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MoTrPAC Data Hub Portal Updates
Jimmy Zhen edited this page May 25, 2023
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- The Graphical Clustering page has been updated to include the mitochondria-specific visualization results. While on the page, users can select to view either the landscape graphical analysis reports or the mitochondria-specific graphical analysis reports.
- Google Analytics event tracking has been implemented to log the downloads of bundled PASS1B-06 datasets.
- For consortium users who signed into the Data Hub portal, clicking on the QC Data Monitor link in the top navbar initially would load the page as expected. If the user navigated away to other page(s) and clicked on the QC Data Monitor link again, the page would not load as expected. This UI issue has now been resolved.
- A new Project Overview page with collapsible sections has been added to the Data Hub portal. Users can access this page via the Help dropdown menu in the top navbar.
- After scrolling down on a page, clicking on a different link in the top navbar would not load the new page at the top of the page in the browser window. This UI issue has now been resolved.
- For consortium users who signed into the Data Hub portal, clicking on the QC Data Monitor link in the top navbar initially would not invoke QC data fetching. This UI issue has now been resolved.
- Hover tooltip UI is added to the Timewise and Training tabs of the result tables on the DEA search page.
- Hover tooltip UI is added to the Timewise and training keywords in the page summary in the Gene-centric View.
- When a user triggers a search submit event at the top-level, all search filters are now reset so that previously selected filters are not persisted. This change applies to the DEA search and Gene-centric View.
- New misc analysis resources bundle has been added to the downloadable PASS1B-06 bundle datasets.
- New version of the Data Hub portal with public access to PASS1B-06 data was released. This release includes a number of significant changes:
- DEA search, data file downloads, Gene-centric view, and landscape graphical clustering are now public accessible.
- Code Repositories, previously an external link to a location on Github, is now a publicly accessible page listing numerous links to a variety of publicly accessible GitHub repositories pertinent to PASS1B-06 data pipelines, QC and analysis.
- The support of Typeahead feature is now available to the Gene-centric View search, as well as the DEA search by gene/metabolite.
- Gene-centric View supports the search and time-series plots of multiple genes.
- DEA search supports the search of either multiple genes or multiple metabolites.
- Search filters are disabled if the returned search results do not include data matching the filters.
- Vena Cava is added to the tissue filter on the file downloads, DEA, Gene-centric View searches.
- A collection of selected bundle PASS1B-06 datasets has been made available on the file downloads page.
- For authenticated external users, they can now access the PASS1B-06 data sample summary, in addition to the limited PASS1A-06 data samples, upon their successful logins to the portal.
- Primary navigation bar has been relocated to the top of the page from the side.
- Users can now access the external, publicly accessible
data-viz.motrpac-data.orgvisualization tool via a link in the Explore dropdown menu in the top navbar.
- A downloadable Somalogic metadata file has been added to the HERITAGE related study page.
- In the PASS1B-06 metabolomics DEA result tables, the
datasetfield contains all the expected assay codes while theassayfield contains just the "metab" value across all rows. This behavior caused the incorrect metabolomics assay values being returned in search queries and affected the search result filtering for metabolomics assays on the Search page. This data issue has now been resolved in search indexing and the UIs.
- On the QC Data Monitor page, when selecting the sub-tabs of the Phase tab, users might have noticed that the tissue labels at the bottom of the "Tissue Submitted by CAS/Assay" grid include of instances of "undefined" labels (e.g. "T68 - undefined" or "T69 - undefined"). This UI issue has now been resolved.
- The updated PASS1A 6-month RRBS data have now been made available to the consortium. On the Browse Data page, when selecting the filters of PASS1A-06 and RRBS, a list of files matching the criteria are returned.
- The merged PASS1A/1B/1C 6-month phenotype data tables have been updated due to the phenotype data updates received from DMAQC. As a result, both of the database and indexing were updated to ensure the newer versions of merged phenotype data tables and DMAQC-provided raw files to be accessible and downloadable in Data Hub portal.
