Open Source Java Simulation Software

JGAP is a Genetic Algorithms and Genetic Programming package written in Java. It is designed to require minimum effort to use, but is also designed to be highly modular. JGAP features grid functionality and a lot of examples. Many unit tests included. Legal notice/Impressum: Klaus Meffert An der Struth 25 D-65510 Idstein sourceforge <at> klausmeffert.de

Important: Groimp migrates to Gitlab. You can find the latest code at "https://gitlab.com/grogra/groimp/". The version on Sourceforge will not be updated anymore. The modelling platform GroIMP is designed as an integrated platform which incorporates modelling, visualisation and interaction. It exhibits several features which makes itself suitable for the field of biological or ALife modelling: The “modelling backbone” consists in the language XL. It is fully integrated, e.g., the user can interactively select the rules to be applied. GroIMP provides classes that can be used in modelling: Turtle commands, further geometrical classes like bicubic surfaces, the class Cell which has been used in the Game Of Life implementation, and so on. The outcome of a model is visualised within GroIMP. In the visual representation of the model output, users can i

IDL specified API for manipulating and processing CellML 1.0 and 1.1. Includes C++ implementation. Accessible from a C++ program, or from any language for which a CORBA language mapping is available Also, a Java wrapper of the API is available.

DimReduction project provide an open-source multiplatform (Java) graphical environment for bioinformatics problems that supports many feature selection algorithms, pattern recognition techniques, criterion functions and graphic visualization tools.

JBioFramework (JBF) is a set of two different chemical separations simulations (2D Electrophoresis and Mass Spectrometry) that are frequently used in chemistry, biochemistry and proteomics research. It is written in the Java programming language and will run on any and all systems that have the JVM installed. As we continue to develop the software over the coming months/years and attempt to quantify the success of our efforts with testing and reviews, user input is very important. Please don't hesitate to review the software below or email Paul Craig [pac8612@rit.edu] with larger descriptions/bugs/feature ideas. Our next scheduled release will contain (in addition to 2DE and MassSpec) a 1D Electrophoresis simulation as well as a tab containing ChemAxon's MarvinSketch [http://www.chemaxon.com/products/marvin/] along with some improved functionality. It should be out shortly as we complete the creation and modification of a permanent domain for the project.

Meredys (MEsoscopic REaction DYnamics Simulator) is a particle based stochastic simulation software designed to model and simulate reaction-diffusion systems. (http://www.ebi.ac.uk/compneur-srv/meredys.html)

Narrator is a graphical modelling tool for the description of dynamical systems and processes. Narrator is SBML compatible.

4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid (stochastic and deterministic) modeling and simulation of (whole) cell environments in 4D. The framework may incorporate any reaction and diffusion algorithms applicable in a 4D grid layout.

Agent-based multiscale model of cancer proliferation dynamics

AgentCell is an agent-based model of cellular biochemical processes and biological behavior.

The Automated Life Ecosystem Simulator is a microbe simulation environment developed in Java.

Basic life is an application that desires to simulate basic life based on some basic chemistry/physics rules. This environment provides particles that can bond, vibrate, react, etc. in order to create basic cells

BiVeS - Biochemical Model Versioning System BiVeS is a tool based on the XMLDiff algorithm. You can think of it as a kind of SVN for models with biological or chemical background encoded in XML.

BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. Models presented are annotated and linked to relevant data resources and are available in various format

The BioSimz project aims to deliver a library (as well as the interface) to conduct large-scale biomolecular simulations at their atomic scales of detail. The initiative idea is to observe the protein crowding in vivo; it now can do much more than that!

Cell Electrophysiology Simulation Environment (CESE)

This software enable cannabis grower to manage and retrieve statistics about culture, tools included have the goal to help growing indoor cannabis.

The target system of this project is to develop mathematically efficient program code generator from cellml like biological models described by mathematical markup languages.

Cervelletto is a neural network simulator. It uses a new neural model based on biological, neurological and psychological studies. [it's not yet completed... just give me some weeks! sorry!]

Software suite for cell modelling

Discrete Event System Specification (DEVS) combined with System Biology Markup Language (SBML) project: a Java-based tool to solve complex biology processes. Support by RTSync Corporation and Arizona Center for Integrated Modeling & Simulation (ACIMS)

DawgPack is an ultra-fast, Cloud-based tool that maps many high coverage genomes and performs analysis to find clues for pathogenesis. It will integrate CNV, SNP, RNA-Seq and ChIP-Seq analyses.

The Disease Simulation Framework (DiSiF) represents a spatial simulation environment for infectious viral disease spread. The framework currently embodies a very simple framework for simulation in 2D space with focus on SARS and the Common Flu.

This is a computer model to study Evo-devo. It is the software of a project described in PLoS Computational Biology.

A platform for the integration of deterministic and stochastic models, for the simulation of the integrated models and for interactive exploration of the model behaviour.