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Applications

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  • See here for ways to install software yourself.
  • You may also contact CSC Service Desk with your software installation request. Given enough requests, we may consider pre-installing a particular application, or purchasing a license for it if the software in question is proprietary.
  • Although we cannot promise to pre-install all requested applications, CSC Service Desk is happy to support you in installing software yourself.

Applications in alphabetical order

A

  • ABAQUS — Dassault Systemes' SIMULIA academic research suite

  • AMS — Modelling suite providing engines like ADF, BAND, DFTB and MOPAC

  • AMS-GUI — AMS integrated GUI

  • ANSYS — ANSYS Academic engineering simulation software suite

  • Accelerated visualization — A selection of GPU accelerated visualization applications

  • Alphafold — Protein 3D structure prediction

  • Amber — Molecular dynamics suite

  • ArcGIS — General purpose GIS software family for viewing, editing and analysing geospatial data

B

  • 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

  • Bioconda — Package manger for installing bioinformatics software

  • Biopython — Python environment with biopython and other bioinformatics related Python libraries

  • Blender — 3D modeling, visualization and rendering software

  • Bowtie2 — Short read aligner

C

  • CD-HIT — Sequence clustering and redundancy removal tool

  • COMSOL Multiphysics — General-purpose simulation software

  • 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

  • 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

  • Cirq-on-iqm — open-source cirq adapter for quantum computing

  • CloudCompare — for visualizing, editing and processing poing clouds

  • CryoSPARC — Tool to analyse Cryo-EM data on Puhti/Mahti

  • Cutadapt — Trimming high-throughput sequencing reads

  • 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

D

  • DDT — Parallel debugger

  • Desktop — Remote desktop environment

  • Diamond — Sequence similarity search tool for proteins and nucloeotides

  • Discovery Studio — Protein modeling environment

E

  • EMBOSS — Toolkit for classical sequence analysis

  • Elmer — Open source multi-physics FEM package

  • Entrez Direct — Entrez direct - command line tool to search and retrieve data from NCBI

  • Exonerate — A generic tool for pairwise sequence comparison

  • eBay's tsv-tools — Utilities for manipulating large tabular data files

F

  • FORCE — for mass-processing of medium-resolution satellite images

  • FastQC — Quality control tool for high throughput sequence data

  • Finnish Tagtools — Finnish Tagtools

  • Freebayes — Genetic variant detector

  • finnish-parse — Dependency Parser for Finnish

G

  • GDAL — for geospatial data formats

  • GOLD — Protein Ligand Docking Software

  • GPAW — Versatile DFT package

  • GRASS GIS — General purpose GIS software family for viewing, editing and analysing geospatial data

  • GROMACS — Fast and versatile classical molecular dynamics

  • Gaussian — Versatile computational chemistry package

  • Geoconda — Python libraries for spatial analysis

  • Grace — Plotting tool for xvg-files in particular

  • gdb — GNU debugger for compiled programs

H

  • HADDOCK3 — High Ambiguity Driven biomolecular DOCKing

  • HFST — Helsinki Finite-State Transducer Technology

  • HFST-fi — Helsinki Finite-State Technology for Finnish

  • HFST-sv — Helsinki Finite-State Technology for Swedish

  • HMMER — Toolkit to create and use sequence profile hidden Markov models

  • HUMAnN — Profiling microbial pathways with metagenomic data

  • HyperQueue — Scheduler for sub-node tasks

I

  • IDL — Programming Language, Numeric Analysis, Manipulation and Visualization of Scientific Data

  • Illumina BaseSpace — Command line client for retrieving data from the Illumina BaseSpace environment

  • Intel Trace Analyzer and Collector (ITAC)

  • Intel VTune Profiler — Performance analysis tool for single core and threading performance

  • 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)

J

  • JAX — Autograd and XLA, brought together for high-performance machine learning

  • Julia Language — High-level, high-performance dynamic programming language for numerical computing

  • 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

K

  • Kaldi — Kaldi Speech Recognition Toolkit

  • Kraken — Taxonomic sequence classification system

  • Krona visualization tool — Visualization tool for taxonomic classification and other hierarchical data

L

  • LAMMPS — Fast molecular dynamics engine with large force field selection

  • LAStools — for LiDAR datasets

  • Lazypipe — A stand-alone pipeline for identifying viruses in host-associated or environmental samples

