From 7b76d7dbdd38d7a2f5eab0008dbee0dde9e54f98 Mon Sep 17 00:00:00 2001 From: Kilian Cavalotti Date: Thu, 19 Dec 2024 09:52:16 -0800 Subject: [PATCH] docs: updated software list --- includes/data/software.yml | 665 ++++++++++++++++++---------------- src/docs/software/updates.xml | 153 ++------ 2 files changed, 371 insertions(+), 447 deletions(-) diff --git a/includes/data/software.yml b/includes/data/software.yml index 5a4372684..3308abd67 100644 --- a/includes/data/software.yml +++ b/includes/data/software.yml @@ -5873,19 +5873,6 @@ software_modules: Sequencing platforms., markedDefault: false, versionName: 2.2.1_py36} - name: chemistry packages: - - categories: chemistry, cheminformatics - defaultVersionName: 2018.09.1_py27 - description: RDKit is a collection of cheminformatics and machine-learning software - written in C++ and Python. - package: py-rdkit - url: http://www.rdkit.org - versions: - - {description: RDKit is a collection of cheminformatics and machine-learning - software written in C++ and Python., markedDefault: false, versionName: 2018.09.1_py36} - - {description: RDKit is a collection of cheminformatics and machine-learning - software written in C++ and Python., markedDefault: false, versionName: 2022.09.1_py39} - - {description: RDKit is a collection of cheminformatics and machine-learning - software written in C++ and Python., markedDefault: true, versionName: 2018.09.1_py27} - categories: chemistry, computational chemistry defaultVersionName: 2.6.0 description: Libint computes molecular integrals. @@ -5898,25 +5885,6 @@ software_modules: versionName: 2.0.3} - {description: Libint computes molecular integrals., markedDefault: false, versionName: 2.6.0} - - categories: chemistry, molecular dynamics - defaultVersionName: '20220426' - description: The QUIP package is a collection of software tools to carry out - molecular dynamics simulations. - package: quip - url: https://github.com/libAtoms/QUIP - versions: - - description: The QUIP package is a collection of software tools to carry out - molecular dynamics simulations. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: '20170901' - - description: The QUIP package is a collection of software tools to carry out - molecular dynamics simulations. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: '20220426' - categories: chemistry, tools defaultVersionName: 3.1.1 description: Open Babel is a chemical toolbox designed to speak the many languages @@ -5926,6 +5894,165 @@ software_modules: versions: - {description: Open Babel is a chemical toolbox designed to speak the many languages of chemical data., markedDefault: false, versionName: 3.1.1} + - categories: chemistry, molecular dynamics + defaultVersionName: '20230802' + description: LAMMPS is a classical molecular dynamics code that models an ensemble + of particles in a liquid, solid, or gaseous state. + package: lammps + url: http://lammps.sandia.gov + versions: + - description: LAMMPS is a classical molecular dynamics code that models an + ensemble of particles in a liquid, solid, or gaseous state. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: '20180316' + - description: LAMMPS is a classical molecular dynamics code that models an + ensemble of particles in a liquid, solid, or gaseous state. + markedDefault: false + properties: + arch: {gpu: 1} + parallel: {mpi: 1} + versionName: '20200303' + - description: LAMMPS is a classical molecular dynamics code that models an + ensemble of particles in a liquid, solid, or gaseous state. + markedDefault: false + properties: + arch: {gpu: 1} + parallel: {mpi: 1} + versionName: '20230802' + - categories: chemistry, docking + defaultVersionName: 1.0.2 + description: A deep learning framework for molecular docking + package: gnina + url: https://github.com/gnina/gnina + versions: + - description: A deep learning framework for molecular docking + markedDefault: false + properties: + arch: {gpu: 1} + versionName: 1.0.2 + - categories: chemistry, computational chemistry + defaultVersionName: 5.2.2 + description: Libxc is a library of exchange-correlation functionals for density-functional + theory. + package: libxc + url: https://www.tddft.org/programs/libxc + versions: + - {description: Libxc is a library of exchange-correlation functionals for density-functional + theory., markedDefault: false, versionName: 3.0.0} + - {description: Libxc is a library of exchange-correlation functionals for density-functional + theory., markedDefault: false, versionName: 5.2.2} + - categories: chemistry, computational chemistry + defaultVersionName: 3.22.1_py39 + description: The Atomic Simulation Environment (ASE) is a set of tools and Python + modules for setting up, manipulating, running, visualizing and analyzing atomistic + simulations. + package: py-ase + url: https://wiki.fysik.dtu.dk/ase/ + versions: + - {description: 'The Atomic Simulation Environment (ASE) is a set of tools and + Python modules for setting up, manipulating, running, visualizing and analyzing + atomistic simulations.', markedDefault: false, versionName: 3.14.1_py27} + - {description: 'The Atomic Simulation Environment (ASE) is a set of tools and + Python modules for setting up, manipulating, running, visualizing and analyzing + atomistic simulations.', markedDefault: false, versionName: 3.22.1_py39} + - categories: chemistry, quantum chemistry + defaultVersionName: 6.0.0 + description: ORCA is a flexible, efficient and easy-to-use general purpose tool + for quantum chemistry. + package: orca + url: https://orcaforum.kofo.mpg.de/ + versions: + - description: ORCA is a flexible, efficient and easy-to-use general purpose + tool for quantum chemistry. