Applications

In alphabetical order By discipline By availability By license

Applications in alphabetical order

A

ABAQUS Dassault Systemes' SIMULIA academic research suite Puhti Computational Engineering Academic AMS Modelling suite providing engines like ADF, BAND, DFTB and MOPAC Puhti Mahti Chemistry Academic AMS-GUI AMS integrated GUI Puhti Mahti Chemistry Academic ANSYS ANSYS Academic engineering simulation software suite LUMI Puhti Mahti Computational Engineering Other Accelerated visualization A selection of GPU accelerated visualization applications LUMI LUMI Puhti Miscellaneous Free AlphaFold Protein 3D structure prediction Puhti Biosciences Free Amber Molecular dynamics suite LUMI Puhti Mahti Chemistry Academic ArcGIS General purpose GIS software family for viewing, editing and analysing geospatial data Geosciences Other

B

BLAST Sequence similarity search tool for nucleotides and proteins Puhti Biosciences Free BRAKER Automatic genome annotator for eucaryots Puhti Biosciences Free BWA Short read aligner Puhti Biosciences Free BamTools Tools for working with BAM formatted files Puhti Biosciences Free BayeScan Tool for identifying candidate loci under natural selection based on allele frequencies in populations Puhti Biosciences Free BioPerl Perl environment with bioperl extension Puhti Biosciences Free Bioconda Package manger for installing bioinformatics software Puhti Biosciences Free Biopython Python environment with biopython and other bioinformatics related Python libraries Puhti Biosciences Free Blender 3D modeling, visualization and rendering software LUMI Puhti LUMI Puhti Miscellaneous Free Bowtie2 Short read aligner Puhti Biosciences Free

C

CD-HIT Sequence clustering and redundancy removal tool Puhti Biosciences Free COMSOL Multiphysics General-purpose simulation software Puhti Puhti Computational Engineering Academic COSMO-RS Toolbox for predictive property calculation of liquids Puhti Chemistry Academic CP2K DFT, quantum chemistry, QM/MM, AIMD etc. in particular for periodic systems LUMI Puhti Mahti Chemistry Free CSD Cambridge Crystallographic Database - organic and metallo-organic crystal structures and tools Puhti Chemistry Academic Chipster_genomes Tool to download aligner indexes used by Chipster to Puhti Puhti Biosciences Free Cirq-on-iqm open-source cirq adapter for quantum computing LUMI Quantum Free CloudCompare for visualizing, editing and processing poing clouds Puhti Puhti Geosciences Free Cutadapt Trimming high-throughput sequencing reads Puhti Biosciences Free

D

DDT Parallel debugger Puhti Mahti Miscellaneous Free Desktop Remote desktop environment LUMI LUMI Puhti Mahti Miscellaneous Free Diamond Sequence similarity search tool for proteins and nucloeotides Puhti Biosciences Free Discovery Studio Protein modeling environment Biosciences Academic

E

EMBOSS Toolkit for classical sequence analysis Puhti Biosciences Free Elmer Open source multi-physics FEM package LUMI Puhti Mahti Computational Engineering Free Entrez Direct Entrez direct - command line tool to search and retrieve data from NCBI Puhti Biosciences Free Exonerate A generic tool for pairwise sequence comparison Puhti Biosciences Free

F

FORCE for mass-processing of medium-resolution satellite images Puhti Geosciences Free FastQC Quality control tool for high throughput sequence data Puhti Biosciences Free Freebayes Genetic variant detector Puhti Biosciences Free

G

GDAL for geospatial data formats LUMI Puhti Mahti Geosciences Free GOLD Protein Ligand Docking Software Puhti Chemistry Biosciences Academic GPAW Versatile DFT package Puhti Mahti Chemistry Free GRASS GIS General purpose GIS software family for viewing, editing and analysing geospatial data LUMI Puhti Puhti Geosciences Free GROMACS Fast and versatile classical molecular dynamics LUMI Puhti Mahti Chemistry Biosciences Free Gaussian Versatile computational chemistry package Puhti Mahti Chemistry Other Grace Plotting tool for xvg-files in particular Puhti Puhti Biosciences Free

H

HMMER Toolkit to create and use sequence profile hidden Markov models Puhti Biosciences Free HUMAnN Profiling microbial pathways with metagenomic data Puhti Biosciences Free HyperQueue Scheduler for sub-node tasks LUMI Puhti Mahti Miscellaneous Free

I

IDL Programming Language, Numeric Analysis, Manipulation and Visualization of Scientific Data Puhti Mahti Mathematics and Statistics Academic Illumina BaseSpace Command line client for retrieving data from the Illumina BaseSpace environment Puhti Biosciences Free Intel Trace Analyzer and Collector (ITAC) Puhti Free Intel VTune Profiler Puhti Free InterProScan Protein signature/motif search tool Puhti Biosciences Free iPyrad toolkit for population genetic and phylogenetic studies of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) Puhti Biosciences Free

J

JAX Autograd and XLA, brought together for high-performance machine learning LUMI Puhti Mahti Data Analytics and Machine Learning Free Julia Language High-level, high-performance dynamic programming language for numerical computing LUMI Puhti Mahti Mathematics and Statistics Free Julia-Jupyter Interactive computational environment for Julia LUMI LUMI Puhti Mahti Miscellaneous Free Jupyter Interactive computational environment for Python LUMI LUMI Puhti Mahti Miscellaneous Free Jupyter for courses A version of the Jupyter app for course environments Puhti Mahti Miscellaneous Free

K

Kraken Taxonomic sequence classification system Puhti Biosciences Free Krona visualization tool Visualization tool for taxonomic classification and other hierarchical data Puhti Biosciences Free

L

LAMMPS Fast molecular dynamics engine with large force field selection LUMI Puhti Mahti Chemistry Free LAStools for LiDAR datasets Puhti Geosciences Other Lazypipe A stand-alone pipeline for identifying viruses in host-associated or environmental samples Puhti Biosciences Free

M

MACS2/3 ChIP-Seq analysis tool Puhti Biosciences Free MATLAB High-level technical computing language LUMI Puhti LUMI Puhti Mathematics and Statistics Academic MIRA Whole genome shotgun and EST sequence Assembler Puhti Biosciences Free MOLPRO Package for accurate ab initio quantum chemistry calculations Puhti Chemistry Non-commercial Maestro Versatile drug discovery and materials modeling suite Puhti Mahti Puhti Mahti Chemistry Biosciences Academic Materials Studio Versatile materials modeling suite Chemistry Academic Megahit Metagenomics assembly Puhti Biosciences Free MetaPhlAn Profiling the composition of microbial communities with metagenomic data Puhti Biosciences Free Minimap2 Short read aligner Puhti Biosciences Free Molden Processing program for molecular and electronic structure calculations Puhti Mahti Chemistry Non-commercial Mothur Package for microbial community analysis of amplicon sequencing data Puhti Biosciences Free MrBayes Program for inferring phylogenies using Bayesian methods Puhti Biosciences Free

