristics: The "Pathology / Specimen Type" field displays available data and returns search results.
- Search by Subject Characteristics: Resolved problem with the "Subject: In vivo / Sex" field that prevented search to return the correct results.
- Data: The Group Disposition Protocols page displays the name of the anesthetic in the Anesthetic field (i.e., study 001-00002-0013-000-7)
- Proteomics: Removed the show/hide menu in the protein annotation page.
- Show search criteria: This page may not update and show the correct query information.
- Observation protocol: Not displaying all information provided (i.e., study 005-00002-0012-000-0).
- Histopathology findings: Not displaying information on Specimen Preparation / Preservation Protocol(s) and Assay Protocols page.
- Microarray: Experiment Information Report does not display Stressor Name(s) and Experiment Description.
- Microarray: CEBS accession number is not displayed on the Experiment Information Report.
- Proteomics: If columns can be sorted on pages that allow the user to download the tabular data displayed on the page, the downloaded file displays the header name in HTML format.
- Data: Study 005-00002-0012-000-0 does not display acetaminophen as a stressor name in the Study Details page.
- Data: Comparators are not being displayed properly because of issues with certain original data sets (studies 005-00002-0012-000-0, 001-00003-0011-000-6, 004-00004-0011-000-0, 006-00001-0011-000-9, and 004-00002-0011-000-8). Data reload will correct this issue. Data submitted for study 003-00001-0011-000-6 did not identify comparators. The comparators are correct in studies 005-00003-0011-000-9 and 001-00002-0013-000-7.
- Data: The timeline on study 003-00001-0011-000-6 looks small. The heuristics used to display the "study duration" increments the duration to one unit larger than the event. In this case, since the event unit is hours, the study duration is day.
CEBS 2.0.1 (beta) Release Summary
Release Date: December 19, 2005
Bug fixes
- Homepage: Fixed "Search by Subject Characteristics" link on the homepage.
- Search pages: The "Reset" button on the search pages no longer forwards to unknown URL on pre-production server.
- Protocols: Corrected issues for most protocols that prevented protocols from being correctly displayed. See below for protocols still not displaying properly.
- Microarray: GO annotations are now retrieved.
- Proteomics: Resolved file corruption issue with compressed (zipped) images.
- Homepage: Updated the "CEBS Content" section.
- Search pages: Added alphanumeric sorting to values within search criteria fields.
- Search results: Added the display of the PI associated with an investigation.
- Clinical results: Added a link to define the abbreviations shown on the Clinical Results page.
- Protocols: Display data for one protocol in one row if values can be displayed in non-empty cell.
- Microarray: Improved performance in selecting microarray hybridizations.
- Administration: Added the ability to change visibility of studies.
- Search by Study Characteristics: Search by PI name no longer works.
- Search by Subject Characteristics: The default value in the Clinical Signs field is "Body Weight-Final". This does not affect the search results, but will appear in the "Show Search Criteria" page.
- Filtering: Searching and then filtering once produces the correct results. Using filter again (or using the browser's back button) may result in incorrect results.
- Show search criteria: This page may not update and show the correct query information.
- Observation protocol: Not displaying all information provided (i.e., study 005-00002-0012-000-0).
- Histopathology findings: Not displaying information on Specimen Preparation / Preservation Protocol(s) and Assay Protocols page.
- Microarray: Experiment Information Report does not display Stressor Name(s) and Experiment Description.
- Microarray: CEBS accession number is not displayed on the Experiment Information Report.
- Proteomics: If columns can be sorted on pages that allow the user to download the tabular data displayed on the page, the downloaded file displays the header name in HTML format.
- Data: Study 005-00002-0012-000-0 does not display acetaminophen as a stressor name in the Study Details page.
- Data: Comparators are not being displayed properly because of issues with certain original data sets (studies 005-00002-0012-000-0, 001-00003-0011-000-6, 004-00004-0011-000-0, 006-00001-0011-000-9, and 004-00002-0011-000-8). Data reload will correct this issue. Data submitted for study 003-00001-0011-000-6 did not identify comparators. The comparators are correct in studies 005-00003-0011-000-9 and 001-00002-0013-000-7.
- Data: The timeline on study 003-00001-0011-000-6 looks small. The heuristics used to display the "study duration" increments the duration to one unit larger than the event. In this case, since the event unit is hours, the study duration is day.
