ARC Software: Difference between revisions

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* [[Bioconda]] -- lets you install thousands of software packages related to biomedical research using the [[Conda on ARC | Conda]] package manager.
* [[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
* [[SignalP]] -- Prediction of Signal Peptides and their cleavage sites in all domains of life


= Chemistry =
= Chemistry =

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.

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.

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.

Statistics