N

NAMD Highly scalable classical molecular dynamics LUMI Puhti Mahti Chemistry Non-commercial NASA Ames Stereo Pipeline (ASP) for processing stereo images Puhti Geosciences Free NWChem A computational chemistry software package designed to perform well on parallel HPC systems Puhti Mahti Chemistry Free Nextflow Nextflow is a scientific workflow management system for creating scalable, portable, and reproducible workflows LUMI Puhti Mahti Biosciences Free NoMachine LUMI Puhti Mahti

O

ORCA General purpose quantum chemistry package Puhti Mahti Chemistry Other Octave High-level interpreted language for numerical computations Puhti Mathematics and Statistics Free Open Babel Program to interconvert file formats currently used in molecular modeling Puhti Mahti Chemistry Free OpenDroneMap (ODM) for processing aerial drone imagery Puhti Geosciences Free OpenFOAM Open source C++ tool box for continuum mechanics problems LUMI Puhti Mahti Computational Engineering Free Orfeo ToolBox (Open Source processing of remote sensing images) for remote sensing applications Puhti Geosciences Free

P

PALM Meteorological model system for atmospheric and oceanic boundary-layer flows LUMI Puhti Mahti Computational Engineering Free PANNZER2/SANSPANZ Automatic protein annotation tool Puhti Biosciences Free PCL for 2D/3D image and point cloud processing Puhti Geosciences Free PDAL for point cloud translations and processing LUMI Puhti Mahti Geosciences Free PLUMED Library and tools for enhanced sampling methods Puhti Mahti Chemistry Free ParaView Free open-source visualization application LUMI Puhti Mahti LUMI Puhti Miscellaneous Free Pennylane Free open-source software framework for quantum machine learning and quantum computing LUMI Quantum Free Picard Tools Tools for working with SAM,BAM,CRAM and VCF files Puhti Biosciences Free Prokka Rapid prokaryotic genome annotation Puhti Biosciences Free PyTorch Machine learning framework for Python LUMI Puhti Mahti Data Analytics and Machine Learning Free Python The programming language and its modules at CSC Puhti Mahti Mathematics and Statistics Free Python Data Collection of Python libraries for data analytics and machine learning Puhti Data Analytics and Machine Learning Free

Q

QGIS General purpose GIS software family for viewing, editing and analysing geospatial data LUMI Puhti Puhti Geosciences Free QIIME Package for microbial community analysis of amplicon sequencing data Puhti Biosciences Free Qiskit open-source toolkit for useful quantum computing LUMI Puhti Mahti Quantum Free Qiskit-on-iqm open-source qiskit adapter for quantum computing LUMI Quantum Free

R

R for GIS R spataial analysis libraries Puhti Geosciences Free RAPIDS Suite of libraries for data analytics and machine learning on GPUs Puhti Mahti Data Analytics and Machine Learning Free RAxML Program for inferring phylogenies with likelihood Puhti Biosciences Free RStudio IDE Integrated development environment for R Puhti Puhti Mathematics and Statistics Other Roary Pan genome pipeline Puhti Biosciences Free r-env R, RStudio Server, SAGA and TensorFlow Puhti Mathematics and Statistics Other

S

SAGA GIS General purpose GIS software family for viewing, editing and analysing geospatial data LUMI Puhti Puhti Geosciences Free SALMON Program to produce transcript-level quantification estimates from RNA-seq data Puhti Biosciences Free SAMtools Utilities for managing SAM/BAM formatted alignment files Puhti Biosciences Free SNAP for remote sensing applications Puhti Puhti Geosciences Free SOFI3D for 3D finite-difference seismic wave simulation Puhti Geosciences Free SPAdes Genome assembly Puhti Biosciences Free STAR Short read aligner Puhti Biosciences Free SageMath Free open-source mathematics software system Puhti Mathematics and Statistics Free Scalasca Puhti Mahti Free Seismic Unix for processing of 2D seismic or GPR data sets. Puhti Geosciences Free Sen2Cor for atmospheric-, terrain and cirrus correction of the Sentinel-2 products Puhti Geosciences Free Sen2mosaic for download, preprocessing and mosaicing of Sentinel-2 products Puhti Geosciences Free Seqtk Tool for processing sequences in the FASTA or FASTQ format Puhti Biosciences Free Snakemake Snakemake is a scientific workflow management system for creating scalable, portable, and reproducible workflows Puhti Biosciences Free Spark High-performance distributed computing framework Data Analytics and Machine Learning Free Stacks Pipeline for building loci from short-read sequences (e.g. RAD-seq data) Puhti Biosciences Free Star-CCM+ Computational Fluid Dynamics software by Siemens Digital Industries Software LUMI Puhti Mahti Computational Engineering Other Structure Inference of population structure in genetics Puhti Biosciences Free

T

TURBOMOLE Efficient program package for electronic structure calculations Puhti Mahti Chemistry Academic TensorBoard The visualization toolkit for TensorFlow LUMI LUMI Puhti Mahti Miscellaneous Free TensorFlow Deep learning library for Python LUMI Puhti Mahti Data Analytics and Machine Learning Free TmoleX GUI for setting up and analyzing TURBOMOLE jobs Puhti Chemistry Academic TopHat Splice junction mapper for RNA-Seq reads Puhti Biosciences Free Trinity Traskriptome assembly tool Puhti Biosciences Free

V

VASP Ab initio DFT electronic structures Puhti Mahti Physics Chemistry Other VMD Molecular visualization program Puhti Mahti Puhti Mahti Chemistry Biosciences Non-commercial Velvet Genome assembler Puhti Biosciences Free VirusDetect Virus identification with sRNA data Puhti Biosciences Free VisIt Free open-source visualization application LUMI Puhti Mahti LUMI Puhti Miscellaneous Free Visual Studio Code Source code editor LUMI LUMI Puhti Mahti Miscellaneous Free

W

WhiteboxTools an advanced geospatial data analysis platform Puhti Geosciences Free wtdbg2 Fast assembler for long-read data Puhti Biosciences Free