- Data: The Group Disposition Protocols for study 001-00002-0013-000-7 incorrectly displays "No" in the Anesthetic field.
CEBS 2.0 (beta) Release Summary
Release Date: December 12, 2005
CEBS 1.6.1 Release Summary
Release Date: November 21, 2005
CEBS Microarray
- Redesigned homepage and left menu.
- Relocated the login and register links to the bottom of all pages.
- Removed links to the submission workflow.
- Updated administrator's menu.
- Updated User's Guide.
CEBS 1.6 Release Summary
Release Date: August 30, 2005
CEBS Microarray
- Implemented a new security framework, which will facilitate single sign-on across CEBS components (e.g., microarray, proteomics).
- Improved the implementation of multiple stressor information. Subsequently, redesigned and implemented the display of multiple stressors and associated experiment factors (e.g., time, dose). In general, each combination of stressor and factor (e.g. acetaminophen-dose) is displayed as a separate column. The effort has been made to optimize the display of certain design. Specifically, if multiple chemical stressors are used in one experiment and each sample is treated by no more than one chemical, the chemical name is now displayed as a column and common factors (e.g. time) from different stressors will be put in the same column to minimize the total number of displayed columns.
- The reverse labeling information for two channel arrays is now explicitly captured from the submitter, and displayed during search/browsing workflow.
- Type of dye used for RNA labeling is now specified at the experiment level, and then populated for each hybridization to facilitate mapping samples to channel(s) of hybridizations. This should significantly reduce the amount of work required for the submitter.
- A timer is added when performing time-consuming computation. Measures have been implemented to monitor the progress of computation that prevent the browser from timing out when waiting for the computational results to return.
- Links and display for LocusLink have been updated to EntrezGene to reflect the change at NCBI.
- The capability to export data from the table to files has been implemented in several pages that display analysis results.
- Modified existing and added additional administration pages.
CEBS 1.5 Release Summary
Release Date: June 6, 2005
CEBS Proteomics Browser
- Study Design context is provided at all levels of data: Images, Spectra, Spots (both raw and expression to control ratio pages), Spot lists.
- Paging implemented in pages displaying Spots (both raw and expression to control ratio pages).
- Sorting implemented in pages displaying Spots (both raw and expression to control ratio pages).
- Workflow enables access to expression ratio data for spots with confirmed protein identification only available. In these pages, protein accession numbers are now available together with the ratio data.
- The Protein Identification page has a much more organized look to it. Sorted by Ref spot, protein id search software (alphabetical) and by descending order of scores in order. Information in the software column is colored by the software used for searching. The number in the column proteinID event now represents the protein hits available for that particular Ref spot. If no proteinID information exists for a particular spot, these spots are displayed at the bottom of the list and n/a is displayed in those rows.
- Pages have been redesigned (columns as well as links better organized, consistency in naming different columns).
- Protein Accession numbers are now hyperlinked to Uniprot as long as they are SwissprotIds. GenBank accession numbers (GIs) have not yet been linked.
- Provided decimal controls on selected data columns.
CEBS SysTox Browser
- Browse the study by a specific stressor type. For example, browse the study in SysTox by stressor name, vehicle name or CAS numbers for the stressor and vehicle.
- Search the study by a specific clinical chemistry test result value or value range. For example, retrieve the study or studies if there is at least one subject within the study that meets the search condition like "total protein level is higher than 5 mg/dl".
- Search the study by a pathology finding (e.g., organ, lesion name, histological site, and lesion qualifier). For example, retrieve the study or studies if there is at least one animal within the study that meets the search condition like "live centrilobular severe necrosis".
CEBS 1.4.1 Release Summary
Release Date: April 1, 2005
I. New CEBS Functionality-Data Upload and Browsing
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A. Submission of Generic One-Channel Data Experiments
Description: enable a user to submit microarray experiments utilizing non-standard one-channel scanner/image processing platforms. CEBS users will be instructed to convert the corresponding array design and data files to the CEBS specified-generic one-channel array design and data file formats prior to submission.
