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
TOTEM_M
Code underlying: Topology Optimization of Thermo-Electro-Mechanical elements (TOTEM)
- Non-convexity
- Power constraint
- SIMP
- + 3
- Other
- Matlab
- HTML
- + 2
Chemistry Development Kit
Open Source cheminformatics library.
- Cheminformatics
- Chemistry
- Computational Chemistry
- Java
- Pawn
- HTML
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
NNPDF
Fitting proton substructure to observation data using neural networks
- Machine learning
- Python
- Jupyter Notebook
- C
- + 5
ESMValCore
ESMValTool Core: core functionalities and driver for ESMValTool, a community diagnostic and performance metrics tool for routine evaluation of Earth System Models in CMIP.
- Big data
- Optimized data handling
- Visualization
- + 1
- Python
- Jupyter Notebook
- HTML
- + 5
ArrayAnalysis
ArrayAnalysis provides a user-friendly solution for transcriptomic data analysis. It allows researchers, regardless of their bioinformatics expertise, to efficiently analyse, explore, and interpret RNA sequencing and microarray datasets.
- Data Analysis
- data visualization
- microarray
- + 2
- R
- HTML
- Batchfile
- + 2
Scholia
Graphical User Interface around Wikidata that uses SPARQL to collect data
- Wikidata
- JavaScript
- Python
- HTML
- + 3
Paired omics data platform
If you do metabolomics experiments with mass spectra and have sequenced the genomes of the samples, then the platform can help you link them.
- Inter-operability & linked data
- TypeScript
- JavaScript
- HTML
- + 3
MAGMa
MAGMa is an online application for the automatic chemical annotation of mass spectrometry data.
- Big data
- Visualization
- Python
- JavaScript
- Makefile
- + 5
grlc
Builds a web API from SPARQL queries hosted on GitHub to accessing triple store data.
- garlic
- Inter-operability & linked data
- Python
- HTML
- TeX
- + 4