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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
  • BLAST — Sequence similarity search tool for nucleotides and proteins
  • BRAKER — Automatic genome annotator for eucaryots
  • BWA — Short read aligner
  • BamTools — Tools for working with BAM formatted files
  • BayeScan — Tool for identifying candidate loci under natural selection based on allele frequencies in populations
  • BioPerl — Perl environment with bioperl extension
  • Biopython — Python environment with biopython and other bioinformatics related Python libraries
  • Bowtie2 — 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
  • CryoSPARC — Tool to analyse Cryo-EM data on Puhti/Mahti
  • Cutadapt — Trimming high-throughput sequencing reads
  • Diamond — Sequence similarity search tool for proteins and nucloeotides
  • EMBOSS — Toolkit for classical sequence analysis
  • Entrez Direct — Entrez direct - command line tool to search and retrieve data from NCBI
  • 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
  • GROMACS — Fast and versatile classical molecular dynamics
  • Grace — Plotting tool for xvg-files in particular
  • HADDOCK3 — High Ambiguity Driven biomolecular DOCKing
  • 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
  • Kraken — Taxonomic sequence classification system
  • Krona visualization tool — Visualization tool for taxonomic classification and other hierarchical data
  • Lazypipe — A stand-alone pipeline for identifying viruses in host-associated or environmental samples
  • MACS2/3 — ChIP-Seq analysis tool
  • MIRA — Whole genome shotgun and EST sequence Assembler
  • Maestro — Versatile drug discovery and materials modeling suite
  • MaxQuant  — A proteomics software for processing of Mass-spectromtery data
  • 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
  • PANNZER2/SANSPANZ — Automatic protein annotation tool
  • Picard Tools — Tools for working with SAM,BAM,CRAM and VCF files
  • Prokka — Rapid prokaryotic genome annotation
  • QIIME — 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
  • SPAdes — Genome assembly
  • STAR — Short read aligner
  • 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)
  • 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
  • VMD — Molecular visualization program
  • Velvet — Genome assembler
  • VirusDetect — Virus identification with sRNA data
  • XHMM (eXome-Hidden Markov Model) — Copy number variation calling from targeted sequencing data
  • iPyrad — toolkit for population genetic and phylogenetic studies of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS)
  • wtdbg2 — Fast assembler for long-read data

Chemistry

  • AMS — Modelling suite providing engines like ADF, BAND, DFTB and MOPAC
  • AMS-GUI — AMS integrated GUI
  • Amber — Molecular dynamics suite
  • 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
  • GOLD — Protein Ligand Docking Software
  • GPAW — Versatile DFT package
  • GROMACS — Fast and versatile classical molecular dynamics
  • Gaussian — Versatile computational chemistry package
  • HADDOCK3 — High Ambiguity Driven biomolecular DOCKing
  • LAMMPS — Fast molecular dynamics engine with large force field selection
  • MOLPRO — Package for accurate ab initio quantum chemistry calculations
  • Maestro — Versatile drug discovery and materials modeling suite
  • Molden — Processing program for molecular and electronic structure calculations
  • NAMD — Highly scalable classical molecular dynamics
  • NWChem — A computational chemistry software package designed to perform well on parallel HPC systems
  • ORCA — General purpose quantum chemistry package
  • Open Babel — Program to interconvert file formats currently used in molecular modeling
  • PLUMED — Library and tools for enhanced sampling methods
  • Quantum ESPRESSO — Electronic-structure calculations and materials modeling at the nanoscale
  • TURBOMOLE — Efficient program package for electronic structure calculations
  • TmoleX — GUI for setting up and analyzing TURBOMOLE jobs
  • 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
  • PyTorch — Machine learning framework for Python
  • Python Data — Collection of Python libraries for data analytics and machine learning
  • RAPIDS — Suite of libraries for data analytics and machine learning on GPUs
  • Spark — High-performance distributed computing framework
  • TensorFlow — Deep learning library for Python
  • Whisper — General-purpose speech recognition model

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
  • GRASS GIS — General purpose GIS software family for viewing, editing and analysing geospatial data
  • Geoconda — Python libraries for spatial analysis
  • LAStools — for LiDAR datasets
  • NASA Ames Stereo Pipeline (ASP) — for processing stereo images
  • OpenDroneMap (ODM) — for processing aerial drone imagery
  • Orfeo ToolBox (Open Source processing of remote sensing images) — 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
  • SNAP — for remote sensing applications
  • SOFI3D — for 3D finite-difference seismic wave simulation
  • 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
  • WhiteboxTools — an advanced geospatial data analysis platform
  • Zonation — Spatial conservation prioritization framework

Language Research and Other Digital Humanities and Social Sciences

Mathematics and Statistics

  • IDL — Programming Language, Numeric Analysis, Manipulation and Visualization of Scientific Data
  • Julia Language — 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
  • RStudio IDE — Integrated development environment for R
  • SageMath — Free open-source mathematics software system
  • r-env — R, RStudio Server, SAGA and TensorFlow

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
  • Intel Trace Analyzer and Collector (ITAC) — MPI profiling and tracing tool
  • Intel VTune Profiler — Performance analysis tool for single core and threading performance
  • 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
  • Scalasca — Performance profiler for parallel programs
  • TensorBoard — The visualization toolkit for TensorFlow
  • VisIt — Free open-source visualization application
  • Visual Studio Code — Source code editor
  • cProfile — Built-in profiler for Python programs
  • compute-sanitizer — Functional correctness checking suite included in the CUDA toolkit
  • cuda-gdb — Nvidia extension of the GNU debugger GDB
  • gdb — GNU debugger for compiled programs
  • ncu — Nvidia CUDA kernel profiler
  • nsys — Nvidia GPU and CPU profiler
  • nvprof — Nvidia profiling tool that collects and views profiling data
  • pdb — Built-in Python debugger
  • perf — Command line tool for performance analysis