Mike Chelen's Library tagged bioinformatics →  View Popular

Cheminformatics Benchmark Toolkit --------------------------------- Why? Because we want to: 1. measure if a patch improves performance 2. compare cheminformatics toolkits Project ------- This is an open project, and anyone can contribute or patch the tests, in order to attempt to create a balanced and fair test suite impartial to the toolkit being tested. Versioning ---------- When reporting results for a toolkit for a test, always report the version of ChemInfBenchmark release, as well as the test number as listed below. The tests --------- Toolkits should always to the bare minimum; any extra things will only make the outcome unfavourable, but toolkits may do that if they wish. 1. Convert an SD file to XYZ 2. Calculate the molecular mass of the entries in an SD file 3. Convert an SD file to CML 2.5 4. Perform a substructure match on all of the entries in an SD file 5. Parse a collection of SMILES - this will be a measure of performance and completeness 6. Detect rings in a collection of molecules. 7. Parse (not perform the search) for a collection of SMARTS patterns - this will be a measure of performance and completeness Running tests ------------- Each test is run via a configure file. A test can be run by $ ant -Dconfig=test-config.xml run

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chemistry informatics cheminformatics bioinformatics open science source

BioPuppy is an minimal Linux OS and electronic workbench for bio-informatics and computational biology. It has been designed to meet the needs of beginners, learners, students, staffs and Research scholars. BioPuppy is available as a live CD cum installation CD [and in USB Pen drive] and containing all the required software to boot the computer with ready to use bio-informatics tools. BioPuppy is based of the Puppy Linux. The another objective of this BioPuppy is small in size. Our estimated size of BioPuppy is ~150MB.

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biopuppy Linux livecd bioinformatics open source puppylinux

Bio-Linux 5.0 is a fully featured, powerful, configurable and easy to maintain bioinformatics workstation. Bio-Linux provides more than 500 bioinformatics programs on an Ubuntu Linux base. There is a graphical menu for bioinformatics programs, as well as easy access to the Bio-Linux bioinformatics documentation system and sample data useful for testing programs.

You can install Bio-Linux on your machine, either as the only operating system, or as part of a dual-boot setup which allows you to use your current system and Bio-Linux on the same hardware.

Bio-Linux also runs Live from the DVD. This runs in the memory of your machine and does not involve installing anything. This is a great, no-hassle way to try out Bio-Linux, demonstrate or teach with it, or to work with when you are on the move.

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biolinux biology linux bioinformatics

A collaborative workflow builder and enactor for e-Sciences, in particular bioinformatics.

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taverna workflow escience bioinformatics

We are organizing a special session on “Data Mining in Protein Interaction Networks” in ISIBM conference (2009 ISIBM International Joint Conferences on Bioinformatics, Systems Biology and Intelligent Computing). Please refer the call for paper in http://www.isibm.org/IJCBS/sessions.html for more information of this special sessions (The main conference web site is at http://www.isibm.org/IJCBS/index.html).

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bioinformatics

CloudBurst: Highly Sensitive Short Read Mapping with MapReduce
Michael Schatz
Center for Bioinformatics and Computational Biology, University of Maryland


Next-generation DNA sequencing machines are generating an enormous amount of sequence data, placing unprecedented demands on traditional single-processor read mapping algorithms. CloudBurst is a new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics. It is modeled after the short read mapping program RMAP, and reports either all alignments or the unambiguous best alignment for each read with any number of mismatches or differences. This level of sensitivity could be prohibitively time consuming, but CloudBurst uses the open-source Hadoop implementation of MapReduce to parallelize execution using multiple compute nodes.

CloudBurst's running time scales linearly with the number of reads mapped, and with near linear speedup as the number of processors increases. In a 24-processor core configuration, CloudBurst is up to 30 times faster than RMAP executing on a single core, while computing an identical set of alignments. In a large remote compute clouds with 96 cores, CloudBurst reduces the running time from hours to mere minutes for typical jobs involving mapping of millions of short reads to the human genome. CloudBurst is available open-source as a model for parallelizing other bioinformatics algorithms with MapReduce.

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cloudburstbio mapreduce cloudburst bioinformatics genetics

Hadoop comes bundled with launch scripts to simplify initializing an Amazon Elastic Compute Cloud (EC2) cloud for Hadoop. Once initialized, running CloudBurst is identical to running on a local cluster. If you use EC2 regularly with the same datasets (i.e. the human genome as a reference), you will probably want to copy the data once to Amazon Simple Storage Service (S3) so you can quickly copy the data from S3 to your cloud at low cost.

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cloudburstbio bioinformatics ec2

The Bioclipse project is aimed at creating a Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). Bioclipse, as any RCP application, is based on a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc.

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eclipse bioclipse bioinformatics biology