Biology
Introduction
Research Computing and the HPC Center, as the organization that is directly responsible for development and support of the research computing resources on campus - both hardware and software - are fully committed to supporting biological research computing at the University of Florida. As a part of our commitment to this mission we have a full-time Biological Applications Support specialist and a part-time Biological Computing Training specialist. This section of the HPC wiki is dedicated to all things related to biological research computing at UF. See the Category:Biology for a complete listing of related pages or keep reading. We believe that the success of our support of the biological computing efforts at UF depends on the stability of the four main corner stones - hardware resources, software availability and support, training and documentation, and direct consulting and problem solving. The following sections address each of these major points.
Hardware
BioC - Biocomputing Cluster
UF Research Computing has a matching program for researchers that would like to invest in shared hardware resources at the HPC Center. See the Faculty Update from July 27th, and the PDF with the full description of the program. Contact Erik Deumens for details of the matching program or if you'd like to participate in the next round.
- Based on the results of the first round of the matching program a dedicated computing cluster for biological computing (BioC) will be purchased in the near future. Discussions on the hardware and policies for the BioC cluster are on-going.
- Meetings will be held to provide the biological research community that invested into the BioC opportunities to define usage processes, scope out requirements, and come to a consensus on the hardware specifications that will satisfy the majority. Please use the BioC requirements wiki page and its accompanying discussion page for preliminary information gathering on usage scenarios and requirements beforehand.
Main HPC Cluster
Both investors and non-investor users can also use the main HPC cluster. The Main and the BioC clusters provide access to the same software, though they are configured differently and have different usage policies. See Getting Started, Job Submission Queues and Schedulers for the documentation on the main cluster usage.
Fisher Bioinformatics Cluster
The Fisher Bioinformatics Cluster at the UF Genetics Institute is an older, though still capable, computing resource that is accessible to the UFGI affiliated faculty and the researchers they supervise. Fisher is particularly useful for smaller computing jobs and teaching efforts. Fisher has ten 8-core nodes with 12GB of RAM each and a 16-core node with 128GB of RAM. Contact Matt Gitzendanner or Taum Hanlon for more details.
Software
Galaxy
There is a local instance of the world renowned Galaxy platform for biological computing at UF HPC. Please read the UF HPC Galaxy documentation or proceed directly to the HPC Galaxy interface.
Modules
To ease the burden of setting up, administering, and maintaining a robust computing environment for the multitude of the applications used by biological researchers we implemented an environmental modules system based on lmod software at UF HPC. Please read documentation on using software via modules at UF HPC or peruse the currently much more extensive documentation written by the written by the lmod author.
Software installation
If you research requires installation of a particular application or a suite of software whether command-line (CLI) or web based we're here to help. Please submit a software installation request in the support system and we'll promptly review it and if possible install and configure the application for you as well as provide a modulefile for it. Both CLI and Galaxy tool requests should be submitted in the same manner.
Software Support
We provide support for building your own software on HPC resources as well as for particular job submission problems encountered in the day-to-day usage of the biocomputing software at the UF HPC. Please submit a help request in the support system at any time. We do not do data analysis consulting, but would be happy to refer you to a bioinformaticist who could help you. We, in our turn, will provide the hardware and software support for the data analysis pipeline they create for you.
Databases
- For BLAST databases, which serve both Galaxy and the command line blast see
/scratch/hpc/bio/blastdb/db. - For Bowtie indexes see
/scratch/hpc/bio/bowtie. - For Bwa indexes that can also be used by RiboPicker see
/scratch/hpc/bio/bwa. - For Reference Genomes see
/scratch/hpc/bio/genomes. Currently, H. sapiens hg19 and D. melanogaster (from FlyBase) genomes are available.
Documentation
HPC Biological Computing Wiki
We will provide UF HPC specific documentation for the hardware and the software available at the HPC in this wiki. Please see the Category:Biology for a full list of available documentation.
UFGI Bioinformatics wiki
The UFGI Bioinformatics Wiki] is a valuable resource on using biological research specific software in a high-performance computing environment at the UF. The Short Read Aligner comparison and software guide are very useful to read.
Training
Matt and Alex are in charge of preparing tutorials and hands-on classes on all aspects of the biological research computing at the UF. Please contact us if you have a particular training request or would like to have us present an HPC related tutorial or have a Galaxy or cluster-based hands-on exercise at the class you teach.
- 2011 - Fall Semester - a series of Training Sessions have concluded.
- 2012 - Spring Semester training sessions are being scheduled. They are free for all to attend, but tend to focus on Biological Applications and infrastructure.