X

XHMM (eXome-Hidden Markov Model) Copy number variation calling from targeted sequencing data Puhti Biosciences Free

Z

Zonation Spatial conservation prioritization framework Puhti Puhti Geosciences Free

Applications by discipline

Biosciences

AlphaFold Protein 3D structure prediction Puhti Free BLAST Sequence similarity search tool for nucleotides and proteins Puhti Free BRAKER Automatic genome annotator for eucaryots Puhti Free BWA Short read aligner Puhti Free BamTools Tools for working with BAM formatted files Puhti Free BayeScan Tool for identifying candidate loci under natural selection based on allele frequencies in populations Puhti Free BioPerl Perl environment with bioperl extension Puhti Free Bioconda Package manger for installing bioinformatics software Puhti Free Biopython Python environment with biopython and other bioinformatics related Python libraries Puhti Free Bowtie2 Short read aligner Puhti Free CD-HIT Sequence clustering and redundancy removal tool Puhti Free Chipster_genomes Tool to download aligner indexes used by Chipster to Puhti Puhti Free Cutadapt Trimming high-throughput sequencing reads Puhti Free Diamond Sequence similarity search tool for proteins and nucloeotides Puhti Free Discovery Studio Protein modeling environment Academic EMBOSS Toolkit for classical sequence analysis Puhti Free Entrez Direct Entrez direct - command line tool to search and retrieve data from NCBI Puhti Free Exonerate A generic tool for pairwise sequence comparison Puhti Free FastQC Quality control tool for high throughput sequence data Puhti Free Freebayes Genetic variant detector Puhti Free GOLD Protein Ligand Docking Software Puhti Academic GROMACS Fast and versatile classical molecular dynamics LUMI Puhti Mahti Free Grace Plotting tool for xvg-files in particular Puhti Puhti Free HMMER Toolkit to create and use sequence profile hidden Markov models Puhti Free HUMAnN Profiling microbial pathways with metagenomic data Puhti Free Illumina BaseSpace Command line client for retrieving data from the Illumina BaseSpace environment Puhti Free InterProScan Protein signature/motif search tool Puhti Free Kraken Taxonomic sequence classification system Puhti Free Krona visualization tool Visualization tool for taxonomic classification and other hierarchical data Puhti Free Lazypipe A stand-alone pipeline for identifying viruses in host-associated or environmental samples Puhti Free MACS2/3 ChIP-Seq analysis tool Puhti Free MIRA Whole genome shotgun and EST sequence Assembler Puhti Free Maestro Versatile drug discovery and materials modeling suite Puhti Mahti Puhti Mahti Academic Megahit Metagenomics assembly Puhti Free MetaPhlAn Profiling the composition of microbial communities with metagenomic data Puhti Free Minimap2 Short read aligner Puhti Free Mothur Package for microbial community analysis of amplicon sequencing data Puhti Free MrBayes Program for inferring phylogenies using Bayesian methods Puhti Free Nextflow Nextflow is a scientific workflow management system for creating scalable, portable, and reproducible workflows LUMI Puhti Mahti Free PANNZER2/SANSPANZ Automatic protein annotation tool Puhti Free Picard Tools Tools for working with SAM,BAM,CRAM and VCF files Puhti Free Prokka Rapid prokaryotic genome annotation Puhti Free QIIME Package for microbial community analysis of amplicon sequencing data Puhti Free RAxML Program for inferring phylogenies with likelihood Puhti Free Roary Pan genome pipeline Puhti Free SALMON Program to produce transcript-level quantification estimates from RNA-seq data Puhti Free SAMtools Utilities for managing SAM/BAM formatted alignment files Puhti Free SPAdes Genome assembly Puhti Free STAR Short read aligner Puhti Free Seqtk Tool for processing sequences in the FASTA or FASTQ format Puhti Free Snakemake Snakemake is a scientific workflow management system for creating scalable, portable, and reproducible workflows Puhti Free Stacks Pipeline for building loci from short-read sequences (e.g. RAD-seq data) Puhti Free Structure Inference of population structure in genetics Puhti Free TopHat Splice junction mapper for RNA-Seq reads Puhti Free Trinity Traskriptome assembly tool Puhti Free VMD Molecular visualization program Puhti Mahti Puhti Mahti Non-commercial Velvet Genome assembler Puhti Free VirusDetect Virus identification with sRNA data Puhti Free XHMM (eXome-Hidden Markov Model) Copy number variation calling from targeted sequencing data Puhti Free iPyrad toolkit for population genetic and phylogenetic studies of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) Puhti Free wtdbg2 Fast assembler for long-read data Puhti Free

Chemistry

AMS Modelling suite providing engines like ADF, BAND, DFTB and MOPAC Puhti Mahti Academic AMS-GUI AMS integrated GUI Puhti Mahti Academic Amber Molecular dynamics suite LUMI Puhti Mahti Academic COSMO-RS Toolbox for predictive property calculation of liquids Puhti Academic CP2K DFT, quantum chemistry, QM/MM, AIMD etc. in particular for periodic systems LUMI Puhti Mahti Free CSD Cambridge Crystallographic Database - organic and metallo-organic crystal structures and tools Puhti Academic GOLD Protein Ligand Docking Software Puhti Academic GPAW Versatile DFT package Puhti Mahti Free GROMACS Fast and versatile classical molecular dynamics LUMI Puhti Mahti Free Gaussian Versatile computational chemistry package Puhti Mahti Other LAMMPS Fast molecular dynamics engine with large force field selection LUMI Puhti Mahti Free MOLPRO Package for accurate ab initio quantum chemistry calculations Puhti Non-commercial Maestro Versatile drug discovery and materials modeling suite Puhti Mahti Puhti Mahti Academic Materials Studio Versatile materials modeling suite Academic Molden Processing program for molecular and electronic structure calculations Puhti Mahti Non-commercial NAMD Highly scalable classical molecular dynamics LUMI Puhti Mahti Non-commercial NWChem A computational chemistry software package designed to perform well on parallel HPC systems Puhti Mahti Free ORCA General purpose quantum chemistry package Puhti Mahti Other Open Babel Program to interconvert file formats currently used in molecular modeling Puhti Mahti Free PLUMED Library and tools for enhanced sampling methods Puhti Mahti Free TURBOMOLE Efficient program package for electronic structure calculations Puhti Mahti Academic TmoleX GUI for setting up and analyzing TURBOMOLE jobs Puhti Academic VASP Ab initio DFT electronic structures Puhti Mahti Other VMD Molecular visualization program Puhti Mahti Puhti Mahti Non-commercial

