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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.
COB editor is a collaborative editor for biological ontology (e.g., Gene Ontology) building. Building on the idea of modular ontology from KR research, it supports multiple people to work on the same ontology.
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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.
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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.
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.
Cellontro models and simulates cells, other biological entities, and biochemical networks. Specify your models using XML and Java, or SBML. Cellontro is now completely contained within the Xholon sourceforge project.
The JChemPaint Applet and Swing Application are Java programs for drawing 2D chemical structures like those found in most chemistry textbooks. It is based on the Chemistry Development Kit (cdk.sf.net). Downloads, tracker, and source code repository can be found on https://jchempaint.github.io
A dialect of XUL implementing most of Mozilla XUL's Fourth Draft. XML User Interface Language (XUL) is a method for easily creating GUI applications. Lux XUL supports Python scripting via Jython 2.1.
PSIMAP is the Protein Structural Interactome MAP, a map of all the domain level protein-protein interactions in the Protein Data Bank (PDB). PSIsoft is an archive of the software used to generate and analyse PSIMAP.
ISYS (Integrated SYStem) is a Java-based plugin framework for loosely-coupled integration of independently developed components. It provides both service-oriented and event-based communication whose semantics may be contributed by component developers.
LineageEvolver is a simulation system for molecular evolution. Sequence evolution is simulated using modular processes such as substitutions, gene duplication/death, horizontal gene transfer, and more.
neochip is a collection of algorithms for high-density oligonucleotide microarrays. The current version contains heuristic algorithms that attempt to improve the quality of arrays by re-designing their layout (the location of the probes on the chip).
JAligner is an open source Java implementation of the dynamic programming algorithm Smith-Waterman with Gotoh's improvement for biological local pairwise sequence alignment with the affine gap penalty model.