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STJUDE-SRM is a laboratory management system designed to support shared resource facility (or core lab) activities. It was designed and developed by the Hartwell Center for Bioinformatics and Biotechnology at St. Jude Children's Research Hospital.
GSCope3 performs microarray data analysis to find correlations between BLSOM clusters and any form of omic knowledge expressed in OSML. Includes example metabolic pathway, gene ontology, genome position, transcription and PPI knowledge in OSML format.
Spectre for mass spectrometry. (Quantitiave) analysis of multiple ls-ms(ms) runs, using mzXML import of raw data. (working on mzDATA). Provides filters, alignment- and export tools.
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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.
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.
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.
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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.
This software is to help the those connected with Biology,Biotechnology,Bio Informatics.The user can select from the choices of proteins, nucleotides,etc(All those found on NCBI's website)and search for the specific results
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.
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.
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.
PANDA (Protein And Nucleotide Data Archive) unifies the archival of the sequences from Taxonomy,GenBank,RefSeq,UniProt,PDB,and PRF on a regular interval to build and maintain a Protein and Nucleotide data archive. This project is part of BRC project fund
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.
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.