Software Development Software Bioinformatics

For sites that offer resources for developing bioinformatics software, such as APIs, libraries, etc. etc.

• Top/Computers/Open Source
• Top/Computers/Programming

• AcePerl - OO Interface to AceDB
  
• The XEMBL Project - XEMBL provides access to the EMBL/GenBank/DDBJ Nucleotide Sequence Database, providing output in various XML standards.
  
• The Darwin Manual - Guide to running this programming language. Library contains programs to compute pairwise alignments, phylogenetic trees, multiple sequence alignments, and to make secondary structure predictions.
  
• Bielefeld University Bioinformatics Server - BiBiServ supports Internet-based collaborative research, software development and distance education in bioinformatics.
  
• The Scriptome - A set of software tools that filter, format, and merge data in tabular or common biological formats. Organized as a classified collection of Perl one-liners.
  
• Cell Electrophysiology Simulation Environment (CESE) - A framework to perform electrophysiological simulations. Useful for simulations of action potentials, individual ionic currents, and changes in ionic concentrations.
  
• NCICB Core Infrastructure - The National Cancer Institute's Center for Bioinformatics produces the caCORE infrastructure, an open-source enterprise architecture for cancer informatics.
  
• DW Computing - Web design, computer sales, and custom programming, including bioinformatics.
  
• Bionconductor - The Bioconductor project produces an open source software framework that will assist biologists and statisticians working in bioinformatics, with primary emphasis on inference using DNA microarrays, built mostly using R.
  
• Brainwave Biosolutions - Bioinformatics Company focused on the development of data mining products, databases, visualization and analysis tools.
  
• MolTalk - Software development for structural bioinformatics. Runs on Unix, Windows and MacOSX.
  
• BioPHP - An open source project to develop PHP code and scripts for biocomputing. A wiki-like service allows collaboration between developers.
  
• The Systems Biology Markup Language - Information on the SBML project which helps develop a variety of software packages for SBML, a computer-readable format for representing models of biochemical reaction networks in software.
  
• BioRuby - BioRuby project aims to implement an integrated environment for Bioinformatics with Ruby language.
  
• BioWarehouse Database Integration System - Integrates multiple public bioinformatics databases into a single relational database system within a common bioinformatics schema.
  
• BioJava.org - The BioJava Project is an open-source project dedicated to providing Java tools for processing biological data.
  
• Pathway Tools - Predict metabolic pathways from genomes and graphically depict pathways. Visualize gene expression data on a metabolic pathway map. Generate a metabolic wall chart. Includes a genome browser and support for transcriptional regulatory networks.
  
• BioPython - The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.
  
• Biochemical Algorithms Library - C++ framework for rapid software prototyping in molecular modeling.
  
• The BioSharp Project - BioSharp is an open-source project to provide a framework for processing biological data using C# and other .net languages.
  
• Phylogenetic Analysis Library - PAL library is a Java toolkit for determining evolutionary trends.
  
• NeoBio - An open source library of Java bioinformatics algorithms. The current version consists mainly of sequence alignment algorithms such as Needleman- Wunsch and Smith-Waterman.
  
• AceDB - A hierarchical database system for displaying genomic data (originally C. elegans), suitable also for displaying other scientific data.
  
• BioQuery - Tools that searches multiple biomedical databases from your desktop.
  
• EST2uni - A tool to analyze a set of ESTs. Cleans, clusters and annotates the sequences and prepares a web site to browse the results in a complete automatic way.
  
• High Throughput Screening Tools - Analytical tools and SQL scripts that solve common problems in drug discovery.
  
• Sight - Extendable parallel system for automatic genome analysis. Software for analysing all potential genes in a defined genome region. Given two marker names, can output reports of genomic features between them. Features for converting between naming systems, s
  
• InterMine - A general-purpose object-oriented data warehouse system developed as part of the FlyMine project and made available as stand-alone open-source software.
  
• Dynamite - Code generator for writing dynamic programming programs.
  
• JCell - A Java based framework to reconstruct genetic interactions from microarray data.
  
• BioLisp.org - BioLisp.org is a public resource supporting scientists who use Lisp to develop intelligent applications in the biological sciences. We collect and disseminate Lisp biocomputing code, and gather pointers to Lisp and other Intelligent BioComputing methods.
  
• PISE - Given an abstract definition of a program's parameters, PISE can generate whatever style of interface from the configuration module.
  
  

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