2020-08-24 BioData Catalyst Ecosystem Release Notes

Introduction

The 2020-08-24 release marks the second release for the NHLBI BioData Catalyst ecosystem. This release includes several new features along with documentation and tutorials (e.g. genome-wide association studies) to help new users get started on the system. This release also includes enhanced support for machine learning in the workspace environments and support for GA4GH industry standard in Dockstore for workflows. Please find more detail on the new features and user support materials in the sections below.

The 2020-08-24 data release includes the addition of TOPMed Freeze 8 data for a subset of studies on BioData Catalyst. Freeze8 multi-sample VCFs are available for 29 studies, of which 10 studies are new to the ecosystem. For each study and consent group, VCF files are available on a per chromosome basis and in an un-tarred format, in contrast to the Freeze5 multi-sample VCFs which are hosted as tar bundles. For the 10 studies new to BioData Catalyst, CRAM files and unharmonized clinical files are also available for access. The data release further includes updates of many studies to the latest versions that are available on dbGaP. The next data release will include Freeze8 multi-sample VCFs for additional TOPMed studies in addition to unharmonized clinical data and CRAM files for studies that are not yet hosted on the system. Please refer to the Data Release section below for more information as well as the on the BioData Catalyst website.

Significant new features

• GENESIS tutorial and public project: Seven Bridges has made a public project available that introduces users to the GENESIS R package and related R packages (SeqArray, SeqVarTools, and SNPRelate) used in mixed model association testing in sequence data. The examples in the project help users understand the code that is used in the GENESIS public apps (), prepare data for input to those apps, and interact with the results. The “GENESIS Tutorial” public project can be found in the list of Seven Bridges public projects on the top navigation bar of the platform.

• Launch machine learning packages in Jupyterlab Notebooks: Users on Seven Bridges can now use a docker image with that support machine learning analyses when working in Jupyterlab Notebooks. This docker image can be found in the Data Cruncher feature: Select “Create new analysis” and then, under the Environment setup menu, select “SB Machine Learning - TensorFlow 2.0, Python 3.7.”

New user support materials and documentation

• Overview of the ecosystem: This collaboratively developed guides new users through the process of understanding what the BioData Catalyst is to getting started using the ecosystem.

• Tips for reliable and efficient analysis set-up: provides recommendations on how to set up your initial set of analyses, tips for running tools/workflows, and specifications for computational resources on Seven Bridges.

• Genetic Association Testing Using GENESIS Workflows:

Data release

The table below highlights which TOPMed studies were included in the 2020-08-24 data release. Freeze 8 multi-sample VCFs were added for the 29 studies listed in the table below. This includes 19 studies which were previously hosted on BioData Catalyst with Freeze 5b data available and 10 studies which are new to BioData Catalyst. For each study and consent group, VCF files are available on a per chromosome basis and in an un-tarred format. For the 10 studies which are new to BioData Catalyst, CRAM files and unharmonized clinical files are also available for access. Additionally, 10 of these studies were updated to the latest version. The data is now available for access across the entire ecosystem.

For detailed platform release notes please consult the following resources:

• Gen3 release notes