Open Source Java Bio-Informatics Software

This ohnlp project has released "pipelines" that were contributed by members of the OHNLP Consortium. The pipelines are based on the Apache UIMA framework. medKAT/P, MedCoref, MedTagger, MedXN, and cTAKES are licensed under Apache License V2.0. MedTime is licensed under GNU General Public License version 3.0 (GPLv3). cTAKES development has moved to apache.org. See http://ctakes.apache.org/

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, ...

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.

FM100 is a computer simulation of the Farnsworth-Munsel 100 hue colour (color) vision test. The results of the test can be used to assess the user's colour vision.

User friendly PDB (Protein Data Bank) file editor with graphic user interface for protein crystallographers to expedite selective parallel edit / data extraction / analysis of their PDB files

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

http://www.princeton.edu:80/pr/pwb/01/0326/1b.shtml http://www.cs.princeton.edu/immsim/ Immsim is an immune system simulation used by Immunology students and researchers. Currently it is being used at Princeton University.

Tree Growth Open Source Software is a Java based version of the forest growth simulator for north west Germany BWINPro.

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)

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

In addition to computing co-expression clusters, Maccu fishes potential co-expressed genes for a given bait set. All results can be further processed via graph-level operations so that we can compare graphs based on different reference data.

In addition to RPKM (Reads Per Kbp per Million reads) values, RACKJ computes read counts for exons and splicing events. In so doing, it is feasible to compare two samples and identify genes with most significant difference in exon(splicing)-level.

VitaPad is an application used to visualize biological pathways and map experimental data to them

The final build of this software now is distributed in R, embedded in "RedeR': an R/Bioconductor package for hierarchical and nested network analysis... more about RedeR: http://bioconductor.org/packages/2.9/bioc/html/RedeR.html

A Java library to facilitate SED-ML support for systems biology applications to read, validate, edit, and write SED-ML documents in compliance with MIASE guidelines. Also contains modules to execute simulation tasks and produce outputs. This project also contains the SED-ED editor application for SED-ML.

As of 2018-06-28, this project has moved to https://github.com/AdamaJava. This copy of the code will remain but all new code updates and releases will be from the new site. Java code developed by the Australian ICGC team for operating on next-generation sequencing data. This code is currently being maintained and expanded by the QIMR Berghofer Genome Informatics team (http://www.qimrberghofer.edu.au/lab/genome-informatics/) More details and documentation can be found on the wiki: http://sourceforge.net/p/adamajava/wiki/Home/

Agent-based multiscale model of cancer proliferation dynamics

Projet de 2e année d'ingé

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.

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

BioX (pronounce as bio cross) is a system for the management of local and remote (currently supporting RMI, CORBA and SOAP Web Services) components such as files and services (e.g. BLAST). Additionally, the components can be composed to workflows.

Biogranat (Molecular Biology Graph Visualisation and Analysis Tool) is a new tool for the analysis and visualisation of large datasets.

A biobank registry system for handling data regarding human biological samples.

CB-Commander is a plugin based tool that tries to integrate high throughput sequencing algorithms. It allows researchers to design and execute their experiments through a user friendly interface.