Difference between revisions of "Creating a canonical prokaryotic biochemical pathway map"

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{{Projectproposal
 
{{Projectproposal
 
|Contact person=Jaap Heringa
 
|Contact person=Jaap Heringa
 +
|Contact person2=Mengjin Liu (FrieslandCampina)
 +
|Contact person3=Dongmei Deng (ACTA)
 
|Master areas=Bioinformatics
 
|Master areas=Bioinformatics
 
|Fulfilled=No
 
|Fulfilled=No

Latest revision as of 16:14, 7 February 2014


About Creating a canonical prokaryotic biochemical pathway map


Description

Friesland Campina Research, Deventer & Academic Centre for Dentistry Amsterdam

This project is the collaboration between the Department of Oral Microbiology of the Dentistry Faculty of the Amsterdam University and Friesland Campina Research in Deventer. The project will be mainly carried out in Deventer.

Description:

At the moment, there are several canonical biochemical pathways maps available, such as e.g. the Roche Wall Chart of Biochemical Pathways. However, most of these are based on Eukaryotic metabolic data. To our knowledge, no such canonical biochemical pathway map has been created for bacteria. The number of sequenced bacterial genomes has increased significantly the last years, allowing us to study the metabolic networks of microorganisms at the genome-scale. This project will focus on the creation of a curated set of metabolic reactions that are shared in a selected group of microorganisms. A curated canonical metabolic pathway map will be constructed and used for future studies such as pathway analysis and visualization of metabolomics and transcriptomics data.

Tasks:

  • Querying literature, various databases and genome-wide metabolic models for canonical pathway data.
  • Assembly of the retrieved canonical pathway data into one biochemical database.
  • Visualizing the biochemical data in one overall pathway map.

Requirements:

  • Background in biochemistry on an academic level (biology or chemistry training).
  • enthusiastic
  • Good communication skills.

Contact persons:

Mengjin Liu, Corporate Research FrieslandCampina. Tel. 0570-690317 [1] or
Dongmei Deng, Deprtment of Oral Microbiology. Tel. 020-5188437 or [2]

Duration of the internship is 3 to 9 months