This is the home of the Bioinformatics Team (BioITeam) at the University of Texas at Austin.
The BioITeam (bio - i - team, short for bioinformatics team) is a consortium of bio-computing scientists at the University of Texas comprised of scientists from TACC, CCBB, CSSB, GSAF, TI-3D, and SSC.
Make sure you have the BioITeam's environment sourced in your Stampede and Lonestar profiles
Run BLAST+ an order of magnitude faster on Lonestar
split_blast wrapper is now available to make running BLAST queries in parallel easy on Lonestar. You can specify how you want to split your input data, and the wrapper script takes care of the rest: splitting the data, BLASTing it in parallel, and then reassembling the outputs. Run your BLAST query 10 times (roughly!) faster by splitting your input across 10 nodes!
launcher_creator.py on Stampede
launcher_creator.py has been updated to automatically detect whether it's being executed on Lonestar or Stampede, and will generate either an SGE or SLURM launcher as appropriate. The same
launcher_creator.py commands that worked on Lonestar should now work on Stampede.
launcher_creator.py has also been updated with some new options.
Mission of the BioITeam:
Provide "one-stop" unified support for bioinformatics:
educational resources and
We are initially, but not exclusively, focused on tools for next-generation sequencing (NGS) analysis. We are a group of users interested in pooling our efforts with others to reduce the time we spend implementing new software and databases and on training ourselves and others we work with.
Our general model is that TACC serve as the reference implementation for stable software releases so most of the "power computing" can be done at TACC, but in addition acknowledge that most of us use resources in addition to TACC, and often need tools, databases, or other resources not globally supported at TACC.
Due to the number of tools available and the pace of change, we have formed a community to help keep up with documentation, testing, implementation, and education. You are encouraged to become a contributor - just contact one of the BioITeam core members: Scott Hunicke-Smith (UT GSAF), Matt Vaughn (TACC), Dhivya Arasappan (UT GSAF), or Anna Battenhouse (UT - Iyer lab).
Resources available here:
- How to join the BioITeam
- Relevant classes offered at UT System Schools
- SSC Intro to NGS Bioinformatics Course
- Wish list
- Documentation of software (DRAFT) at TACC, CCBB, and GSAF systems
- Documentation of reference genomes, databases, indexes, etc
- BioITeam meeting minutes
- Bioinformatics Pipelines and Scripts
- BME 383J Course Content
- Results of surveys...
- Other helpful resources
- Appsoma-based pipeline development