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Software Highlights

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1-12 of 101

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

2685

OpenChrom

OpenChrom is a vendor independent open source software for chromatography, spectrometry and spectroscopy.

chromatography
mass spectrometry

Java
CSS
HTML

190

NNPDF

Fitting proton substructure to observation data using neural networks

Machine learning
PDF

Python
Jupyter Notebook
C
+ 5

120

BridgeDb Java

Java library for identifier mapping

Data
persistent identifiers

Java
Perl
Shell
+ 5

117

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

105

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

Scholia

Graphical User Interface around Wikidata that uses SPARQL to collect data

Wikidata

JavaScript
Python
HTML
+ 3

Via Appia Visualization

A web application which visualizes the point clouds and additional data gathered in the Via Appia project with WebGL.

Visualization

JavaScript
HTML
CSS

mcfly

Helps you find a suitable neural network configuration for deep learning on time series.

auto-ml
deep learning
Machine learning
+ 1

JavaScript
Python
CSS
+ 1

hyphe

A research-driven web-crawler aimed at building, curating and categorizing a corpus of web actors and the network graph of hyperlinks connecting them.

crawling
Networks
python
+ 1

JavaScript
Python
HTML
+ 3

compareMS2

compareMS2 is a tool for direct comparison of tandem mass spectrometry datasets, typically from liquid chromatography-tandem mass spectrometry (LC-MS/MS), defining a distance as a function of the share of similar spectra. Applications span biomedicine, phylogenetics, forensics and food science.

Forensics
mass spectrometry
phylogenetics
+ 1

JavaScript
C
HTML
+ 2