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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.
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.
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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.
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.
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.
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This software system serves as both a DICOM image viewer as well as a diagramming tool for collaborating notes on the given image sets. This my Computer Science graduate thesis project at Loyola Marymount University.
GeXpert is an expert system that can be used for genetics and metabolic pathway analysis. GeXpert can help Biotechnologists do their work faster, reducing the time required for performing, analyzing and storing the results of Bioinformatics research.
The BGSSJ allows for easy and interactive querying using different gene identifiers (GenBank ID, UniGene, SwissProt, gene symbol), generates a summary page with listings of the frequencies of Gene Ontology annotations for each functional category (cluste
TRANSFOG DAS (Translational and Functional Onco-Genomics Distributed Annotation System) is an XML-based annotation system to allow the discovery and analysis of candidate genes potentially involved in cancer onset and progression.
Manuelito is a Java tool for decrypting posttranslational modification (PTM) patterns of proteins based on MALDI mass spectrometry spectra. It was built for analysing the 'histone code' but it can be applied to any other highly modified protein.
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)
Microarray Explorer (MAExplorer) is a Java microarray data-mining bioinformatics program.
It includes data management, graphics, statistics, clustering, reports, gene data-filtering, user
written MAEPlugins, documentation, tutorials, demo data.
CompuCell3D is a software framework for multimodel simulations of biocomplexity
problems. It has been developed as an ongoing project for the Interdisciplinary Center
for the Study of Biocomplexity at the university of Notre Dame.
SENTENSA Knowledge Miner is a platform independent tool for searching any text. SENTENSA uses robust methods of indexing and searching text, leveraging on experience from more than 20 years of information retrieval.