Computational Engineering

ABAQUS Dassault Systemes' SIMULIA academic research suite Puhti Academic ANSYS ANSYS Academic engineering simulation software suite LUMI Puhti Mahti Other COMSOL Multiphysics General-purpose simulation software Puhti Puhti Academic Elmer Open source multi-physics FEM package LUMI Puhti Mahti Free OpenFOAM Open source C++ tool box for continuum mechanics problems LUMI Puhti Mahti Free PALM Meteorological model system for atmospheric and oceanic boundary-layer flows LUMI Puhti Mahti Free Star-CCM+ Computational Fluid Dynamics software by Siemens Digital Industries Software LUMI Puhti Mahti Other

Data Analytics and Machine Learning

JAX Autograd and XLA, brought together for high-performance machine learning LUMI Puhti Mahti Free PyTorch Machine learning framework for Python LUMI Puhti Mahti Free Python Data Collection of Python libraries for data analytics and machine learning Puhti Free RAPIDS Suite of libraries for data analytics and machine learning on GPUs Puhti Mahti Free Spark High-performance distributed computing framework Free TensorFlow Deep learning library for Python LUMI Puhti Mahti Free

Geosciences

ArcGIS General purpose GIS software family for viewing, editing and analysing geospatial data Other CloudCompare for visualizing, editing and processing poing clouds Puhti Puhti Free FORCE for mass-processing of medium-resolution satellite images Puhti Free GDAL for geospatial data formats LUMI Puhti Mahti Free GRASS GIS General purpose GIS software family for viewing, editing and analysing geospatial data LUMI Puhti Puhti Free LAStools for LiDAR datasets Puhti Other NASA Ames Stereo Pipeline (ASP) for processing stereo images Puhti Free OpenDroneMap (ODM) for processing aerial drone imagery Puhti Free Orfeo ToolBox (Open Source processing of remote sensing images) for remote sensing applications Puhti Free PCL for 2D/3D image and point cloud processing Puhti Free PDAL for point cloud translations and processing LUMI Puhti Mahti Free QGIS General purpose GIS software family for viewing, editing and analysing geospatial data LUMI Puhti Puhti Free R for GIS R spataial analysis libraries Puhti Free SAGA GIS General purpose GIS software family for viewing, editing and analysing geospatial data LUMI Puhti Puhti Free SNAP for remote sensing applications Puhti Puhti Free SOFI3D for 3D finite-difference seismic wave simulation Puhti Free Seismic Unix for processing of 2D seismic or GPR data sets. Puhti Free Sen2Cor for atmospheric-, terrain and cirrus correction of the Sentinel-2 products Puhti Free Sen2mosaic for download, preprocessing and mosaicing of Sentinel-2 products Puhti Free WhiteboxTools an advanced geospatial data analysis platform Puhti Free Zonation Spatial conservation prioritization framework Puhti Puhti Free

Mathematics and Statistics

IDL Programming Language, Numeric Analysis, Manipulation and Visualization of Scientific Data Puhti Mahti Academic Julia Language High-level, high-performance dynamic programming language for numerical computing LUMI Puhti Mahti Free MATLAB High-level technical computing language LUMI Puhti LUMI Puhti Academic Octave High-level interpreted language for numerical computations Puhti Free Python The programming language and its modules at CSC Puhti Mahti Free RStudio IDE Integrated development environment for R Puhti Puhti Other SageMath Free open-source mathematics software system Puhti Free r-env R, RStudio Server, SAGA and TensorFlow Puhti Other

Physics

VASP Ab initio DFT electronic structures Puhti Mahti Other

Quantum

Cirq-on-iqm open-source cirq adapter for quantum computing LUMI Free Pennylane Free open-source software framework for quantum machine learning and quantum computing LUMI Free Qiskit open-source toolkit for useful quantum computing LUMI Puhti Mahti Free Qiskit-on-iqm open-source qiskit adapter for quantum computing LUMI Free

Miscellaneous

Accelerated visualization A selection of GPU accelerated visualization applications LUMI LUMI Puhti Free Blender 3D modeling, visualization and rendering software LUMI Puhti LUMI Puhti Free DDT Parallel debugger Puhti Mahti Free Desktop Remote desktop environment LUMI LUMI Puhti Mahti Free HyperQueue Scheduler for sub-node tasks LUMI Puhti Mahti Free Julia-Jupyter Interactive computational environment for Julia LUMI LUMI Puhti Mahti Free Jupyter Interactive computational environment for Python LUMI LUMI Puhti Mahti Free Jupyter for courses A version of the Jupyter app for course environments Puhti Mahti Free ParaView Free open-source visualization application LUMI Puhti Mahti LUMI Puhti Free TensorBoard The visualization toolkit for TensorFlow LUMI LUMI Puhti Mahti Free VisIt Free open-source visualization application LUMI Puhti Mahti LUMI Puhti Free Visual Studio Code Source code editor LUMI LUMI Puhti Mahti Free

