228 projects tagged "Bioinformatics"

No download Website Updated 22 Mar 2010 Ascalaph

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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 07 Apr 2011 JHeatChart

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Pop 68.64
Vit 1.88

JHeatChart is a one class Java API for generating heat map charts that was created because very few charting APIs seem to contain the facility to create heat maps. It is not a full featured charting API and cannot be used to other charts. The generated charts are created as Java Image objects, which can be incorporated into a GUI or saved to a file.

No download No website Updated 10 Aug 2010 CanvasXpress

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Pop 18.22
Vit 37.24

CanvasXpress is a JavaScript library based on the HTML5 canvas tag that provides a generic and simple way to display genomics data. It supports bar graphs, line graphs, bar-line combination graphs, box plots, dot plots, area graphs, stacked graphs, percentage-stacked graphs, correlation plots, Venn diagrams, heat maps, Newick trees, 2D-scatter plots, 2D-scatter bubble plots, 3D-scatter plots, pie charts, networks (or pathways), and a genome browser. It also supports a few data transformations like log and exponential transformation, z-score, percentile transformation, and ratio. It also supports grouping of samples, zooming, events, and more.

Download Website Updated 14 Apr 2011 Scalable Assembler at Notre Dame

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Pop 21.35
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.

Download Website Updated 17 Mar 2014 LabKey Server

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Pop 110.38
Vit 9.26

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.

No download No website Updated 31 Oct 2011 ODES

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Pop 12.00
Vit 30.68

ODES is a pthreads parallelized exact algorithm to enumerate all maximal sub-graphs of a graph that exceed a specified cutoff density of at least 1/2, even if they overlap.

No download Website Updated 03 Sep 2012 Emergent

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Pop 38.34
Vit 2.71

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 30 Jul 2012 ScalaBLAST

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Pop 38.57
Vit 2.01

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.

Download Website Updated 28 Jul 2012 MSAProbs

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Pop 17.61
Vit 2.01

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 No website Updated 26 Oct 2012 VPLG

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Pop 21.93
Vit 1.99

Visualization of Protein Ligand Graphs (VPLG) uses a graph-based model to describe the structure of proteins on the super-secondary structure level. A protein-ligand graph is computed from the atomic coordinates in a PDB file and the secondary structure assignments of the DSSP algorithm. In this graph, vertices represent secondary structure elements (SSEs, usually alpha helices and beta strands) or ligand molecules, while the edges model contacts and relative orientations between them. The graphs can be visualized, written to a database, and saved in a text-based file format.

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Open Camera

A camera app for Android.

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mcl-edge

A command-line network analysis workbench.