- PASS1A/1C 6-month ATAC-seq result file names were changed in GCP Storage. As a result, both of the database and indexing were updated to ensure the affected files to be accessible and downloadable in Data Hub portal.
- The consortium has been given early access to the PASS1A/1C 6-month data through the Data Hub portal.
- On the Browse Data page, users now have the options to filter files by phases of either PASS1A-06 or PASS1B-06. The PASS1A-06 phase consists of both PASS1A and PASS1C data.
- External links to MoTrPAC Collab (JupyterHub implementation) have been added to the navigation sidebar as well as the Browse Data page.
- An external link to CFDE has been added to the Useful Links page.
- Upon performing a top-level search (e.g. by gene symbol, protein id, or metabolite), certain search filters (e.g. tissue, assay) are now disabled if the returned search results contain no matches. This change applies to the DEA search and Gene-centric View pages.
- A more helpful message is now displayed to users when certain combinations of selected search filters return no matches in the filtered results. This change applies to the DEA search, Gene-centric View, and Browse Data pages.
- Resolved an unintended UI behavior when user clicks on the radio buttons of either Gene or Protein ID after performing a top-level search. Now this click event resets top-level search results. This change applies to the DEA search page only.
- On the QC Data Monitor page and under the main Metabolomics tab, there are now 2 sub-tabs: Processed and Raw, with Processed being the default sub-tab for Metabolomics QC data.
- On the QC Data Monitor page and under the main Proteomics tab, there are now 3 sub-tabs: Processed by BIC, Processed by CAS, and Raw. The default sub-tab for Proteomics QC data is Processed by BIC.
- Resolved an issue pertinent to the Browse Data page when selecting a non-metabolomics assay filter would result in a set of files with merged metabolomics data included.
- On the Sample Summary page, the sample counts for the PASS1A-06 RNA-seq testes and ovaries tissues have now been corrected to 39 instead of 78.
- The announcement banner on the landing page now highlights the MoTrPAC Landscape Preprint availability at bioRxiv.
- The Announcements page now displays a new announcement item with regards to the MoTrPAC Landscape Preprint availability at bioRxiv.
- The QC Data Monitor now displays real-time QC data by querying the Service API for all 6 omics/assays (e.g. metabolomics, proteomics, rna-seq, rrbs, atac-seq, and immunoassay), instead of sourcing from the embedded JSON files.
- The QC Data Monitor now displays 2 new Submit Date and QC Report columns to the QC data tables (except for immunoassay). The rows in the tables are sorted by Submit Date as a default.
- On the Search page and in the Gene-Centric View of the animal analysis, previously when user selected multiple values of a given filter (e.g. "heart", "liver", and "lung" of Tissue), it would return no matches in the search results. Doing so now properly return the expected search results.
- On the Releases page, all prior internally released data are no longer available to consortium users to download directly from the portal. A new notice has been added to the page to inform consortium users to visit the Browse Data page to access the most up-to-date PASS1B-06 data.
- On the Browse Data page, the page summary at the top has been enhanced to be more descriptive and to provide more context about the data. With the Phenotype filter being moved to its own Metadata filter group, an “info” icon has also been added to the Category filter group panel header for showing more information about the filters when the cursor hovers over it. Lastly, the Omics filter group panel has been moved above the Assay filter group panel.
- On the landing page, the animation of the graphic associated Multi-Omics has been changed to a new animation supported by CSS-only in the attempt to reduce dependency on 3rd-party modules.
- On the Browse Data page, a prior implementation of enhancing the functionality of the header checkbox in the table introduced a bug, in which clicking the Next or Previous pagination buttons at the bottom does not change the displayed rows in the table. This has now been fixed.
- In the Gene-Centric View of the animal analysis, the header checkbox in the table of search results is now disabled to prevent all rows from being selected in the table.
- On the Browse Data page, previously when user selects on the checkbox in table header, only the rows on the current paginated page would be selected. Selecting the header checkbox now will select all rows in the table on all paginated pages.
- Google Analytics is now implemented to track all file download requests when users click on the Download selected files button on the Browse Data page.
