General Development Tools » Environmental Bioinformatics Knowledge Base

  Development and Programming

Resource Developer
acslX (“modeling and simulation of dynamic systems and processes”) AEgis Technologies
AMP – Agent Modeling Platform Eclipse Foundation
Analytica Lumina Decision Systems
ANSYS CFD (Computational Fluid Dynamics) ANSYS
ANSYS Fluent (“Flow Modeling Simulation Software”) ANSYS
AnyLogic (“simulation tool that supports Discrete Event, Agent Based, and System Dynamics Simulation”) AnyLogic Company
ARES Commander Edition Graebert GmbH
Ascape (“developing and exploring general-purpose agent-based models”) Ascape development team
behaviorsearch (“Adaptive search and exploration of agent-based model parameters”) behaviorsearch development team
Behaviour Composer Modelling4All project and University of Oxford
BENSOLVE (“MATLAB implementation of Benson’s algorithm”) M.L.-U. Halle-Wittenberg, Germany (Andreas Lohne)
Berkeley Madonna (“modeling and analysis of dynamic systems”) UC Berkeley
Bio-PEPA Workbench Bio-PEPA development team
Breve (“build 3D simulations of multi-agent systems and artificial life”) Jon Klein
C++ C++ development team
Cassandra database (“open source distributed database management system”) Apache Cassandra development team and The Apache Software Foundation
DEVS-Suite DEVS-Suite development team
Discrete Dynamics Lab (“Tools for researching Cellular Automata, Random Boolean Networks, multi-value Discrete Dynamical Networks, and beyond”) DDLab development team
Ecolego Swedish Radiation Safety Authority, Sweden and Norwegian Radiation Protection Authority
Entorama Branimir Cace
exaptive Exaptive, Inc.
Fast Numerical Algorithms for Stiff Reaction-Diffusion Equations University of California, Irvine
FileMaker Filemaker, Inc
FLAME – Flexible Large-scale Agent-based Modeling Environment Software Engineering Group, CSED, STFC
Fortran Free Software Foundation, Inc
GAMA IRD/UPMC International Research Unit, UMMISCO
geppetto (“a web-based […] simulation platform […] to support the simulation of complex biological systems and their surrounding environment”) geppetto development team
Hadoop (“open-source software for […] scalable, distributed computing”) The Apache Software Foundation
Hive (“data warehouse software”) Apache Hive development team and The Apache Software Foundation
HLM – Hierarchical Linear and Nonlinear Modeling Scientific Software International, Inc.
Hypertable (“open source database system”) Hypertable Inc.
IBM SPSS Statistics SPSS Inc. and IBM
isee NetSim (Web-based Simulation Sharing for STELLA and iThink models) isee Systems, Inc.
Jason Jason development team
Java Oracle
JILDT – Jason Induction of Logical Decison Trees JILDT development team
J-MADeM – Multi-modal Agent Decision Making (library integrated into Jason) MADeM development team
Jsim Physiome Project, University of Washington
JSoar Soar Technology, Inc. and Dave Ray
KNIME – Konstanz Information Miner KNIME development team
LISREL (“for structural equation modeling”) Scientific Software International, Inc.
LSD (“platform for the development, use and distribution of simulations”) Laboratory for Simulation Development
Lucene (“text search engine library”) Apache Software Foundation
MADARA – Multi-Agent Distributed Adaptive Resource Allocation madara development team
Maple MapleSoft
MariaDB MariaDB Foundation
MASON – Multi-Agent Simulator Of Neighborhoods GMU Evolutionary Computation Laboratory and GMU Center for Social Complexity
MASS – Multi-Agent Simulation Suite AITIA International Inc
MASyV – Multi-Agent System Visualization MASyV development team
Mathcad PTC
Mathematica Wolfram Research
MATLAB The Mathworks, Inc.
MetaSD (“A system dynamics model archive”) MetaSD development team
Mimosa (“modeling and simulation platform”) Mimosa development team and Cirad
Minitab Minitab Inc.
Mobidyc – MOdelling Based on Individuals for the DYnamics of Communities Mobidyc development team
Model Builder Flavio Coelho
ModelMaker The University of Nottingham and FamilyGenetix
ModelMaker Tools ModelMaker Tools
Modgen – Model generator Statistics Canada
MonetDB (“open source column-oriented database management system”) MonetDB development team
MongoDB (“open-source document database, and […] NoSQL database”) MongoDB, Inc.
MySQL Oracle
NetLogo Uri Wilensky, Center for Connected Learning
Network Fluxus Technology Ltd.
Objective C Apple
Octave John W. Eaton
OpenModel The University of Nottingham
Oracle Oracle
Origin OriginLab Corporation
OriginPro OriginLab Corporation
Pajek Batagelj et al., University of Ljubljana, Slovenia
Pandora (“HPC Agent-Based Modelling framework”) Barcelona Supercomputing Center
Perl Perl development team
PostgreSQL PostgreSQL Global Development Group
Ps-i Lustick Consulting
PyDSTool Robert Clewley, GSU
Python Python Software Foundation
R package R package development team
Rational Rose IBM
Repast Argonne National Laboratory
Ruby Ruby development team (Yukihiro “Matz” Matsumoto)
SAS – Statistical Analysis System SAS Institute Inc.
SAS-EM – SAS Enterprise Miner SAS Institute Inc.
SAS-SDS – SAS Scientific Discovery Solutions SAS Institute Inc.
Scilab (“software for numerical computation”) Scilab Enterprises, former Scilab Consortium and Scilab contributors
SCoP – Simulation Control Program Simulation Resources Inc
SeSAm – Shell for Simulated Agent Systems SeSAm development team
SIMCA Umetrics
Simul8 Simul8 Corp
Simulink The Mathworks, Inc.
SOARS – Spot Oriented Agent Role Simulator SOARS Project and Deguchi Lab, Tokyo Institute of Technology
SPADE – Smart Python multi-Agent Development Environment SPADE development team
SPARK – Simple Platform for Agent-based Representation of Knowledge SPARK development team
Spark (“engine for large-scale data processing”) The Apache Software Foundation
Spotfire Decision Site Software TIBCO Spotfire
Spotfire S-Plus TIBCO Spotfire
StarLogo/ OpenStarLogo MIT
Statistica (with Data and Text Miner) StatSoft
STELLA isee systems
StellaR StellaR development team
Sugarscape Sugarscape development team
Swarm Swarm Development Group
SYSTAT Systat Software, Inc.
TerraME TerraME Develppment Team, Federal University of Ouro Preto
Titanium Appcelerator Inc
trex2-agent (“A formal framework for situated agent deliberation and execution”) trex2-agent development team
Visual Studio Microsoft
WinSAAM University of Pennsylvania
Wolfram SystemModeler Wolfram Research

