XetaBase 1.2 Release Notes

1 What’s new…

For the XetaBase 1.2 release we have focused on improving the infrastructure of the system to enable more control of releases and making IVA more functionally complete to aid the research and clinical use of XetaBase. 

These improvements and new functionality help us move XetaBase towards being a more holistic and stable tool to be used in both clinical and research fields, to interrogate aggregated and indexed genomic data at unprecedented scale. 

The key functionality we have added includes: 

  • Adding Exomiser as an interpretation tool 
  • Adding additional reference data to CellBase 
  • Improving the usability of both the Genome Browser and the reporting section of the clinical analysis 
  • Increasing the number of filters available when using IVA 
  • Adding the ability to lock an interpretation via IVA 

1.1 OpenCGA version 2.4.0

The key functionality we have added includes: 

  • Adding Exomiser as an automatic interpreter 
  • Making it mandatory to provide a status that maps to the Closed category, so cases can be closed when custom statuses are provided 
  • Infrastructure improvements and security upgrades 
  • Index improvements 

1.2 CellBase version 5.2.0

The key functionality we have added includes: 

  • Adding additional reference data sources:  
    • Pubmed 
    • EBI GWAS Catalog 
  • Improvements to the way Variants are Annotated 

1.3 IVA version 2.4.0

The key functionality we have added includes: 

  • Improvements to the Case portal 
    • Displaying the list of cases in the Clinical Analysis browser 
    • Displaying the list of disease panels registered in the current project 
  • Ability to lock an interpretation in the IVA interpretation manager 
  • Adding additional filters for Clinical Analysis browser and case portal 
    • Due date filter 
    • Filter for source in disease panel browser 
  • Updates to the Genome Browser 
    • Improving alignment 
    • Ability to mark features of interest in the karyotype panel and the current chromosome 
    • Ability to select and view the defined features of interest  
  • Report improvements 
    • Adding a standardised report format for all users 
    • Adding link to Signal webpage for each mutational signature ID 
  • Adding a Confirm action step, with the ability to confirm or cancel the last action 

2 Bug fixes

The key bug fixes are: 

  • Remove a hardcoded versioning in CellBase 
  • Genome Browser fixes: 
    • Primary Findings are updated in the features of interest dropdown 
    • Genome Browser in SVB displays correct region if there are no primary findings 
    • Genome Browser always displays the proband sample when applicable 
    • The current chromosome name is displayed in the Genome Browser for Chromosome panels 
    • Sample genotypes and depth are displayed in lollipop tooltip in Genome Browser 
  • Enable IVA 2.3 to support CellBase v4 
  • Add JSON tab to detailed tabs in interpretation_review/primary_finding 
  • Display stderr log in the job browser warning for pending jobs 
  • Replace spaces with underscores for column names for TSV exports of  SVB variants 
  • Correctly display the Column sex in individual grid when passing an empty object 
  • Display correct warning when trying to delete a locked case 
  • Clear due-date after submitting a case 
  • Synchronise Corpasome template version OpenCGA version 
  • Enable OpenCGA Storage Hadoop EMR6.1 to compile with mvn 3.8.5 
  • Update certificates for MongoDB replica set works 
  • Stop LDAP connection hanging 
  • Migrate Hadoop tests to version HDP 3.1 
  • Ensure OpenCGA command line has all endpoints for the meta service 

3 What’s next

For the next XetaBase cycle release we will be focusing on ensuring code quality and updating the quality controls in place, to ensure the reliability and stability of the service now and for future changes. We will also be focussed on fixing some key known issues that have been raised by customers. 

To speak to a member of our team about the the power of XetaBase, please email info@zettagenomics.com

XetaBase 1.1 Release Notes

1 What’s new…

For the XetaBase 1.1 release, we have been focused on making major improvements to the panel searches which means we are able to more quickly return results and enable large panels to be used to search. We have continued to add new reference data and have improved the usability of both the interface and the command line.  

These improvements and new functionality help us move XetaBase towards being a more holistic and stable tool to be used in both clinical and research fields to interrogate aggregated and indexed genomic data at an unprecedented scale. 

The key functionality we have added includes: 

  • Improved usability and functionality of the Genome Browser 
  • Improved deployment mechanism of XetaBase 

1.1 OpenCGA version 2.3.0

The key functionality we have added includes: 

  • Optimised performance of all panel searches, enabling large panel searches to be completed. 
  • Improvements to usability: 
    • Command line improvements 
    • Enabling a default filter to be set and applied for a Study 
    • Adding a lock feature to stop an interpretation being changed or deleted 
    • Enabling the panels used on a case to be limited to a predefined set 
  • Updates to the running and management of the OpenCGA code, including: 
    • Auto-incrementing the version number 
    • Updating naming conventions for better usability 
    • Creating a default SampleIndexConfiguration when a Study is created  

1.2 CellBase version 5.1.0

The key functionality we have added includes: 

  • Adding new reference data for Annotations: 
    • SpliceSite Scores 
    • HGNC IDs for Genes 
    • HGMD database 
  • Updating the running and management of the CellBase code, including: 
    • Improvements to the way the Docker image is handled 
    • Implemention of data release versioning 
    • Improvements to the Kubernetes deployment 

1.3 IVA version 2.3.0

The key functionality we have added includes: 

  • Embedding the Genome Browser in the interface 
  • Adding additional information to the Genome Browser: 
    • Sample information 
    • Better visualisation 
    • Highlighting variants of interest 
  • Additional user notifications when changes are unsaved 
  • Replacing EBI Ontology (GO/HPO) with CellBase 
  • An updated version of the Case Portal (v2) 

1.4 Infrastructure

The key functionality and updates include: 

  • Adding automated infrastructure across other providers (AWS) 
  • Ability to quickly generate simulated test data to improve the development process 
  • Deployment improvements for IVA 
  • Removing BigWig dependency in the Rest API 

2 Bug fixes

The key bug fixes are: 

  • Upgraded Jersey library to fix compatibility issue with Java 11 
  • Fixed JUnit tests 
  • Added a missing field in DiseasePanel data model 
  • Fixed search functionality end point for panels 
  • Fixed clinical variant index 
  • Stop Somatic and Germline rearrangement browsers displaying mixed variants 
  • Removed duplicated features in Gene overview track 
  • Now highlighting the display of the number of elements returned in the disease panel detail tab 
  • Enabled the Family browser filter to autocomplete for phenotype 
  • Fixed issue with the Chromosome filter in the QC section 
  • Increased reliability of the clinical browser 
  • Ensured update of individual phenotypes and disorders works correctly 
  • Corrected the base URL for HPO links for phenotype in the family browser 

3 What’s next

For the XetaBase 1.2 release we will be focusing on improving the deployment of the system to enable more control of release and making IVA more functionally complete to aid the research and clinical use of XetaBase. We will also be focussed on fixing some key known issues that have been raised by customers. 

To speak to a member of our team about the the power of XetaBase, please email info@zettagenomics.com