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[News] Roundup of Bioinformatics Software for GNU/Linux, More Universal Packaging

  • Subject: [News] Roundup of Bioinformatics Software for GNU/Linux, More Universal Packaging
  • From: Roy Schestowitz <newsgroups@xxxxxxxxxxxxxxx>
  • Date: Wed, 04 Nov 2009 00:59:18 +0000
  • Followup-to: comp.os.linux.advocacy
  • Newsgroups: comp.os.linux.advocacy
  • User-agent: KNode/4.3.1
Hash: SHA1

Free and Open Source Bioinformatics Software for Linux

,----[ Quote ]
| 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.


One FatELF Binary To Run Them All

,----[ Quote ]
| 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.



Bioinformatics, Genomes, EC2, and Hadoop

,----[ Quote ]
| 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!


Two Notable Linux Updates

,----[ Quote ]
| 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.



Bioinformatics Open Source Conference, Stockholm, Sweden

,----[ Quote ]
| 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.


UK Developers Prep Open-Source Alternative To Illumina GAâs Primary Analysis

,----[ Quote ]
| 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.

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