Open Source Java Bio-Informatics Software for Windows

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

openModeller is a complete C++ framework for species potential distribution modelling. The project also includes a graphical user interface, a web service interface and an API for Python.

The objective of this project is to make available an open-source version of our Multifactor Dimensionality Reduction (MDR) software. MDR is a nonparametric alternative to logistic regression for detecting and characterizing nonlinear interactions.

A minimalist approach to share text documents and data annotations. Allows a large number of different annotations to be represented. Project files contain: - simple code to hold/read/write data and perform sample processing. - BioC-formatted corpora - BioC tools that work with BioC corpora BioC goals - simplicity - interoperability - broad use - reuse There should be little investment required to learn to use a format or a software module to process that format. We are interested in reuse, and we focus on common NLP tasks that are broadly useful for textmining.

The source code has been migrated and is now hosted on Github: https://github.com/jenetics/jenetics Jenetics is an advanced Genetic Algorithm, Evolutionary Algorithm and Genetic Programming library, respectively, written in modern day Java. It is designed with a clear separation of the several algorithm concepts, e. g. Gene, Chromosome, Genotype, Phenotype, Population and fitness Function. Jenetics allows you to minimize or maximize the given fitness function without tweaking it. In contrast to other GA implementations, the library uses the concept of an evolution stream (EvolutionStream) for executing the evolution steps. Since the EvolutionStream implements the Java Stream interface, it works smoothly with the rest of the Java Stream API. Other repositories: - https://github.com/jenetics/jenetics Maven: - https://mvnrepository.com/artifact/io.jenetics

Java Machine Learning Library is a library of machine learning algorithms and related datasets. Machine learning techniques include: clustering, classification, feature selection, regression, data pre-processing, ensemble learning, voting, ...

CILib is a framework for developing Computational Intelligence software in swarm intelligence, evolutionary computing, neural networks, artificial immune systems, fuzzy logic and robotics.

Conrad is both a high performance Conditional Random Field engine which can be applied to a variety of machine learning problems and a specific set of models for gene prediction using semi-Markov CRFs.

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

Java/XML toolkit for research using Bayesian networks and other graphical models of probability (exact and approximate inference, structure learning, etc.)

This is a Java-based project for complex event extraction from text and co-reference resolution. Currently the code can read BioNLP shared task format (http://2011.bionlp-st.org/) and i2b2 Natural Language Processing for Clinical Data shared task format (https://www.i2b2.org/NLP/DataSets/Main.php). Event extraction includes finding events and the parameters for an event in a text. The method is based on SVM but other ML algorithms can be adopted. The method details are explained in the following paper: Ehsan Emadzadeh, Azadeh Nikfarjam, and Graciela Gonzalez. 2011. Double Layered Learning for Biological Event Extraction from Text. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistic

The BioNLP UIMA Component Repository provides UIMA wrappers for novel and well-known 3rd-party NLP tools used in biomedical text prosessing, such as tokenizers, parsers, named entity taggers, and tools for evaluation.

Contextor is a light-weight simple-to-use Java based library to help developers and researchers working with the general concept of a resource; as examples, resources can be text resources, web resources, images and videos.

Java API for implementing any kind of Genetic Algorithm and Genetic Programming applications quickly and easily. Contains a wide range of ready-to-use GA and GP algorithms and operators to be plugged-in or extended. Includes Tutorials and Examples.

Set of Java packages to apply Genetic Algorithms to any kind of problem. Various genetic operators are implemented and an example shows of how the system could be applied to digital circuit evolution.

JGAL is a Java Genetic Algorithms Library.

OntoCardio is an initiative to build ontologies for the legacy Cardio Database (Resource of bioinformation on cardiovascular diseases). SMI's Protege and its OWL plug-in has been adopted as the ontology construction and programming framework.

Protege is a free, open-source platform that provides a suite of tools to construct domain models and knowledge-based applications with frame-based and Semantic Web ontologies.

Agent-based multiscale model of cancer proliferation dynamics

Bayesian Network tools in Java (BNJ) is an open-source suite of software tools for research and development using graphical models of probability. It is published by the Kansas State University Laboratory for Knowledge Discovery in Databases (KDD).

It moves by itself inside networks like virus infection & plagues, it is being written to solve computer virus problem drastically and responsibly. It is legal, free and open for public domain to improve W3 ICT Security.

BorderFlow implements a general-purpose graph clustering algorithm. It maximizes the inner to outer flow ratio from the border of each cluster to the rest of the graph.

CEGA is a highly extendable layout plugin for Cytoscape based on an Evolutionary Algorithm. In contrast to other layout algorithms, CEGA lets users decide which features are important for the visualization of their graphs.

Darwin 2: Java Framework for Evolutionary Computation (genetic algorithm, GA). A true framework with out-of-the-box functionality and extensibility of all classes. Interface-based pattern with dependency-injection to configure components.

DrPangloss is a python implementation of a three operator genetic algorithm, complete with a java swing GUI for running the GA and visualising performance, generation by generation