New tools for bioinformatics teaching

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Written on Monday, 11 August 2008 00:00

The eBioUSB used for the course

For the third year, the ILRI/BecA EMBNet node organized an introductory course in Bioinformatics at the International Livestock Research Institute (ILRI) campus in Nairobi, Kenya. The objective was to introduce young scientists from east and central Africa to use bioinformatics/computational biology in their research and to present some of the biological resources available on the ILRI-BECA bioinformatics platform.

The course is organized in collaboration with the Swedish University of Agricultural Sciences (SLU), Uppsala University (UU) and Linnaeus Centre for Bioinformatics (LCB) funded by SIDA.

The course was 9 days long, from 5–15 May 2008. 24 participants from Uganda, Sudan, Tanzania, Burundi, Somalia, Cameroon, Ethiopia and Kenya attended the course. Futhermore, the lectures were recorded on DVD and will be used at the University of Buea, Cameroon and Maseno University in Kenya.

The course team (L to R): Erik Lagercrantz, Maria Wilbe, Erik Bongcam-Rudloff, Alvaro Martinez Barrio; (Not in the picture) Etienne de Villiers and Saidimu Apale

Topics covered during the course were: sequence analysis and alignments, EMBOSS/wEMBOSS, Staden package, Unix/Perl basics, genomics and comparative genomics, Artemis and Artemis Comparison Tool and Ensembl.

Saidimu Apale filming the lectures

Many course participants are learning new tools and techniques that will be useful for them when returning to their own laboratories. Last year, each student received a Bioinformatics Live-CD with all programs used during the course, but it was not possible for them to easily save their work. The course team, therefore, came up with a new idea that resulted on an “Bioinformatics workbench on a USB memory stick”, eBioUSB. Each student received one USB stick to use during the course and bring back home for continuous work. By using a USB stick, the students were also able to save all their work directly on the stick.{xtypo_quote_right}I look forward to applying the knowledge I have acquired in the training in my research work and to assist others{/xtypo_quote_right}

The eBioUSB stick is based on a Linux environment: the African UBUNTU system. The USB solution has the advantage that it can be used in any computer without changing any settings. It has a complete desktop environment (e.g. office package, text editor and mail client).

The programs that were necessary for the course and installed on eBioUSB were:

• ClustalW
• ClustalX
• NCBI BLAST
• NCBI Tools
• EMBOSS
• wEMBOSS
• Staden
• PHYLIP
• Artemis
• Artemis comparison Tool
• JalView
• BioPerl

 

The course participants at ILRI, Kenya, May 9, 2008

We have created 2 different USB sticks: one that can be ran on old computers and the one used for the course can be used on newer machines resulting on a higher speed system.

Future improvements of the eBioUSB include incorporating the SwissProt database for running most common analysis locally.

The “BioMacKit” a Bioinformatics Portable Teaching Kit that was created last year was used this time to access a complete mirror of various programs and databases used during the course (More information: EMBnet.news, Vol 13 Nr 2:7, 2007).

The course evaluation resulted on an average 4.9 of maximum 5 points encouraging the teachers to organize a new course next year. Student comments of the course:

“Interesting and highly applicable to our work though not so easy for beginners”

“I enjoy working with the emboss software because it has many programs and each has a manual, thus quite user friendly”

“I look forward to applying the knowledge I have acquired in the training in my research work and to assist others”

“The USB stick enables me to reproduce exactly what I have learned”

“I learned a lot about databases that were available to me and programs I could use to analyze protein and DNA sequences”

Read more  EMBnet.news Volume 14 Nr. 2, July 2008 881.60 Kb