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The Self-Organizing Map Maker for Education and Research. Features include 3D-visualization of the training process, various 2D and 3D map topologies, easy extensibility to additional topologies.
Modern MATLAB-based modelling software for 13C metabolic flux analysis (MFA).
Support available in Google group (https://groups.google.com/d/forum/13cmfa-openflux).
PAICE is a rapid bioinformatics pathway visualization tool for KEGG-compatible accessions derived from Illumina Solexa next-gen and Affymetrix datasets. It colors KEGG pathways while appreciating detection-calls and duplicate gene copies.
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A bioinformatics tool for the annotation and tag-counting of next-gen Illumina Solexa datasets. TASE works with CASAVA 1.0 builds, providing annotation, tag counts and visualization in a rapid manner.
Cca-forum unifies the Common Component Architecture tools and tutorial. It includes the CCA specifications, the Ccaffeine framework for HPC, and related tools. These support multilanguage scientific and parallel computing.
A web based information management system for macromolecular (protein) crystallography X-ray experiments.
This project has moved to https://forge.ill.eu/projects/ispyb
NMRShiftDB is an open-source, open-access, open-submission, open-content web database for chemical structures and their nuclear magnetic resonance data.
A collection of applets used to demonstrate physics and math principles. The applets include: a ray diagram drawing applet, a collision of disks applet, an electromagnetic field mapper and a 3d hydrogen orbital simulation.
Meredys (MEsoscopic REaction DYnamics Simulator) is a particle based stochastic simulation software designed to model and simulate reaction-diffusion systems. (http://www.ebi.ac.uk/compneur-srv/meredys.html)
4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid (stochastic and deterministic) modeling and simulation of (whole) cell environments in 4D. The framework may incorporate any reaction and diffusion algorithms applicable in a 4D grid layout.
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 bi-directional BLAST tool for orthologue listing with extended facilities (global alignment; paralogue list; GO onthology; dN/dS; etc) working on Win32 compiled versions of NCBI BLAST,FASTA,EMBOSS, and PAML. FILES AVAILABLE AT THE HOMEPAGE.(JAVA coded)