Skip to content

Table of Contents

Applications by discipline

Note

In addition to technical support, CSC also provides expert consulting in questions related to sciences and methods. For more details, see our science-specific support pages at research.csc.fi or directly contact our Service Desk.

Biosciences

  • BAMtools Tools for working with BAM formatted files
  • BayeScan Tool for identifying candidate loci under natural selection based on allele frequencies in populations.
  • Bioconda Package manger for installing bioinformatics software
  • BioPerl Perl environment with bioperl extension
  • BioPython Python environment with biopython and other bioinformatics related Python libraries
  • BLAST Sequence similarity search tool for nucleotides and proteins
  • Bowtie2 Short read aligner
  • BWA Short read aligner
  • CD-hit Sequence clustering and redundancy removal tool
  • Chipster Easy-to-use analysis platform for RNA-seq, single cell RNA-seq and other NGS data
  • Chipster_genomes Tool to download aligner indexes used by Chipster to Puhti
  • Cutadapt Trimming high-throughput sequencing reads
  • Diamond Sequence similarity search tool for proteins and nucloeotides
  • Discovery Studio Protein modeling environment.
  • Edirect Entrez direct - command line tool to search and retrieve data from NCBI
  • EMBOSS Toolkit for classical sequence analysis
  • Exonerate A generic tool for pairwise sequence comparison.
  • FastQC Quality control tool for high throughput sequence data
  • Freebayes Genetic variant detector
  • GOLD Protein Ligand Docking Software
  • Grace Plotting tool for xvg-files in particular
  • Gromacs Fast and versatile classical molecular dynamics
  • HMMER Toolkit to create and use sequence profile hidden Markov models
  • HUMAnN2 Profiling microbial pathways with metagenomic data
  • Illumina BaseSpace Command line client for retrieving data from the Illumina BaseSpace environment
  • InterProScan Protein signature/motif search tool
  • Ipyrad toolkit for population genetic and phylogenetic studies of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS)
  • Kraken2 Taxonomic sequence classification system
  • Krona Visualization tool for taxonomic classification and other hierarchical data
  • Lazypipe A stand-alone pipeline for identifying viruses in host-associated or environmental samples
  • MaxQuant A proteomics software for processing of Mass-spectromtery data
  • MIRA Whole genome shotgun and EST sequence Assembler
  • MACS2 ChIP-Seq analysis tool
  • Maestro Versatile drug discovery and materials modeling suite
  • Megahit Metagenomics assebly
  • MetaPhlAn Profiling the composition of microbial communities with metagenomic data
  • Minimap2 Short read aligner
  • Mothur Package for microbial community analysis of amplicon sequencing data
  • MrBayes Program for inferring phylogenies using Bayesian methods
  • Pannzer Automatic protein annotation tool
  • Picard Tools for working with SAM,BAM,CRAM and VCF files
  • Prokka Rapid prokaryotic genome annotation
  • QIIME2 Package for microbial community analysis of amplicon sequencing data
  • RAxML Program for inferring phylogenies with likelihood
  • Roary Pan genome pipeline
  • Salmon Program to produce transcript-level quantification estimates from RNA-seq data
  • Samtools Utilities for managing SAM/BAM formatted alignment files
  • Seqtk Tool for processing sequences in the FASTA or FASTQ format
  • Stacks Pipeline for building loci from short-read sequences (e.g. RAD-seq data)
  • SPAdes Genome assembly
  • STAR Short read aligner
  • Structure Inference of population structure in genetics
  • Tophat Splice junction mapper for RNA-Seq reads
  • Trinity Traskriptome assembly tool
  • Velvet Genome assembler
  • VirusDetect Virus identification with sRNA data
  • VMD Molecular visualization program
  • wtdbg2 Fast assembler for long-read data
  • XHMM Copy number variation calling from targeted sequencing data

