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BecA Hub in action The hub Service units Bioinformatics / LIMS
BecA Hub in action The hub Service units Bioinformatics / LIMS | Bioinformatics / LIMS unit |
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Etienne deVilliers, email: This e-mail address is being protected from spam bots, you need JavaScript enabled to view it System Administrator: The BecA Hub Bioinformatics Platform provides advanced computational capabilities in bioinformatics to all BecA Hub scientists to:
The initial focus of the platform is to be an easy-to-use platform for advanced sequence analysis. We make available high-speed, specialized hardware and sophisticated commercial and academic software. To make these useful, we maintain the latest copies of all major sequence databases. Investigators can use these components to perform one-time projects or to build up their own ongoing analysis pipeline. Bioinformatics unit services: We provide scientific and technical staff that can assist with or collaborate on individual projects. As part of the Bioinformatics Platform, we also have access to the advice and expertise of associated BecA staff members. The Bioinformatics Platform is a specialist node of The European Molecular Biology Network (EMBnet) (http://www.embnet.org). EMBnet is a consortium of collaborating bioinformatics groups located in Europe and a number of groups outside Europe. Each group is represented by a ‘node’, and is responsible for the maintenance of local services for their users (e.g. education, training, software, database distribution, technical support, helpdesk). The combined expertise of the nodes allows EMBnet to provide services to the bioinformatics community that encompass more than can be provided by a single node. Bioinformatics unit hardware: The BecA Hub Bioinformatics Platform is hosted on a High Performance Computer (HPC) platform located on the BecA, Nairobi campus. 
The HPC platform is a 66 CPU Linux cluster, based on AMD 64-bit Opteron technology and build with ROCKS version 4.1. Each compute node contains two 64-bit Opteron processors with 2 GB of memory. Nodes are interconnected with high-speed 1 Gbits/sec networking. In total, the system has 72 GB of memory and more than 3 TB of disk space. Platform LSF scheduling software manages job scheduling. Paracel BlastMachine runs parallelized versions of NCBI BLAST, PSI-BLAST, and MegaBLAST. It utilizes 20 of the 66 CPUs on the HPC. The BlastMachine accelerates the BLAST algorithms by dividing a job across multiple processors and can divide both the database and the query among groups of processors. Paracel GeneMatcher2 - accelerates dynamic programming algorithms such as Smith-Waterman, HMMer and Genewise. Several other Unix file-, web- and data servers are available. Some things you can do using the bioinformatics platform:
Capacity building: Bioinformatics is a relatively new specialist area. We need to raise awareness of the field here in Africa and expose local scientists to its potential. The West has spent millions of dollars sequencing the genomes of humans, animals, plants and parasites and the resulting data are freely available on the Internet. This is a vast body of knowledge that local scientists can use to solve their specific problems or to answer research questions. All scientists in Africa need to make use of these data are a computer, good Internet access and bioinformatics skills. 
Raising awareness and building capacity in Bioinformatics in Africa is a major focus of the Bioinformatics Platform. This is accomplished through regular training courses and research projects undertaken at the BecA platform. In association with the Swedish University of Agricultural Sciences and the Linnaeus Centre for Bioinformatics, in Uppsala, Sweden, BecA runs an annual two-week “Introduction to Bioinformatics” training course. Since 2005, we have trained more than 100 students from more than five eastern and central Africa countries in the field of bioinformatics. Download the Bioinformatic unit brochure  Bioinformatics unit brochure 302.28 Kb
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Site last modified:
Thu, 22 July 2010,
04:38:50 AM
Thu, 22 July 2010,
04:38:50 AM
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