Applications by availability

Puhti

ABAQUS Dassault Systemes' SIMULIA academic research suite Computational Engineering Academic AMS Modelling suite providing engines like ADF, BAND, DFTB and MOPAC Chemistry Academic AMS-GUI AMS integrated GUI Chemistry Academic ANSYS ANSYS Academic engineering simulation software suite Computational Engineering Other AlphaFold Protein 3D structure prediction Biosciences Free Amber Molecular dynamics suite Chemistry Academic BLAST Sequence similarity search tool for nucleotides and proteins Biosciences Free BRAKER Automatic genome annotator for eucaryots Biosciences Free BWA Short read aligner Biosciences Free BamTools Tools for working with BAM formatted files Biosciences Free BayeScan Tool for identifying candidate loci under natural selection based on allele frequencies in populations Biosciences Free BioPerl Perl environment with bioperl extension Biosciences Free Bioconda Package manger for installing bioinformatics software Biosciences Free Biopython Python environment with biopython and other bioinformatics related Python libraries Biosciences Free Blender 3D modeling, visualization and rendering software Miscellaneous Free Bowtie2 Short read aligner Biosciences Free CD-HIT Sequence clustering and redundancy removal tool Biosciences Free COMSOL Multiphysics General-purpose simulation software Computational Engineering Academic COSMO-RS Toolbox for predictive property calculation of liquids Chemistry Academic CP2K DFT, quantum chemistry, QM/MM, AIMD etc. in particular for periodic systems Chemistry Free CSD Cambridge Crystallographic Database - organic and metallo-organic crystal structures and tools Chemistry Academic Chipster_genomes Tool to download aligner indexes used by Chipster to Puhti Biosciences Free CloudCompare for visualizing, editing and processing poing clouds Geosciences Free Cutadapt Trimming high-throughput sequencing reads Biosciences Free DDT Parallel debugger Miscellaneous Free Diamond Sequence similarity search tool for proteins and nucloeotides Biosciences Free EMBOSS Toolkit for classical sequence analysis Biosciences Free Elmer Open source multi-physics FEM package Computational Engineering Free Entrez Direct Entrez direct - command line tool to search and retrieve data from NCBI Biosciences Free Exonerate A generic tool for pairwise sequence comparison Biosciences Free FORCE for mass-processing of medium-resolution satellite images Geosciences Free FastQC Quality control tool for high throughput sequence data Biosciences Free Freebayes Genetic variant detector Biosciences Free GDAL for geospatial data formats Geosciences Free GOLD Protein Ligand Docking Software Chemistry Biosciences Academic GPAW Versatile DFT package Chemistry Free GRASS GIS General purpose GIS software family for viewing, editing and analysing geospatial data Geosciences Free GROMACS Fast and versatile classical molecular dynamics Chemistry Biosciences Free Gaussian Versatile computational chemistry package Chemistry Other Grace Plotting tool for xvg-files in particular Biosciences Free HMMER Toolkit to create and use sequence profile hidden Markov models Biosciences Free HUMAnN Profiling microbial pathways with metagenomic data Biosciences Free HyperQueue Scheduler for sub-node tasks Miscellaneous Free IDL Programming Language, Numeric Analysis, Manipulation and Visualization of Scientific Data Mathematics and Statistics Academic Illumina BaseSpace Command line client for retrieving data from the Illumina BaseSpace environment Biosciences Free Intel Trace Analyzer and Collector (ITAC) Free Intel VTune Profiler Free InterProScan Protein signature/motif search tool Biosciences Free JAX Autograd and XLA, brought together for high-performance machine learning Data Analytics and Machine Learning Free Julia Language High-level, high-performance dynamic programming language for numerical computing Mathematics and Statistics Free Kraken Taxonomic sequence classification system Biosciences Free Krona visualization tool Visualization tool for taxonomic classification and other hierarchical data Biosciences Free LAMMPS Fast molecular dynamics engine with large force field selection Chemistry Free LAStools for LiDAR datasets Geosciences Other Lazypipe A stand-alone pipeline for identifying viruses in host-associated or environmental samples Biosciences Free MACS2/3 ChIP-Seq analysis tool Biosciences Free MATLAB High-level technical computing language Mathematics and Statistics Academic MIRA Whole genome shotgun and EST sequence Assembler Biosciences Free MOLPRO Package for accurate ab initio quantum chemistry calculations Chemistry Non-commercial Maestro Versatile drug discovery and materials modeling suite Chemistry Biosciences Academic Megahit Metagenomics assembly Biosciences Free MetaPhlAn Profiling the composition of microbial communities with metagenomic data Biosciences Free Minimap2 Short read aligner Biosciences Free Molden Processing program for molecular and electronic structure calculations Chemistry Non-commercial Mothur Package for microbial community analysis of amplicon sequencing data Biosciences Free MrBayes Program for inferring phylogenies using Bayesian methods Biosciences Free NAMD Highly scalable classical molecular dynamics Chemistry Non-commercial NASA Ames Stereo Pipeline (ASP) for processing stereo images Geosciences Free NWChem A computational chemistry software package designed to perform well on parallel HPC systems Chemistry Free Nextflow Nextflow is a scientific workflow management system for creating scalable, portable, and reproducible workflows Biosciences Free NoMachine ORCA General purpose quantum chemistry package Chemistry Other Octave High-level interpreted language for numerical computations Mathematics and Statistics Free Open Babel Program to interconvert file formats currently used in molecular modeling Chemistry Free OpenDroneMap (ODM) for processing aerial drone imagery Geosciences Free OpenFOAM Open source C++ tool box for continuum mechanics problems Computational Engineering Free Orfeo ToolBox (Open Source processing of remote sensing images) for remote sensing applications Geosciences Free PALM Meteorological model system for atmospheric and oceanic boundary-layer flows Computational Engineering Free PANNZER2/SANSPANZ Automatic protein annotation tool Biosciences Free PCL for 2D/3D image and point cloud processing Geosciences Free PDAL for point cloud translations and processing Geosciences Free PLUMED Library and tools for enhanced sampling methods Chemistry Free ParaView Free open-source visualization application Miscellaneous Free Picard Tools Tools for working with SAM,BAM,CRAM and VCF files Biosciences Free Prokka Rapid prokaryotic genome annotation Biosciences Free PyTorch Machine learning framework for Python Data Analytics and Machine Learning Free Python The programming language and its modules at CSC Mathematics and Statistics Free Python Data Collection of Python libraries for data analytics and machine learning Data Analytics and Machine Learning Free QGIS General purpose GIS software family for viewing, editing and analysing geospatial data Geosciences Free QIIME Package for microbial community analysis of amplicon sequencing data Biosciences Free Qiskit open-source toolkit for useful quantum computing Quantum Free R for GIS R spataial analysis libraries Geosciences Free RAPIDS Suite of libraries for data analytics and machine learning on GPUs Data Analytics and Machine Learning Free RAxML Program for inferring phylogenies with likelihood Biosciences Free RStudio IDE Integrated development environment for R Mathematics and Statistics Other Roary Pan genome pipeline Biosciences Free SAGA GIS General purpose GIS software family for viewing, editing and analysing geospatial data Geosciences Free SALMON Program to produce transcript-level quantification estimates from RNA-seq data Biosciences Free SAMtools Utilities for managing SAM/BAM formatted alignment files Biosciences Free SNAP for remote sensing applications Geosciences Free SOFI3D for 3D finite-difference seismic wave simulation Geosciences Free SPAdes Genome assembly Biosciences Free STAR Short read aligner Biosciences Free SageMath Free open-source mathematics software system Mathematics and Statistics Free Scalasca Free Seismic Unix for processing of 2D seismic or GPR data sets. Geosciences Free Sen2Cor for atmospheric-, terrain and cirrus correction of the Sentinel-2 products Geosciences Free Sen2mosaic for download, preprocessing and mosaicing of Sentinel-2 products Geosciences Free Seqtk Tool for processing sequences in the FASTA or FASTQ format Biosciences Free Snakemake Snakemake is a scientific workflow management system for creating scalable, portable, and reproducible workflows Biosciences Free Stacks Pipeline for building loci from short-read sequences (e.g. RAD-seq data) Biosciences Free Star-CCM+ Computational Fluid Dynamics software by Siemens Digital Industries Software Computational Engineering Other Structure Inference of population structure in genetics Biosciences Free TURBOMOLE Efficient program package for electronic structure calculations Chemistry Academic TensorFlow Deep learning library for Python Data Analytics and Machine Learning Free TmoleX GUI for setting up and analyzing TURBOMOLE jobs Chemistry Academic TopHat Splice junction mapper for RNA-Seq reads Biosciences Free Trinity Traskriptome assembly tool Biosciences Free VASP Ab initio DFT electronic structures Physics Chemistry Other VMD Molecular visualization program Chemistry Biosciences Non-commercial Velvet Genome assembler Biosciences Free VirusDetect Virus identification with sRNA data Biosciences Free VisIt Free open-source visualization application Miscellaneous Free WhiteboxTools an advanced geospatial data analysis platform Geosciences Free XHMM (eXome-Hidden Markov Model) Copy number variation calling from targeted sequencing data Biosciences Free Zonation Spatial conservation prioritization framework Geosciences Free iPyrad toolkit for population genetic and phylogenetic studies of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) Biosciences Free r-env R, RStudio Server, SAGA and TensorFlow Mathematics and Statistics Other wtdbg2 Fast assembler for long-read data Biosciences Free