Corresponding Use Cases:
2.1 Submit A Microarray Experiment (Form Input)
2.3 Upload Microarray Data Files
2.1.1 Submit New Array Design
Associated CEBS Goal:
Develop Large Context-Annotated Data Sets-users will be able to submit to CEBS a wider variety of one-channel microarray data, thereby increasing the scope of potential microarray experiment submissions to CEBS and consequently the number and variety of one-channel hybridizations available for analysis.
B. Super User Queries
Description: enable CEBS users specified by NIEHS to query all experiments in CEBS, regardless of the "visibility", or data access rules, for each experiment. Corresponding Use Cases:
3.1 Basic Microarray Experiment Search
Associated CEBS Goal:
Develop Large Context-Annotated Data Sets-providing selected CEBS users with "Super User" query rights will enable analysis of all protected-access experiments by NIEHS-designated users.
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A. Analysis of Generic One-Channel Data
Description: enable the preprocessing and utilization of the CEBS microarray analysis tools for one-channel data not generated with the Affymetrix scanner/image processing platform.
Corresponding Use Cases:
5.8 Perform Generic One-Channel Preprocessing
Associated CEBS Goal:
Aiding in development of new algorithms and computational tools that allow predictive modeling of gene interactions and networks-enables the user analyze a wider variety of one-channel microarray data.
B. Extend caBIO to C. Elegans Genome (Originally Scheduled for CEBS 1.4)
Description: The CEBS annotation engine, caBIO, will be extended to provide coverage for the C. Elegans genome. As of the CEBS 1.4.1 release, caBIO will cover the following genomes: Human, Mouse, Rat, and C. Elegans.
Corresponding Use Cases:
5.7 Comparison of Gene Expression Between Paired Samples in Same Array
5.6 Compare Gene Expression Between Samples
7.8 Perform Gene Expression Analysis based on Gene Ontology
7.9 View Expression Report for a Gene Ontology Category
Associated CEBS Goal:
Aiding in development of new algorithms and computational tools that allow predictive modeling of gene interactions and networks-enables the user to broadcast differentially expressed genes from a C. Elegans array experiment onto categories of biological activity (CBAs) such as GO, KEGG, and BioCarta.
CEBS 1.4 Release Summary
Release Date: November 22, 2004
I. New CEBS Functionality-Data Upload and Browsing
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A. Forgotten Login Support
Description: enable a user who has forgotten his/her login (username and/or password) to retrieve the login (both username and password) via a "hint" term the user specified in the process of signing up for a CEBS account. Once the hint word is verified, the user's password and username are forwarded to the user's email.
Corresponding Use Cases:
1.1 Register As A New User (User Now Provides "Hint" Term for Login Retrieval)
1.9 Retrieve Forgotten Login Information
Associated CEBS Goal:
Develop Large Context-Annotated Data Sets-forgotten password support will make it much easier for the user to retrieve his/her password, thereby enhancing ease of use of CEBS, in particular, the process of submitting microarray experiments.
B. Replacement and Addition of Hybridizations to Experiments
Description: enable a user to replace one or more hybridizations previously submitted for an experiment and/or associate additional hybridizations with the experiment. Thus, the user will be able to replace hybridizations that prove to be of unacceptable quality as well as associate additional hybridizations with an experiment previously submitted to CEBS.
Corresponding Use Cases:
2.10 Associate Additional Hybridizations with Previously Submitted Experiment
2.11 Replace Hybridizations Associated with Previously Submitted Experiment
Associated CEBS Goal:
Develop Large Context-Annotated Data Sets-the ability of the user to replace hybridizations of unacceptable quality corresponding to a previously submitted experiment and to associate additional hybridizations with the experiment will greatly enhance the usability of CEBS. Thus, the user will be able to update the hybridizations corresponding to experiments in CEBS in a convenient manner consistent with the existing microarray experiment submission capability in CEBS.
C. Icoria to CEBS Pipeline
Description: NIEHS, Icoria (formerly Paradigm Genetics) and SAIC will work together to develop a semi-automated microarray data pipeline corresponding to NIEHS-sponsored studies performed by Icoria. The pipeline for the CEBS Microarray 1.4 release will be based upon of a series of document standards agreed to by NIEHS, Icoria, and SAIC and will consist of a defined set of data and annotation elements for each NIEHS study to be loaded into CEBS; this set of data and annotation elements will cover all MIAME elements currently captured by the CEBS microarray experiment submission module.
