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Java/XML toolkit for research using Bayesian networks and other graphical models of probability (exact and approximate inference, structure learning, etc.)
Simulare is a simulation engine and application built on java. At first it'll simulate an aquarium but planned to evolve latter. One objective is a simple UI so everybody can use it. Imagine a fish farmer optimizing his production with this software! ;)
EcoloSim is a Simulation Framework for simple spatial models in biology and ecology, in Java.
Typical problems are behavior of a herd of cattle, growth of microbe cells and other populations.
Annotated Gel Markup Language is a simple markup language that is being proposed to markup data obtained by 2D gel electrophorosis.The goal of AGML is to enable proteomics research move into the browsing mode of searching through existing databases.
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Jaybird is java-language based, source & xml & codebyte class inter-converting tool.
You can write your Envolvable Code with it;
You can make your computer write program itself;
You can run program without compiling time;
You can manage source as data
...BioSap selects unique oligos for microarrays by detecting user-defined parameters and running parallel instances of Featurama and Blast on compute engines, producing xml output files.
Cooperative effort to develop a Java-XML API and architecture to manage and share health concepts and processes eficiently. Includes a framework to develop healthcare applications (from PDA reminders to hospital information systems) quickly and easily.
The SchemaWalker is a Java application able to read a any schema and produce XForms web pages for user selected nodes grouped into webpages to allow editing of XML data files.
A simple tool for molecular biologists (or similar) to estimate the size of electrophoresis gel bands. This can be applied to SDS-Page-,Native-Protein-, DNA, RNA, *whatever* gels as long as a weight/size standard lane is present on the gel.