Platform


April 1, 2020

What's New

March 30, 2020

What's New

  • Fixed how medications are queried for Survival Curve plots. (CR-214)

  • Correct how Survival Curve statistics are shown when multiple cohorts are selected. (CR-201)

  • Once insights ETL can support persistence to both Elasticsearch and Postgres the scheduler needs to begin running separate, parallel jobs to dual write. (CR-161)

March 27, 2020

What's New

  • Added a depth query parameter to the Ontologies get-codings-related-codings endpoint to perform multi-step traversals. (LO-6629)

March 26, 2020

What's New

  • Subject Search Beta: Expression filters have been added. (CR-189)

  • Subject Search Beta: Structural variant filters have been added. (CR-188)

Bug Fixes

  • The account switcher layout issues for Firefox have been resolved. (LO-6625)

March 25, 2020

What's New

  • Subject Search Beta: Copy number variant filters have been added. (CR-187)

March 16, 2020

What's New

  • The Custom Apps page has been redesigned. (LO-6582)

March 13, 2020

What's New

  • Added several enhancements to the Insights Survival Curve module like censoring and improved data and statistics outputs. (CR-25)

  • Added Cox proportional-hazards model analysis to the Insights Survival Curve statistics. (CR-174)

  • Fixed a bug with ingesting VCFs that had a float value for genotype quality. (CR-170)

  • The Cohorts page has been redesigned. (LO-3925)

March 9, 2020

What's New

  • When inviting the same LIFE Extend user to multiple projects, the newest invite will always control which project gets the user's LIFE Extend data. (LO-5766)

Bug Fixes

  • Searching for users by name under account management works again. (LO-6560)

March 5, 2020

Bug Fixes

  • The access control policy editor will now no longer show "Loading Group..." forever when it is unable to find the group. (LO-6536)

What's New

  • Add successful Copied to clipboard message to Copy to Clipboard buttons found under Subject Viewer and Insights > Edit Layout > Raw Edit. (LO-6484)

  • The Omics Tests table now supports pagination and infinite scroll. (CR-5)

March 4, 2020

What's New

  • The Omics Test Details page has a new visualization for the indexed, uploaded, and ingestion dates. (CR-134)

Bug Fixes

  • DICOM files can now be opened in DICOM Viewer. (CR-135)

March 3, 2020

What's New

  • Project tags can now be selected as conditions for Insights Survival Curves. (CR-118)

  • Updated Consent tab to include Versioning (LO-6426)

March 2, 2020

Bug Fixes

  • Users can now leave the demo account. (LO-6497)

February 26, 2020

What's New

  • BETA: A new Transcribe feature is available in the Subject Viewer for some accounts. Convert your speech dictation into medications and conditions which can then be saved to the patient record! (CR-132)

February 25, 2020

What's New

  • Updated the Survival Curve line style to no longer be linear and instead use a step function for display. (CR-126)

Bug Fixes

  • Fixed an issue with shareable file links not working when unauthenticated. (CR-124)

February 20, 2020

What's New

  • BETA: Added option to run TensorBoard in a Jupyter Notebook server. (LO-6465)

February 11, 2020

What's New

  • The Task view now uses the new inline file viewer to present inputs and outputs. (LO-6340)

  • Added ability to specify notification preferences for surveys. Subjects participating in the survey will only receive notifications about the survey through the channels allowed. (LO-6295)

February 5, 2020

Bug Fixes

  • Fixed an issue where failed genomic conversion jobs were not properly being re-queued. (LO-6350)

February 4, 2020

What's New

  • Access control policies can now specify file as a resource type to limit their scope to files only. (LO-6331)

February 3, 2020

Bug Fixes

  • Deep linking to a patient's detail page will redirect to the correct project (LO-6267)

What's New

  • "Use All Groups?" is now disabled by default when creating a new access control policy. (LO-6310)

  • Registration for consent and survey participants via "PHC Me" will now require first and last name as part of the registration process so that PHC Administrators can see names associated with subjects when they don't complete the demographics form. (LO-6092)

January 29, 2020

What's New

  • Enable the ability to link with patients and track medication adherence via LX combined with our PHC survey functionality. (LO-5415)

January 28, 2020

What's New

  • Adjusted the Edit Layout slider in Insights and Subject Viewer so that it doesn't cover up as much of the screen. (LO-5615)

  • The following observations code will be standardized in Insights: 8302-2/height => cm,29463-7/weight => kg,15074-8/glucose => mg/dL,53061-8/ketones => mg/dL,8280-0/waist circumference => cm (LO-6231)

