Master's Thesis: Pure Structural RNA Alignment via Independent Set

This page is related to the thesis project "Pure Structural RNA Alignment"

Summary

topic	Pure Structural RNA Alignment via Independent Set
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official start
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main advisor	Dr. Gunnar W. Klau
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General rules and agreements

We will meet once a week unless agreed on otherwise. The regular meeting will take place tba in Gunnar's office.

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

Goal of the thesis

Taking on a graph-based view on purely structural RNA alignment leads to an independent set problem. The goal of this thesis is to study the special structure of the problem instances arising from the RNA application and to develop (practically) efficient algorithms.

The algorithms should be implemented within the software library LiSA. LiSA is a C++ library, a large part of which deals with computational RNA analysis.

The algorithm should be compared to state-of-the-art tools (testing environment available within LiSA) on different, meaningful input. The thesis should describe all efforts in a sound, scientific way and document the theoretical investigations as well as the computational results properly.

Literature

tba

Time table

week 1-23	tba
week 24	buffer time

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.