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.

• Applications by discipline
  • Biosciences
  • Chemistry
  • Computational Engineering
  • Data Analytics and Machine Learning
  • Geosciences
  • Language Research and Other Digital Humanities and Social Sciences
  • Mathematics and Statistics
  • Physics
  • Quantum
  • Miscellaneous

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

• Bioconda — Package manger for installing bioinformatics software

• 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

• Discovery Studio — Protein modeling environment

• 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

• 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

• 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

• Materials Studio — Versatile 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

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

• 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

• Finnish Tagtools — Finnish Tagtools

• 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

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

• finnish-parse — Dependency Parser for Finnish

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 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

• 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

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