RSS 73 projects tagged "Bioinformatics"

Download Website Updated 14 Oct 2013 SimThyr

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Pop 45.48
Vit 4.47

SimThyr is a continuous simulation program for pituitary-thyroid feedback control. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses, and patients.

Download Website Updated 28 Jul 2012 MSAProbs

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Pop 17.72
Vit 2.03

MSAProbs is a protein multiple sequence alignment algorithm. It achieves the statistically highest alignment accuracy on popular benchmarks: BALIBASE, PREFAB, SABMARK, and OXBENCH, compared to ClustalW, MAFFT, MUSCLE, ProbCons, and Probalign.

Download Website Updated 30 Jul 2012 ScalaBLAST

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Pop 38.46
Vit 2.03

ScalaBLAST is a high-performance multiprocessor implementation of the NCBI BLAST library. It supports all 5 primary program types (blastn, blastp, tblastn, tblastx, and blastx) and several output formats (pairwise, tabular, and XML). It will run on most multiprocessor systems which have MPI installed, and can run over a wide variety of interconnects, including infiniband, quadrics, and ethernet. It is designed to run a large number of queries against either large or small databases. It parallelizes the BLAST calculations by dynamically scheduling them across processors using a fault-resilient scheme.

No download Website Updated 03 Sep 2012 Emergent

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Pop 40.37
Vit 2.74

Emergent is a neural network simulator with a built-in scripting language which allows for the creation and analysis of complex, sophisticated models of the brain in the world. Networks and all of their state variables are visually inspected in 3D, allowing quick "visual regression" of network dynamics and robot behavior. Emergent is a direct descendant of the PDP and PDP++ neural network packages.

Download Website Updated 17 Mar 2014 LabKey Server

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Pop 108.07
Vit 13.92

LabKey Server is open source software that helps scientists manage, analyze, and share complex datasets. It supports tandem mass spectrometry, flow cytometry, assays for neutralizing antibodies, Luminex, observational studies, and secure, Web-based collaboration. The software is modular, configurable, and customizable. It can be installed in your institution on any modern hardware and operating system. It is designed to integrate with your existing systems, instruments, and work flows, and to be readily adapted by skilled programmers to novel methods of inquiry. The project is under active development by a team of professional software engineers and a community of active contributors. New versions are released about four times per year.

Download Website Updated 14 Apr 2011 Scalable Assembler at Notre Dame

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Pop 22.18
Vit 1.04

The Scalable Assembler at Notre Dame (SAND) replaces the early stages of the Celera Assembler with scalable versions that can run on collections of commodity computers. By harnessing clusters, clouds, grids, or just random machines in your office, many bioinformatics tasks can be reduced from weeks or months down to minutes or hours.

No download Website Updated 22 Mar 2010 Ascalaph

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Pop 22.07
Vit 38.58

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

No download Website Updated 18 Dec 2010 SwissParser

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Pop 23.02
Vit 2.30

SwissParser allows you to define in a few lines a parser able to deal with the flat file format used in bioinformatics software such as UniProt, KEGG, etc.

Download Website Updated 21 Nov 2011 GoFigure2

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Pop 46.17
Vit 41.30

GoFigure2 is a cross-platform application for visualization, processing, and analysis of out-of-core multidimensional microscopy data (5D data sets). Users can visualize images, segment cells in 3d, track cells through time, and detect cell divisions to generate lineages. Results are stored in a MySQL database back-end. Once data has been processed, cell-based object features are quantified and can be used for sorting, color-coding, analysis, or exported to external tools. GoFigure2 was developed for biology research including studying the development of embryos (zebrafish and mouse), synthetic biology (signaling), and for drug screening.

Download No website Updated 10 Jul 2009 SPADE

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Pop 34.35
Vit 41.73

The Structural Proteomics Application Development Environment (SPADE) provides a community suite for developing and sharing protein structure and sequence tools. It includes a custom molecular viewer, sequence alignment editor, many reusable tools, and a chemical probing suite to support experimental verification of predicted structural models.

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Project Spotlight

Calligra

An integrated suite of office and creative applications.

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Project Spotlight

Collax Groupware Suite

A complete collaboration, e-mail, and messaging server with Outlook MAPI support.