Sprint 16

Associated Release of ISB-CGC-Common: 3.1

Please Note:

NOTE 1: A number of TCGA and CCLE case IDs shown below will have been removed from all cohorts since they are no longer available from NCI’s Genomics Data Commons, and ISB-CGC is trying to mirror that data as closely as possible.

TCGA cases: TCGA-33-4579, TCGA-35-3621, TCGA-66-2746, TCGA-66-2747, TCGA-66-2750, TCGA-66-2751, TCGA-66-2752, TCGA-AN-A0FE, TCGA-AN-A0FG, TCGA-BH-A0B2, TCGA-BR-4186, TCGA-BR-4190, TCGA-BR-4194, TCGA-BR-4195, TCGA-BR-4196, TCGA-BR-4197, TCGA-BR-4199, TCGA-BR-4200, TCGA-BR-4205, TCGA-BR-4259, TCGA-BR-4260, TCGA-BR-4261, TCGA-BR-4263, TCGA-BR-4264, TCGA-BR-4265, TCGA-BR-4266, TCGA-BR-4270, TCGA-BR-4271, TCGA-BR-4272, TCGA-BR-4273, TCGA-BR-4274, TCGA-BR-4276, TCGA-BR-4277, TCGA-BR-4278, TCGA-BR-4281, TCGA-BR-4282, TCGA-BR-4283, TCGA-BR-4284, TCGA-BR-4285, TCGA-BR-4286, TCGA-BR-4288, TCGA-BR-4291, TCGA-BR-4298, TCGA-BR-4375, TCGA-BR-4376, TCGA-DM-A286, TCGA-E2-A1IP, TCGA-F4-6857, TCGA-GN-A261, TCGA-O2-A5IC, TCGA-PN-A8M9

CCLE cases: LS123, LS1034

NOTE 2: The number of cases and samples when viewed in the User Interface as compared to the BigQuery tables vary across all three projects (TCGA, TARGET, and CCLE). This is because the user interface reflects the data available at the Genomic Data Commons, whereas data in BigQuery reflects either data at the original TCGA data coordinating center supplemented with Genomic Data Commons Data (for TCGA and CCLE), or for TARGET, data received from the TARGET data coordinating center, not the Genomic Data Commons.

NOTE 3: We have removed Google Genomics functionality from the user interface. You will still be able to access CCLE open access data in Google Genomics from the command line. We are open to adding Google Genomics controlled data back into the user interface if you have a use case for it. Also we are restructuring the handling of multiple Programs of data. Please feel free to provide feedback <https://groups.google.com/a/isb-cgc.org/forum/#!newtopic/feedback>_.

NOTE 4: For TARGET data the clinical and Gene Expression files themselves are available in the system. The bam files will be available soon!

New Enhancements

• You will be returned a more detailed error message when uploading your own user data.
• On the Data Availability section on the cohort details page now displays the HG38 somatic mutation information for program TCGA, and HG38 miRNA data for TARGET.
• Users can now plot HG38 Somatic Mutation data for TCGA, and HG38 miRNA data for TARGET.
• On the cohort creation page you can now filter with the HG38 somatic mutation data by gene for program TCGA using the Molecular tab.
• The mouse over feature will display the long name for disease code and project short name for all programs.

Bug Fixes

• There is now a 2000 character limit for the workbook title section.
• When selecting the cohort link to complete analysis section on a worksheet will send you to the existing cohort list table page.
• Latency issues when working with the cohort creation page have been resolved.
• When working with TCGA data the IGV browser will not give you a 401 or a 404 error.
• On the IGV Browser when working with TCGA genomic build hg38 you will no longer get a 404 error.
• On the cohort creation page when working with User Data tab, the left filter panel sorts the other filter.
• Cohorts created with API specific filters are now accessible on their cohort details page.

