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Cover image for COPASI

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
12
2686
Cover image for ASTRA Toolbox

ASTRA Toolbox

The ASTRA Toolbox is a Python and MATLAB library of flexible, high-performance GPU-accelerated primitives for 2D and 3D tomography.

  • CT
  • GPU
  • Image reconstruction
  • + 4
  • C++
  • Cuda
  • MATLAB
  • + 8
2
1372
Cover image for Parallel Ice Sheet Model (PISM)

Parallel Ice Sheet Model (PISM)

An open-source modelling framework for ice sheets and glaciers

  • C++
  • geophysics
  • Glacier
  • + 5
  • C++
  • Python
  • TeX
  • + 9
33
876
Cover image for AMUSE

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
  • + 26
6
280
Cover image for SAGECal

SAGECal

Fast, memory efficient and GPU accelerated radio interferometric calibration program

  • Big data
  • GPU
  • High performance computing
  • C
  • C++
  • Cuda
  • + 5
4
183
Cover image for spec2vec

spec2vec

spec2vec is a novel similarity measure for comparing mass spectrometry data, which learns peak representations using Word2Vec.

  • Machine learning
  • Text analysis & natural language processing
  • Python
  • Batchfile
  • Makefile
10
179
Cover image for NNPDF

NNPDF

Fitting proton substructure to observation data using neural networks

  • Machine learning
  • PDF
  • Python
  • Jupyter Notebook
  • C
  • + 5
7
120
Cover image for FAIR Data Point

FAIR Data Point

RESTful web service that enables data owners to expose their data sets using rich machine-readable metadata.

  • Big data
  • Inter-operability & linked data
  • Python
  • Makefile
  • Dockerfile
6
115
Cover image for MAGMa

MAGMa

MAGMa is an online application for the automatic chemical annotation of mass spectrometry data.

  • Big data
  • Visualization
  • Python
  • JavaScript
  • Makefile
  • + 5
3
98
Cover image for matchms

matchms

Python library for fuzzy comparison of mass spectrum data and other Python objects

  • Big data
  • Optimized data handling
  • Python
  • TeX
  • Batchfile
  • + 1
14
97
Cover image for DeepRank

DeepRank

Deep learning framework for data mining protein-protein interactions using CNN

  • Big data
  • Machine learning
  • Optimized data handling
  • Python
  • R
  • C
  • + 2
8
89
Cover image for iScore

iScore

A framework and predictor based on support vector machine and random walk graph kernel for scoring protein-protein interfaces.

  • Big data
  • Machine learning
  • Protein-Protein Interaction
  • Python
  • Cuda
  • Makefile
  • + 1
4
80