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 4.2.1 + - description: ORCA is a flexible, efficient and easy-to-use general purpose + tool for quantum chemistry. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 5.0.0 + - description: ORCA is a flexible, efficient and easy-to-use general purpose + tool for quantum chemistry. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 5.0.3 + - description: ORCA is a flexible, efficient and easy-to-use general purpose + tool for quantum chemistry. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 6.0.0 + - categories: chemistry, quantum chemistry + defaultVersionName: 2.9.7 + description: OCEAN is a versatile and user-friendly package for calculating + core edge spectroscopy including excitonic effects. + package: ocean + url: http://monalisa.phys.washington.edu/OCEAN/index.html + versions: + - description: OCEAN is a versatile and user-friendly package for calculating + core edge spectroscopy including excitonic effects. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 2.9.7 + - categories: chemistry, crystallography + defaultVersionName: 2.0.20 + description: A C++ toolkit for working with macromolecular coordinate files. + package: mmdb2 + url: https://www.ccp4.ac.uk/ + versions: + - {description: A C++ toolkit for working with macromolecular coordinate files., + markedDefault: false, versionName: 2.0.20} + - categories: chemistry, computational chemistry + defaultVersionName: 7.0.2 + description: NWChem is an ab initio computational chemistry software package + which also includes quantum chemical and molecular dynamics functionality. + package: nwchem + url: https://nwchemgit.github.io + versions: + - description: NWChem is an ab initio computational chemistry software package + which also includes quantum chemical and molecular dynamics functionality. + markedDefault: false + properties: + arch: {gpu: 1} + parallel: {mpi: 1} + versionName: '6.8' + - description: NWChem is an ab initio computational chemistry software package + which also includes quantum chemical and molecular dynamics functionality. + markedDefault: false + properties: + arch: {gpu: 1} + parallel: {mpi: 1} + versionName: 7.0.2 + - categories: chemistry, crystallography + defaultVersionName: 2.1.20180802 + description: Crystallographic automation and complex data manipulation libraries. + package: clipper + url: https://www.ccp4.ac.uk/ + versions: + - {description: Crystallographic automation and complex data manipulation libraries., + markedDefault: false, versionName: 2.1.20180802} + - categories: chemistry, cheminformatics + defaultVersionName: 2018.09.1_py27 + description: RDKit is a collection of cheminformatics and machine-learning software + written in C++ and Python. + package: py-rdkit + url: http://www.rdkit.org + versions: + - {description: RDKit is a collection of cheminformatics and machine-learning + software written in C++ and Python., markedDefault: false, versionName: 2018.09.1_py36} + - {description: RDKit is a collection of cheminformatics and machine-learning + software written in C++ and Python., markedDefault: false, versionName: 2022.09.1_py39} + - {description: RDKit is a collection of cheminformatics and machine-learning + software written in C++ and Python., markedDefault: false, versionName: 2024.3.2_py312} + - {description: RDKit is a collection of cheminformatics and machine-learning + software written in C++ and Python., markedDefault: true, versionName: 2018.09.1_py27} - categories: chemistry, computational chemistry defaultVersionName: 2021-1 description: Schrödinger Suites (Small-molecule Drug Discovery Suite, Material @@ -5997,72 +6124,59 @@ software_modules: license: {restricted: 1} parallel: {mpi: 1} versionName: 2021-1 - - categories: chemistry, quantum chemistry - defaultVersionName: 1.95A - description: TeraChem is general purpose quantum chemistry software designed - to run on NVIDIA GPU architectures. - package: terachem - url: http://www.petachem.com/ + - categories: chemistry, computational chemistry + defaultVersionName: 5.4.1 + description: The Vienna Ab initio Simulation Package (VASP) is a computer program + for atomic scale materials modelling, e.g. electronic structure calculations + and quantum-mechanical molecular dynamics, from first principles. + package: vasp + url: https://www.vasp.at versions: - - description: TeraChem is general purpose quantum