Associated CEBS Goal:
Develop Large Context-Annotated Data Sets-a semi-automated data submission process for experiments carried out at Icoria will facilitate population of CEBS with high-quality data sets emanating from NIEHS-sponsored studies.
D. SysTox Object Model
Description: the first version of the SysTox object model will be designed and implemented for this release. The SysTox OM will enable the capture and browsing of in-life toxicological data, as well as the linking of tox data with transcriptomics, proteomics, and eventually metabonomics data. In summary, SysTox, along with SysBio, serve as the infrastructure that will deliver on the ultimate vision for CEBS: predictive toxicology.
Associated CEBS Goal:
Develop Large Context-Annotated Data Sets-SysTox will enable the user to provide the toxicological context for all studies submitted to CEBS, as well as browse and analyze CEBS studies per in-life study tox data.
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A. Gene Ontology (GO)-Based Analysis Tools
Description: enable the user to view differentially expressed genes via a GO categories in the context of all of the genes in that category. Overall statistical evaluation will be performed at each GO gene category level as an indication of the overall perturbation of gene expression in certain functional, biological categories. The biological functional aspects that have undergone the most significant changes between biological samples or treatment conditions can be identified via the CEBS GO Analysis Tools.
Corresponding Use Cases:
7.8 Perform Gene Expression Analysis based on Gene Ontology
7.9 View Expression Report for a Gene Ontology Category
Associated CEBS Goal:
Aiding in development of new algorithms and computational tools that allow predictive modeling of gene interactions and networks-enables the user to broadcast differentially expressed genes onto GO categories, providing a Gene Ontology-based biological context for microarray gene expression data.
B. SysTox-Based Browsing in CEBS
Description: SysTox browsing capabilities for CEBS Microarray 1.4 will enable the user to browse studies via stressor and test results, retrieving detailed stressor and treatment information for animals and animal groups.
Corresponding Use Cases:
1.0 Specify Study Search Criteria
2.0 Search Studies by Stressor
3.0 Search Studies by Test Results
4.0 View Stressor and Treatment Information for Animals in Selected Group(s)
5.0 View Test Results for Selected Group(s)
Associated CEBS Goal:
Aiding in development of new algorithms and computational tools that allow predictive modeling of gene interactions and networks-enable the user to browse in-life toxicological data and access the corresponding transcriptomics and proteomics data.
C. Cross-Experiment Comparison and Visualization Tools
Description: enables the comparison and analysis of processed hybridization data across two or more experiments utilizing the same array design.
Corresponding Use Cases:
10.1. Perform Pre-Processing Across Different Experiments (Same Array Design)
10.2. Visualization of Microarray Gene Expression Data from Different Experiments (Same Array Design)
10.3. Compare Microarray Gene Expression Data from Different Experiments (Same Array Design)
Associated CEBS Goal:
Aiding in development of new algorithms and computational tools that allow predictive modeling of gene interactions and networks-enables the user to compare data across two or more experimental studies, thereby enlarging the possible comparative data sets that can be analyzed in CEBS.
D. Extend caBIO to C. Elegens Genome
Description: The CEBS annotation engine, caBIO, will be extended to provide coverage for the C. Elegens genome. As of the CEBS Microarray 1.4 release, caBIO will cover the following genomes: Human, Mouse, Rat, and C. Elegens.
Corresponding Use Cases:
5.7 Comparison of Gene Expression Between Paired Samples in Same Array
5.6 Compare Gene Expression Between Samples
7.8 Perform Gene Expression Analysis based on Gene Ontology
7.9 View Expression Report for a Gene Ontology Category
Associated CEBS Goal:
Aiding in development of new algorithms and computational tools that allow predictive modeling of gene interactions and networks-enables the user to broadcast differentially expressed genes from a C. Elegens array experiment onto GO categories of biological activity (CBAs).
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A. Experiment Submission
Description: the user will be asked to specify a principal investigator to associate with an experiment submission, whereas prior to this release the user's PI was automatically associated with an experiment submission.
Corresponding Use Cases:
2.1 Submit A Microarray Experiment (Form Input)
Associated CEBS Goal:
Develop Large Context-Annotated Data Sets-facilitates ease of use as "power users" who are very familiar with the CEBS microarray experiment submission module will be able to rapidly submit experiments on behalf of several principal investigators in a facile manner.