- All API requests for Data Hub portal searches are now required to use access tokens to enhance the protection for the search backend.
- The UIs and behaviors of the range filters (e.g.
logFC,p_value) for portal search have been updated due to the updates in the search backend. - The response time has been significantly improved when user clicks on the download search results button.
- A file size column has been added to the table UI on the Browse Data page.
- The file download modal UI has been updated to support the single zip file download rather than the individual file downloads.
- The response time has been significantly improved for the data to be initially fetched and rendered on the Browse Data page.
- Fixed bug in which clicking on the QC Data Monitor link panel on the main Search page returns no data being shown on the page.
- The data file browse/download backend service was completed and deployed to production. With this backend service, the data files selected by a given user can now be grouped and downloaded in a single zip file rather than being downloaded one file at a time.
- The QC Data Monitor backend component - QC automation pipeline - was completed and deployed to production. The QC automation pipeline includes a database which will become the new data source of QC Data Monitor moving forward. UI changes to the QC Data Monitor will be introduced subsequently after further testing.
- The sample counts, including immunoassay, have now been updated for the PASS1B-06 rat data and accessible on the Summary page on data hub portal.
- A preview version of the Gene-Centric View feature, allowing users to visualize time series trends via line plots with error bars, is now available on the data hub portal. This preview currently only support the RNA-seq and proteomics assays available in the PASS1B-06 DEA data. The BIC will continue to extend and provide ongoing support for this feature.
- Both of the timewise and training DEA results of RRBS and ATAC-seq assays in PASS1B-06 have now been added to the searchable data on the portal. As a result, a number of frontend changes have also been implemented to support the additional and large amount of network-transferred data.
- A preview version of the data file browse/download feature, allowing the selection of smaller subset of files, is now available on the data hub portal. This preview currently only support the analysis and results files available in the PASS1B-06 rat data. The BIC will continue to extend and provide ongoing support for this feature.
- A tooltip-like pop-up description has been added to the p-value and adj p-value column headers in the timewise DEA data search results table.
- Google Analytics is now implemented to track the search result download events.
- Fixed bug in rounding exponential numbers to 4 decimals in the DEA data search results (e.g. p-value, selection FDR).
- Fixed bug in sorting DEA data search results table columns with numeric values (e.g. p-value, selection FDR).
- Removed external links on feature IDs in the DEA data search results table because certain protein IDs (used as feature IDs) are not valid protein IDs.
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A preview version of the search feature is now available on the data hub portal. This preview currently only support the search of PASS1B-06 DEA data (excluding RRBS and ATAC-seq). The BIC will continue to extend and provide ongoing support for this feature.
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A preview version of the graphical analysis reports also becomes available on the data hub portal. This feature can be accessed in the animal analysis section of the portal.
- The QC summary report of RNA-seq has been revised and the QC Data Monitor now reflects the up-to-date RNA-seq QC samples in the summary tables.
- Currently with 2 endpoints, a new API service based on serverless architecture has been introduced to replace the prior container-based backend services used by new user registration and data download on the Data Hub portal.
- The citation has been updated to reflect the publication of the HERITAGE Family Study paper.
- Data from older versions of internal releases are no longer available for download on the Data Hub portal, but available as part of the latest release (v2.0) which includes all the raw data and most updated results. The respective download links and command-line instructions have been removed from the Releases page.
- The QC summary reports of metabolomics, RNA-seq, and ATAC-seq have been revised and the QC Data Monitor now reflects the up-to-date QC samples in the summary tables.
- As a default, the metabolomics and proteomics summary tables in the QC Data Monitor are sorted by QC Date, while the other tables are sorted by CAS temporarily.
- Various shades of background color have been applied to cells with values greater than
0in the Issues and Raw Manifest columns. - The team page has been revised to reflect the addition of new members as well as the role changes of existing members.
- QC Data Monitor has now been migrated from ShinyApp.io to the MoTrPAC infrastructure. The BIC will continue to extend and provide ongoing support for this feature.
Feedback and comments? Please reach out to us at motrpac-helpdesk@lists.stanford.edu