Master's Thesis: Peptide Sequencing Using Mathematical Programming

This page is related to the thesis project "Peptide Sequencing Using Mathematical Programming "

Summary

topic	Peptide Sequencing Using Mathematical Programming
student	Sandro Andreotti
official start	19 Jun 2007
official end	18 Dec 2007
main advisor	Dr. Gunnar W. Klau
2nd reviewer	Prof. Dr. Paul Wrede

General rules and agreements

We will meet once a week unless agreed on otherwise.

General information about MSc theses in bioinformatics at FU Berlin can be found here.

Goal of the thesis

The goal is to develop, implement, and evaluate a novel concept for de novo peptide sequencing and spectral alignment based on antisymmetric paths in the spectrum graph.

Thesis

I encourage writing theses in English language. This is no strict rule, however. Presentation quality and clarity are more important than sticking to this recommendation. There is a vast amount of literature on good scientific writing. Here are just a few examples:

• Elements of Style (Strunk & White). A cheap and excellent primer. Everybody should use it.
• For professional use: The Chicago Manual of Style.
• S. P. Jones: How to write a great research paper. Most of the advice holds for theses as well.
• San Francisco Edit: Twelve Steps to Developing an Effective First Draft of Your Manuscript. There's more advice on their web page.
• Dave Patterson's writing advice
• The "ten simple rules" edition by Philip Bourne on PLOS Computational Biology.

Remark: Perhaps more than other advisors, I appreciate reading clearly structured theses and the absence of grammatical and spelling mistakes. This holds true even for early draft versions of the thesis.

Grading

The final grade will largely be based on the written thesis. More precisely, the composition of the final grade is as follows: 70% thesis, 20% implementation and documentation, 10% presentations, collaboration, progress.