Known Issues in Sprint 16 as of 06/14/2017

• Analysis Type : Seq peek Formatting Elongated on occasion
• In the Webapp, the log scale on graphs does not function properly for duplicated worksheets.
• On the existing cohorts table list page, the confirmation delete ‘blue x’ button does not remove selected cohort if you select another option e.g Set Operation. The same issue can be found in reverse if you select the ‘blue x’ on the confirmation page for set operation you can then select the delete button and see the cohort on the confirmation panel.
• Swap values is not working properly for the plot settings.
• The set operation for existing cohorts complement is behaving exceptionally slow.
• A duplication of the exact cohort happens when you select the confirmation multiple times while the page is loading working with Set Operations.
• When working with a new worksheet or a duplicate worksheet with workbooks for categorical features e.g bar chart you can select the log option. The log option only applies to numerical options.
• When working with workbooks, if you select the delete confirmation button multiple times while the page is loading you will be sent to an error page.
• You currently cannot plot user uploaded data when working with workbooks.
• When plotting, certain values will be displayed as numerical when it should be a categorical value e.g Tobacco Smoking History.
• On the IGV browser when working with TCGA data build hg38 you get a No feature found with name “efgr” at the bottom of the iGV browser page.
• On the cohort creation page for TCGA data the filters disease code and project short name NA is an option which is not a valid disease.

Data Migration

Associated Releases of ISB-CGC-Common: 3.0 and ISB-CGC-API: 3.0

Multiple Program Datasets

In collaboration with the GDC we now have TARGET pediatric cancer data available for analysis in the user interface. You are now able to create cohorts and plot analysis with information from TARGET, TCGA, and CCLE data.

In addition, we have replaced the previous APIs with a new version that supports the new user interface.

We have also released the analyzed data types that are based on genome build GRCh38 for TCGA and TARGET data. GRCh37 (HG19) is also still available for TCGA, TARGET, and CCLE datasets.

Workbooks, cohorts, and variables favorites list created before the data structure migration will still be available for analysis and have been labeled as legacy and version 1. If you have difficulty using version 1 workbooks, please contact us

Please Note:

NOTE 1: A number of TCGA and CCLE case IDs shown below will have been removed from all cohorts since they are no longer available from NCI’s Genomics Data Commons, and ISB-CGC is trying to mirror that data as much as possible.

TCGA cases: TCGA-33-4579, TCGA-35-3621, TCGA-66-2746, TCGA-66-2747, TCGA-66-2750, TCGA-66-2751, TCGA-66-2752, TCGA-AN-A0FE, TCGA-AN-A0FG, TCGA-BH-A0B2, TCGA-BR-4186, TCGA-BR-4190, TCGA-BR-4194, TCGA-BR-4195, TCGA-BR-4196, TCGA-BR-4197, TCGA-BR-4199, TCGA-BR-4200, TCGA-BR-4205, TCGA-BR-4259, TCGA-BR-4260, TCGA-BR-4261, TCGA-BR-4263, TCGA-BR-4264, TCGA-BR-4265, TCGA-BR-4266, TCGA-BR-4270, TCGA-BR-4271, TCGA-BR-4272, TCGA-BR-4273, TCGA-BR-4274, TCGA-BR-4276, TCGA-BR-4277, TCGA-BR-4278, TCGA-BR-4281, TCGA-BR-4282, TCGA-BR-4283, TCGA-BR-4284, TCGA-BR-4285, TCGA-BR-4286, TCGA-BR-4288, TCGA-BR-4291, TCGA-BR-4298, TCGA-BR-4375, TCGA-BR-4376, TCGA-DM-A286, TCGA-E2-A1IP, TCGA-F4-6857, TCGA-GN-A261, TCGA-O2-A5IC, TCGA-PN-A8M9

CCLE cases: LS123, LS1034

NOTE 2: The number of cases and samples when viewed in the User Interface as compared to the BigQuery tables vary across all three projects (TCGA, TARGET, and CCLE). This is because the user interface reflects the data available at the Genomic Data Commons, whereas data in BigQuery reflects either (for TCGA and CCLE) data at the original TCGA data coordinating center supplemented with Genomic Data Commons Data, or for TARGET, data received from the TARGET data coordinating center, not the Genomic Data Commons.

