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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.
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.
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.
Total Network Visibility for Network Engineers and IT Managers
Network monitoring and troubleshooting is hard. TotalView makes it easy.
This means every device on your network, and every interface on every device is automatically analyzed for performance, errors, QoS, and configuration.
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.
By integrating heterogeneous original data with uniform RDF format, creating additional ontology mappings between GO terms, and introducing a set of reasoning rulebases, we proposed a RDF model GORouter.
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.
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.
TaxonDNA is a simple but extensible system for performing simple DNA (and other) sequence manipulations in Java. We hope to create a simple framework which can be quickly extended to create bioinformatics applications.
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.
Osprey is a software platform for visualization of complex interaction networks. Osprey builds data-rich graphical represetations from Gene Ontology (GO) annotated interactions maintained by the BioGRID.