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Manatee is a web-based gene evaluation and genome annotation tool. Manatee can store and view annotation for prokaryotic and eukaryotic genomes.1 weekly downloads
Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.2,105 weekly downloads
The PDL module gives standard perl the ability to COMPACTLY store and SPEEDILY manipulate the large N-dimensional data sets that are the bread and butter of scientific computing.12 weekly downloads
The Disease Ontology has moved to Github. New project page: https://github.com/DiseaseOntology Disease Ontology is a stuctured controlled vocabulary originally based upon and mapped to medical billing codes. The goal of this ontology is to create a comprehensive hierachical controlled vocabulary to represent subsumptive disease relationships.4 weekly downloads
The Systems Biology Ontology project (SBO) goal is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling.
!!! PTEROS DEVELOPMENT MOVED TO GITHUB !!! New project page: https://github.com/yesint/pteros New documentation page: https://yesint.github.io/pteros/ Pteros is the C++ library for custom molecular modeling and simulations codes designed for researchers, not for C++ gurus. Provides facilities for PDB, XTC and TRR files IO, powerful selections, geometry transformations, RMSD fitting and alignment, etc.
A web-based software package for comparative genomics1 weekly downloads
A novel and comprehensive quantification tool for proteomics data
Coati is a web development framework and API for genome databases that supports multiple database vendors and database schemas.
This project contains the software for extracting bioinformatics data (sequences, features and annotations) from TIGR's legacy schemas as well as support for efficiently loading data into chado from BSML.
An intuitive molecular editor and visualization tool4,091 weekly downloads
WE HAVE MIGRATED TO GITHUB. https://github.com/ebi-chebi/ChEBI
This project is designed to be able to take standard NMEA data available from most boats and broadcast APRS WX reports. Other telemetry like battery voltage, tank levels, etc, as well as data logging will be supported.
pricewizard compares prices from different feeds and other SOAP-sources works with zip-locator to show best price for location
Software and systems that currently support the data processing, annotation and Genbank submission pipelines for viral projects at JCVI.
Encode Arabic provides tools for encoding and decoding Arabic in Haskell, Python, Perl, or LaTeX. Interprets the ArabTeX notation to generate original orthography or phonetic transcription. Supports Buckwalter and other romanizations. Converts legacy byte encodings into Unicode. http://github.com/otakar-smrz/encode-arabic
A cross-platform interface for the *.mfj file format.4 weekly downloads
Development and implementation of a Local Control Bus for use in Model Railroad Applications, and based on CAN hardware bus protocols.
An open source toolbox for protein-protein docking with internal backbone flexibility that can be executed on GPU cards, using PyMOL molecular viewer for user interface. Implemented in CUDA with the eventual transition into OpenCL.
OpenSourceDCC is an online repository for open source data coordinating center software derived from completed and ongoing NIH/NHLBI funded projects at the Channing Lab at Brigham and Women's Hospital/Harvard Medical School.
Harmonize + gene = Harmogene Efficiently create sets of genome annotations ("consensus annotations") from one or more source genomes using simple rules and and apply those annotations to one or more target genomes. See the Trac page for more info.
CAMERA is a research environment and repository for metagenomic data
From project management to general decision making, SWOT is a key tool. Lack of packages (specially Open Source) driven me to create a multiplatform tool, using available, free resources.
A Silverlight framework that makes it easy to develop games and applications simulating creatures that interacts with eachother.