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Software Highlights

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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

2686

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

280

BridgeDb Java

Java library for identifier mapping

Data
persistent identifiers

Java
Perl
Shell
+ 5

117

Twiqs

Software behind the web server twiqs.nl, which has provided free access to statistics about Dutch tweets since 2010

Big data
Text analysis & natural language processing
Visualization

Perl
Java
HTML
+ 3

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

eEcology Annotation Tool

Visualize and annotate GPS measurements of bird movements.

Inter-operability & linked data
Visualization

HTML
Python
Mako
+ 5

PIQMIe

A web tool for mass spectrometry-based proteomics data analyses

Data Analysis
mass spectrometry
Optimized data handling
+ 2

HTML
JavaScript
Python
+ 3

iReceptor Gateway

A Distributed Data Management System and Scientific Gateway for Mining Next Generation Sequence Data from Immune Responses.

immunogenomics
Immunology
iReceptor

PHP
Blade
Shell
+ 7

eEcology Tracker calendar

Calendar overview with daily statistics of GPS-trackers used to track bird movements.

Visualization

Python
Makefile
JavaScript
+ 5

Analizo

Analizo is a free, multi-language, extensible source code analysis. It supports the extraction and calculation of a fair number of source code metrics, generation of dependency graphs, and software evolution analysis.

Software Evolution
Source Code Metrics
Static Analysis

Perl
C++
C
+ 7

CBRAIN

CBRAIN is a flexible Ruby on Rails framework for accessing and processing of large data on high-performance computing infrastructures.

CBRAIN
cluster
Data Analysis
+ 6

Ruby
HTML
JavaScript
+ 3

IRIDA

Integrated Rapid Infectious Disease Analysis (IRIDA) platform is a user-friendly, distributed, open source bioinformatics and analytical web platform that was developed to support real-time infectious disease outbreak investigations using whole genome sequencing data.

genomics
infectious disease

Java
JavaScript
TypeScript
+ 6