NOTE 3: We have removed Google Genomics functionality from the user interface. You will still be able to access CCLE open access data in Google Genomics from the command line. We are open to adding Google Genomics controlled data back into the user interface if you have a use case for it. Also we are restructuring the handling of multiple Programs of data. Please feel free to provide feedback <https://groups.google.com/a/isb-cgc.org/forum/#!newtopic/feedback>_.

NOTE 4: For TARGET data the clinical and Gene Expression files themselves are available in the system. The bam files will be available soon!

New Enhancements

• You will be returned a more detailed error message when uploading your own user data.
• The user interface now displays the same nomenclature as the Genomic Data Commons (GDC).

Bug Fixes

• The user data upload is enabled and users can now upload their own datasets and create cohorts using existing programs and newly uploaded data by the user.
• You can now have multiple Google Cloud Projects associated to your account and use only one bucket and dataset on one project with no interference.

Known Issues in this Data Structure Migration Sprint as of 05/25/2017

• Analysis Type : Seq peek Formatting Elongated on occasion
• The CCLE data in GUI is not parallel to the CCLE data in BigQuery.
• When a user duplicates a worksheet, then tries to implement the log scale it will not function properly.
• On the existing cohorts table list page, the confirmation delete ‘blue x’ button does not remove selected cohort if you select another option e.g Set Operation. The same issue can be found in reverse if you select the ‘blue x’ on the confirmation page for set operation you can then select the delete button and see the cohort on the confirmation panel.
• On the cohort view files page there are capitalization bugs on the Platform filter.
• Swap values is not working properly for the plot settings.
• The set operation for existing cohorts complement is behaving exceptionally slow.
• A duplication of the exact cohort happens when you select the confirmation multiple times while the page is loading working with Set Operations.
• When working with a new worksheet or a duplicate worksheet with workbooks for categorical features e.g bar chart you can select the log option. The log option only applies to numerical options.
• When working with workbooks, if you select the delete confirmation button multiple times while the page is loading you will be sent to an error page.
• When working on a scatter plot the Tobacco Smoking being used as the Legend is displayed in numerical values when it should be displayed as categorical values.
• The character limit for a workbook title name is currently inactive, if you exceed the possible limit you will be sent to an error page.
• You currently cannot plot user uploaded data when working with workbooks.
• Selecting cohort from worksheet “To Complete Analysis” section will send you to a 400 Bad Request error.
• You will experience latency issues when working with the create a new cohort page.
• When plotting, certain values will be displayed as numerical when it should be a categorical value e.g Tobacco Smoking History.
• On the File List page you currently unable to access the bam files for the IGV Browser associated to build hg38 when working with TCGA data.

Sprint 14

Associated Release of ISB-CGC-Common: 2.13

Please Note:

NOTE 1: We have removed Google Genomics functionality from the user interface. You will still be able to access CCLE open access data in Google Genomics from the command line. We are open to adding Google Genomics controlled data back into the user interface if you have a use case for it. Also we are restructuring the handling of multiple Programs of data. Please feel free to provide feedback (feedback link).

NOTE 2: There will be a reduced number of releases and features over the next month (or so) while we do some rework required for enabling the distribution of additional data sets and types copied from the NCI GDC. The new data type is TARGET data, and different analyzed data types are based on the hg38 genome builds. Stay tuned in likely the early part of 2017.

