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The Biomolecule Naming Service (BNS) is loosely inspired by DNS servers used to resolve host names and IP addresses. BNS uses the Lightweight Directory Access Protocol (LDAP) to resolve gene/protein names and identifiers.
Project VDW serves as a repository for all things pertaining to Van Der Waerden sequences. Volunteers to run the distributed client, mathematicians to help with theory, and anyone interested in VDW sequences are welcome!
ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.1 or later. HOME @ http://rsb.info.nih.gov/ij/
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The Comparative Toxicogenomics Database (under development) will be a publicly-available, web-based database of genes and proteins of human toxicological significance. It is being developed using an Oracle 9i database, Tomcat, and Python.
Network Visualization is a mature part of computer science that is enjoying a good deal of growth, partially fueled by Bioinformatics. Network is a synonym for Graph, and both refer to a collection of nodes and edges.
The OO component based XML processing framework.The goal is to make the XML developer's life easier.It's going ot achieve that by providing reusable components for all stages of XML processsing with easy language and application binding.
J-Sim (previously known as JavaSim) is a component-based, compositional simulation environment written in Java. It is built upon the autonomous component architecture (ACA), a component architecture at the implementation level.
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idyuts is \"I Dare You to Use This Shell\"; a pre-hibernate approach to replacing an ORM written with jython functors into a pure-Java language command pattern. The \"pipeline codegen artifacts\" are simple IoC templates, and trivial to adapt
HORUS is a system for knowledge acquisition, hypothesis generation, inference and learning. It is an interactive, internet environment accessible to a diverse community of users (public-access or membership basis) - see also UMKAILASH project for more.
A ContextTree is a way of dynamically forming relationships between information: the same information can be viewed in different ways, depending on what you want from it.
jrgp is a strong-typed Genetic Programming system, which features a graphical interface (gool) to setup and run GP-problems and a tool (fs-d) that greatly simplifies the definition of a GP-problem.
JReferences is a tool to store and retrieve bibliographic references from a file or MySQL database.
It reads BibTeXML, DocBook XML and RIS type references, and can output these and BibTex.
A bibtex like alternative is also provided for DocBook XML docu
Port of Numerical Python to Jython (Java Python) to support all mathematical operations (linear algebra, matrices, DSP, wavelets, FFT, arrays...) and thus compete with commercial packages such as Matlab. It can be easily embedded in Java programs.
A clearing house for various pieces of open source software which use the GenCAM data format for input or output of electronic interconnect (PWB, PCB, PWA, PCA) information.
This is a collection of different little tools written in MATLAB, JAVA, Python. They all have to to do with Imaging & Microscopy for life science research and related topics or problems. Some of them are meant to be used with ImageJ and MicroManager.
aVolve is an evolutionary/genetic algorithm designed to evolve single-cell organisms in a micro ecosystem. It currently uses the JGAP Genetic algorithm, but does include a primitive genetic algorithm written in Python.
this is a small project which provides several mathematical function useful for a chemist or somebody working with mass specs.
The goal is to provide several cuda and c based functions which can be easily accessed using java, groovy and python.
Automated supernova finder is a software package to automatically compare FITS images to a nominated reference image with the aim of finding supernovae or other optical transient phenomena.
The RNA Ontology Consortium proposed a translation the RNA backbone angles to 46 clusters ('suites') and hence unique names. This project calculates the suites from RNA 3D structures, and to search on a Java-based index structure of known folds.
The co-simulation adapation platform serves as programming framework and middleware to enable coupling of distributed, heterogeneous numerical models. The framework facilitates the adaptation and integration of new sub-models into a common simulation platform.
A library for handling vectors, tensors, and more.
VectTens is an object-oriented numerical library designed to manipulate vectors, tensors, and other mathematical quantities in a simple and efficient manner.