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
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
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
BridgeDb Java
Java library for identifier mapping
- Data
- persistent identifiers
- Java
- Perl
- Shell
- + 5
matchms
Python library for fuzzy comparison of mass spectrum data and other Python objects
- Big data
- Optimized data handling
- Python
- TeX
- Batchfile
- + 1
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
Xenon
If you are using remote machines to do your computations, and don’t feel like learning and implementing many different APIs, Xenon is the tool for you.
- batch-job
- distributed computing
- FTP
- + 11
- Java
- Shell
- Batchfile
nanopub
The nanopub library provides a high-level, user-friendly python interface for searching, publishing and retracting nanopublications.
- Inter-operability & linked data
- Python
- Shell
- Batchfile
Xenon command line interface
A command line interface for the Xenon library that allows you to use remote machines to do your computations.
- High performance computing
- Java
- Common Workflow Language
- Dockerfile
- + 2
eEecology Classification
Automatic classification of accelerometer data using a supervised learning approach.
- Machine learning
- Java
- JavaScript
- HTML
- + 3
LUE
LUE is software for storing and manipulating large amounts of information for large numbers of objects. The software is useful, and currently mainly used, in the context of environmental modelling of biological and physical systems, represented by agents and fields.
- Agent-based modeling
- environmental modelling
- field based modelling
- + 6
- C++
- Python
- CMake
- + 6
PathVisio
PathVisio is a free open-source software to curate biological pathway models.
- bioinformatics
- PathVisio
- Systems Biology
- + 2
- Java
- HTML
- JavaScript
- + 4