/tag/bio
AlphaFold and UVA HPC
Description This package provides an implementation of the inference pipeline of AlphaFold 3.
Software Category: bio
For detailed information, visit the AlphaFold
website.
Available Versions To find the available versions, run:
module spider alphafold For detailed information about a particular version, including the load command, run module spider <name/version>. For example:
module spider alphafold/3.0.0 ModuleVersion Module Load Command alphafold3.0.0 module load gcc/11.4.0 alphafold/3.0.0 alphafold2.3.0 module load apptainer/1.3.4 alphafold/2.3.0 AlphaFold 3 Model Parameters The AlphaFold 3 model parameters are subject to the Terms of Use defined here. Our module does not contain the model parameters; instead, each user must submit their own request to DeepMind.
The Bioconda Environment and UVA HPC
Bioconda Python packages Many bioinformatics Python packages are now maintained and available for the popular Anaconda Python distribution. Python packages for the Anaconda distribution are distributed through a variety of different bundles, called channels. The bioconda channel is specifically set up for the maintenance and distribution of popular bioinformatics packages.
Available Versions The current installation of Bioconda
incorporates the most popular packages. To find the available versions and learn how to load them, run:
module spider bioconda The output of the command shows the available Bioconda
module versions.
For detailed information about a particular Bioconda
module, including how to load the module, run the module spider command with the module’s full version label.
Bioinformatics and UVA HPC
Overview Many commonly used bioinformatics software packages on the HPC clusters are available as individual modules or as Python packages bundled in the bioconda modules.
Please see our HowTo for more information about using this software on the HPC system.
Software Availability If a particular package is not available, several options are available. If it is sufficiently widely used, Research Computing staff will install it as a new module. If we determine that it is too specialized, you can install it yourself. Please use permanent storage such as your home directory to install software. If you have difficulty we can assist you to install the package.
