🚀 go-pugleaf

Dear all

We have a job opening for a programmer in our lab.
The details will be available on the Edinburgh university website
soon,
but to register your interest, please email me jimicarlo@gmail.com,
with PROGRAMMER JOB in the title and I'll alert you when it goes
online.

Here's a brief description...

Opening for a computer scientist to help solving one of the
fundamental problems of Cell Biology: the elucidation of protein-
protein interactions
Wellcome Trust Centre for Cell Biology, University of Edinburgh, UK

Ideal professional background:
Database administration (PostgreSQL), database application
development, algorithms, data structure, Java (C++, web programming),
data mining, data visualization.

Ideal personal attributes:
Interested in application (of informatics to proteomics/life
sciences), inspired by wider scope of things, awake, asking questions.

Our group:
We are a young group of currently seven people from Germany, UK,
Denmark, Brazil, and China. The group has started five years ago in
Milan, Italy, and relocated about two years ago to Edinburgh. We are
embedded in one of the best Cell Biology Institutes of the UK
interacting with some of the world's best researchers in Cell Biology.
Our own work focuses on acquiring data of proteins by mass
spectrometry and on designing computational tools to mine this data
for valuable information.

Our aim:
We want to find out which proteins do interact in the cell. There are
many thousand proteins in a human cell, most having their own distinct
function. However, proteins usually act in complexes. Protein
complexes can be isolated and their protein components be investigated
by mass spectrometry. The analysis does reveal the identity of the
proteins in the complex but not which proteins interact directly. This
information is currently not accessible at all or only for a very
limited number of complexes. We are therefore developing a new
approach that will deliver this information.

Our approach:
We chemically link proteins in complexes and preserve in this way
their proximity for the mass spectrometric analysis. The proteins are
then degraded in a controlled way into peptides. A few of the peptides
are actually a pair of peptides stably linked to one an other by the
chemical linker and thus containing the information we desire. These
cross-linked peptides are at the centre of our interest. We detect
them together with all the other peptide by mass spectrometry and then
need to identify them. We do so by matching all spectra to a database
containing all possible peptide combinations. In this way we find the
peptide pair that matches best to our mass spectrometric data. The
approach is computationally very challenging: 1000 proteins give
easily rise to 1,000,000 peptides and hence to 5x1011 peptide pairs. A
person in our lab has been working since 14 months on this
computational problem and the open post is to reinforce these efforts.

Our requirements:
Any candidate applying for this position should be knowledgeable about
the techniques needed for the design of efficient algorithms and be
able to use appropriate mathematical tools for analysing their
performance. Moreover he/she should understand the importance of the
data structures used in a particular implementation of an algorithm,
and how the data structure that is used can affect the running time.
Desirable skills include: knowledge of Java, databases (PostgreSQL)
and web-based programming.

Our offer:
Desired start date ASAP. Funding is secured until 30.04.2009. The
salary depends on the experience level (20-30,000 GBP/year) and is
fixed by the European Commission who is the source of funding. In
addition, travel allowance is paid according to the rules of the
European Commission (up to 4,000 GBP/year).

Our website: http://rappsilber.bio.ed.ac.uk/

Good luck!  We look forward to hearing from you.

Jimi