Known issues in this Sprint 14 as of 11/30/2016

• Analysis Type : Seq peek Formatting Elongated
• The CCLE data in GUI is not parallel to the CCLE data in BigQuery.
• User will occasionally be sent to the Social Network Login page when trying to login. If this occurs, please go the the home page of the Web Application and try again.
• If the user shares a cohort they do not receive a confirmation email.
• Cannot plot any data if you use CCLE data cohort on a worksheet.
• When a user duplicates a worksheet, then tries to implement the log scale it will not function properly.
• If a researcher leaves the workbooks inactive the page freezes.
• On the existing cohort list page for the delete button, select the blue x does nothing. It should be disabled.
• On the cohort view files page there are capitalization bugs on the Platform filter.
• Swap values is not working properly for the plot settings.
• Some plot setting are saved or retrieved when working with worksheets.
• The set operation for existing cohorts intersection is behaving exceptionally slow.

Issues that are resolved in sprint 14 as of 11/30/2016

New Enhancements

No new enhancements in this release.

Bug Fixes

• The user can no longer see BCGSC expression as an option when plotting genes if user does not select center filter on worksheet.
• Worksheets added to an existing workbook now behave the same as the original worksheet.
• Cohort set operations no longer performing exceptionally slow.

Sprint 13

Associated Release of ISB-CGC-Common: 2.12

Please Note: We are removing Google Genomics from the user interface. You will still be able to access CCLE open access data in Google Genomics from the command line. We are open to adding Google Genomics controlled data back into the user interface if you have a use case for it. Please feel free to provide feedback.

Known issues in this Sprint 13 as of 11/16/2016

• Analysis Type : Seq peek Formatting is Elongated
• The CCLE data in GUI is not parallel to the CCLE data in BigQuery.
• User will occasionally be sent to the Social Network Login page when trying to login. If this occurs, please go the the home page of the Web Application and try again.
• If the user shares a cohort they do not receive a confirmation email.
• Cannot plot any data if you use CCLE data cohort on a worksheet.
• When a user duplicates a worksheet, then tries to implement the log scale it will not function properly.
• If a researcher leaves the workbooks inactive the page freezes.
• On the existing cohort list page for the delete button, selecting the blue x does nothing. It will be be disabled in a future release.
• On the cohort view files page there are capitalization bugs on the Platform filter.
• Swap values is not working properly for the plot settings.
• Some plot setting are saved or retrieved when working with worksheets.
• Worksheets added to an existing workbook behave differently than the original worksheet.
• The user can see BCGSC expression as an option when plotting genes if user does not select center filter on worksheet.
• The set operation for existing cohorts intersection is behaving exceptionally slow.

Issues that are resolved in Sprint 13 as of 11/16/2016

New Enhancements

• A warning will be displayed if the user is trying to plot with required data missing e.g. must select an analysis, gene or variable, and a cohort to create a plot.
• On the project details page user will be sent to upload new study in existing project tab when they select upload data.
• When the user plots a graph with NA values, you will be returned a notification stating no valid data was found.
• There is no longer text overlapping on the Cloud Hosted Datasets readthedocs page in the documentation.

Bug Fixes

• The user can no longer add the same gene symbol twice if list to the same worksheet even if they have given their list different names.
• When the user selects multiple cohorts for color by feature for scatter plot all cohorts selected display on the graph.
• On the existing cohorts table for public cohorts, the new workbook and set operations buttons are now active.
• For all analysis types the x-axis and y-axis with certain variables text will no longer overlap and is displayed clearly.
• The upload data button is disabled on the review files page when no buckets or datasets are associated.
• Someone with multiple eRA accounts will be no longer have issues when trying to access controlled data.