January 25, 2020

Bug Fixes

  • Survey invitations will no longer intermittently fail. This was causing users to have to accept invites multiple times before they could get in. (LO-6235)

January 23, 2020

What's New

  • From the File Viewer, it is now possible to create a shareable link that can be used to access and view the file directly in the new File Viewer. (LO-6241)

  • From the Files Table View, you can now click on a file row to launch an inline viewer of the content for supported file types like text files, PDFs, notebooks, and images. (LO-6240)

Bug Fixes

  • In masked mode, a subject's name will now be hidden in the Surveys module within the Subject Viewer. (LO-6190)

January 22, 2020

What's New

  • Omics Explorer: If you find yourself using the same filter options, you can now save them as a "saved filter", by providing a name and description. After saved filters are created, quickly apply them from the dropdown. Only project admins or the saved filter owner can modify them. (LO-5334)

  • Fixed: "failed to fetch gene sets" error message, when switching accounts. (LO-5869)

January 21, 2020

What's New

Bug Fixes

  • Deleting a project will no longer cause users that are part of that project to receive errors. (LO-5803)

January 17, 2020

What's New

  • Our FHIR API now supports ClinicalImpression resources. (LO-6219)

  • PHC Administrators can create and receive automated email alerts from preset rules based on subjects' survey responses. (LO-5862)

January 15, 2020

Bug Fixes

  • Align chart settings panel below page header on Insights (LO-6199)

  • Fixed a bug in task-service where large FHIR input types would fail to download. (LO-6193)

What's New

  • Refine layout and styles of Single Value Metric in Insights (LO-6192)

  • Improved performance for Tasks that have large storage requirements in terms of inputs. (LO-6187)

January 14, 2020

What's New

  • Added option to update the genome build for a project in the Edit Project dialog. (LO-6166)

January 13, 2020

What's New

  • Fix Insights color swatches not displaying in load palette popover (LO-6131)

  • Improve contrast of disabled icon buttons in PageHeader (LO-6174)

  • Align header data label, values, and open editor icon in Subject View edit mode (LO-6162)

  • Project tile layout adjustments (LO-6138)

January 9, 2020

What's New

  • The Insights filter now appears in modal. It can be opened using the filter icon at the far right end of the blue header. (LO-6121)

  • Insights: The Filter box is now collapsible, and it is collapsed by default. (LO-3607)

  • Surveys now allow for radio button group selection questions (LO-6099)

Bug Fixes

  • In masked mode, the Subject Viewer timeline slider only uses the masked date of birth information, e.g. year of birth. (LO-5894)

January 8, 2020

What's New

  • Added ability to schedule surveys within the survey builder. (LO-6081)

  • Allow the user to search by survey results from the subject search UI. (LO-6083)

  • The drug associations table in the variant details view of Omics Explorer now additionally default sorts by evidence level, allowing for the most clinically validated rows to be sorted to the top. (LO-6084)

  • Improved web accessibility throughout PHC, including keyboard and screenreader support for modals/dialogs, popover menus, etc. (LO-5937)

  • Added the display of the state reason to failed Tasks in order to display additional information for why a Task failed. (LO-6097)

  • Insights: Bar Charts now have the option to display Y-value counts as raw counts or normalized as percentages. (LO-5961)

Bug Fixes

  • The Omics Explorer Structural Variant Gene filter allows for searching by gene pairs, e.g gene1-gene2 (LO-5912)

January 7, 2020

What's New

  • We are FDA Title 21 CFR Part 11 compliant. (LO-5488)

January 3, 2020

What's New

  • Changes to layouts in Insights and Subject Viewer are committed with the button now labeled "Save changes". (LO-5945)

Bug Fixes

  • Fixed a bug in how variants were being split by transcript for display in the Omics Explorer which was causing multiple empty records to appear. (LO-6110)

January 2, 2020

What's New

  • Layouts in Insights and Subject Viewer are now consistently labeled Layouts rather than Dashboards. (LO-5943)

  • We have added the ability to filter short genetic variants by population allele frequency to the cohort building filters in the Subject Search in addition to the Omics Explorer. (LO-5688)

  • Improved how Tasks are restarted from the Tasks UI view. (LO-6042)

December 19, 2019

What's New

  • The Analytics DSL gnosis_count domain now returns the count of distinct variants. (LO-6046)

