228 projects tagged "Bioinformatics"

No download Website Updated 05 Aug 2010 CellProfiler

Pop 23.02
Vit 2.11

CellProfiler is a system for analyzing cell images. It is designed for biologists without training in computer vision or programming to make quantitative measurements of cells in thousands of images automatically. It is implemented using Matlab, but compiled standalone versions are available.

Download Website Updated 22 Jul 2010 COPASI

Pop 24.08
Vit 3.10

COPASI is a software application for modeling and simulation of biochemical networks. The software package has a GUI that lets users define biochemical network models by entering chemical reactions and kinetic equations. A powerful simulation engine can then perform simulations of the dynamics of the networks and carry out many different computational analyses. COPASI can simulate dynamics using either an ODE approach or a stochastic chemical kinetics approach (Gillespie-type algorithms).

Download Website Updated 24 May 2010 OBSearch

Pop 37.15
Vit 2.90

OBSearch is a distributed similarity search index. It can (for example) match programs and help to detect Open Source/Libre license violations, find music that sounds like Sisters of Mercy, or match huge vectors of randomly generated integers just for fun.

Download Website Updated 20 Apr 2010 SIBsim4

Pop 17.92
Vit 5.39

The SIBsim4 project is based on sim4, which is a program designed to align an expressed DNA sequence with a genomic sequence, allowing for introns. SIBsim4 is an extensive rewrite of the sim4 program to improve execution speed and provide more informative output.

Download Website Updated 09 Apr 2010 Blossoc

Pop 20.20
Vit 5.94

Blossoc is a linkage disequilibrium association mapping tool that attempts to build (perfect) genealogies for each site in the input, score these according to non-random clustering of affected individuals, and judge high-scoring areas as likely candidates for containing disease affecting variation. Building the local genealogy trees is based on a number of heuristics that are not guaranteed to build true trees, but have the advantage over more sophisticated methods of being extremely fast. Blossoc can therefore handle much larger data sets than more sophisticated tools, but at the cost of sacrificing some accuracy.

Download Website Updated 01 Apr 2010 Xholon

Pop 28.88
Vit 2.77

Xholon is a flexible tool for multi-paradigm (UML 2, ABM, SBML, NN, GP, PSys, CA, etc.) modeling, simulation, design, execution, and transformation. It is based on generic Java and XML building blocks, and optionally packaged as an Eclipse plugin for UML/SysML/FSM simulation. The Xholon project explores the idea of software as systems of linked nodes, organized hierarchically. The Xholon toolkit supports this back-to-basics approach, and demonstrates practical benefits through examples from numerous domains.

No download Website Updated 22 Mar 2010 Ascalaph

Pop 21.31
Vit 39.11

Ascalaph is a general purpose 3D graphical molecular modeling suite that performs molecular mechanics and molecular dynamics simulations as well as quantum mechanics calculations.

Download Website Updated 10 Mar 2010 The Digital Seed Vault

Pop 42.67
Vit 3.10

The Digital Seed Vault is a seed stock database mainly developed for researchers in the plant sciences. It can also be used by people who handle a lot of different seeds, e.g. garden enthusiasts, seed breeders, or seed producers.

Download Website Updated 02 Dec 2009 Bio2RDF

Pop 28.35
Vit 2.50

The Bio2RDF software is a package which resolves bio2rdf.org semantic Web identifiers corresponding to bioinformatics data and knowledge bases into RDF files which can be consumed by any generic RDF processor.

Download Website Updated 12 Nov 2009 Mauve

Pop 34.29
Vit 5.14

Mauve constructs global multiple alignments of rearranged genome sequences. It also provides an interactive display of multi-species sequence conservation and any annotated features in those genomes. It can be applied for sequence comparison of both finished or incomplete genomes in multiple contigs. The resulting display is useful for identifying functional chromosomal regions under selective pressure and for performing ortholog assignment based on conserved gene order. Mauve writes global alignments in eXtended Multi-FastA (XMFA) format, a phylogenetic guide tree in Newick format, and the location of genomic islands. It identifies the breakpoints of genomic rearrangement and can provide a reduction of the genomes to a signed permutation matrix suitable for inference of rearrangement history.


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Open Camera

A camera app for Android.


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A command-line network analysis workbench.