Open Source Java Information Analysis Software for BSD

Framework for text mining, data integration and data analysis. Keywords: ontology and graph alignment, relation mining, warehouse, semantic database integration, bioinformatics, systems biology, microarray, Java.

Thea, Tools for High-throughput Experiment Analysis, is an integrated information processing system dedicated to the annotation of data issued from classification systems with biological information coming from a knowledge base.

Annotated Gel Markup Language is a simple markup language that is being proposed to markup data obtained by 2D gel electrophorosis.The goal of AGML is to enable proteomics research move into the browsing mode of searching through existing databases.

FORce based Cluster Editing (FORCE) is a Java software heuristically solving the graph cluster editing problem on weighted edges using BLAST E-values. It further provides a training mode for heuristic parameter estimation.

Sequence studio main package provides classes and interfaces for various kinds of sequence alignment. Differently from regular expressions it computes similarity with two initially unknown strings. Project page provides code generating applet.

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.

Workbench for visualizing biological networks (regulatory, interaction, and metabolic). Can be used as a front-end for BNDB datawarehouses, but also as stand-alone tool.

The CHIP Cluster Generator attempts to create spatio-temporal cluster data in an automated fashion to help evaluate epidemic detection software. The spatio-temporal data will then be used to determine robustness of spatial detection algorithms.

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.

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.

Use statistical methods to analyze time-course data (gene expression microarray and RNA-seq data in particular, but not limited to). Apply significance tests to filter out only significant genes or time series. Cluster time series into similar groups. Generate network models, including linear or non-linear models. Variable selection and optimization routines included. Written in Scala and R. The application is a cross-platform desktop app with a simple GUI and is fully functional currently. The app was and is developed at the University of Rochester (http://cbim.urmc.rochester.edu) under the GPL 3.0 license. This is a fork of that project.

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.

The Genomic Diversity and Phenotype Data Model (GDPDM) captures molecular and phenotypic diversity data. MySQL databases are used to implement the schema. This project develops software tools (written in Java, Perl, etc.) associated with this model.

GeNetDB, contraction of Genetic Network Database, is a bioinformatic platform destined to the study of genetic regulatory networks. It contains in one place the data and the way to study them, providing the user an access to all tools needed for his work

Executable program that measures sizes and other properties of colonies arrayed in a grid format (intended for 768, 384, or 96 colonies on agar plates) from jpeg images

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

Jeep is a modular, abstract and distributed evolutionnary programming core written in Java, allowing to grow autonomous agents as well a gene pool (as in genetic algorithms).

MASQOT-GUI is an open-source, platform-independent application for two-channel microarray spot quality control. Included is a set of tools for gridding, segmentation, quantification, multivariate spot quality assessment and data visualization.

MicroArray Genome Imaging and Clustering Tool (MAGIC tool) is a platform-independant java program for analyzing MicroArray data (.tiff scans & .txt godlists) via graphs and clustering operations (including QT-clustering). http://www.bio.davidson.edu/magic

NeoBio is a Java class library of Computational Biology Algorithms. The current version consists mainly of pairwise sequence alignment algorithms such as the classical dynamic programming methods of Needleman-Wunsch and Smith-Waterman.

OBOES (Open Biomedical Ontology-Based Enrichment and Search) is an information-theory-based platform that embeds new integrative methods allowing biologists to evaluate new hypotheses.

PIVOT is a simple yet flexible visualization tool based on Circos (Krzywinski et al., 2009), which offers a fast and aesthetical visualization of data and information. The Protein Interaction Visualization and Observation Tool (PIVOT) was developed specifically for the visualization of protein interaction. It is difficult to spot the proteins that have an interaction when given a large list of proteins but with PIVOT, it is easy to identify the them at a glance. PIVOT displays an image showing all the proteins and draws a connection between proteins that have an interaction.

PROMPT is a system for retrieval, analysis, mapping and comparison of proteins. It allows easy mapping of different types of sequence IDs, data retrieval and integration, a multitude of analysis and comparison algorithms and a full-blown easy to use GUI.

Phenex is an application for annotating taxa and phenotypes in character matrix files with ontology terms. Phenex saves ontology annotations alongside traditional character matrix data using the NeXML format standard for evolutionary data. Current Phenex development is taking place at GitHub: https://github.com/phenoscape/Phenex

The Phenoscape project attempts to formalize the description of evolutionary characters to make them interoperable and computable with the body of phenotype annotation being generated by model organism databases, and other biomedical research.