chemistry software designed - to run on NVIDIA GPU architectures. + - description: The Vienna Ab initio Simulation Package (VASP) is a computer + program for atomic scale materials modelling, e.g. electronic structure + calculations and quantum-mechanical molecular dynamics, from first principles. markedDefault: false properties: arch: {gpu: 1} license: {restricted: 1} - versionName: 1.96H-beta - - description: TeraChem is general purpose quantum chemistry software designed - to run on NVIDIA GPU architectures. - markedDefault: true + parallel: {mpi: 1} + versionName: 6.1.1 + - description: The Vienna Ab initio Simulation Package (VASP) is a computer + program for atomic scale materials modelling, e.g. electronic structure + calculations and quantum-mechanical molecular dynamics, from first principles. + markedDefault: false properties: arch: {gpu: 1} license: {restricted: 1} - versionName: 1.95A - - categories: chemistry, molecular dynamics - defaultVersionName: 1.0.0 - description: A collection of tools for characterizing membrane structure and - dynamics within simulated trajectories of molecular systems. - package: mosaics - url: https://github.com/MOSAICS-NIH/MOSAICS - versions: - - description: A collection of tools for characterizing membrane structure and - dynamics within simulated trajectories of molecular systems. + parallel: {mpi: 1} + versionName: 6.3.2 + - description: The Vienna Ab initio Simulation Package (VASP) is a computer + program for atomic scale materials modelling, e.g. electronic structure + calculations and quantum-mechanical molecular dynamics, from first principles. markedDefault: false properties: + arch: {gpu: 1} + license: {restricted: 1} parallel: {mpi: 1} - versionName: 1.0.0 - - categories: chemistry, computational chemistry - defaultVersionName: g16.B01 - description: Gaussian is a general purpose computational chemistry software - package. - package: gaussian - url: https://www.gaussian.com - versions: - - description: Gaussian is a general purpose computational chemistry software - package. + versionName: 6.4.1 + - description: The Vienna Ab initio Simulation Package (VASP) is a computer + program for atomic scale materials modelling, e.g. electronic structure + calculations and quantum-mechanical molecular dynamics, from first principles. markedDefault: false properties: arch: {gpu: 1} license: {restricted: 1} - versionName: g16.A03 - - description: Gaussian is a general purpose computational chemistry software - package. - markedDefault: false + parallel: {mpi: 1} + versionName: 6.4.3 + - description: The Vienna Ab initio Simulation Package (VASP) is a computer + program for atomic scale materials modelling, e.g. electronic structure + calculations and quantum-mechanical molecular dynamics, from first principles. + markedDefault: true properties: arch: {gpu: 1} license: {restricted: 1} - versionName: g16.B01 - - categories: chemistry, computational chemistry - defaultVersionName: 5.2.2 - description: Libxc is a library of exchange-correlation functionals for density-functional - theory. - package: libxc - url: https://www.tddft.org/programs/libxc - versions: - - {description: Libxc is a library of exchange-correlation functionals for density-functional - theory., markedDefault: false, versionName: 3.0.0} - - {description: Libxc is a library of exchange-correlation functionals for density-functional - theory., markedDefault: false, versionName: 5.2.2} + parallel: {mpi: 1} + versionName: 5.4.1 - categories: chemistry, molecular dynamics defaultVersionName: 2.3.2 description: PLUMED is an open source library for free energy calculations in @@ -6088,17 +6202,6 @@ software_modules: can be used for the simulation of molecules in gases, fluids, zeolites, aluminosilicates, metal-organic frameworks, carbon nanotubes and external fields.', markedDefault: false, versionName: 2.0.3_py27} - - categories: chemistry, docking - defaultVersionName: 1.0.2 - description: A deep learning framework for molecular docking - package: gnina - url: https://github.com/gnina/gnina - versions: - - description: A deep learning framework for molecular docking - markedDefault: false - properties: - arch: {gpu: 1} - versionName: 1.0.2 - categories: chemistry, quantum chemistry defaultVersionName: '4.1' description: CP2K is a quantum chemistry and solid state physics software package @@ -6123,20 +6226,6 @@ software_modules: arch: {gpu: 1} parallel: {mpi: 1} versionName: '4.1' - - categories: chemistry, computational chemistry - defaultVersionName: 3.22.1_py39 - description: The Atomic Simulation Environment (ASE) is a set of tools and Python - modules for setting up, manipulating, running, visualizing and analyzing atomistic - simulations. - package: py-ase - url: https://wiki.fysik.dtu.dk/ase/ - versions: - - {description: 'The Atomic Simulation Environment (ASE) is a set of tools and - Python modules for setting up, manipulating, running, visualizing and analyzing - atomistic simulations.', markedDefault: false, versionName: 3.14.1_py27} - - {description: 