ARC Software: Difference between revisions
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= Software Management = | |||
For some general consideration for setting up software in your home directory see [[Managing software on ARC]]. | For some general consideration for setting up software in your home directory see [[Managing software on ARC]]. | ||
* [[Conda on ARC | Conda]] and Miniconda | * [[Conda on ARC | Conda]] and Miniconda | ||
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* [[CESM]] | * [[CESM]] | ||
= | = Biomedical research = | ||
* [[ | |||
* [[Bioconda]] -- lets you install thousands of software packages related to biomedical research using the [[Conda on ARC | Conda]] package manager. | |||
* [[SignalP]] -- Prediction of Signal Peptides and their cleavage sites in all domains of life | |||
= Chemistry = | = Chemistry = | ||
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* [[ORCA]] - an ab initio quantum chemistry program package that contains modern electronic structure methods. | * [[ORCA]] - an ab initio quantum chemistry program package that contains modern electronic structure methods. | ||
* [[GROMACS]] - Classical molecular dynamics simulator. | * [[GROMACS]] - Classical molecular dynamics simulator. | ||
* [[Quantum ESPRESSO]] - an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials. | |||
* [[CPMD]] -- | |||
= Computational Fluid Dynamics = | = Computational Fluid Dynamics = | ||
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= Neuroimaging = | = Neuroimaging = | ||
* [[AFNI on ARC | AFNI]] | |||
* [[Freesurfer on ARC | Freesurfer]] | * [[Freesurfer on ARC | Freesurfer]] | ||
* [[FSL on ARC | FSL]] | * [[FSL on ARC | FSL]] | ||
* [[fmriprep on ARC | fmriprep]] | * [[fmriprep on ARC | fmriprep]] | ||
* [[Statistical Parametric Mapping on ARC | SPM 12]] | * [[Statistical Parametric Mapping on ARC | SPM 12]] | ||
= Physics = | |||
* [[ROOT]] - An open-source data analysis framework used by high energy physics and others. | |||
= Statistics = | = Statistics = | ||
| Line 57: | Line 68: | ||
* [[Stan on ARC | rstan]] | * [[Stan on ARC | rstan]] | ||
[[Category:ARC]] | [[Category:ARC]] | ||
{{Navbox ARC}} | {{Navbox ARC}} | ||
Latest revision as of 21:07, 1 October 2024
Software Management
For some general consideration for setting up software in your home directory see Managing software on ARC.
- Conda and Miniconda
General Tools
File Format Libraries
Atmospheric research
Biomedical research
- Bioconda -- lets you install thousands of software packages related to biomedical research using the Conda package manager.
- SignalP -- Prediction of Signal Peptides and their cleavage sites in all domains of life
Chemistry
- Gaussian 16 - a commercial software package for electronic structure modelling.
- ORCA - an ab initio quantum chemistry program package that contains modern electronic structure methods.
- GROMACS - Classical molecular dynamics simulator.
- Quantum ESPRESSO - an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
- CPMD --
Computational Fluid Dynamics
- ANSYS - Fluent and CFX - commercial CFD software.
- OpenFOAM - Open-source toolkit for creating CFD applications.
Finite Element Modelling
- ANSYS - ANSYS Fluent - commercial software for finite element-based structural analysis.
- Abaqus - Commercial software for finite element-based analysis.
- Nektar++ -- a tensor product based finite element package designed to allow one to construct efficient classical low polynomial order h-type solvers (where h is the size of the finite element) as well as higher p-order piecewise polynomial order solvers.
Geospatial Analysis
Machine Learning
Mathematical Libaries and Applications
- MATLAB - Commercial general-purpose high-level programming environment for linear algebra, statistics, image processing and a wide range of other calculations.
- Mathematica - Commercial general-purpose high-level programming package for both symbolic and numerical calculations.
Microscopy
Neuroimaging
Physics
- ROOT - An open-source data analysis framework used by high energy physics and others.