Mahti

AMS Modelling suite providing engines like ADF, BAND, DFTB and MOPAC Chemistry Academic AMS-GUI AMS integrated GUI Chemistry Academic ANSYS ANSYS Academic engineering simulation software suite Computational Engineering Other Amber Molecular dynamics suite Chemistry Academic CP2K DFT, quantum chemistry, QM/MM, AIMD etc. in particular for periodic systems Chemistry Free DDT Parallel debugger Miscellaneous Free Elmer Open source multi-physics FEM package Computational Engineering Free GDAL for geospatial data formats Geosciences Free GPAW Versatile DFT package Chemistry Free GROMACS Fast and versatile classical molecular dynamics Chemistry Biosciences Free Gaussian Versatile computational chemistry package Chemistry Other HyperQueue Scheduler for sub-node tasks Miscellaneous Free IDL Programming Language, Numeric Analysis, Manipulation and Visualization of Scientific Data Mathematics and Statistics Academic JAX Autograd and XLA, brought together for high-performance machine learning Data Analytics and Machine Learning Free Julia Language High-level, high-performance dynamic programming language for numerical computing Mathematics and Statistics Free LAMMPS Fast molecular dynamics engine with large force field selection Chemistry Free Maestro Versatile drug discovery and materials modeling suite Chemistry Biosciences Academic Molden Processing program for molecular and electronic structure calculations Chemistry Non-commercial NAMD Highly scalable classical molecular dynamics Chemistry Non-commercial NWChem A computational chemistry software package designed to perform well on parallel HPC systems Chemistry Free Nextflow Nextflow is a scientific workflow management system for creating scalable, portable, and reproducible workflows Biosciences Free NoMachine ORCA General purpose quantum chemistry package Chemistry Other Open Babel Program to interconvert file formats currently used in molecular modeling Chemistry Free OpenFOAM Open source C++ tool box for continuum mechanics problems Computational Engineering Free PALM Meteorological model system for atmospheric and oceanic boundary-layer flows Computational Engineering Free PDAL for point cloud translations and processing Geosciences Free PLUMED Library and tools for enhanced sampling methods Chemistry Free ParaView Free open-source visualization application Miscellaneous Free PyTorch Machine learning framework for Python Data Analytics and Machine Learning Free Python The programming language and its modules at CSC Mathematics and Statistics Free Qiskit open-source toolkit for useful quantum computing Quantum Free RAPIDS Suite of libraries for data analytics and machine learning on GPUs Data Analytics and Machine Learning Free Scalasca Free Star-CCM+ Computational Fluid Dynamics software by Siemens Digital Industries Software Computational Engineering Other TURBOMOLE Efficient program package for electronic structure calculations Chemistry Academic TensorFlow Deep learning library for Python Data Analytics and Machine Learning Free VASP Ab initio DFT electronic structures Physics Chemistry Other VMD Molecular visualization program Chemistry Biosciences Non-commercial VisIt Free open-source visualization application Miscellaneous Free

LUMI

ANSYS ANSYS Academic engineering simulation software suite Computational Engineering Other Accelerated visualization A selection of GPU accelerated visualization applications Miscellaneous Free Amber Molecular dynamics suite Chemistry Academic Blender 3D modeling, visualization and rendering software Miscellaneous Free CP2K DFT, quantum chemistry, QM/MM, AIMD etc. in particular for periodic systems Chemistry Free Cirq-on-iqm open-source cirq adapter for quantum computing Quantum Free Desktop Remote desktop environment Miscellaneous Free Elmer Open source multi-physics FEM package Computational Engineering Free GDAL for geospatial data formats Geosciences Free GRASS GIS General purpose GIS software family for viewing, editing and analysing geospatial data Geosciences Free GROMACS Fast and versatile classical molecular dynamics Chemistry Biosciences Free HyperQueue Scheduler for sub-node tasks Miscellaneous Free JAX Autograd and XLA, brought together for high-performance machine learning Data Analytics and Machine Learning Free Julia Language High-level, high-performance dynamic programming language for numerical computing Mathematics and Statistics Free Julia-Jupyter Interactive computational environment for Julia Miscellaneous Free Jupyter Interactive computational environment for Python Miscellaneous Free LAMMPS Fast molecular dynamics engine with large force field selection Chemistry Free MATLAB High-level technical computing language Mathematics and Statistics Academic NAMD Highly scalable classical molecular dynamics Chemistry Non-commercial Nextflow Nextflow is a scientific workflow management system for creating scalable, portable, and reproducible workflows Biosciences Free NoMachine OpenFOAM Open source C++ tool box for continuum mechanics problems Computational Engineering Free PALM Meteorological model system for atmospheric and oceanic boundary-layer flows Computational Engineering Free PDAL for point cloud translations and processing Geosciences Free ParaView Free open-source visualization application Miscellaneous Free Pennylane Free open-source software framework for quantum machine learning and quantum computing Quantum Free PyTorch Machine learning framework for Python Data Analytics and Machine Learning Free QGIS General purpose GIS software family for viewing, editing and analysing geospatial data Geosciences Free Qiskit open-source toolkit for useful quantum computing Quantum Free Qiskit-on-iqm open-source qiskit adapter for quantum computing Quantum Free SAGA GIS General purpose GIS software family for viewing, editing and analysing geospatial data Geosciences Free Star-CCM+ Computational Fluid Dynamics software by Siemens Digital Industries Software Computational Engineering Other TensorBoard The visualization toolkit for TensorFlow Miscellaneous Free TensorFlow Deep learning library for Python Data Analytics and Machine Learning Free VisIt Free open-source visualization application Miscellaneous Free Visual Studio Code Source code editor Miscellaneous Free