Data Visualization

Resource Developer
ArcGIS (geographical information system mapping and visualization) Esri
ArcPad Esri
Arcv2CAD Guthrie CAD/GIS Software Pty Ltd.
ARES Commander Edition Graebert GmbH
Artboard (“vector-based drawing software” for Mac OS X) Mapdiva, LLC
BioLayout Express3D (“visualization and analysis of network graphs”) BioLayout Express3D Team
Boxshade (“program for creating good looking printouts from multiple-aligned […] sequences”) Boxshade Development Team
CAD Viewer Tailor Made Software
CAD2Shape Guthrie CAD/GIS Software Pty Ltd.
CartoDB Vizzuality team
Cartographica ClueTrust
CartoMobile ClueTrust
ChemPoint (“Environmental Data Management System”) Starpoint Software Inc.
Cytoscape Cytoscape Consortium and Institut Pasteur
DeltaGraph (“combines […] statistical tools with […] data visualization capabilities”) Red Rock Software, Inc.
Didger (“geoprocessing and data conversion tool”) Golden Software Inc.
DIVA-GIS (“mapping and geographic data analysis”) DIVA-GIS development team
Downhole Explorer (“drillhole presentation and plotting program”) Downhole Explorer development team
Encom Discover (“desktop Geographical Information System”) Encom and Pitney Bowes
E-Net (“software for analyzing ego network data”) Analytic Technologies
EVS Pro – Environmental Visualization System Pro – 3D Mapping C Tech
GEON Integrated Data Viewer UNAVCO
Google Earth Pro (“3D interactive globe that can be used to aid planning, analysis and decision making”) Google
Google Map Maker (“allows […] to add and update geographic information for […] users to see in Google Maps and Google Earth”) Google
Grapher – “Graphing software” Golden Software Inc.
GraphPad Prism GraphPad Software, Inc.
Graphviz (“Graph Visualization Software”) Graphviz Development Team
Gwyddion (“a modular program for SPM (scanning probe microscopy) data visualization and analysis”) Gwyddion development team
ImageJ ImageJ development team
IPython – Shell interface for interactive computing in multiple programming languages IPython development team
Java Treeview (“Viewer for Microarray Data in the PCL or CDT format”) Stanford University School of Medicine (A. J. Saldanha) and Java Treeview development team
Krackplot (“Network visualization”) Analytic Technologies
MapBox MapBox team
MapInfo Professional (“desktop mapping application”) MapInfo and Pitney Bowes
MapInfo Vertical Mapper (“tool for geospatial data analysis”) MapInfo and Pitney Bowes
MapTales MapTales team
NCAR Graphics University Corporation for Atmospheric Research
NetDraw (“program for visualizing social network data”) Analytic Technologies
OpenGL (“developing portable, interactive 2D and 3D graphics applications”) Silicon Graphics International Corp. (SGI) and Khronos Group
Origin OriginLab Corporation
OriginPro OriginLab Corporation
Ortelius (mapping software for Mac OS X) Mapdiva, LLC
ParaView ParaView project team
QGIS (“Create, edit, visualise, analyse and publish geospatial information”) QGIS development team
RExcel (Excel add-in to use R from Microsoft Excel) RExcel development team
SigmaPlot Systat Software Inc.
SigmaStat Systat Software Inc.
Soundcities Stanza team
Tableau Tableau Software
Tecplot Tecplot Inc
Visio stencils for UML and SysML Software Stencils development team (P. Hruby)
WellCAD (combines “display, editing and analysis capabilities for well data”) Advanced Logic Technology
WhiteStar data WhiteStar Corporation
Worldmapper (“collection of world maps, where territories are re-sized on each map according to the subject of interest”) Worldmapper Team