Difference between revisions of "Biology"
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[[Category:Biology]] | [[Category:Biology]] | ||
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==Introduction== | ==Introduction== | ||
| − | Research Computing as the organization that is directly responsible for development and support of the research computing resources on campus - both hardware and software - is 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 [mailto:om@ | + | Research Computing as the organization that is directly responsible for development and support of the research computing resources on campus - both hardware and software - is 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 [mailto:om@rc.ufl.edu Biological Applications Support] specialist and a part-time [mailto:magitz@ufl.edu 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== | ==Hardware== | ||
| − | + | BioComputing Researchers enjoy exclusive access to 192 cores provided by the ''bio'' queue that automatically sends jobs to the main investor queue once the bio queue is full. | |
| − | BioComputing | + | |
| + | Large memory servers are available in the ''bigmem'' queue and contain from 500GB to 1TB of RAM. | ||
==Software== | ==Software== | ||
===Galaxy=== | ===Galaxy=== | ||
| − | There is a local instance of the world renowned [http://wiki.g2.bx.psu.edu/ Galaxy] platform for biological computing at UFRC. Please read the UFRC Galaxy [[Galaxy|documentation]] or proceed directly to the [http://galaxy. | + | There is a local instance of the world renowned [http://wiki.g2.bx.psu.edu/ Galaxy] platform for biological computing at UFRC. Please read the UFRC Galaxy [[Galaxy|documentation]] or proceed directly to the [http://galaxy.rc.ufl.edu/ HPC Galaxy interface]. |
===Modules=== | ===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 [http://www.tacc.utexas.edu/tacc-projects/mclay/lmod lmod software] at UFRC. Please read documentation on using software via modules at [[Modules|UFRC]] or peruse the currently much more extensive documentation | + | 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 [http://www.tacc.utexas.edu/tacc-projects/mclay/lmod lmod software] at UFRC. Please read documentation on using software via modules at [[Modules|UFRC]] or peruse the currently much more extensive documentation written by the [http://www.tacc.utexas.edu/tacc-projects/mclay/lmod lmod author]. |
===Software installation=== | ===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 [http://support. | + | 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 [http://support.rc.ufl.edu 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=== | ===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 UFRC. Please submit a help request in the [http://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 UFRC. Please submit a help request in the [http://support.rc.ufl.edu 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== | ==Databases== | ||
| − | * For BLAST databases, which serve both Galaxy and the command line blast see <code>/ | + | * For BLAST databases, which serve both Galaxy and the command line blast see <code>/data/reference/blast/db</code>. |
| − | * For Bowtie indexes see <code>/ | + | * For Bowtie indexes see <code>/data/reference/bowtie</code>. |
| − | * For Bwa indexes that can also be used by [[RiboPicker]] see <code>/ | + | * For Bowtie2 indexes see <code>/data/reference/bowtie2</code>. |
| − | * For Reference Genomes see <code>/ | + | * For Bwa indexes that can also be used by [[RiboPicker]] see <code>/data/reference/bwa</code>. |
| + | * For Reference Genomes see <code>/data/reference/genomes</code>. | ||
==Documentation== | ==Documentation== | ||
| − | |||
We will provide UFRC 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. | We will provide UFRC 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. | ||
==Training== | ==Training== | ||
| − | [mailto:magitz@ufl.edu Matt] and [mailto:om@ | + | [mailto:magitz@ufl.edu Matt] and [mailto:om@rc.ufl.edu 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. See the [[Trainings]] page for the current training schedule. |
Latest revision as of 21:23, 14 December 2022
Introduction
Research Computing as the organization that is directly responsible for development and support of the research computing resources on campus - both hardware and software - is 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
BioComputing Researchers enjoy exclusive access to 192 cores provided by the bio queue that automatically sends jobs to the main investor queue once the bio queue is full.
Large memory servers are available in the bigmem queue and contain from 500GB to 1TB of RAM.
Software
Galaxy
There is a local instance of the world renowned Galaxy platform for biological computing at UFRC. Please read the UFRC 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 UFRC. Please read documentation on using software via modules at UFRC 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 UFRC. 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
/data/reference/blast/db. - For Bowtie indexes see
/data/reference/bowtie. - For Bowtie2 indexes see
/data/reference/bowtie2. - For Bwa indexes that can also be used by RiboPicker see
/data/reference/bwa. - For Reference Genomes see
/data/reference/genomes.
Documentation
We will provide UFRC 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.
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. See the Trainings page for the current training schedule.