Sri Lankan EMBnet node: progress report

Kanchana Senanayake

Institute of Biochemistry, Molecular Biology and Biotechnology (IBMBB), University of Colombo,

Sri Lanka

Mission - IBMBB

“INITIATE, PROMOTE, FACILITATE Advance Research & Human Resource Development in Molecular Life Sciences to achieve National and International Development”

The Institute of Biochemistry, Molecular Biology and Biotechnology is an independent institute of the University of Colombo established in 2004. It is located in the main campus of the University of Colombo.

Its main activities are in human resource training and research and development in Molecular Life Sciences and allied fields. It has two masters programs (Master of Science in Molecular Life Sciences, Master of Science in Cellular and Molecular Life Sciences), MPhil/PhD programs and several research programs in genomics/proteomics. A Master of Science program in Bioinformatics is currently being developed.

Figure 1. A computer cluster and screenshots from some of the applications it runs.

Institute of Biochemistry, Molecular Biology and Biotechnology was first elected as the Sri Lankan national node in 2007. Since then we have managed to achieve several goals such as dissemination of knowledge through workshops and training programs and setting up resources in bioinformatics. Being the only institute of this kind in Sri Lanka we are aware of our responsibility to provide technical support and knowledge to Sri Lankan Molecular Biologists on using Bioinformatics tools for their research and to provide access to online databases and tools in bioinformatics.

Figure 2. The IBMBB building.

Using the knowledge and hands on experience gained by the training received in Sweden we have managed to configure a bioinformatics cluster with a local installation of the BLAST tools and the mirror of the BLAST database and it also includes the EMBOSS explorer which is a GUI for the EMBOSS tools. This cluster is temporarily hosted at the URL www.ibmbb.edu.lk on the public domain.

• BLAST search tool; www.ibmbb.edu.lk/blast
• EMBOSS explorer; www.ibmbb.edu.lk/emboss

There is also a local installation of the ebiokit which includes Ensembl genome browser, Biomart, MRS, Galaxy and wEMBOSS toolkits for Bioinformatics. The “ebiokit”, a collection of open source bioinformatics programs was installed at the IBMBB by Prof. Erik Bongcam-Rudloff’s research team at the Swedish University of Agricultural Sciences, Sweden.

For further details regarding IBMBB please visit www.ibmbb.lk