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* [http://lists.ufl.edu/cgi-bin/wa?A0=HPC-ANNOUNCE-L HPC announcement list]. All Research Computing users are automatically subscrib * [http://lists.ufl.edu/cgi-bin/wa?A0=HPC-BIO-L HPC Biocomputing discussion list] - This is an open subscription list for UF Bi

Biological Computing Category in the UF HPC Wiki

HPC infrastructure related documentation.

|{{#vardefine:url|https://developer.nvidia.com/hpc-sdk}} ...x, the HPC SDK provides the tools you need to build NVIDIA GPU-accelerated HPC applications.

...itz@ufl.edu Biological Computing Training] specialist. This section of the HPC wiki is dedicated to all things related to biological research computing at ...laxy|documentation]] or proceed directly to the [http://galaxy.rc.ufl.edu/ HPC Galaxy interface].

<!--HPC pre-built Bowtie Indexes are located in ''/scratch/hpc/bio/bowtie''. They should be available for bowtie use automatically. If you

Apptainer/Singularity is the most widely used container system for HPC. It is designed to execute applications at bare-metal performance while bei ...reproducibly build, share, and archive your workload from workstations, to HPC, to the edge.

====Using HPC GO database from a graphical Blast2GO application==== To use the HPC GO database with a graphical Blast2GO interface running locally on your com

|{{#vardefine:url|https://reframe-hpc.readthedocs.io/en/latest/index.html}} Unit testing framework for HPC clusters.

...neers interested in porting their codes to a wide-variety of heterogeneous HPC hardware platforms and architectures with significantly less programming ef

Intel processor optimized versions of cap3 and formcon are installed at HPC.

...in an object oriented manner. pyrpipe can be used on local computers or on HPC environments to manage analysis of RNA-Seq data. Users can use the easy-to-

Note: Docker is not usable on HPC clusters, so use -with-singularity, environment modules, or conda for runni

...following Ribosomal RNA databases are available for use with RiboPicker at HPC:

Open OnDemand is a web platform for accessing and managing HPC resources. If you're encountering issues while using Open OnDemand, here ar

..._campaign=HPC_Update_31_Lmod_Alternative_to_Environment_Modules_2013-01-30 HPC Admin Magazine].

...veraged tree topologies. jModelTest 2 includes High Performance Computing (HPC) capabilities and additional features like new strategies for tree optimiza

...within the software you used for transferring the files or by logging into HPC and running the following commands:

...Galaxy are access to the high-speed campus Research Network, use of large HPC cluster resources for running jobs, transparent user account access and con

....rc.ufl.edu/1.24/stacks http://stacks.rc.ufl.edu/1.24/stacks] and use your HPC credentials to log in and view the results. The exact URI is constructed as

All modules are automatically unloaded when you log out of the HPC system, and in most cases, there is no need to use the unload command.<br>

...$MYSQL_DB" must be changed to the database name used for the run. Use your HPC credentials to access the protected web portal.

...mance profiler for invaluable optimization advice across native and Python HPC codes, and Linaro Performance Reports for advanced reporting capabilities.

...s running as Docker container. However, Docker is not compatible with the HPC. AlphaFold has been installed as an apptainer container and

...same usage pattern you learned on Windows. However, when you log into the HPC system to get the job done via the command-line (CLI) interface you have to

See the [[Samtools|samtools HPC wiki page]] for more details on Samtools.

<!-- Note to HPC Staff: paste the list generated by the "library()" command between the <pre

...r home directory as the location for temporary files. It is a violation of HPC policy for jobs to write to your home directory.

#Alexandros Stamatakis. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and