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.

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 computing resource that is accessible to the UF biological researchers and is particularly useful for teaching efforts. Contact Matt Gitzendanner or Taum Hanlon for more details.

Software

Galaxy

The world renowned Galaxy platform for biological computing is being set up at the UF HPC. Please read the UF HPC Galaxy documentation or proceed directly to the HPC Galaxy.

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 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.

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.

We will provide UF HPC specific documentation for the software available at the HPC.

Training

Matt and Alex are preparing a series of 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 or have a Galaxy or cluster-based hands-on exercise at the class you teach.