Applications by license

Free

Accelerated visualization A selection of GPU accelerated visualization applications LUMI LUMI Puhti Miscellaneous AlphaFold Protein 3D structure prediction Puhti Biosciences BLAST Sequence similarity search tool for nucleotides and proteins Puhti Biosciences BRAKER Automatic genome annotator for eucaryots Puhti Biosciences BWA Short read aligner Puhti Biosciences BamTools Tools for working with BAM formatted files Puhti Biosciences BayeScan Tool for identifying candidate loci under natural selection based on allele frequencies in populations Puhti Biosciences BioPerl Perl environment with bioperl extension Puhti Biosciences Bioconda Package manger for installing bioinformatics software Puhti Biosciences Biopython Python environment with biopython and other bioinformatics related Python libraries Puhti Biosciences Blender 3D modeling, visualization and rendering software LUMI Puhti LUMI Puhti Miscellaneous Bowtie2 Short read aligner Puhti Biosciences CD-HIT Sequence clustering and redundancy removal tool Puhti Biosciences CP2K DFT, quantum chemistry, QM/MM, AIMD etc. in particular for periodic systems LUMI Puhti Mahti Chemistry Chipster_genomes Tool to download aligner indexes used by Chipster to Puhti Puhti Biosciences Cirq-on-iqm open-source cirq adapter for quantum computing LUMI Quantum CloudCompare for visualizing, editing and processing poing clouds Puhti Puhti Geosciences Cutadapt Trimming high-throughput sequencing reads Puhti Biosciences DDT Parallel debugger Puhti Mahti Miscellaneous Desktop Remote desktop environment LUMI LUMI Puhti Mahti Miscellaneous Diamond Sequence similarity search tool for proteins and nucloeotides Puhti Biosciences EMBOSS Toolkit for classical sequence analysis Puhti Biosciences Elmer Open source multi-physics FEM package LUMI Puhti Mahti Computational Engineering Entrez Direct Entrez direct - command line tool to search and retrieve data from NCBI Puhti Biosciences Exonerate A generic tool for pairwise sequence comparison Puhti Biosciences FORCE for mass-processing of medium-resolution satellite images Puhti Geosciences FastQC Quality control tool for high throughput sequence data Puhti Biosciences Freebayes Genetic variant detector Puhti Biosciences GDAL for geospatial data formats LUMI Puhti Mahti Geosciences GPAW Versatile DFT package Puhti Mahti Chemistry GRASS GIS General purpose GIS software family for viewing, editing and analysing geospatial data LUMI Puhti Puhti Geosciences GROMACS Fast and versatile classical molecular dynamics LUMI Puhti Mahti Chemistry Biosciences Grace Plotting tool for xvg-files in particular Puhti Puhti Biosciences HMMER Toolkit to create and use sequence profile hidden Markov models Puhti Biosciences HUMAnN Profiling microbial pathways with metagenomic data Puhti Biosciences HyperQueue Scheduler for sub-node tasks LUMI Puhti Mahti Miscellaneous Illumina BaseSpace Command line client for retrieving data from the Illumina BaseSpace environment Puhti Biosciences Intel Trace Analyzer and Collector (ITAC) Puhti Intel VTune Profiler Puhti InterProScan Protein signature/motif search tool Puhti Biosciences JAX Autograd and XLA, brought together for high-performance machine learning LUMI Puhti Mahti Data Analytics and Machine Learning Julia Language High-level, high-performance dynamic programming language for numerical computing LUMI Puhti Mahti Mathematics and Statistics Julia-Jupyter Interactive computational environment for Julia LUMI LUMI Puhti Mahti Miscellaneous Jupyter Interactive computational environment for Python LUMI LUMI Puhti Mahti Miscellaneous Jupyter for courses A version of the Jupyter app for course environments Puhti Mahti Miscellaneous Kraken Taxonomic sequence classification system Puhti Biosciences Krona visualization tool Visualization tool for taxonomic classification and other hierarchical data Puhti Biosciences LAMMPS Fast molecular dynamics engine with large force field selection LUMI Puhti Mahti Chemistry Lazypipe A stand-alone pipeline for identifying viruses in host-associated or environmental samples Puhti Biosciences MACS2/3 ChIP-Seq analysis tool Puhti Biosciences MIRA Whole genome shotgun and EST sequence Assembler Puhti Biosciences Megahit Metagenomics assembly Puhti Biosciences MetaPhlAn Profiling the composition of microbial communities with metagenomic data Puhti Biosciences Minimap2 Short read aligner Puhti Biosciences Mothur Package for microbial community analysis of amplicon sequencing data Puhti Biosciences MrBayes Program for inferring phylogenies using Bayesian methods Puhti Biosciences NASA Ames Stereo Pipeline (ASP) for processing stereo images Puhti Geosciences NWChem A computational chemistry software package designed to perform well on parallel HPC systems Puhti Mahti Chemistry Nextflow Nextflow is a scientific workflow management system for creating scalable, portable, and reproducible workflows LUMI Puhti Mahti Biosciences Octave High-level interpreted language for numerical computations Puhti Mathematics and Statistics Open Babel Program to interconvert file formats currently used in molecular modeling Puhti Mahti Chemistry OpenDroneMap (ODM) for processing aerial drone imagery Puhti Geosciences OpenFOAM Open source C++ tool box for continuum mechanics problems LUMI Puhti Mahti Computational Engineering Orfeo ToolBox (Open Source processing of remote sensing images) for remote sensing applications Puhti Geosciences PALM Meteorological model system for atmospheric and oceanic boundary-layer flows LUMI Puhti Mahti Computational Engineering PANNZER2/SANSPANZ Automatic protein annotation tool Puhti Biosciences PCL for 2D/3D image and point cloud processing Puhti Geosciences PDAL for point cloud translations and processing LUMI Puhti Mahti Geosciences PLUMED Library and tools for enhanced sampling methods Puhti Mahti Chemistry ParaView Free open-source visualization application LUMI Puhti Mahti LUMI Puhti Miscellaneous Pennylane Free open-source software framework for quantum machine learning and quantum computing LUMI Quantum Picard Tools Tools for working with SAM,BAM,CRAM and VCF files Puhti Biosciences Prokka Rapid prokaryotic genome annotation Puhti Biosciences PyTorch Machine learning framework for Python LUMI Puhti Mahti Data Analytics and Machine Learning Python The programming language and its modules at CSC Puhti Mahti Mathematics and Statistics Python Data Collection of Python libraries for data analytics and machine learning Puhti Data Analytics and Machine Learning QGIS General purpose GIS software family for viewing, editing and analysing geospatial data LUMI Puhti Puhti Geosciences QIIME Package for microbial community analysis of amplicon sequencing data Puhti Biosciences Qiskit open-source toolkit for useful quantum computing LUMI Puhti Mahti Quantum Qiskit-on-iqm open-source qiskit adapter for quantum computing LUMI Quantum R for GIS R spataial analysis libraries Puhti Geosciences RAPIDS Suite of libraries for data analytics and machine learning on GPUs Puhti Mahti Data Analytics and Machine Learning RAxML Program for inferring phylogenies with likelihood Puhti Biosciences Roary Pan genome pipeline Puhti Biosciences SAGA GIS General purpose GIS software family for viewing, editing and analysing geospatial data LUMI Puhti Puhti Geosciences SALMON Program to produce transcript-level quantification estimates from RNA-seq data Puhti Biosciences SAMtools Utilities for managing SAM/BAM formatted alignment files Puhti Biosciences SNAP for remote sensing applications Puhti Puhti Geosciences SOFI3D for 3D finite-difference seismic wave simulation Puhti Geosciences SPAdes Genome assembly Puhti Biosciences STAR Short read aligner Puhti Biosciences SageMath Free open-source mathematics software system Puhti Mathematics and Statistics Scalasca Puhti Mahti Seismic Unix for processing of 2D seismic or GPR data sets. Puhti Geosciences Sen2Cor for atmospheric-, terrain and cirrus correction of the Sentinel-2 products Puhti Geosciences Sen2mosaic for download, preprocessing and mosaicing of Sentinel-2 products Puhti Geosciences Seqtk Tool for processing sequences in the FASTA or FASTQ format Puhti Biosciences Snakemake Snakemake is a scientific workflow management system for creating scalable, portable, and reproducible workflows Puhti Biosciences Spark High-performance distributed computing framework Data Analytics and Machine Learning Stacks Pipeline for building loci from short-read sequences (e.g. RAD-seq data) Puhti Biosciences Structure Inference of population structure in genetics Puhti Biosciences TensorBoard The visualization toolkit for TensorFlow LUMI LUMI Puhti Mahti Miscellaneous TensorFlow Deep learning library for Python LUMI Puhti Mahti Data Analytics and Machine Learning TopHat Splice junction mapper for RNA-Seq reads Puhti Biosciences Trinity Traskriptome assembly tool Puhti Biosciences Velvet Genome assembler Puhti Biosciences VirusDetect Virus identification with sRNA data Puhti Biosciences VisIt Free open-source visualization application LUMI Puhti Mahti LUMI Puhti Miscellaneous Visual Studio Code Source code editor LUMI LUMI Puhti Mahti Miscellaneous WhiteboxTools an advanced geospatial data analysis platform Puhti Geosciences XHMM (eXome-Hidden Markov Model) Copy number variation calling from targeted sequencing data Puhti Biosciences Zonation Spatial conservation prioritization framework Puhti Puhti Geosciences iPyrad toolkit for population genetic and phylogenetic studies of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) Puhti Biosciences wtdbg2 Fast assembler for long-read data Puhti Biosciences