M

  • MACS2/3 — ChIP-Seq analysis tool

  • MATLAB — High-level technical computing language

  • MIRA — Whole genome shotgun and EST sequence Assembler

  • MOLPRO — Package for accurate ab initio quantum chemistry calculations

  • Maestro — Versatile drug discovery and materials modeling suite

  • Materials Studio — Versatile 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

  • Molden — Processing program for molecular and electronic structure calculations

  • Mothur — Package for microbial community analysis of amplicon sequencing data

  • MrBayes — Program for inferring phylogenies using Bayesian methods

  • MySQL — MySQL database client

N

  • NAMD — Highly scalable classical molecular dynamics

  • NASA Ames Stereo Pipeline (ASP) — for processing stereo images

  • NWChem — A computational chemistry software package designed to perform well on parallel HPC systems

  • Nextflow — Nextflow is a scientific workflow management system for creating scalable, portable, and reproducible workflows

  • NoMachine

  • ncu — Nvidia CUDA kernel profiler

  • nsys — Nvidia GPU and CPU profiler

  • nvprof — Nvidia profiling tool that collects and views profiling data

O

P

  • PALM — Meteorological model system for atmospheric and oceanic boundary-layer flows

  • PANNZER2/SANSPANZ — Automatic protein annotation tool

  • PCL — for 2D/3D image and point cloud processing

  • PDAL — for point cloud translations and processing

  • PLUMED — Library and tools for enhanced sampling methods

  • ParaView — Free open-source visualization application

  • Pennylane — Free open-source software framework for quantum machine learning and quantum computing

  • Picard Tools — Tools for working with SAM,BAM,CRAM and VCF files

  • Prokka — Rapid prokaryotic genome annotation

  • PyTorch — Machine learning framework for Python

  • Python — The programming language and its modules at CSC

  • Python Data — Collection of Python libraries for data analytics and machine learning

  • pdb — Built-in Python debugger

  • perf — Command line tool for performance analysis

Q

  • QGIS — General purpose GIS software family for viewing, editing and analysing geospatial data

  • QIIME — Package for microbial community analysis of amplicon sequencing data

  • Qiskit — open-source toolkit for useful quantum computing

  • Qiskit-on-iqm — open-source qiskit adapter for quantum computing

  • Quantum ESPRESSO — Electronic-structure calculations and materials modeling at the nanoscale

R

  • R for GIS — R spataial analysis libraries

  • RAPIDS — Suite of libraries for data analytics and machine learning on GPUs

  • RAxML — Program for inferring phylogenies with likelihood

  • RStudio IDE — Integrated development environment for R

  • Roary — Pan genome pipeline

  • r-env — R, RStudio Server, SAGA and TensorFlow

S

  • SAGA GIS — General purpose GIS software family for viewing, editing and analysing geospatial data

  • SALMON — Program to produce transcript-level quantification estimates from RNA-seq data

  • SAMtools — Utilities for managing SAM/BAM formatted alignment files

  • SNAP — for remote sensing applications

  • SOFI3D — for 3D finite-difference seismic wave simulation

  • SPAdes — Genome assembly

  • STAR — Short read aligner

  • SageMath — Free open-source mathematics software system

  • Scalasca

  • 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

  • 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

  • Spark — High-performance distributed computing framework

  • Stacks — Pipeline for building loci from short-read sequences (e.g. RAD-seq data)

  • Star-CCM+ — Computational Fluid Dynamics software by Siemens Digital Industries Software

  • Structure — Inference of population structure in genetics

T

  • TURBOMOLE — Efficient program package for electronic structure calculations

  • TensorBoard — The visualization toolkit for TensorFlow

  • TensorFlow — Deep learning library for Python

  • TmoleX — GUI for setting up and analyzing TURBOMOLE jobs

  • TopHat — Splice junction mapper for RNA-Seq reads

  • Trimmomatic — Trim Illumina paired-end and single-read data

  • Trinity — Transcriptome assembly tool

U

  • UDPipe — UDPipe Kielipankki version

V

  • VASP — Ab initio DFT electronic structures

  • VMD — Molecular visualization program

  • Velvet — Genome assembler

  • VirusDetect — Virus identification with sRNA data

  • VisIt — Free open-source visualization application

  • Visual Studio Code — Source code editor

W

  • Whisper — General-purpose speech recognition model

  • WhiteboxTools — an advanced geospatial data analysis platform

  • wtdbg2 — Fast assembler for long-read data

X

Z

  • Zonation — Spatial conservation prioritization framework