Phenoscape internship experience

Hello all,

As an online student of Bioinformatics based in Nairobi, Kenya, I had a strong desire to undertake a project that would enhance my knowledge and skills in software development. Hence, after completing MSc. Course work at the University of Manchester, UK, I was happy to be awarded an internship from the Phenoscape project for an 11-week traineeship beginning September 21st, 2009 at the National Evolutionary Synthesis Center (NESCent). This project seeks to establish the developmental and genetic basis of the astonishing morphological heterogeneity across diverse species. In addressing this, a rich and rigorous knowledge base, PhenoscapeKB, constituting evolutionary variable characters across a clade of fishes connected to mutant phenotypes from ZFIN has been developed. Core to the PhenoscapeKB is the modeling of the character entities   using ontologies thus facilitating the knowledge synthesis via logical/mathematical reasoning.

During the internship, I successfully developed a Java-based prototype application for handling ontology term requests, gained in-depth skills and knowledge in software development, made two presentations to the informatics group and above all established a long-term collaboration with the Phenoscape project team.  I am currently working remotely with the team (via Skype and e-mail) and developing my MSc. thesis under the close supervision of Prof Todd Vision (the UNC co-PI in the project). In addition, based on the knowledge acquired during the traineeship, I plan to conduct a basic course in bio-ontologies and Java programming for bioinformatics for members of the regional student group of East Africa in mid 2010.

The traineeship provided an open and stimulating learning environment sustained by the weekly seminars, journal club presentations and the informal yet fruitful discussions. The constant willingness of project team members to guide and share knowledge and above all, the scientific mentorship was profoundly motivating.

I must say that the traineeship provided the best learning experience I have ever had and will go along way in shaping my career in Computational biology.


Mtakai Ngara

International Institute of Tropical Agriculture (IITA), Nairobi, Kenya

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