Academic

ABAQUS Dassault Systemes' SIMULIA academic research suite Puhti Computational Engineering AMS Modelling suite providing engines like ADF, BAND, DFTB and MOPAC Puhti Mahti Chemistry AMS-GUI AMS integrated GUI Puhti Mahti Chemistry Amber Molecular dynamics suite LUMI Puhti Mahti Chemistry COMSOL Multiphysics General-purpose simulation software Puhti Puhti Computational Engineering COSMO-RS Toolbox for predictive property calculation of liquids Puhti Chemistry CSD Cambridge Crystallographic Database - organic and metallo-organic crystal structures and tools Puhti Chemistry Discovery Studio Protein modeling environment Biosciences GOLD Protein Ligand Docking Software Puhti Chemistry Biosciences IDL Programming Language, Numeric Analysis, Manipulation and Visualization of Scientific Data Puhti Mahti Mathematics and Statistics MATLAB High-level technical computing language LUMI Puhti LUMI Puhti Mathematics and Statistics Maestro Versatile drug discovery and materials modeling suite Puhti Mahti Puhti Mahti Chemistry Biosciences Materials Studio Versatile materials modeling suite Chemistry TURBOMOLE Efficient program package for electronic structure calculations Puhti Mahti Chemistry TmoleX GUI for setting up and analyzing TURBOMOLE jobs Puhti Chemistry

Non-commercial

MOLPRO Package for accurate ab initio quantum chemistry calculations Puhti Chemistry Molden Processing program for molecular and electronic structure calculations Puhti Mahti Chemistry NAMD Highly scalable classical molecular dynamics LUMI Puhti Mahti Chemistry VMD Molecular visualization program Puhti Mahti Puhti Mahti Chemistry Biosciences

Other

ANSYS ANSYS Academic engineering simulation software suite LUMI Puhti Mahti Computational Engineering ArcGIS General purpose GIS software family for viewing, editing and analysing geospatial data Geosciences Gaussian Versatile computational chemistry package Puhti Mahti Chemistry LAStools for LiDAR datasets Puhti Geosciences ORCA General purpose quantum chemistry package Puhti Mahti Chemistry RStudio IDE Integrated development environment for R Puhti Puhti Mathematics and Statistics Star-CCM+ Computational Fluid Dynamics software by Siemens Digital Industries Software LUMI Puhti Mahti Computational Engineering VASP Ab initio DFT electronic structures Puhti Mahti Physics Chemistry r-env R, RStudio Server, SAGA and TensorFlow Puhti Mathematics and Statistics

NoMachine LUMI Puhti Mahti

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