December 17, 2019

What's New

  • Subject search can be overwhelming, so we've added ways to scope searches based on tags assigned to the data so the data you expect to see is returned. (LO-3264)

  • Fixed query for Condition autosuggest on Subject Search when a Tag is selected (LO-5849)

  • Made an improvement to the Ashion test ingest Task to only extract the files it needs to cut down on the amount of time it takes to execute. (LO-6044)

Bug Fixes

  • Fixes issues with the Condition autosuggest rendering improperly when a Tag is selected for filtering (LO-5848)

December 16, 2019

What's New

  • Add PageHeader background to Surveys screens (LO-6029)

Bug Fixes

  • Supervised consent now functions properly. (LO-6031)

December 13, 2019

What's New

  • FitBit intraday data is now available to sync from mobile apps for research studies that have approval to do so. (LO-5753)

  • Add PageHeader background to Consent screens (LO-6019)

  • Add PageHeader background to User Defined Functions screens (LO-6023)

  • Added a new "Expression Rank Order" filter to the Omics Explorer for sorting expression values by rank. (LO-5662)

December 11, 2019

What's New

  • Users now must re-enter username and password in order to electronically sign informed consent for projects that are configured to be FDA Title 21 CFR Part 11 compliant. (LO-5850)

  • Add PageHeader background to: Cohorts, Files, Genomics, Knowledge, Playground, Projects, Tasks and Workflows pages (LO-6010)

December 10, 2019

What's New

  • Show MSI and TMB values independentlyRevert to stacked info in sequence switcher popover (LO-5996)

Bug Fixes

  • The "date" field for tests in the Omics Explorer is now formatted properly (LO-6007)

December 9, 2019

What's New

  • Added better survey result support for free text question types. (LO-6000)

  • Insights: Multi Cohort support for Single Value Modules (LO-5966)

  • Added GA4GH Data Repository Service support for PHC files. Files can now be referenced using a DRS URI in a Task input: drs://ga4gh.us.lifeomic.com/{file ID} (LO-5906)

December 6, 2019

Bug Fixes

  • Fixed queries timing out when initially opening the Omics Explorer for large projects. These changes include displaying the variant count as the sum of both canonical and non-canonical variants. (LO-5972)

  • The Consent Management page respects masked mode and only shows initials when masked mode is enabled. (LO-5205)

What's New

  • Added phone number input mask to subject info form. (LO-5897)

  • Participant surveys are now organized by status in the PHC Me app for easier access and management. (LO-5901)

December 5, 2019

What's New

  • Omics Explorer: Sequence selector contents have been reorganized. TMB and MSI results now display next to the selector. (LO-5938)

  • Insights: Add multi-cohort support to survival curves (LO-5965)

  • Insights: the 'All' cohort is now selectable as an option when selecting multiple cohorts (LO-5822)

  • Improved how variants with multiple transcripts are displayed in the Omics Explorer. (LO-5910)

  • Insights: Add multi-cohort support to line charts (LO-5820)

  • Insights: Add multi-cohort support to scatter charts (LO-5819)

Bug Fixes

  • Fixed an issue where navigating to Insights from the Cohort screen would not properly preset the selected cohort (LO-5924)

  • We have improved the filtering of Short Genetic Variants by Zygosity in the Subject Search view. (LO-5865)

December 4, 2019

Bug Fixes

  • Survey reminders will no longer be sent out for completed survey responses. (LO-5964)

  • Fixed issue where cohorts weren't honored on some patient aggregation queries. (LO-5922)

  • Fixed an issue where ingesting multiple Ashion tests against the same subject resulted in some of the results getting overwritten due to non unique output file names. (LO-5968)

What's New

  • Added the ability to specify an email address to receive failed task notifications for FMI, Nantomic, and Ashion ingest tasks. (LO-5969)

December 3, 2019

Bug Fixes

  • Survey reminders will now be sent out for all overdue survey responses even in large projects. (LO-5958)

What's New

  • The option to return to the old Omics Explorer has been removed, now that the new version has proven to be fully functional. (LO-5944)

December 2, 2019

What's New

  • Select up to four cohorts to compare on an Insights layout (LO-5859)

  • Insights: Add multi-cohort support to pie charts (LO-5821)

  • Insights: Add multi-cohort support to bar charts (LO-3828)

  • As an administrator, you can now see the last time a user logged in by navigating to the Users page of the account. (LO-5719)

