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