Search Results for "bio toolkit" - Page 2
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Showing 80 open source projects for "bio toolkit"
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SPADE
A toolkit for developing and deploying protein structure algorithms.
The Structural Proteomics Application Development Environment is a Python tool kit for developing and deploying bioinformatics applications. Handles graphics, analysis, and modeling of protein sequence and structure. Source and Win installers available. SPADE source code can be cloned from http://www.github.com/deaconjs/SPADE. -
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Gene Ontology Browser
Browser for viewing Gene Ontology (GO) .obo files.
Go Browser allows you to view a gene ontology on your local machine. You can go up and down the hierarchy and inspect the terms. It's a good way of familiarising yourself and orienting yourself in the GO system. It's built using the Baby X toolkit, so has no dependencies other than xlib. Baby X has now also been ported to Windows, so a Windows version is available. -
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AJT is a set of utility classes for Java for handling some bioinformatics data, graphics file export, GUI widgets, and classes that should long have been added to the official Java API.
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CADET
Chromatography Analysis and Design Toolkit
We have moved to GitHub: https://github.com/modsim/cadet The Chromatography Analysis and Design Toolkit (CADET) is developed at the Institute of Bio- and Geosciences 1 (IBG-1) under supervision of Dr. Eric von Lieres. The core of the CADET software is a fast and accurate solver for the General Rate Model (GRM) of packed bed liquid chromatography. The CADET solver covers a wide range of GRM variants, combining different transport and binding models with state-of-the-art mathematical... -
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FishingCNV
Copy number variation (CNV) detection in exome sequencing data
FishingCNV, a software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data. The inputs are standard coverage files produced by Genome Analysis ToolKit (GATK), and the output is a file containing putative CNVs. The program comes in 2 different releases * GUI version (FishingCNV_X.X.X.zip) * Command line version (FishingCNV_X.X_pipeline) Browse through our files to find the different releases. -
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Adamant Space
3D-Game with large geodic Maps (Globes) - include multiple Game-Genres
... Covering GameGenres but about Covering (most basic) Features of Reality like Needs/Consume/Production/Trade as Base for Economy. Defined MileStones on RoadMap are: GEO: physical Model of Enviroment, BIO: Flora&Fauna with LifeCycle (wo Darwin), PSY: Life do AI to get their Food&Water&etc., ARCH for Constructions and Building. If that MileStone got archieved adding Features means adding GameFun and next Add is: ECO -- a real Economy of real economizing Individuals which represent real Markets. -
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The Boolean Network Toolkit is an efficient and easy-to-use object-oriented C++ library which enables researchers to simulate ad carry out experiments (like attractor sampling and Derrida plot computation) on large boolean networks.
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Defind
detect genomic deletions using NGS data
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Dress Up RNA seq
End-to-end automated pipeline of RNA seq packages for an HPC system
The purpose of DressUp is to create an end-to-end RNA seq pipeline in which all of the steps of analyzing data from an Illumina sequencer is done in one step in an HPC environment. RNA seq programs included are TopHat, CuffLinks, CuffDiff, CuffMerge, FastQC, and trimming using the FastX toolkit. DressUp facilitates RNA seq programs by streamlining various packages into a single script. That script executes the RNA seq programs on a batch cluster system. Upon execution of the script, jobs... -
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Java Proteomic Library
A java proteomic development toolkit.
The JPL project is no longer updated and maintained. It has evolved after being completely reengineered and upgraded. The new project is available at http://mzjava.expasy.org. -
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Swift Sequence Alignment Program
GPU-based DNA sequence alignment program using Smith-Waterman
Swift is a DNA sequence alignment program that produces gapped alignment using the Smith-Waterman algorithm. It takes in a query file (FASTA format) and a reference file (FASTA format) as input. It outputs the reference name, read name, gapped alignment, alignment score, alignment start and end positions, and alignment length. I gave a talk on Swift in the GPU Technology Conference 2012. The talk can be accessed at... -
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An integrated bioinformatics toolkit for analysis of ChIPseq data from the Illumina DNA sequencing platform. Includes filtering, quality control, simulation, peakfinding, visualization, and comparison of samples.
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3D Realtime Simulation der Evolution des Lebens. Frei erweiterbares Gen/Mutations-System mit Direct3D-Engine. <b>Wichtig ".NET 2.0 beta"-basierent !</b> Also wird zumindest ein Visual Basic 2005 Express Beta benötigt.
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GEOMI2
The 2nd version of GEOMI
... GEOMI-2, provides a large number of novel tools for visual analysis of large networks. The new version gives more tools for visual explorations and interactions of such networks for patterns and trends in three dimensions. Some provided tools are very domain specific such as for bio-networks and social networks. The new framework has been developed at University of Sydney, Australia. Check project's current status at http://www.cs.usyd.edu.au/~visual/geomi2 -
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PileLine (Pileup pipeLine) is a toolkit for efficient handling of genomic position (GP) files, produced by next-generation sequencing experiments. It is designed to be memory efficient by performing on-disk operations over sorted GP files.
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BEAT: Bio-Ontology Enrichment and Alignment Toolkit is a software framework to handle persistence, alignment, queries, reasoning on ontologies. It is specifically targeted to the bio-ontology domain and to the Semantic Web. While Beat can already be used
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Object oriented reusable software classes designed to be used to construct larger software projects developed in multiple software languages.
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Utility to convert PED genome file into RAW SNP format. Creates multiple files per person. Supports big files. The same conversion utility has been included into "aisconvert" toolkit, so this project is rather deprecated.
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A tool to construct the metabolic networks from KEGG, and compare the constructed metabolic networks. Phylogenetic trees can be constructed along the case.
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The DNA Sequence Read Toolkit is a set of programs to convert data from DNA sequencing instruments into formats suitable for archiving, viewing or for onward processing (for example alignment or assembly).
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Volumetric file viewer for the human brain. Easy, powerful and flexible fMRI/MRI brain research and clinical neuro-surgery tool. Using state of the art open VTK 3D library, the proven Qt GUI toolkit, coded in Python.
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The Xholon project explores: 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.
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Free software tools released by the Virtual Institute for Microbial Stress and Survival, including WIST (a toolkit for LIMS development) and PCAPStore (a file repository for LIMS).
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Molecular Graphics and Dynamics. Molecular model builder. Part of the Ascalaph Designer http://sourceforge.net/projects/asc-designer/ project. Windows & Linux.