November 26, 2019

Bug Fixes

  • Fixed the default germline filter for short variants in the Omics Explorer Summary View to include the proper gene set. (LO-5913)

November 23, 2019

What's New

  • Updated eConsent emails to give recipients more clarity in what they're being invited to do. (LO-5838)

November 22, 2019

Bug Fixes

  • FHIR bundle POST requests that resulted in updates were only updating the last resource in the bundle. This is now fixed so that all updates in the bundle are applied. (LO-5893)

November 20, 2019

What's New

  • Created a project-level email address field that will override the account-level email address in emails sent out about a specific project. The project email address can be set in the project creation modal. (LO-5837)

  • Updated survey emails to give recipients more clarity in what they're being invited to do, which now includes the Project Name, Survey Name, and Survey Description fields. (LO-5835)

  • Added beta version of the Reports Module and made technical updates to the patient viewer Graph and Table Modules to improve performance. (LO-5645)

  • Added the ability to change the genome build within a project if no genomic data has been ingested. (LO-5868)

Bug Fixes

  • Inviting existing users to take a survey will no longer send out an invitation to the user, and instead will send the user an email telling them about the new survey and asking them to login and complete it. (LO-5879)

November 19, 2019

What's New

  • Removed the restriction for editing the survey name and description after the survey is published. (LO-5836)

  • In the User page within Manage Account, an Administrator can now search the user list by first name, last name, or name fields. (LO-5721)

November 18, 2019

Bug Fixes

  • Prevent long running analytics query from retrying by the middle services and inundating analytics database (LO-5825)

November 15, 2019

What's New

  • We've added more flexibility to policies so that an administrator can give PHC users access to only the data they need. (LO-5181)

  • More room has been allocated for Subject Viewer swimlane traces in graphs where they are combined with non-swimlane traces. (LO-5842)

  • We've added a new page within the Manage Account area to view all users who have any level of access within your account called Users. (LO-5718)

  • We're automating our roadmap and release notes documentation so they will be comprehensive, accurate, and timely. (LO-5519)

November 14, 2019

What's New

  • LIFE Extend now support HealthKit, FitBit, and Oura integrations for activity, weight, and sleep data. (LO-4571)

Bug Fixes

  • Fixed a bug in the genomics summary API that was causing a 500 status code for certain malformed variant sets. (LO-5833)

  • Fixed a bug that did not redirect to the correct page when switching accounts from the Omics Explorer. (LO-5526)

November 13, 2019

What's New

  • We've added consent management documentation to our user guide. (LO-5782)

Bug Fixes

  • Fixed a persmissions issue with managing Gene Sets. (LO-5840)

  • Fixed the IGV Genome Viewer links in the Omics Explorer to load the proper genomic sets. (LO-5816)

November 12, 2019

Bug Fixes

  • We fixed an issue where subjects/participants were only able to be invited to one survey at a time. (LO-5499)

November 12, 2019

What's New

  • Omics Explorer: A "Clear All" button was added to quickly clear all selected filters. Sorting can now be applied to the drug associations table in the variant details.

Bug Fixes

  • The Subject Search panels no longer show dual scrollbars and the results are easier to select.
  • The Safari issue with Omics Explorer variant details stacking on top of each other has been resolved.
  • The Safari issue with Omics Explorer where clicking the test/sequence switcher would cause the button to become blank has been resolved.

November 11, 2019

What's New

  • We've added a new page in Account Info to view a list of all users with any access level in the account.
  • Omics Explorer: The TMB value/score is now displayed alongside the status. The drug associations table now sorts all of the variant matches (green dots) to the top by default.

Bug Fixes

  • The Subject Search panels no longer cut off your search result options, allowing you to scroll.

November 6, 2019

What's New

  • Subject viewer performance improvements and minor bug fixes.
  • Redesigned breadcrumb links in the header, allowing for better web accessibility.
  • Omics Explorer: The top header section has been redesigned with a new background to help break up the content. The test/sequence switcher has been redesigned. MSI and TMB information for a test can now be found inside of the test/sequence switcher, if it's available. The page is now full-width, allowing more data to be displayed, if applicable.

October 28, 2019

What's New

  • Survey Builder: Made a number of styling improvements.
  • Omics Explorer: Added hover tooltips for long text entries in Drug Associations table.
  • Subject Search: Added a 'Has none' option for Medications, Procedures, Observations, Conditions and Data Availability. Renamed 'Has at least one' to 'Has Any.'
  • Circle Administration: Changed 'Circle Post' to 'Circle Announcement' to prevent confusion.
  • Circle Administration: Fixed an overflow issue on the circle detail page that caused the top row of tabs to get clipped.

