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Free and Open Source Bioinformatics Software for Linux
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| Bioinformatics, as defined by the National
| Center for Biotechnology Information
| (BCBI), is the field of science in which
| biology, computer science, and information
| technology merge into a single discipline.
|
| Bioinformatics is being used largely in the
| field of human genome research by the Human
| Genome Project, which has been determining
| the sequence of the entire human genome
| (about 3 billion base pairs) and is
| essential in using genomic information to
| understand diseases. It is also used
| largely for the identification of new
| molecular targets for drug discovery.
`----
http://www.junauza.com/2009/11/free-and-open-source-bioinformatics.html
One FatELF Binary To Run Them All
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| Even Linux's advocates are unthrilled at
| one of its sticking points: binaries built
| for one breed of Linux don't always run on
| another. And since unifying Linux into a
| common distribution is about as likely as
| herding a circus ring full of cats into a
| clown car, people who want to distribute
| prebuilt binaries for Linux have few
| choices. Here's a new choice: FatELF, or
| universal binaries for Linux.
`----
http://www.informationweek.com/blog/main/archives/2009/11/one_fatelf_bina.html;jsessionid=2FUHMLDEHPUMDQE1GHRSKH4ATMY32JVN
Recent:
Bioinformatics, Genomes, EC2, and Hadoop
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| Built on top of a 64-bit Ubuntu distribution, the JCVI
| Cloud Bio-Linux gives scientists the ability to launch EC2
| instances chock-full of the latest bioinformatics packages
| including BLAST (Basic Local Alignment Search Tool),
| glimmer (Microbial Gene-Finding System), hmmer (Biosequence
| Analysis Using Profile Hidden Markov Models), phylip
| (Phylogeny Inference Package), rasmol (Molecular
| Visualization) genespring (statistical analysis, data
| mining, and visualization tools), clustalw (general purpose
| multiple sequence alignment), the Celera Assembler (de novo
| whole-genome shotgun DNA sequence assembler), and the NIH
| EMBOSS utilities. The Celera Assembler can be used to
| assemble entire bacterial genome sequences on Amazon EC2
| today!
`----
http://aws.typepad.com/aws/2009/09/bioinformatics-genomes-ec2-and-hadoop.html
Two Notable Linux Updates
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| The other release worth checking out is the updated version of Open
| Discovery, a USB turnkey bioinformatics Linux distribution with a customized
| MPI specifically designed for multi-core processors. Open Discovery 2 ships
| with an MPI compiled GROMACS V-3 3, the molecular dynamics software
| application. You can download Open Discovery 2 here.
`----
http://www.genomeweb.com/blog/linux-updates-take-note
Related:
Bioinformatics Open Source Conference, Stockholm, Sweden
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| The Bioinformatics Open Source Conference (BOSC) will be held on 27 and 28
| June in Stockholm, Sweden.
|
| A variety of open source bioinformatics packages are used by the research
| community across many application areas and enable research in the genomic
| and post-genomic era. Open source bioinformatics software has facilitated
| innovation, dissemination and adoption of new computational methods, reusable
| software components and standards.
`----
http://cordis.europa.eu/fetch?CALLER=EN_NEWS&ACTION=D&SESSION=&RCN=30699
UK Developers Prep Open-Source Alternative To Illumina GAâs Primary Analysis
Software
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| A team of UK bioinformaticians is in the process of finalizing Swift, an
| open-source software package for primary analysis of second-generation
| sequencing data. The software was initially developed for Illumina data, but
| will eventually process SOLiD images too.
`----
http://www.bioinform.com/issues/12_40/features/149961-1.html
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