Donaldson Group

The Donaldson Group at the Biotechnology Centre of Oslo

Research Interests

Our interests include computer modelling of biological processes, especially those related to cell signaling. Modelling requires access to a variety of data that needs to be collected or generated. These activities include data warehousing, data mining, prediction of protein-protein interactions and biological text-mining.

Our recent work on a consolidated protein interaction database can be found at http://irefindex.uio.no/ .

Projects

	iRefIndex http://irefindex.uio.no/ iRefIndex (interaction Reference Index) provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein. iRefIndex uses the Sequence Global Unique Identifier (SEGUID) to group proteins and interactions into redundant groups. This method allows users to integrate their own data with the iRefIndex in a way that ensures proteins with the exact same sequence will be represented only once.
	Magrathea http://magrathea.uio.no/ Magrathea is prototype software demostrating the principals of coordinated agent modeling.
	The Biolibrarian Proposal The Biolibrarian proposal proposes the creation of new positions at university libraries around the world. It is envisioned that molecular biologists could meet with a Biolibrarian in the same way that they meet with and use the services of a librarian. The Biolibrarian could help molecular biologist researchers to locate pathways, complexes and interactions that their molecules of interest are involved in.
	DiG: Disease Groups http://donaldson.uio.no/wiki/DiG:_Disease_groups The Disease Groups project groups together phenotypically related disease-gene associations found in OMIM's Morbid Map. The resulting map of disease genes may be used to explore relationships between disease genes in the human protein-interactome.

Group Members

• Ian Donaldson
• Katerina Michalickova
• Paul Boddie
• Sabry Razick
• Antonio Mora
• Hanna Nemchenko

Local Seminar Series

The Biotechnology Centre of Oslo holds a weekly Bioseminar on Tuesdays at 3pm in room 10 of Forskningsparken at. Gaustadalléen 21 (see map here).

The Bioinformatics Seminars are held every Wednesday at 12:15 by the Joint Centre for Bioinformatics in Oslo, located at Gaustadalléen 25 (see map here).

Courses

Ian Donaldson is organizing this year's Molecular Biotechnology Course at the Biotechnology Centre of Oslo. You can find the MNBTS 9000 course web page here and the latest schedule here.

Introductory Perl is taught by Antonio Mora and Ian Donaldson as part of the MBV3070 course.

Antonio Mora and Ian Donaldson also hold the "Applied readings in mathematics, computer science and biology" course every second Autumn term. See MBV-INF4410.

Contact

ian.donaldson at biotek.uio.no

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