'The Atomic Simulation Environment (ASE) is a set of tools and - Python modules for setting up, manipulating, running, visualizing and analyzing - atomistic simulations.', markedDefault: false, versionName: 3.22.1_py39} - categories: chemistry, tools defaultVersionName: 3.1.1.1_py39 description: Python bindings for Open Babel. @@ -6144,113 +6233,142 @@ software_modules: url: http://openbabel.org/ versions: - {description: Python bindings for Open Babel., markedDefault: false, versionName: 3.1.1.1_py39} - - categories: chemistry, electrostatics - defaultVersionName: '1.5' - description: APBS solves the equations of continuum electrostatics for large - biomolecular assemblages. - package: apbs - url: http://www.poissonboltzmann.org/ + - categories: chemistry, modelling + defaultVersionName: 0.3.2_py312 + description: Boltz-1 is the state-of-the-art open-source model that predicts + the 3D structure of proteins, RNA, DNA, and small molecules. + package: py-boltz + url: https://jclinic.mit.edu/boltz-1/ versions: - - {description: APBS solves the equations of continuum electrostatics for large - biomolecular assemblages., markedDefault: false, versionName: '1.5'} - - categories: chemistry, quantum chemistry - defaultVersionName: 6.0.0 - description: ORCA is a flexible, efficient and easy-to-use general purpose tool - for quantum chemistry. - package: orca - url: https://orcaforum.kofo.mpg.de/ - versions: - - description: ORCA is a flexible, efficient and easy-to-use general purpose - tool for quantum chemistry. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: 4.2.1 - - description: ORCA is a flexible, efficient and easy-to-use general purpose - tool for quantum chemistry. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: 5.0.0 - - description: ORCA is a flexible, efficient and easy-to-use general purpose - tool for quantum chemistry. + - description: Boltz-1 is the state-of-the-art open-source model that predicts + the 3D structure of proteins, RNA, DNA, and small molecules. markedDefault: false properties: - parallel: {mpi: 1} - versionName: 5.0.3 - - description: ORCA is a flexible, efficient and easy-to-use general purpose - tool for quantum chemistry. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: 6.0.0 + arch: {gpu: 1} + versionName: 0.3.2_py312 - categories: chemistry, molecular dynamics - defaultVersionName: '20230802' - description: LAMMPS is a classical molecular dynamics code that models an ensemble - of particles in a liquid, solid, or gaseous state. - package: lammps - url: http://lammps.sandia.gov + defaultVersionName: '2023.1' + description: GROMACS is a versatile package to perform molecular dynamics, i.e. + simulate the Newtonian equations of motion for systems with hundreds to millions + of particles. + package: gromacs + url: http://www.gromacs.org versions: - - description: LAMMPS is a classical molecular dynamics code that models an - ensemble of particles in a liquid, solid, or gaseous state. + - description: GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds + to millions of particles. markedDefault: false properties: + arch: {gpu: 1} parallel: {mpi: 1} - versionName: '20180316' - - description: LAMMPS is a classical molecular dynamics code that models an - ensemble of particles in a liquid, solid, or gaseous state. + versionName: '2016.3' + - description: GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds + to millions of particles. markedDefault: false properties: arch: {gpu: 1} parallel: {mpi: 1} - versionName: '20200303' - - description: LAMMPS is a classical molecular dynamics code that models an - ensemble of particles in a liquid, solid, or gaseous state. + versionName: '2018' + - description: GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds + to millions of particles. markedDefault: false properties: arch: {gpu: 1} parallel: {mpi: 1} - versionName: '20230802' - - categories: chemistry, molecular dynamics - defaultVersionName: '2023.1' - description: GROMACS is a versatile package to perform molecular dynamics, i.e. - simulate the Newtonian equations of motion for systems with hundreds to millions - of particles. - package: gromacs - url: http://www.gromacs.org - versions: + versionName: '2021.3' - description: GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. markedDefault: false properties: - arch: {gpu: 1} + arch: {gpu: 1} + parallel: {mpi: 1} + versionName: '2023.1' + - categories: chemistry, molecular dynamics + defaultVersionName: '20220426' + description: The QUIP package is a collection of software tools to carry out + molecular dynamics simulations. + package: quip + url: https://github.com/libAtoms/QUIP + versions: + - description: The QUIP package is a collection of software tools to carry out + molecular dynamics simulations. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: '20170901' + - description: The QUIP package is a collection of software tools to carry out + molecular dynamics simulations. + markedDefault: false + properties: parallel: {mpi: 1} - versionName: '2016.3' - - description: GROMACS is a versatile package to perform molecular dynamics, - i.e. simulate the Newtonian equations of motion for systems with hundreds - to millions of particles. + versionName: '20220426' + - categories: chemistry, x-ray spectroscopy + defaultVersionName: 0.9.80_py312 + description: Larch is a open-source library and set of applications for processing + and analyzing X-ray absorption and fluorescence spectroscopy data and X-ray + fluorescence and diffraction image data from synchrotron beamlines. + package: py-xraylarch + url: https://xraypy.github.io/xraylarch/ + versions: + - {description: Larch is a open-source library and set of applications for processing + and analyzing X-ray absorption and fluorescence spectroscopy data and X-ray + fluorescence and diffraction image data from synchrotron beamlines., markedDefault: false, + versionName: 0.9.80_py312} + - categories: chemistry, molecular dynamics + defaultVersionName: 1.65.0 + description: Qbox is a First-Principles Molecular Dynamics code. + package: qbox + url: http://www.qboxcode.org + versions: + - description: Qbox is a First-Principles Molecular Dynamics code. markedDefault: false properties: - arch: {gpu: 1} parallel: {mpi: 1} - versionName: '2018' - - description: GROMACS is a versatile package to perform molecular dynamics, - i.e. simulate the Newtonian equations of motion for systems with hundreds - to millions of particles. + versionName: 1.65.0 + - categories: chemistry, molecular dynamicx + defaultVersionName: 0.2.2_py39 + description: FATSLiM stands for “Fast Analysis Toolbox for Simulations of Lipid + Membranes” and its goal is to provide an efficient, yet robust, tool to extract + physical parameters from MD trajectories. + package: py-fatslim + url: https://fatslim.github.io/ + versions: + - {description: 'FATSLiM stands for “Fast Analysis Toolbox for Simulations of + Lipid Membranes” and its goal is to provide an efficient, yet robust, tool + to extract physical parameters from MD trajectories.', markedDefault: false, + versionName: 0.2.2_py39} + - categories: chemistry, crystallography + defaultVersionName: '1.4' + description: A macromolecular superposition library. + package: ssm + url: https://www.ccp4.ac.uk/ + versions: + - {description: A macromolecular superposition library., markedDefault: false, + versionName: '1.4'} + - categories: chemistry, quantum chemistry + defaultVersionName: 1.95A + description: TeraChem is general purpose quantum chemistry software designed + to run on NVIDIA GPU architectures. + package: terachem + url: http://www.petachem.com/ + versions: + - description: TeraChem is general purpose quantum chemistry software designed + to run on NVIDIA GPU architectures. markedDefault: false properties: arch: {gpu: 1} - parallel: {mpi: 1} - versionName: '2021.3' - - description: GROMACS is a versatile package to perform molecular dynamics, - i.e. simulate the Newtonian equations of motion for systems with hundreds - to millions of particles. - markedDefault: false + license: {restricted: 1} + versionName: 1.96H-beta + - description: TeraChem is general purpose quantum chemistry software designed + to run on NVIDIA GPU architectures. + markedDefault: true properties: arch: {gpu: 1} - parallel: {mpi: 1} - versionName: '2023.1' + license: {restricted: 1} + versionName: 1.95A - categories: chemistry, quantum chemistry defaultVersionName: '7.1' description: Quantum ESPRESSO is an integrated suite of Open-Source computer @@ -6293,150 +6411,59 @@ software_modules: properties: parallel: {mpi: 1} versionName: '7.1' - - categories: chemistry, quantum chemistry - defaultVersionName: 2.9.7 - description: OCEAN is a versatile and user-friendly package for calculating - core edge spectroscopy including excitonic effects. - package: ocean - url: http://monalisa.phys.washington.edu/OCEAN/index.html - versions: - - description: OCEAN is a versatile and user-friendly package for calculating - core edge spectroscopy including excitonic effects. - markedDefault: false - properties: - parallel: {mpi: 1} - versionName: 2.9.7 - categories: chemistry, molecular dynamics - defaultVersionName: 1.65.0 - description: Qbox is a First-Principles Molecular Dynamics code. - package: qbox - url: http://www.qboxcode.org + defaultVersionName: 1.0.0 + description: A collection of tools for characterizing membrane structure and + dynamics within simulated trajectories of molecular systems. + package: mosaics + url: https://github.com/MOSAICS-NIH/MOSAICS versions: - - description: Qbox is a First-Principles Molecular Dynamics code. + - description: A collection of tools for characterizing membrane structure and + dynamics within simulated trajectories of molecular systems. markedDefault: false properties: parallel: {mpi: 1} - versionName: 1.65.0 - - categories: chemistry, molecular dynamicx - defaultVersionName: 0.2.2_py39 - description: FATSLiM stands for “Fast Analysis Toolbox for Simulations of Lipid - Membranes” and its goal is to provide an efficient, yet robust, tool