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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

  • AlphaFold Protein 3D structure prediction
  • 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
  • BRAKER Automatic genome annotator for eucaryots
  • 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
  • HUMAnN 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 assembly
  • 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
  • Nextflow Nextflow is a scientific workflow management system for creating scalable, portable, and reproducible workflows
  • 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
  • Snakemake Snakemake is a scientific workflow management system for creating scalable, portable, and reproducible workflows
  • 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
  • COSMO-RS Toolbox for predictive property calculation of liquids
  • 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
  • COMSOL Multiphysics General-purpose simulation software
  • Elmer Open source multi-physics FEM package
  • 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

  • JAX Autograd and XLA, brought together for high-performance machine learning
  • Python Data Collection of Python libraries for data analytics and machine learning
  • 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

  • Ames Stereo Pipeline for processing stereo images
  • 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
  • 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
  • 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
  • Seismic-unix for processing of 2D seismic or GPR data sets.
  • 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
  • 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 Tagtools Finnish Tagtools
  • finnish-parse Dependency Parser for Finnish
  • 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
  • r-env R, RStudio Server, SAGA and TensorFlow
  • RStudio Integrated development environment for R
  • SageMath Free open-source mathematics software system

Physics

  • VASP Ab initio DFT electronic structures

Quantum

  • Cirq-on-iqm open-source cirq adapter for quantum computing
  • CUDA Quantum open-source platform for hybrid quantum-classical computing
  • Pennylane Free open-source software framework for quantum machine learning and quantum computing
  • Qiskit open-source toolkit for useful quantum computing
  • Qiskit-on-iqm open-source qiskit adapter for quantum computing

Miscellaneous