All software
COPASI
COPASI is an open source software for simulation and analysis of biochemical networks and their dynamics. It provides simulations using ODEs, SDEs, or Gillespie's stochastic simulation algorithm, with optional discrete events. COPASI provides several analyses, optimization, and parameter estimation.
- Dynamics
- optimization
- Parameter estimation
- + 3
- C++
- Java
- Fortran
- + 17
Chemistry Development Kit
Open Source cheminformatics library.
- Cheminformatics
- Chemistry
- Computational Chemistry
- Java
- Pawn
- HTML
AMUSE
Combine existing numerical codes in an easy to use Python framework. With AMUSE you can simulate objects such as star clusters, proto-planetary disks and galaxies.
- High performance computing
- Multi-scale & multi model simulations
- Workflow technologies
- C
- Fortran
- Python
- + 23
BridgeDb Java
Java library for identifier mapping
- Data
- persistent identifiers
- Java
- Perl
- Shell
- + 5
OpenChrom
OpenChrom is a vendor independent open source software for chromatography, spectrometry and spectroscopy.
- chromatography
- mass spectrometry
- Java
- HTML
- CSS
Twiqs
Software behind the web server twiqs.nl, which has provided free access to statistics about Dutch tweets since 2010
- Big data
- Text analysis & natural language processing
- Visualization
- Perl
- Java
- HTML
- + 3
Glotaran
Glotaran: A Java-Based Graphical User Interface for the R Package TIMP
- global analysis
- target analysis
- time-resolved spectroscopy
- Java
- HTML
BlueObelisk Euclid
A library of numeric, geometric and XML routines
- Java
- HTML
CMLXOM
Java library for working with Chemical Markup Language files.
- Chemical Markup Language
- Chemistry
- XML
- Java
- XSLT
- HTML
- + 1
Research Software Directory
A content management system for research software, which promotes the visibility, reuse, and impact of research software.
- FAIR
- Research Software Impact
- Software Citation
- TypeScript
- Java
- PLpgSQL
- + 8
PanTools
PanTools is a pangenomic toolkit for comparative analysis of large number of genomes. It is developed in the Bioinformatics Group of Wageningen University, the Netherlands. Please cite the relevant publication(s) from the list of publications if you use PanTools in your research.
- Data Analysis
- Gene classification
- pangenomics
- Java
- Snakemake
- Python
- + 1
KLIFS KNIME nodes
If you are working in the KNIME worflow platform and need data about your favorite kinase receptor ligand interaction, then these nodes are for you.
- Workflow technologies
- Java
- Shell
- Scala