Open Source Java Bio-Informatics Software

The Chemistry Development Kit (CDK) is a scientific, LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java. The main home page of the CDK is now at: http://cdk.github.io

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

An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).

This is a framework used to decompose hierarchical graphs, i.e.,graphs which were created from or contain a hierarchy of modules. Each module is reused several times in the hierarchy. This may be useful to reverse-engineer human constructs like electronic equipment, manufactured machines, or bureaucratic hierarchies; but also to decompose natural constructs like gene-relation or protein-relation nets.

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, ...

The Systems Biology Workbench(SBW) is a framework for application intercommunications. It uses a broker-based, distributed, message-passing architecture, supports many languages including Java, C++, Perl & Python, and runs under Linux,OSX & Win32. It comes with a large number of modules, encompassing the whole modeling cycle: creating computational models, simulating and analyzing them, visualizing the information, in order to improve the models. All using community standards, such as SED-ML, SBML and MIRIAM.

ISYS (Integrated SYStem) is a Java-based plugin framework for loosely-coupled integration of independently developed components. It provides both service-oriented and event-based communication whose semantics may be contributed by component developers.

JOELib/JOELib2 is a cheminformatics library which supports SMARTS substructure search, descriptor calculation, processing/filtering pipes, conversion of file formats, 100% pure Java, and interfaces to external programs (e.g. Ghemical) are available.

Parsers for biological data based on scanner generators like Flex (C), Re2c(C), Jflex (Java) and Ifickle (Tcl). This scanner generators are providing easier maintainance, development and higher speed than hand written scanners. Scanner output is SQL.

Object oriented reusable software classes designed to be used to construct larger software projects developed in multiple software languages.

AJT is a set of utility classes for Java for handling some bioinformatics data, graphics file export, GUI widgets, and classes that should long have been added to the official Java API.

Anna is lightweight Java framework to build pipeline systems of any kind. It will take care of recurrent needs such as dependency management, data serialisation and synchronization as well as parallelization of execution.

Avian Freeware Suite (AFS) provides two things: Developers with libraries for Java Swing Widgets, XML handling, Fortran95 and Pascal; End users (Medical students, doctors, scientists) with productivity tools they can use (quizzes, XML databasing & PDF)

The BMF is a Software Framework developed in Java language for the creation of web applications on the server platform also Open source, in clinical, administrative and management for a healthcare company.

Basic Electronical Medical Management (BEMM) is an application to control medical data of a set of patients. It is built on top of open source technologies, to provide an integration skeleton of mvn, Datanucleus, Spring, Vaadin, Acceleo technologies.

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.

The BioUtils - Proteomics package is a lightweight Java framework for handling commonly used data produced and needed in the field of Mass spectrometry in general and especially in the field of Proteomics. It's stable, intuitive to use and good integrated with Java 6 SDK and later.

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.

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

A comparative map and trait visualization framework enabling visual integration of genomic data from disparate data sources and allowing rich client-side interactivity and manipulation. Extensible through plugins for new datasources and algorithms.

CSBI is a component based framework that allows for inter-component data sharing and access. GINY is an Open Source Graph Library.

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.