Infrastructure Development

The BICF is devoted to the development of software platforms that increase accessibility of data management and analytical tools across UTSW and beyond.

Over the past few years, the BICF has invested resources in four flagship projects including:

  • Development of a complete bioinformatics pipeline and annotation/decision-support software for the clinical NGS program
  • Bioinformatics-pipeline for UTSW’s Microbiome Core
  • Development of the Kidney Cancer Explorer as a prototype pan-cancer data commons and clinical decision support system
  • Development of the Cognition Explorer for integrated clinical and molecular data sharing
  • Launch of UDAWS as a framework for deployment of bioinformatics pipelines across the UTSW research community.

Emphasis over the upcoming 5 years is anticipated in the following areas:

Pan-cancer Data Commons: The BICF developed the Kidney Cancer Explorer (KCE) as a prototype data management system to facilitate hypothesis generation from clinical and genomic data. Using KCE’s framework, we will expand this project to create a pan-cancer data commons (PC-DC), allowing researchers to build patient cohorts utilizing integrated data analyses. KCE is the result of a fruitful collaboration between the core and the Kidney Cancer Program at UT Southwestern. The project is supported by CPRIT grant and through a Specialized Program of Research Excellence Award (SPORE) from the National Cancer Institute.

Cognition Explorer: A data management system for integrated clinical and molecular data sharing in Alzheimer’s disease (AD) and related neurodegenerative disease research across UT Southwestern Medical Center (UTSW). This project is in collaboration with the Cognition and Memory Research Program at UT Southwestern.

UT Southwestern Data Analysis Workflow System (U-DAWS): A framework to create scalable and reproducible analysis workflows using Git, Nextflow and Docker, called U-DAWS. Currently these workflows are available in a point-and-click web portal (Astrocyte Workflows) for UTSW researchers and download for anyone to use. Example pipelines available are:

  • ChIP-seq
  • ATAC-seq
  • scRNA-Seq
  • SRA downloading
  • Germline Variant Calling (Exome, Whole Genome, Gene Panel)
  • Somatic Mutation Variant Calling
  • RNA-seq Differential Gene Expression
  • Microbiome 16S rRNA Sequence Analysis

Clinical NGS: The BICF provides all of the tools necessary for monitoring wet bench quality control, identifying the unique genetic makeup of tumor samples and associate genetic alternations with clinical and genetic annotations.