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
- Trimmomatic Trim Illumina paired-end and single-read data
- Trinity Transcriptome 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
- Python The programming language and its modules at CSC
- 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
- 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
- Accelerated visualization A selection of GPU accelerated visualization applications
- Blender 3D modeling, visualization and rendering software
- DDT Parallel debugger
- Desktop Remote desktop environment
- HyperQueue Scheduler for sub-node tasks
- Julia-Jupyter Interactive computational environment for Julia
- Jupyter Interactive computational environment for Python
- Jupyter for courses A version of the Jupyter app for course environments
- MySQL MySQL database client.
- ParaView Free open-source visualization application
- TensorBoard The visualization toolkit for TensorFlow
- VisIt Free open-source visualization application
- Visual Studio Code Source code editor