October 25, 2019

What's New

  • The filters on the Subjects page now match other expansion panels throughout the app.
  • FHIR Search is now available as an input from the Task UI creation modal.
  • The Omics Explorer variant tables cap the text length so that long data no longer forces the column width to be too wide. If you need to see all of the information, click the variant row to open the variant details.

October 23, 2019

What's New

  • Observation terminology search will now include matches in the Code and Display, rather than only the Display.
  • Insights observation bar charts can now handle grouping by codeable concept display values.
  • The Omics Explorer beta has now become the default when clicking Omics Explorer links throughout the application.

October 15, 2019

What's New

  • The navigation sidebar now remembers if you had it open or closed and respects your decision on refreshes.
  • Keyboard shortcuts were added! Press shift+? to launch a help modal containing all of the shortcuts currently supported.
  • The Tasks pages got a few upgrades. The table now infinitely scrolls the contents to save you a manual click to "Load More". Clicking a table row now takes you to the details for the specified task. Clicking the ellipsis exposes the view logs and rerun actions, as you'd expect. The details page uses the expansion panels like Omics Explorer.
  • The Files page also received the same table upgrade treatment with infinite scroll.
  • The Surveys page received some love. Filters are now at the top of the page and can be applied by clicking the radio option - there's no longer a manual "Filter" click! Clicking a survey from the table navigates you straight to editing the survey. A physical back button has been added to the nested pages to get you back to the root view. From the surveys table, click the people icon to be taken straight to the invitations for that particular survey.
  • The Subjects page received some new features. Clicking the "Reset" button now collapses all open filters. Observation chips now use a tooltip to display additional information about the chosen observation(s). Want to filter Subjects by Procedures? Done!
  • [Omics Explorer beta] The variant details are now easier to read and no longer chop off important information you may care about. The table view now takes the maximum browser height, allowing you to view more data on the screen.

Bug Fixes

  • We fixed a bug in Insights with bar charts allowing you to select more than one group-by when it shouldn't have.
  • We fixed a bug with the Subjects Search Observations filter allowing you to select invalid options.

October 02, 2019

What's New

  • Improved the look and feel and consistency of dialogs and the insights header.
  • Added a Load More button to the survey response list so that more than 25 survey responses can be viewed.
  • Insights observation bar charts can now handle grouping by codeable concept values, numeric/quantity values and string values. This makes it possible to visualize the distribution of observation values in a project or cohort.
  • Added gene expression level filter option to Subject Search.
  • [Variants Summary beta] Added variant details view to variant summary view.

September 23, 2019

What's New

  • Gene expression filter options have been added to the Subject Search.
  • [Omics Explorer beta] Project level gene expression metrics have been added. Clicking on a variant in the table launches the variant details modal. The details modal now contains alternate variant transcripts (where applicable). Bug fixes and performance improvements.

September 19, 2019

What's New

  • Clicking the Omics Explorer link from Subject Search no longer opens Omics Explorer in a separate tab.
  • [Omics Explorer beta] Gene expression levels are now displayed alongside the other variant types. Short, structural, copy number, and expression variants will now display a gene or exact match indicator under the CKB column in the variants table. The variants table was redesigned to allow for more separation from the filters.

September 16, 2019

What's New

  • [Omics Explorer beta] Table data can now be sorted by clicking on a column. "Splice region" is added as a variant filter. The drug associations table now displays exact and gene matches properly.

September 11, 2019

What's New

  • Redesigned buttons, header, and sidebar navigation.
  • Improved Observation Value search-as-you-type experience in Subjects Search.
  • [Omics Explorer beta] A new Omics Explorer experience is available! Navigate to the existing Omics Explorer page and click "Try it out!" on the beta popup. If you hit any issues, you can always go back to the original version by using the back button on your browser or clicking the patient name in the header, followed by the Omics Explorer link.

August 23, 2019

Bug Fixes

  • Subject Search observation queries now handle manual entry for >, <, >=, and <=

August 15, 2019

What's New

  • Tasks can now be created using FHIR data as an input.
  • Cleaned up the Subject Filters so they are more intuitive.
  • Addressed issue of persisting error messages in Subject Search.

August 10, 2019

What's New

  • PHC invitation emails have a new look and a link that can be used to accept the invite in case the code entry page is closed prior to acceptance.
  • All FHIR resources that are created or updated will now have a lastUpdated field and can be searched using the _lastUpdated query parameter.

