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
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
BridgeDb Java
Java library for identifier mapping
- Data
- persistent identifiers
- Java
- Perl
- Shell
- + 5
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
Code and data underlying the publication: City3D: Large-scale Building Reconstruction from Airborne LiDAR Point Clouds
Code and data underlying the publication: City3D: Large-scale Building Reconstruction from Airborne LiDAR Point Clouds
- Building
- Point Cloud
- Surface-reconstruction
- + 1
- C
- C++
- Other
- + 8
Scholia
Graphical User Interface around Wikidata that uses SPARQL to collect data
- Wikidata
- JavaScript
- Python
- HTML
- + 3
NPLinker Web Application
This is the NPLinker web application, developed with Plotly Dash. It enables interactive visualization of NPLinker predictions and is designed to be run locally or in a containerized environment.
- Data mining
- Genome
- Metabolome
- + 2
- Python
- CSS
- Dockerfile
- + 1
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
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