Sprint 12

Associated Release of ISB-CGC-Common: 2.11

Known issues in this Sprint 12 as of 11/02/2016

• The user can add same gene twice if list to the same worksheet it they have different names.
• Analysis Type : Seq peek Formatting Elongated
• The CCLE data in GUI is not parallel to the CCLE data in BigQuery.
• If a user creates a cohort with sample type filter Cell Lines and CCLE the total number of samples count off by one.
• User will occasionally be sent to the Social Network Login page when trying to login. If this occurs, please go the the home page of the Web Application and try again.
• If the user shares a cohort they do not receive a confirmation email.
• When the user selects multiple cohorts for color by feature for scatter plot they do not display in chart.
• Cannot plot any data if you use CCLE data cohort on a worksheet.
• When the user plots a graph with NA values the UI returns a blank graph.
• When a user duplicates a worksheet, then tries to implement the log scale it will not function properly.
• If a researcher leaves the workbooks inactive the page freezes.
• On the existing cohort list page for the delete button, selecting the blue x does nothing. It should be disabled.
• On the cohort view files page capitalization bugs on the Platform filter.
• Swap values is not working properly for the plot settings.
• Some plot settings are saved or retrieved when working with worksheets.
• On the existing cohorts table for public cohorts, the new workbook and set operations buttons are currently inactive.
• Worksheets added to an existing workbook behave differently than the original worksheet.

Issues that are resolved in sprint 12 as of 11/02/2016

New Enhancements

• Introduce user data upload functionality see documentation here.
• More fluid zoom feature when working with analysis worksheets.
• Case Sensitivity is now maintained in creating and displaying Workbook names throughout the entire user interface.
• You can now create a new cohort from the menu bar.
• Variables menu bar is displayed similar to the rest of the favorites variables.
• On the dashboard, all create new buttons/links are identical.
• Owner of what is shared is now the only person who can add or remove others.
• Removed BCGSC gene expression from the UI gene specification selection for plot analysis.

Bug Fixes

• X or Y- Axis for text no longer overlaps on worksheet for any analysis type, except for violin plot.
• The Legend is no longer displayed elongated when you use multiple cohort for color by feature for violin plot.
• miRNA_expression_values_fixed table in dataset 2016_07_09_tcga_data_open reflect only hg19.mirbase20 files.
• You are now able to duplicate a workbook that has been shared with you by someone else.
• Added pseudo-counts to the mosaic plots on the create new cohort page. This allows you to be sure of always being able to see (and select) the smallest contributors in these mosaics.
• Removing the filter from the filter confirmation from the create new cohort page, this will remove it from the rest of filter selections.
• Select the “check-all” feature on the create new cohort page will no longer cause duplicates on the selected filters panel.
• Create cohort from plot selection now works with all analysis types.
• Data inconsistencies between the create new cohort histogram filter and the most recent BigQuery datasets has been addressed and resolved.

Sprint 11

Associated Release of ISB-CGC-Common: 2.10

Known issues in this Sprint 11 as of 9/21/2016

• The user can add same gene twice if list to the same worksheet it they have different names.
• The Bar chart on the worksheet panel renders overlapping text.
• Analysis Type : Seq peek Formatting Elongated
• The CCLE data in GUI is not parallel to the CCLE data in BigQuery.
• If a user creates a cohort with sample type filter Cell Lines and CCLE the total number of samples count off by one.
• User will occasionally be sent to the Social Network Login page when trying to login. If this occurs, please go the the home page of the Web Application and try again.
• If the user shares a cohort they do not receive a confirmation email.
• The Legend is displayed elongated when you use multiple cohort for color by feature for violin plot.
• When the user selects multiple cohorts for color by feature for scatter plot they do not display in chart.
• Cannot plot any data if you use CCLE data cohort on a worksheet.
• When the user plots a graph with NA values the UI returns a blank graph.
• When a user duplicates a worksheet, then tries to implement the log scale it will not function properly.
• There are duplicate rows in the molecular data table in BigQuery.

Issues that are resolved in Sprint 11 as of 9/21/2016

New Enhancements

• Text in confirmation box of a duplication of a workbook has been enhanced.
• On the registered Google Cloud Projects page, icon has been added for the user to go directly to the Google Cloud Console page if desired.
• When the a Service Account is removed from the Access Control List, the project owner is sent an email with an explanation as to why the account was removed.
• IGV File List page displays of which page user is browsing.