to extract - physical parameters from MD trajectories. - package: py-fatslim - url: https://fatslim.github.io/ - versions: - - {description: 'FATSLiM stands for “Fast Analysis Toolbox for Simulations of - Lipid Membranes” and its goal is to provide an efficient, yet robust, tool - to extract physical parameters from MD trajectories.', markedDefault: false, - versionName: 0.2.2_py39} - - categories: chemistry, crystallography - defaultVersionName: 3.4.4 - description: VESTA is a 3D visualization program for structural models, volumetric - data such as electron/nuclear densities, and crystal morphologies. - package: vesta - url: http://jp-minerals.org/vesta/en/ - versions: - - {description: 'VESTA is a 3D visualization program for structural models, - volumetric data such as electron/nuclear densities, and crystal morphologies.', - markedDefault: false, versionName: 3.4.4} + versionName: 1.0.0 - categories: chemistry, computational chemistry - defaultVersionName: 5.4.1 - description: The Vienna Ab initio Simulation Package (VASP) is a computer program - for atomic scale materials modelling, e.g. electronic structure calculations - and quantum-mechanical molecular dynamics, from first principles. - package: vasp - url: https://www.vasp.at + defaultVersionName: g16.B01 + description: Gaussian is a general purpose computational chemistry software + package. + package: gaussian + url: https://www.gaussian.com versions: - - description: The Vienna Ab initio Simulation Package (VASP) is a computer - program for atomic scale materials modelling, e.g. electronic structure - calculations and quantum-mechanical molecular dynamics, from first principles. - markedDefault: false - properties: - arch: {gpu: 1} - license: {restricted: 1} - parallel: {mpi: 1} - versionName: 6.1.1 - - description: The Vienna Ab initio Simulation Package (VASP) is a computer - program for atomic scale materials modelling, e.g. electronic structure - calculations and quantum-mechanical molecular dynamics, from first principles. - markedDefault: false - properties: - arch: {gpu: 1} - license: {restricted: 1} - parallel: {mpi: 1} - versionName: 6.3.2 - - description: The Vienna Ab initio Simulation Package (VASP) is a computer - program for atomic scale materials modelling, e.g. electronic structure - calculations and quantum-mechanical molecular dynamics, from first principles. + - description: Gaussian is a general purpose computational chemistry software + package. markedDefault: false properties: arch: {gpu: 1} license: {restricted: 1} - parallel: {mpi: 1} - versionName: 6.4.1 - - description: The Vienna Ab initio Simulation Package (VASP) is a computer - program for atomic scale materials modelling, e.g. electronic structure - calculations and quantum-mechanical molecular dynamics, from first principles. + versionName: g16.A03 + - description: Gaussian is a general purpose computational chemistry software + package. markedDefault: false properties: arch: {gpu: 1} license: {restricted: 1} - parallel: {mpi: 1} - versionName: 6.4.3 - - description: The Vienna Ab initio Simulation Package (VASP) is a computer - program for atomic scale materials modelling, e.g. electronic structure - calculations and quantum-mechanical molecular dynamics, from first principles. - markedDefault: true - properties: - arch: {gpu: 1} - license: {restricted: 1} - parallel: {mpi: 1} - versionName: 5.4.1 - - categories: chemistry, computational chemistry - defaultVersionName: 7.0.2 - description: NWChem is an ab initio computational chemistry software package - which also includes quantum chemical and molecular dynamics functionality. - package: nwchem - url: https://nwchemgit.github.io - versions: - - description: NWChem is an ab initio computational chemistry software package - which also includes quantum chemical and molecular dynamics functionality. - markedDefault: false - properties: - arch: {gpu: 1} - parallel: {mpi: 1} - versionName: '6.8' - - description: NWChem is an ab initio computational chemistry software package - which also includes quantum chemical and molecular dynamics functionality. - markedDefault: false - properties: - arch: {gpu: 1} - parallel: {mpi: 1} - versionName: 7.0.2 - - categories: chemistry, crystallography - defaultVersionName: 2.1.20180802 - description: Crystallographic automation and complex data manipulation libraries. - package: clipper - url: https://www.ccp4.ac.uk/ - versions: - - {description: Crystallographic automation and complex data manipulation libraries., - markedDefault: false, versionName: 2.1.20180802} - - categories: chemistry, crystallography - defaultVersionName: 2.0.20 - description: A C++ toolkit for working with macromolecular coordinate files. - package: mmdb2 - url: https://www.ccp4.ac.uk/ + versionName: g16.B01 + - categories: chemistry, electrostatics + defaultVersionName: '1.5' + description: APBS solves the equations of continuum electrostatics for large + biomolecular assemblages. + package: apbs + url: http://www.poissonboltzmann.org/ versions: - - {description: A C++ toolkit for working with macromolecular coordinate files., - markedDefault: false, versionName: 2.0.20} + - {description: APBS solves the equations of continuum electrostatics for large + biomolecular assemblages., markedDefault: false, versionName: '1.5'} - categories: chemistry, crystallography - defaultVersionName: '1.4' - description: A macromolecular superposition library. - package: ssm - url: https://www.ccp4.ac.uk/ + defaultVersionName: 3.4.4 + description: VESTA is a 3D visualization program for structural models, volumetric + data such as electron/nuclear densities, and crystal morphologies. + package: vesta + url: http://jp-minerals.org/vesta/en/ versions: - - {description: A macromolecular superposition library., markedDefault: false, - versionName: '1.4'} + - {description: 'VESTA is a 3D visualization program for structural models, + volumetric data such as electron/nuclear densities, and crystal morphologies.', + markedDefault: false, versionName: 3.4.4} - categories: chemistry, quantum chemistry defaultVersionName: '7.1' description: Quantum ESPRESSO is an integrated suite of Open-Source computer @@ -6470,18 +6497,6 @@ software_modules: arch: {gpu: 1} parallel: {mpi: 1} versionName: '7.1' - - categories: chemistry, x-ray spectroscopy - defaultVersionName: 0.9.80_py312 - description: Larch is a open-source library and set of applications for processing - and analyzing X-ray absorption and fluorescence spectroscopy data and X-ray - fluorescence and diffraction image data from synchrotron beamlines. - package: py-xraylarch - url: https://xraypy.github.io/xraylarch/ - versions: - - {description: Larch is a open-source library and set of applications for processing - and analyzing X-ray absorption and fluorescence spectroscopy data and X-ray - fluorescence and diffraction image data from synchrotron beamlines., markedDefault: false, - versionName: 0.9.80_py312} - categories: chemistry, molecular dynamics defaultVersionName: 8.1.1_py312 description: A high performance toolkit for molecular simulation. @@ -8625,7 +8640,7 @@ software_modules: arch: {gpu: 1} versionName: 1.0.0 - categories: devel, lib - defaultVersionName: 1.79.0 + defaultVersionName: 1.87.0 description: Boost is a set of libraries for the C++ programming language that provide support for tasks and structures such as linear algebra, pseudorandom number generation, multithreading, image processing, regular expressions, @@ -8669,6 +8684,14 @@ software_modules: properties: parallel: {mpi: 1} versionName: 1.79.0 + - description: Boost is a set of libraries for the C++ programming language + that provide support for tasks and structures such as linear algebra, pseudorandom + number generation, multithreading, image processing, regular expressions, + and unit testing. + markedDefault: false + properties: + parallel: {mpi: 1} + versionName: 1.87.0 - categories: devel, data analytics defaultVersionName: 0.3_py27 description: 'Launching and controlling spark on HPC clusters ' diff --git a/src/docs/software/updates.xml b/src/docs/software/updates.xml index 08d6471d9..a9fec88f9 100644 --- a/src/docs/software/updates.xml +++ b/src/docs/software/updates.xml @@ -5,6 +5,33 @@ Sherlock software update feed https://www.sherlock.stanford.edu/docs/software/list + + New module: chemistry/py-boltz version 0.3.2_py312 + Boltz-1 is the state-of-the-art open-source model that predicts the 3D structure of proteins, RNA, DNA, and small molecules. + https://jclinic.mit.edu/boltz-1/ + https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.3.2_py312#py-boltz + chemistry, modelling + kilian@stanford.edu (Kilian Cavalotti) + Thu, 19 Dec 2024 09:50:55 -0800 + + + New version: chemistry/py-rdkit version 2024.3.2_py312 + RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python. + http://www.rdkit.org + https://www.sherlock.stanford.edu/docs/software/list/?add:v=2024.3.2_py312#py-rdkit + chemistry, cheminformatics + kilian@stanford.edu (Kilian Cavalotti) + Thu, 19 Dec 2024 09:05:51 -0800 + + + New version: devel/boost version 1.87.0 + Boost is a set of libraries for the C++ programming language that provide support for tasks and structures such as linear algebra, pseudorandom number generation, multithreading, image processing, regular expressions, and unit testing. + http://www.boost.org + https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.87.0#boost + devel, lib + kilian@stanford.edu (Kilian Cavalotti) + Thu, 19 Dec 2024 08:50:48 -0800 + New module: chemistry/openmm version 7.1.1 @@ -653,131 +680,5 @@ kilian@stanford.edu (Kilian Cavalotti) Thu, 19 Sep 2024 14:04:21 -0700 - - New version: math/opencv version 4.10.0 - OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. - https://opencv.org - https://www.sherlock.stanford.edu/docs/software/list/?add:v=4.10.0#opencv - math, lib - kilian@stanford.edu (Kilian Cavalotti) - Thu, 19 Sep 2024 10:53:59 -0700 - - - New version: devel/hdf5 version 1.14.4 - HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. - https://www.hdfgroup.org/hdf5 - https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.14.4#hdf5 - devel, data - kilian@stanford.edu (Kilian Cavalotti) - Wed, 18 Sep 2024 18:31:37 -0700 - - - New version: devel/openmpi version 5.0.5 - The Open MPI Project is an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. - https://www.openmpi.org - https://www.sherlock.stanford.edu/docs/software/list/?add:v=5.0.5#openmpi - devel, mpi - kilian@stanford.edu (Kilian Cavalotti) - Wed, 18 Sep 2024 18:13:22 -0700 - - - New module: devel/py-scalene version 1.55.4_py312 - Scalene is a high-performance, high-precision CPU, GPU, and memory profiler for Python with AI-powered optimization proposals - https://github.com/plasma-umass/scalene - https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.55.4_py312#py-scalene - devel, profiling - kilian@stanford.edu (Kilian Cavalotti) - Wed, 18 Sep 2024 15:56:16 -0700 - - - New module: devel/py-scalene version 1.55.4_py39 - Scalene is a high-performance, high-precision CPU, GPU, and memory profiler for Python with AI-powered optimization proposals - https://github.com/plasma-umass/scalene - https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.55.4_py39#py-scalene - devel, profiling - kilian@stanford.edu (Kilian Cavalotti) - Wed, 18 Sep 2024 15:56:16 -0700 - - - New version: system/py-nvidia-ml-py version 12.560.30_py312 - Python bindings to the NVIDIA Management Library. - https://pypi.org/project/nvidia-ml-py/ - https://www.sherlock.stanford.edu/docs/software/list/?add:v=12.560.30_py312#py-nvidia-ml-py - system, tools - kilian@stanford.edu (Kilian Cavalotti) - Wed, 18 Sep 2024 14:30:30 -0700 - - - New version: system/py-nvidia-ml-py version 12.560.30_py39 - Python bindings to the NVIDIA Management Library. - https://pypi.org/project/nvidia-ml-py/ - https://www.sherlock.stanford.edu/docs/software/list/?add:v=12.560.30_py39#py-nvidia-ml-py - system, tools - kilian@stanford.edu (Kilian Cavalotti) - Wed, 18 Sep 2024 14:30:30 -0700 - - - New version: devel/java version 21.0.4 - Java is a general-purpose computer programming language that is concurrent, class-based, object-oriented,[14] and specifically designed to have as few implementation dependencies as possible. - http://www.oracle.com/technetwork/java/index.html - https://www.sherlock.stanford.edu/docs/software/list/?add:v=21.0.4#java - devel, language - kilian@stanford.edu (Kilian Cavalotti) - Tue, 17 Sep 2024 11:24:55 -0700 - - - New version: devel/nccl version 2.23.4 - NCCL (pronounced 'Nickel') is a stand-alone library of standard collective communication routines, such as all-gather, reduce, broadcast, etc., that have been optimized to achieve high bandwidth over PCIe. - https://github.com/NVIDIA/nccl - https://www.sherlock.stanford.edu/docs/software/list/?add:v=2.23.4#nccl - devel, lib - kilian@stanford.edu (Kilian Cavalotti) - Mon, 16 Sep 2024 15:17:35 -0700 - - - New module: devel/nsight-systems version 2024.4 - NVIDIA Nsight™ Systems is a system-wide performance analysis tool designed to visualize an application’s algorithms, identify the largest opportunities to optimize, and tune to scale efficiently across any quantity or size of CPUs and GPUs, from large servers to our smallest systems-on-a-chip (SoCs). - https://developer.nvidia.com/nsight-systems - https://www.sherlock.stanford.edu/docs/software/list/?add:v=2024.4#nsight-systems - devel, profiling - kilian@stanford.edu (Kilian Cavalotti) - Mon, 16 Sep 2024 15:03:22 -0700 - - - New module: system/xcb-util-cursor version 0.1.5 - The XCB util modules provides a number of libraries which sit on top of libxcb, the core X protocol library, and some of the extension libraries. - https://xcb.freedesktop.org/ - https://www.sherlock.stanford.edu/docs/software/list/?add:v=0.1.5#xcb-util-cursor - system, tools - kilian@stanford.edu (Kilian Cavalotti) - Mon, 16 Sep 2024 15:03:06 -0700 - - - New module: system/xcb-proto version 1.17.0 - xcb-proto provides the XML-XCB protocol descriptions that libxcb uses to generate the majority of its code and API. - https://xcb.freedesktop.org/ - https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.17.0#xcb-proto - system, tools - kilian@stanford.edu (Kilian Cavalotti) - Mon, 16 Sep 2024 15:02:57 -0700 - - - New module: system/libxcb version 1.17.0 - The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. - https://xcb.freedesktop.org/ - https://www.sherlock.stanford.edu/docs/software/list/?add:v=1.17.0#libxcb - system, tools - kilian@stanford.edu (Kilian Cavalotti) - Mon, 16 Sep 2024 15:02:46 -0700 - - - New version: devel/cuda version 12.6.1 - CUDA is a parallel computing platform and application programming interface (API) model created by Nvidia. It allows software developers and software engineers to use a CUDA-enabled graphics processing unit (GPU) for general purpose processing. - https://developer.nvidia.com/cuda-toolkit - https://www.sherlock.stanford.edu/docs/software/list/?add:v=12.6.1#cuda - devel, language - kilian@stanford.edu (Kilian Cavalotti) - Mon, 16 Sep 2024 11:22:27 -0700 -