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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
2599
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
1292
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
  • CMake
  • + 9
33
782
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
175
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
163
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
104
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
95
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
89
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
77
Cover image for Vantage6

Vantage6

An open-source platform for supporting the development of federated learning projects

  • federated learning
  • healthcare
  • privacy preserving analysis
  • + 1
  • Python
  • TypeScript
  • HTML
  • + 6
8
43
Cover image for Research Software Directory

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
  • + 7
25
38
Cover image for OMUSE

OMUSE

A Python environment to interface and couple oceanographic and other earth system model codes.

  • High performance computing
  • Multi-scale & multi model simulations
  • Fortran
  • Python
  • HTML
  • + 10
8
25