Difference between revisions of "Biology"

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.

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 [[Category:Biology]]
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 ==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 [mailto:om@hpc.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.
+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==
-===BioC - Biocomputing Cluster===
+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.
-UF Research Computing has a matching program for researchers that would like to invest in shared hardware resources at the HPC Center. See the [http://www.aa.ufl.edu/072711 Faculty Update from July 27th], and the [http://www.hpc.ufl.edu/doc/RCMatchingProgram.pdf PDF] with the full description of the program. Contact [mailto:deumens@ufl.edu 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.
+Large memory servers are available in the ''bigmem'' queue and contain from 500GB to 1TB of RAM.
-===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 [https://fisher.bioinformatics.ufl.edu/wordpress/ 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 [mailto:magitz@ufl.edu Matt Gitzendanner] or [mailto:taum@ufl.edu Taum Hanlon] for more details.
 ==Software==
 ===Galaxy===
-The world renowned [http://wiki.g2.bx.psu.edu/ Galaxy] platform for biological computing is being set up at the UF HPC. Please read the UF HPC Galaxy [[Galaxy|documentation]] or proceed directly to the [http://galaxy.hpc.ufl.edu/ HPC 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===
-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 UF HPC. Please read documentation on using software via modules at [[Modules|UF HPC]] or peruse the currently much more extensive documentation written by the written by the [http://www.tacc.utexas.edu/tacc-projects/mclay/lmod lmod author].
+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===
-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.hpc.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.
+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===
-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 [http://support.hpc.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.
+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==
+* For BLAST databases, which serve both Galaxy and the command line blast see <code>/data/reference/blast/db</code>.
+* For Bowtie indexes see <code>/data/reference/bowtie</code>.
+* For Bowtie2 indexes see <code>/data/reference/bowtie2</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==
-===HPC Biological Computing Wiki===
+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 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 [https://fisher.bioinformatics.ufl.edu/wiki/index.php/Main_Page UFGI Bioinformatics Wiki]] is a valuable resource on using biological research specific software in a high-performance computing environment at the UF. The [https://fisher.bioinformatics.ufl.edu/wiki/index.php/Short_Read_Aligner_Information Short Read Aligner] comparison and [https://fisher.bioinformatics.ufl.edu/wiki/index.php/Software software guide] are very useful to read.
 ==Training==
-[mailto:magitz@ufl.edu Matt] and [mailto:om@hpc.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.
+[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.
-* 2011 - Fall Semester - a series of [[Training Sessions 2011 Fall|Training Sessions]] has been scheduled. They are free for all to attend, but will tend to focus on Biological Applications and infrastructure.