August 2, 2019

What's New

  • Improvements to Observation filter in subject search, including "exists" operator and autosuggest for CodeableConcepts

Bug Fixes

  • UDF saving now handles empty parameters more gracefully

July 25, 2019

What's New

  • Tasks can now be scheduled to run at a future date, or configured to run on a recurring schedule

July 16, 2019

What's New

  • Enhanced Observation filter in Subject Search
  • Single Value module type added to Insights
  • Various Survey Builder improvements
  • Trial Matching user interface updates
  • Improved spacing on Omics Explorer tables
  • Circle management style improvements
  • Added gnomAD exome annotations to the Omics Explorer short variants table

July 10, 2019

What's New

  • PHC users who administer LIFE Fasting circles will now be able to manage those circles and post announcements directly in the PHC.

July 8, 2019

What's New

  • The project link tiles have been redesigned for a consistent look across the app
  • Improve survey invite
  • Left align loader to be visible with wide tables
  • Add separate links for fusion genes, point all genes to NCBI
  • Structural variant column status -> effect
  • Remove status requirement when searching on copy number gene
  • Standardize to 'variant'
  • Shuffle Omics Explorer filters to be standardized order
  • Add default sort, set structural variants to 'status'
  • Add lab reported significance values for structural variants subject search

July 2, 2019

What's New

  • Added quantity support for surveys.
  • Improved Time Range Selector.
  • Added ability to search for “has at least one” type of specimen.

June 28, 2019

What's New

  • The loading animation has been redesigned.
  • Insights and Subject Viewers tiles have been updated to match other tiles.
  • Added Run Time column to Tasks list view.

Bug Fixes

  • Links are now more readable in the account description hero tile.

June 17, 2019

What's New

June 10, 2019

What's New

  • The account landing page has been redesigned. The account description is now displayed for all users as a hero tile. Quick link options are available from the landing page to access account information, billing, and usage pages. A subset of all projects are displayed from the landing page as well. Click "See All" if you don't see the project(s) you're looking for!

June 5, 2019

What's New

  • The project picker is redesigned and now displays all available projects at once. Project tiles were updated too!
  • Removed the 5gb file size limit for doing file renames.
  • Ontology support added to:
  • A Data explorer has been added to the Subject Viewer layout editor. Layout configuration editors can now experiment with JMESPath expressions to query FHIR JSON and pull out data elements for display.
  • Subject Viewer graphs will now try to convert data points in the same trace to a common unit.
  • Subject Viewer layout editors can now configure what unit a trace should convert its data points too.
  • A configuration option was added to the Subject Viewer to allow overlaid traces of the same unit to share the same y-axis range.
  • dbNSFP annotations have been added to short variants with results viewable in the Omics Explorer.

May 21, 2019

What's New

  • Added VCF related columns quality, filter, and read depths to the Omics Explorer for short variants.
  • Updated the Tasks UI to provide a more enhanced view of the status of tasks (queued, initializing, running, canceled, complete) and better filtering support within a project.
  • Added project ID to projects list. To get project ID visit /phc/project/projects and click the List View button.
  • Added the ability to select and view copy number variants in OE.
  • Added the ability to search for subjects with copy number data in subject viewer.

May 9, 2019

Bug Fixes

  • Loading more subjects in the subject search now appends the new result set to the existing result set.

May 1, 2019

Bug Fixes

  • If you happened to notice the scatter plot was broken, it's fixed now.
  • Subsumption based filtering for medications is working again.

April 30, 2019

What's New

  • The sidebar navigation is redesigned with a new look and an expand/collapse feature. By default, it is expanded showing all navigation options. To get more screen real estate, click the arrow icon to collapse it. When the sidebar is collapsed, hovering over the navigation icons will display a tooltip with more information about the page.

April 26, 2019

What's New

  • Redesigned account management access and pages. To access previous pages under Account Management and Manager Users, click the account name in the header. If the user is part of a single account, they'll be taken straight to the new account management page; otherwise, an account switcher dialog will appear and the user should click "Manage" next to the account to access the new page.
  • Filtering on medications when searching for subjects now supports ontology service functionality. When selecting medications that subsume other medications users may now optionally include all subsumed medications in the filter.
  • Added the ability to search table contents in Subject Viewer tables.
  • ReferralRequest and Specimen resource types can now be added to the Subject Viewer header.

