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
• 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
• 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
• 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 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

Miscellaneous

• Accelerated visualization A selection of GPU accelerated visualization applications
• CUDA Quantum open-source platform for hybrid quantum-classical computing
• DDT Parallel debugger
• Desktop Remote desktop environment
• HyperQueue Scheduler for sub-node tasks
• Julia-Jupyter Interactive computational environment with Julia
• Jupyter Interactive computational environment with Python
• Jupyter for courses A version of the Jupyter app for course environments
• MySQL MySQL database client.
• ParaView Free open-source visualization application
• Pennylane Free open-source software framework for quantum machine learning and quantum computing
• Qiskit open-source toolkit for useful quantum computing
• TensorBoard The visualization toolkit for TensorFlow
• VisIt Free open-source visualization application
• Visual Studio Code Source code editor

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