The Patient and Sample System for Information Management (PASSIM) is a system for annotation and storage of data, associated with the collection of samples in biomedical studies.
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.
Gridder is a group of portlets that simplify the use and administration of grid services. Especially for job submission management. Gridder also extends and documents the functionality of the OGCE Bundle. It is plenty of useful documentation.
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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.
Chemical Evaluation Framework (CEF) is a molecular structure based software to assist in hazard assessment. Download requires Java 6 update 1. Source code is contained in jar files. Download contains GSH reactivity plugin.
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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.
Open2Dprot is an open-source proteomics project for the development of bioinformatic tools for n-dimensional protein expression data analysis of quantified protein expression across multiple samples from research experiments.
A collection of novel phylogenetics algorithms that assists biologists, geneticists, and bioinformaticians in the analysis and interpretation of phylogenetic data.
SOMMS is an analysis program for mass spectra intended for bio-informatics research. Its goal is to relate theoretical spectra with raw data. A previous version, accompanying an article published in Rapid Comm. in Mass Spectrometry, was written in Perl.
A plugin for segmentation and analysis of images of vascular networks.
A plugin package for ImageJ that assists with quantification and characterization of vascular networks. The tool regularizes lighting, segments the vessels, and generates a skeletal description that reflects the biological structures of interest.
PARs is a bioinformatics tool for the analysis of cis-regulatory DNA sequences. Composed of two parts: a suite of sequence analysis algorithms for predicting cis-binding sites in DNA sequences and a GUI for visualisation and exploration of the results.
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.
Comprehensive Meta Prediction and Annotation Services for Proteins: The new all-in-one prediction tool that can be easily extended to include any SOAP/WSDL-enabled prediction servers. A concise user interface lets you use the results instantly.
The JefNET (Java Evolutionary Framework Network) Proj. consists of three subprojects: JEF, Dna, JXTAJef. Our intent is to provide a distributed genetic programming framework for the Java language, and a network in which classes can spontaneously evolve.
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
The Canopy project is an initiative to merge and expand the functionality of Perl-speaks-NONMEM (PsN), Census, Xpose and PopED. The goal is to produce a coherent, inclusive and convenient platform for pharmacometric data analysis.
BioDOM is a JAVA library for easy creation of XML files according to simple XML schemas for describing biological data. It can also be used to convert other commonly used biological (possibly non-)XML data into these new formats.
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.