Bug Fixes

• For a Cubby hole plot the x - axis name can be seen clearly.
• On a duplicate worksheet when working with gene specifications, user is able to select between all options multiple times.
• Page becomes elongated when the user builds a Cubby Hole plot.
• The selected variables for the plot setting on a worksheet are saved after the user leaves the workbook.
• When registering a Google Cloud Project the user is displayed the list of emails associated to the GCP only once.

Sprint 10

Associated Release of ISB-CGC-Common: 2.9

Known issues in this sprint 10 as of 9/07/2016

• The user can add same gene twice if list to the same worksheet it they have different names.
• The Bar chart on the worksheet panel renders overlapping text.
• Analysis Type : Seq peek Formatting Elongated
• The CCLE data in GUI is not parallel to the CCLE data in BigQuery.
• If a user creates a cohort with sample type filter Cell Lines and CCLE the total number of samples count off by one.
• User will occasionally be sent to the Social Network Login page when trying to login. If this occurs, please go the the home page of the Web Application and try again.
• Page becomes elongated when the user builds a Cubby Hole plot.
• X-axis name cut off for cubby hole plot when x-axis has only 3 criteria.
• If the user shares a cohort they do not receive a confirmation email.
• The Legend is displayed elongated when you use multiple cohort for color by feature for violin plot.
• When the user selects multiple cohorts for color by feature for scatter plot they do not display in chart.
• When the user creates a duplicate worksheet,the bar chart with a gene with specification protein can freeze when selecting an option for the Select Feature.
• Cannot plot any data if you use CCLE data cohort on a worksheet.
• When the user plots a graph with NA values the UI returns a blank graph.
• When a user duplicates a worksheet, some functionality related to plotting will not function properly on the duplicate worksheet.

Issues that are resolved in sprint 10 as of 9/07/2016

New Enhancements

• Dictionary mapping feature types to units for use in plot displays added to worksheets.
• The user now has the option to make the axis logarithmic if the plot can display continuous numerical data for eg. mRNA expression levels.
• The NIH username entry is now case insensitive for dbGaP authorization.
• The mouse over feature works when the user has created a long workbook name on the existing workbooks table page.
• The mouse over functionality was added to the worksheet name within a workbook.

Bug Fixes

• The order by ascending or descending feature is now working properly for the existing workbooks table page.
• Tobacco Smoking History filter in the create cohort page displays the filters in descriptive values.
• The user can now select all existing cohorts when on the add cohort(s) to worksheet page.
• The gene specification selection on the worksheet page is now working properly.
• When a user shares a workbook with someone the person who received viewer access to the workbook is sent a confirmation email. If the person who shared the workbook then deletes the workbook before it's opened, then the person clicks the invitation link the person is sent to the unknown invitation page. The button to go back to the Dashboard page appears like this, "Your Dashboard"
• The user is sent an email when the Service Account is removed the Access controlled list for having a user associated to the project who is not dbGaP authorized.

Sprint 9

Associated Release of ISB-CGC-Common: 2.8

Known issues in Sprint 9 as of 8/24/2016

• The user can add same gene twice if list to the same worksheet it they have different names.
• The Bar chart on the worksheet panel renders overlapping text.
• Analysis Type : Seq peek Formatting Elongated.
• The CCLE data in GUI is not parallel to the CCLE data in BigQuery.
• If a user creates a cohort with sample type filter Cell Lines and CCLE the total number of samples count off by one.
• User will occasionally be sent to the Social Network Login page when trying to login. If this occurs, please go the the home page of the Web Application and try again.
• Page becomes elongated when the user builds a Cubby Hole plot.
• X-axis name cut off for cubby hole plot when x-axis has only 3 criteria.
• When the user shares a cohort they do not receive a confirmation email.
• User will be spammed with email every one minute when their service account is removed from the ACL control list. To stop this, please either delete your service account from the ISB-CGC interface, or remove the GCP project member(s) who is (are) not authorized to access the controlled data set. (see documentation here). We are planning to reduce the frequency of the notification emails to once per day.
• The Legend is displayed elongated when you use multiple cohort for color by feature for violin plot.
• When the user selects multiple cohorts for color by feature for scatter plot they do not display in chart.
• When the user creates a duplicate worksheet,the bar chart with a gene with specification protein can freeze when selecting an option for the Select Feature.
• When a user shares a workbook with someone the person who received viewer access to the workbook is sent a confirmation email. If the person who shared the workbook then deletes the workbook before it's opened, then the person clicks the invitation link the person is sent to the unknown invitation page. The button to go back to the Dashboard page appears like this, "Your Dashboard{"
• Cannot plot any data if you use CCLE data cohort on a worksheet.