Bug Fixes

  • Subject search performance improvements.

April 23, 2019

What's New

April 12, 2019

What's New

  • Patient name search will now perform partial prefix matches. For example searching for either "Lav" or "Vander" will find "Lavelle Vandervort".
  • Patient name search is now more strict in that unrelated full names will no longer match. For example searching for "Lavelle Vandervort" will no longer find "Max Vandervort". Also, full name matches will only find the patient when the Patient record contains the full name.

April 10, 2019

What's New

  • Omics Explorer now provides a quick link to view the variant in IGV if a given sequence has an associated read set available.
  • Redesigned user menu. The new user menu is focused on user-specific tasks such as links to manage your profile, accept invitations to accounts, and sign out.
  • Redesigned header. The header now has a new look, but should feel familiar. Switching an account can now be accomplished by clicking the account name in the header, selecting from a list of accounts, and then confirming the action.
  • Redesigned page titles. Each page will display the project name followed by the current page the user is on.
  • Exposed observation data as a filter in subject search.
  • Added a link to the PHC User Guides from the navigation menu.

Bug Fixes

  • Account descriptions have been enhanced to now allow Account avatars.
  • Patient Viewer bug fixes.

Mar 21, 2019

What's New

  • Patient Viewer table header labels are now configurable.
  • Patient Viewer now enables JMESPath configuration for table values. This enables adding any fhir resource value to the table.

Bug Fixes

  • Cohort comparison is no longer required for insight's survival curves. The user can update the survival curve with the cohort dropdown or query language input.
  • Minor improvements to remove clutter in patient viewer graphs.

Mar 20, 2019

What's New

  • Subject Viewer default time range can now be configured.
  • Users can now change the marker type and line style of Subject Viewer graphs.
  • Survival curves have been added to Insights.
  • Search capabilities for files explorer.

Bug Fixes

  • Subject Viewer performance improvements.

Mar 15, 2019

  • Patient Viewer will now use the full width of the window for greater horizontal space.
  • Patient Viewer will now lazy load data for improved performance.
  • JSON files are now directly viewable via the Files listing.
  • The Files listing now shows Date Uploaded for files.
  • Various small bug fixes and style improvements

Mar 12, 2019

What's New

  • Modules (graphs, tables, etc.) within Subject Viewer are now able to be collapsed/expanded by the user. Administrators can collapse modules by default within a given layout to save space.
  • Graphs and traces can now be optionally set to be ‘shown’ or ‘not shown’ as a default for each configured layout.
  • [GA] New virtual directory browsing UI for the Files page. Files with slashes (/) will be treated as a directory as you would expect on a traditional OS file system (i.e., examples/case1/file.txt)

Mar 5, 2019

What's New

  • [beta] New virtual directory browsing UI for the Files page. Files with slashes (/) will be treated as a directory as you would expect on a traditional OS file system (i.e., examples/case1/file.txt)

Bug Fixes

  • General performance improvements to the UI

Feb 28, 2019

What's New

  • Enable one trace within a given plot to overlay vertical visual shading (a swim-lane effect) over other traces.
  • FHIR bundle POST requests are now rate limited to 10 request per 10 seconds per account.

Bug Fixes

  • Subject viewer performance improvements.

Feb 26, 2019

What's New

  • All pages in the PHC now have a button to generate a sharable link. The shareable link will be copied to the clipboard and can be sent to other users so they can easily navigate to the exact page and view.
  • The PHC login screen has been updated with new style and branding, but the functionality is the same.
  • The FHIR resource ingest API (both single item POST/PUT and bundle POST) is now backed by a FIFO queue so it is faster and more robust. As a result it may take some time for large batches to show up in queries.
  • Patient viewer will now hide traces that have no data in the selected time range to conserve space.
  • Added Zygosity to the Omics Explorer variant table, subject search, and the insights query API.
  • Account descriptions now support rich-text through an interactive editor. These account descriptions will allow customers to provide documentation of goals and high level overviews for the account.
  • Patient viewer can now easily compare different quantitative trends by providing a new administrative option to overlay multiple observational graph traces.

Feb 12, 2019

What's New

  • Added GPU support to Task service. Task service supports instance types that have 4 or 8 GPUs available.

Feb 6, 2019

What's New

  • Added synonymous as a coding effect option on Omics Explorer
  • Added explicit account trust option when sending invites. This allows an administrator to restrict the login method used to accept an invite and in turn restrict the login methods for users who are granted access to the account.