Chemistry

  • Amber Molecular dynamics suite
  • AMS Modelling suite providing engines like ADF, BAND, DFTB and MOPAC
  • AMS-GUI AMS integrated GUI
  • CP2k DFT, quantum chemistry, QM/MM, AIMD etc. in particular for periodic systems
  • CSD Cambridge Crystallographic Database - organic and metallo-organic crystal structures and tools
  • Gaussian Versatile computational chemistry package
  • GOLD Protein Ligand Docking Software
  • GPAW Versatile DFT package
  • Gromacs Fast and versatile classical molecular dynamics
  • LAMMPS Fast molecular dynamics engine with large force field selection
  • Maestro Versatile drug discovery and materials modeling suite
  • Materials Studio Versatile materials modeling suite
  • MOLDEN Processing program for molecular and electronic structure calculations
  • MOLPRO Package for accurate ab initio quantum chemistry calculations
  • NAMD Highly scalable classical molecular dynamics
  • NWChem A computational chemistry software package designed to perform well on parallel HPC systems.
  • Open Babel Program to interconvert file formats currently used in molecular modeling
  • ORCA General purpose quantum chemistry package
  • Plumed Library and tools for enhanced sampling methods
  • TmoleX GUI for setting up and analyzing TURBOMOLE jobs
  • Turbomole Efficient program package for electronic structure calculations
  • VASP Ab initio DFT electronic structures
  • VMD Molecular visualization program

Computational Engineering

  • Abaqus Dassault Systemes' SIMULIA academic research suite
  • ANSYS ANSYS Academic engineering simulation software suite
  • CFDEMcoupling Open source toolbox for CFD-DEM coupling
  • COMSOL Multiphysics General-purpose simulation software
  • Elmer Open source multi-physics FEM package
  • LS-DYNA General-purpose finite element program
  • Nektar++ Spectral/hp element framework
  • OpenFOAM Open source C++ tool box for continuum mechanics problems
  • PALM Meteorological model system for atmospheric and oceanic boundary-layer flows
  • Star-CCM+ Computational Fluid Dynamics software by Siemens Digital Industries Software

Data Analytics and Machine Learning

  • Python Data Collection of Python libraries for data analytics and machine learning
  • MXNet Deep learning library for Python
  • PyTorch Machine learning framework for Python
  • RAPIDS Suite of libraries for data analytics and machine learning on GPUs
  • Spark High-performance distributed computing framework
  • TensorFlow Deep learning library for Python

Geosciences

  • ArcGIS General purpose GIS software family for viewing, editing and analysing geospatial data
  • CloudCompare for visualizing, editing and processing poing clouds
  • FORCE for mass-processing of medium-resolution satellite images
  • GDAL for geospatial data formats
  • Geoconda - Python spatial analysis libraries
  • GRASS GIS General purpose GIS software family for viewing, editing and analysing geospatial data
  • LAStools for LiDAR datasets
  • Mapnik for rendering maps
  • OpenDroneMap for processing aerial drone imagery
  • Orfeo ToolBox for remote sensing applications
  • PCL for 2D/3D image and point cloud processing
  • PDAL for point cloud translations and processing
  • pktools for remote sensing applications
  • QGIS General purpose GIS software family for viewing, editing and analysing geospatial data
  • R for GIS R spataial analysis libraries
  • SAGA GIS General purpose GIS software family for viewing, editing and analysing geospatial data
  • Sen2Cor for atmospheric-, terrain and cirrus correction of the Sentinel-2 products
  • Sen2mosaic for download, preprocessing and mosaicing of Sentinel-2 products
  • SNAP for remote sensing applications
  • Sofi3d for 3D Finite-Difference Seismic Wave Simulation
  • SPLITS for time series analysis of remotely sensed parameters
  • WhiteboxTools an advanced geospatial data analysis platform
  • Zonation Spatial conservation prioritization framework

Language Research and Other Digital Humanities and Social Sciences

  • eBay's tsv-tools Utilities for manipulating large tabular data files
  • finnish-parse Dependency Parser for Finnish
  • Finnish Tagtools Finnish Tagtools
  • HFST Helsinki Finite-State Transducer Technology
  • HFST-fi Helsinki Finite-State Technology for Finnish
  • HFST-sv Helsinki Finite-State Technology for Swedish
  • Kaldi Kaldi Speech Recognition Toolkit
  • UDPipe UDPipe Kielipankki version

Mathematics and Statistics

  • IDL Programming Language, Numeric Analysis, Manipulation and Visualization of Scientific Data
  • Julia High-level, high-performance dynamic programming language for numerical computing
  • MATLAB High-level technical computing language
  • Octave High-level interpreted language for numerical computations.
  • Python programming language and its modules at CSC.
  • r-env-singularity R, RStudio Server, SAGA and TensorFlow (Singularity container)
  • RStudio Integrated development environment for R
  • SageMath Free open-source mathematics software system

Physics

  • VASP Ab initio DFT electronic structures

Miscellaneous

  • DDT Parallel debugger
  • MySQL MySQL database client.
  • ParaView Free open-source visualization application
  • VisIt Free open-source visualization application