Issues that are resolved in sprint 9 as of 8/24/2016

New Enhancements

• When the researcher is on the Register Service Account page, after they have submitted the Service Account associated to their Google Cloud Project a table that shows who is authorized will be prompted.
• There is now a column that says “Has NIH Identity”, before it said, “Has eRA Commons”.
• When the researcher creates a new cohort with more than 20 filters chosen the URL exceeds the limit of 2K characters and this affects the count for the Details panel. Therefore the user is now prompted with an alert box that will say, “You have selected too many filters. The current counts shown will not be accurate until one or more filter options are removed.” if this is ever the case.
• In the user details page, if the researcher has not registered a Google Cloud Project it will say, “Register a Google Cloud Project” on the link.

###Bug Fixes

• The researcher can now delete whom they share cohort with from existing cohorts table.
• After 24-hours of use, a dbGaP authorized user can re-authenticate through the link provided in the user details page.
• The variable favorites list table page can now support a long title for the variable list.
• The filter name will appear aligned in the verification panel when the filter is name too
  long for the create in cohort filter confirmation selection on the create new cohort page.
• Grouped Data Type filter counts (Methylation, RNA Seq, miRNA Seq) now behave like the other count groups. The counts will behave as grouped values.
• The user can no longer select a categorical variable for selection for Histogram plot.
• The Filter token displays are now shown in 'readable' names when working with cohort filters.
• Controlled access BAM files are now viewable viewable in the IGV browser after the user has authorized their credentials.
• The user can now unlink an eRA commons account from their Google Identity in the user detail page.
• The violin plot was inconsistently failing. We have updated the JavaScript, therefore the Violin plot no longer fail.

Sprint 8

Associated Release of ISB-CGC-Common: 2.7

New Functionality Released in this Sprint

• The researcher can now create a cohort of participants and samples based on the presence of a gene mutation in a specified gene. Look for the new “Molecular” tab when you are creating a cohort.
• The bioinformatics programmer now has the ability to associate their Google Cloud Project’s Service Account. This allows the researcher to run computational pipelines from Google Virtual Machines using TCGA Controlled data (e.g. BAM files) for seven days before they have to reauthorize. For more information please select here.

Known issues in Sprint 8 as of 8/10/2016

• The user can add same gene twice if list to the same worksheet it they have different names.
• The Bar chart on the worksheet panel renders overlapping text.
• Cannot delete whom you share cohort with from existing cohorts table.
• Analysis Type : Seq peek Formatting Elongated
• The CCLE data in GUI is not exactly coordinated the CCLE data in BigQuery.
• If a user creates a cohort with sample type filter Cell Lines and CCLE the total number of samples count is off by one.
• After 24-hours of use, a dbGaP authorized user has to logout and then log back in to be prompted with NIH login link to re-access controlled data.
• User will occasionally be sent to the Social Network Login page when trying to login. If this occurs, please go the the home page of the Web Application and try again.
• Page becomes elongated when the user builds a Cubby Hole plot.
• X-axis name cut off for Cubby Hole plot when x-axis has only 3 criteria.
• When the user shares a cohort they do not receive a confirmation email.
• When a name is too long for variable favorites list table, the Last Updated” column will appear cut off.
• Filter name will appear off the verification panel when the filter is name too long for the create in cohort filter selection.
• Grouped Data Type filter counts (Methylation, RNA Seq, miRNA Seq) don't behave like other count groups. The counts behave as though the values were for distinct categories.
• User will be spammed with email every one minute when their service account is removed from the ACL control list. To stop this, please either delete your service account from the ISB-CGC interface, or remove the GCP project member(s) who is (are) not authorized to access the controlled data set. (see documentation here). We are planning to reduce the frequency of the notification emails to once per day.
• The user can select a categorical variable for selection for Histogram plot, and will return a graph with no data.
• The Legend is displayed elongated when you use multiple cohort for color by feature for violin plot.
• When the user selects multiple cohorts for color by feature for scatter plot they do not display in chart.
• When the user creates a duplicate worksheet,the bar chart with a gene with specification protein can freeze when selecting an option for the Select Feature.

