Software
Physics/Astronomy
- Space Telescope Science Institute - a link to a variety of software packages
- FITS Liberator - the ESA/ESO/NASA Photoshop tool for processing astonomical images
- ESO's Scisoft - a bundle of scientific software served by the ESO
- PyFITS - part of the bundle
- PyRAF
- STSDAS and TABLES
- Numdisplay
- NumPy - a MATLAB-like package used by Scisoft, but not developed by them
- MultiDrizzle
- stsci_python
- Specview
- StarView
- FITS
- AstroGrid - a software interface to the many Virtual Observatories
Databases
- PostgreSQL - open source database, fast query speed as ranked against other databases
- Berkeley Database - efficient open source database from Oracle
- MySQL - "The world's most popular open source database"
- SQLite - a software library that implements a self-contained, serverless, zero-configuration, transactional SQL database engine
- Java Database - Sun's supported distribution of the open source Apache Derby database
Data Mining Software
- TANGARA - free data mining software
- Orange
- Weka
- RapidMiner - has a free community as well as a commercial enterprise edition
- Sipina - SIPINA is a Data Mining Software which implements various supervised learning paradigms. SIPINA is an academic tool, it is free for all kind of activities.
API Software
- An API for searching Twitter - written by Matt Sanford
Bioinformatics Software
- Bellerophon Server - Bellerophon is a program for detecting chimeric sequences in a multiple sequence dataset by comparative analysis.
- DAMBE, AMIADA, and goldMINER - Dr. Xuhua Xia's tools for data analysis in biology and evolution, analyzing microarray data, and automated gene annotation and classification
- DnaSP - DNA Sequence Polymorphism - a software package for the analysis of nucleotide polymorphism from aligned DNA sequence data
- Sanger Institute - a research genome institute and powerhouse of bioinformatics software
- Sanger Institute's ACT - a DNA sequence comparison viewer based on Artemis
- alien_hunter - an application for the prediction of putative Horizontal Gene Transfer (HGT) events
- DECIPHER - DECIPHER tracks submicroscopic duplications and deletions of DNA in patients together with phenotypes exhibited by those patients
- est_db - software suite and database system designed to support expressed sequence tag (EST) sequencing projects
- EMBOSS - a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole.
- BioPerl - toolkit of perl modules useful in building bioinformatics solutions. Many volunteers have written modules using the tookit.
- Wise2 - compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.
- MEGA - Molecular Evolutionary Genetics Analysis - the primary phylogenetic tree building program
Data Visualization
- Processing - MIT Media Lab's open source data visualization programming environment
- Many Eyes - IBM's Many Eyes is a free online library of tools that give you options for visually exploring all kinds of data - even for analyzing text documents. It also lets you share and embed your visualizations.
- InfoVis Javascript Toolkits wiki page - lots of links to associated toolkits
- JavaScript Information Visualization Toolkit (JIT) - A blog about the JavaScript Infoviz Toolkit and other stuff
- Tamara Munzer's graph tree software packages
- Knime - A data exploration platform that enables the user to visually create data flows, selectively execute some or all analysis steps, and investigate the results through interactive views on data and models.
- Human-Computer Interaction Lab - U. Maryland's data visualization labs. They have developed an array of visualization tools, free for academic use.
- TimeSearcher - visual exploration of large time-series data applied in financial, medical, and genomic domains
- Hierarchical Clustering Explorer - includes a rank-by-feature framework
- Lifelines2 - aids discovery of temporal categorical patterns across multiple records
- Piccolo - A new way to create graphical applications with effects such as zooming, animation and multiple representations.
- UUorld (pronounced world) - provides 3d visualization of geographical data, exportable to Google maps. Free version and pro version.
- amCharts - Generates flash charts and maps for your website. Also provides WPF charts. Free version and pro version.