Jan 1, 2019

What's New

  • OAuth application ecosystem for registering OAuth apps hosted outside of the platform that users develop and want to interact with the platform.

Nov 30, 2018

What's New

  • Tags filter for Subjects

Nov 27, 2018

What's New

  • Subject viewer header reorganization
  • Subject filters added for Race and Ethnicity
  • Omics Explorer - Allows a user to review annotated somatic and germline variants in a faceted filter search interface. A few notable facets are: chromosome, protein changes, gene sets (i.e. ACMG 59), genes, and ClinVar significance/review status.
  • Gene Sets via Knowledge tile
  • Updated genomic filters for subjects

Nov 15, 2018

What's New

  • New subject filters: Medications and Conditions

Nov 7, 2018

What's New

  • New subject filters: Medications and Conditions

Sept 27, 2018

What's New

  • User interface refresh with side navigation menu and action tiles together replacing tabs
  • Configurable Insights with many options and module types:
    • Scatter plot
    • Bar/column/histogram charts
    • Pie chart
    • Line chart
    • OncoPrint for DNA mutations
    • PCA for gene expression
    • Heat map for gene expression
  • Insights query system to filter subjects list for graphing purposes
  • Subject Viewer header configuration
  • Tag filtering for Subject Viewer charts, tables and header
  • Age rounding depending on life stage
  • Feature Toggled: Cohort saving from the Subjects list filter system
  • Feature Toggled: Insights focus on entire project or a selected cohort

Aug 13, 2018

What's New

  • DICOM images are now viewable on the platform.
  • v6.0.1 of the LifeOmic CLI was released this morning. It includes some major changes to the command formats. This new version has better support of the application. Please let us know if you find any issues when using the new version. https://github.com/lifeomic/cli/releases/tag/v6.0.1

Aug 8, 2018

What's New

  • API keys - One can use client credentials to do headless auth, but the API keys provide a simpler way for users to create and use their own keys. Plus, the access is scoped to that of the user the API key was created for.

Jun 12, 2018

What's New

  • A UI style refresh that gives more vertical space and some more attractive styling.
  • V2 patient search - the search options will be limited until insights is enabled for the project by the project administrator.
  • Insights - these will be blank until Insights is enabled for the project
  • Masked Mode - this mode masks identifying information for subjects.

May 5, 2018

What's New

  • Viewing subjects' data with a specific data layout can now be modified and saved to share with other users of the platform.
    • Create a custom layout for any specific use-case:
      • Research
      • Oncology / Tumor boards
      • Treatment overview
      • ...
  • Tasks - you can now create docker container based tasks and run them in the PHC where the data resides.

Apr 4, 2018

What's New

  • Released htsget APIs and a hosted web version of IGV.js genome viewer for viewing whole genome (or smaller) BAM files.

Apr 1, 2018

What's New

  • PHC web console generally available.
  • Implemented bulk ingest for FHIR resources. This provides an optimized way to insert large FHIR data-sets in a scalable manner.

Mar 1, 2018

What's New

  • Platform HITRUST certified.
  • SAML2 two-factor authentication for Single-sign on.
  • Attribute-based access control (ABAC) for fine grained management of feature and data access.
  • CLI for easy platform API access from a terminal in an interactive or scripted environment.

Feb 16, 2018

What's New

  • LifeOmic has joined GA4GH as an organization member.
  • PHC web console now has a unified spinner/loading indicator. :-)
  • Platform status and metrics can now be watched and subscribed to here: https://status.us.lifeomic.com
  • FHIR DSTU3 API support

Jan 1, 2018

What's New

  • Beta of PHC Web Console to early partners.
  • Beta of LIFE Fasting Tracker on iOS.
  • The platform can now handle and manage any type of file no matter how big or small (bam, vcf, and any future file extension)
  • GA4GH APIs to power genomic data access
  • Sequence FHIR resource support in the API - including interlinking between GA4GH and FHIR.
  • Now you can search for Conditions by SNOMED code, for example.
  • Added RNA and Expression Level endpoints to the GA4GH service to allow users to search/filter through expression data.

Nov 1, 2017

What's New

  • Platform HIPAA compliance.
  • Precision health cloud REST APIs are released.
  • Automated 1-minute monitoring of platform health and alerting.

Aug 10, 2017

What's New

  • Organization of customer account data by projects (data-sets)
  • Single Sign-on with support for Google and Facebook
  • FHIR DSTU2 API support

Last update: June 28, 2019