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Bio-Linux操作系统简介  

2011-11-26 09:38:34|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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Feature article contributed by Bela Tiwari, Lead Bioinformatician, NERC Environmental Bioinformatics Centre, United Kingdom
    
Bio-Linux 6.0 is a 64-bit workstation system developed for biologists and bioinformaticians by the NERC Environmental Bioinformatics Centre (NEBC) (Figure 1). Bio-Linux 6.0 is based on the popular Ubuntu Linux system, providing the benefits of a free, user-friendly, comprehensive computing environment, as well as many useful bioinformatics tools.

Bio-Linux 6.0 desktop view

Figure 1.
Bio-Linux 6.0 desktop view.

Bio-Linux 6.0 comes with over 500 bioinformatics programs pre-installed, including
software for handling sequence data from Roche 454 and Illumina systems, and R libraries of interest to biologists, such as vegan, ShortReads, Rsamtools, and the the biocLite selection of packages from Bioconductor (Figure 2). Bio-Linux also has all the standard software one would expect on a bioinformatics system including the blast and blast+ packages of NCBI software, many alignment and phylogenetic programs, and much more.

Bio-Linux 6.0 comes with over 500 bioinformatics programs pre-installed


Figure 2.
Bio-Linux 6.0 comes with over 500 bioinformatics programs pre-installed.

All of the bioinformatics software is available from the command line of course. There is also a graphical drop down menu from which the user can launch some of the popular bioinformatics tools (
Figure 3). Bio-Linux also includes an introductory tutorial and associated data files linked from the desktop. Even new users, who are unfamiliar with Linux, should find it relatively easy to familiarize themselves with this system.

Bio-Linux 6.0 features a graphical drop down menu from which one can launch some of the popular bioinformatics tools


Figure 3.
Bio-Linux 6.0 features a graphical drop down menu from which one can launch some of the popular bioinformatics tools.

Bio-Linux comes with a comprehensive
documentation system (Figure 4) that is linked from the desktop and provides information on all the bioinformatics software on the system, categorised according to functionality. There are also pages for popular bioinformatics software that can be added to the system with a single command, so that users can easily expand the system to meet their analysis needs. A folder of sample data is also linked to the desktop, allowing users to try out new programs easily.

Bio-Linux comes with a comprehensive documentation system


Figure 4.
Bio-Linux comes with a comprehensive documentation system.

Other Features
The NEBC has a limited number of branded, bootable Bio-Linux USB sticks available to give away. To request a promotional USB stick, please send a small self-addressed, padded envelope to the NERC Environmental Bioinformatics Centre, Centre for Ecology and Hydrology, Benson Lane, Crowmarsh Gifford, Wallingford, England, OX10 8BB.

Useful Links
 
Note:
Bio-Linux 6.0 is a 64-bit system that requires a 64-bit computer. Most machines bought in the last 3 years should be fine. A minimum of 1 GB of memory is recommended but more memory is better. Further details can be found in the Ubuntu documentation for hardware requirements.

Please note: If you know of any bioinformatics research programs, software, hardware, meetings, workshops, training sessions, web servers, degree or certificate programs that we should feature in future issues of this newsletter, please email Ian Forsythe at if@ualberta.ca.
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