21. ALinks - alinks is a set of POJO describing pedigree graphs.
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22. Ambit - chemical structures database - AMBIT consists of a MySQL database and functional modules providing storage of chemical compounds and allowing a variety of flexible structure, similarity and other queries. Written in Java, with the use of The Chemistry Development Kit.
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23. Amino Acid Finder - Ever got confused while remembering all the various physical properties of all the standard 20 amino acids? Then use Amino Acid Finder!!
It has a built-in database and contains information about all the physical properties and lets you to search them
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24. AMORSS: redox enzymes simulation system - This project is A Mitochondrial OxydoReduction Simulation System. It consists of two linked projects: a program for displaying and analysing large biomolecular systems (Floral) and a multi-agent simulator for biomolecular oxydoreduction systems (AMORSS).
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25. Analytical Data Interchange - This project provides open software for working with analytical instrumentation data using the ASTM "ANDI" standard.
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26. Analytical Information Markup Language - This project supports ASTM E13.15 "Analytical Data Magement" in it's work defining AnIML, an XML standard for representing, managing and interchanging analytical chemistry data.
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27. Anna - Anna is lightweight Java framework to build pipeline systems of any kind.
It will take care of recurrent needs such as dependency management, data serialisation and synchronization as well as parallelization of execution.
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28. AnnaF - AnnaF is an automatic gene annotation framework, that is used to do some automatic annotation for C. higginsianum. It was also tested on F. graminearum and should work well for fungi in general.
AnnaF was build upon the pipeline framework Anna.
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29. Annotated Gel Markup Language Project - 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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30. AnnotationQuery - A command-line program to manipulate annotated genetic sequences (initially in EMBL format). The user supplies a pattern to identify which features or qualifiers to process. These can then be deleted, renamed etc
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31. Anthill - Anthill is a framework to support the design, implementation and evaluation of P2P applications based on ideas such as multi-agent and evolutionary programming borrowed from the complex adaptive systems area.
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32. Antimony - Antimony is a human-readable, human-writable model definition language. libAntimony is a library that will read and write Antimony and SBML files and provides an API for other programs to import Antimony models into their own internal formats.
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33. APBS - APBS is a software package for the numerical solution of the Poisson-Boltzmann equation, a popular continuum model for describing electrostatic interactions between molecular solutes over a wide range of length scales. <http://apbs.sf.net/>.
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34. Aqua - AQUA is a suite of programs for Analyzing the QUAlity of biomolecular structures that were determined via NMR spectroscopy. AQUA was developed by Ton Rullmann and Jurgen Doreleijers in the NMR Spectroscopy Department, Utrecht.
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35. Arcadia - Arcadia is a light-weight, cross-platform, C++ desktop application designed for visualizing biological networks such as metabolic pathways.
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36. Area-split proportional to pointinfluenc - Acre calculates growing-space or stand-density of trees and creats pictures of it. It can also be used to calculate weighted Voronoi-Diagrams (splits up an area to the neares point or to the point with the greatest influence at a certain place).
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37. array2net - Array2Net is a tool for visualizing gene co-expression network of expression profiling data.
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38. ArrayExpress Tab2MAGE - Tab2MAGE uses a flexible spreadsheet format for MIAME annotation of microarray experiments. Tab2MAGE spreadsheets may be submitted directly to ArrayExpress, or used to generate MAGE-ML for data exchange.
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39. ArrayPipeline - ArrayPipeLine is a web-based Laboratory Information Management system, using MySQL, Perl CGI and R. It enables high-throughput analysis of microarray data, providing automation of data handling, and rapid creation and implementation of analysis pipelines
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40. arrayplex - ArrayPlex integrates various forms of microarray data from diverse annotation and primary data sources. It provides a programmatic framework (API set) for collaborative development and deploys as easy to maintain client-server architecture.
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