Software Applications

'Modules' are a convenient way to provide access to the wide range of applications we have already installed on the cluster.

Command Description Example
module load <module name> Loads , (default version) module load Python
module load <module name>/<version> Loads , module load Python/3.11.6-foss-2023a
module purge Removes all loaded modules
module list Lists currently loaded modules.
module spider Lists all available modules.
module spider <module name> Searches (fuzzy) available modules for module spider python

For a full list of module commands run man module or visit the lmod documentation.

4ti2 is a software suite for algebraic, geometric, and combinatorial problems on linear spaces. It is available on the cluster via a module.

Available Modules

module load 4ti2/1.6.11
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Available Modules

module load crystal/23.1.0.1
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Available Modules

module load gaussian/16
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Macaulay2 is a software system for research in algebraic geometry and commutative algebra. It is designed to be easy to use and provides a powerful programming environment. It is particularly well-suited for computations in algebraic geometry, commutative algebra, and related areas.

Available Modules

module load macaulay2/1.24.11
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Available Modules

module load mathematica/14.2.1
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AFNI (Analysis of Functional NeuroImages) is a leading software suite of C, Python, R programs and shell scripts primarily developed for the analysis and display of multiple MRI modalities

Available Modules

module load afni/24.2.03
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AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known.

Available Modules

module load apptainer/alphafold2
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AlphaFold can predict protein structures with atomic accuracy even where no similar structure is known.

Available Modules

module load alphafold3/3.0.1
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Ansys Fluent is proprietary fluid simulation software

Available Modules

module load /
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ORCA is a general-purpose quantum chemistry program package that features virtually all modern electronic structure methods.

Available Modules

module load orca/6.1.0
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Provides PyTorch 2.2 with CUDA and cuDNN via NVIDIA NGC container

Available Modules

module load apptainer/pytorch/24.04
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Bohra

Available Modules

module load apptainer/bohra/2.3.7
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CCP4

Available Modules

module load /
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Available Modules

module load /
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GLOBEClaritas is a proprietary software package for 2D and 3D land and marine seismic data processing.

Available Modules

module load apptainer/GLOBEClaritas/2024.1.2
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AlphaFold2 using MMseqs2. Easy to use protein structure and complex prediction using AlphaFold2 and Alphafold2-multimer

Available Modules

module load apptainer/colabfold/1.5.3/1.5.3
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Visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project

Available Modules

module load apptainer/connectome_workbench/2.0.1
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Available Modules

module load /
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DeepPoseKit is a Python toolkit with a high-level API for 2D pose estimation of user-defined keypoints using deep learning

Available Modules

module load apptainer/deepposekit/0.3.9
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Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.

Available Modules

module load apptainer/dorado/0.9.1
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fMRIPrep neuroimaging preprocessing via Apptainer container

Available Modules

module load fmriprep/25.1.2
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FSL is a library of analysis tools for FMRI, MRI and diffusion brain imaging data

Available Modules

module load apptainer/FSL/6.0.7.12
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Genealogies Unbiased By recomBinations In Nucleotide Sequences - Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences.

Available Modules

module load apptainer/gubbins/3.3.5
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Guppy is a data processing toolkit that contains the Oxford Nanopore Technologies' basecalling algorithms, and several bioinformatic post-processing features.

Available Modules

module load apptainer/guppy-gpu/6.4.6
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HUMAnN (the HMP Unified Metabolic Analysis Network) is a method for efficiently and accurately profiling the abundance of microbial metabolic pathways and other molecular functions from metagenomic or metatranscriptomic sequencing data.

Available Modules

module load /
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Available Modules

module load matlab/r2024b
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Ollama is a free and open source inference runtime for large language model (LLM) applications.

Available Modules

module load /
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OpenPose is a real-time multi-person keypoint detection library developed by the CMU Perceptual Computing Lab. It supports body, face, hand, and foot pose estimation using deep learning.

Available Modules

module load apptainer/openpose/1.7
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Available Modules

module load samtools/1.20
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Space Ranger is a set of analysis pipelines that process 10x Genomics Visium data with brightfield or fluorescence microscope images, allowing users to map the whole transcriptome in a variety of tissues.

Available Modules

module load /
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Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data

Available Modules

module load apptainer/TBProfiler/6.2.1
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Whisper (speech-to-text)

Available Modules

module load /
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XDSGUI is a graphical user interface for XDS, SHELX and ARCIMBOLDO for processing and phasing results for X-ray, neutron and electron diffraction data.

Available Modules

module load /
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Zstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set.

Available Modules

module load zstd//1.5.6-e7rjt2q
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