Issues that are resolved in Sprint 8 as of 8/10/2016

New Enhancements

• The user now has the option to select all or deselect all possible filters for any tab that has more than 10 possible options in the create new cohort page.
• The user can now set all existing tables by either ascending or descending order.
• The cohort_id has been added to the detail cohort page. This allows the user to reference a desired cohort with ease in the API endpoints.
• When creating a new cohort, the user is given the full description for sample type in the selected filters panel.

Bug Fixes

• Histological Type entries in create new cohort page on the user interface now match the Google BigQuery entries in terms of capitalization.
• Filters for data type counts in left panel currently is now working properly.
• When a user sets a cohort as Color by feature for violin plot legend will be set to cohort. Then when the user sets another color by feature it will update the legend.
• The user can no longer make a gene list without selecting a gene first.
• The user can now list the Last Modified section for the existing cohort table by either ascending or descending order.
• In the create new cohort page for the data type tab, the user can now select either True or False for DNA Sequencing, Protein, and SNP Copy Number filters.
• When the user edits a new cohort and sets the edited cohort to return zero samples, the user will be prompted to select different set of filters.

Sprint 7

Associated Release of ISB-CGC-Common: 2.6

Known issues in this sprint 7 as of 7/19/2016

• The user can add same gene twice if two identical worksheets with different names are uploaded.
• The Bar chart on the worksheet panel renders overlapping text.
• User cannot delete whom you share cohort with from existing cohorts table.
• Analysis Type : Seq peek Formatting Elongated.
• The CCLE data in GUI is not parallel to the CCLE data in BigQuery.
• If a user creates a cohort with sample type filter Cell Lines and CCLE the total number of samples count off by one.
• Histological Type entries in create new cohort page on the user interface should match the Google BigQuery entries in terms of capitalization.
• When a user sets a cohort as Color by feature for violin plot legend will remain cohort.
• After 24 hour dbGaP authorization runs out the user is unable to re authenticate. (If you have this issue, please log out and log back in to be prompted with login link for dbGaP authorization.)
• Filters for data type counting in left panel are not working properly. For DNA Sequencing, Protein and SNP Copy Number no false filter can be selected. Also if you click true it will not filter properly.

Issues that are resolved in sprint 7 as of 7/19/2016

New Enhancements

• Created ability in GUI to make cohorts based on presence of an HPV status.
• Created ability in GUI to make cohorts based on BMI value.
• In the details panel for existing cohort have a section that shows the ISB-CGC cohort_id.
• Enhancements of GUI to view submenu item in different screen sizes and resolutions.
• New version of IGV javascript installed.

Bug Fixes

• User can still add same filter to existing cohorts and filter down their cohort, but will now be clearer.
• Optimized Security in the user interface.
• If a user opens a shared cohort it will appear once on the dashboard.
• Pathologic State Filter in create cohort Stage is displayed capitalized.
• Filter counts with 0 value do list when editing a pre-existing cohort.
• After 24 hour dbGaP authorization runs out the user is able to re authenticate.
• User can not create new gene list without giving the gene list a name.