Bachelor Thesis: Visualization of RNA alignments

This page is related to the thesis project "Visualization of RNA alignments"

Summary

topic	Visualization of RNA alignments
student	Robert Weißmann
start	4 Jun 2007
official start	11 Jun 2007
official end	6 Aug 2007
main advisor	Dr. Gunnar W. Klau
add. advisor	Markus Bauer
2nd reviewer	Prof. Dr. Knut Reinert

General rules and agreements

We will meet once a week unless agreed on otherwise. The regular meeting will take place Mondays, 13:59 in Gunnar's office.

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

Goal of the thesis

The goal of the thesis is to develop a visualization of multiple RNA secondary structure alignments within the software library LiSA. LiSA is a C++ library, a large part of which deals with computational RNA analysis. The basis for the visualization is the MultipleStructuralAlignment class, which holds the aligned sequences and a consensus base pair probability matrix. In a first step, the structure logos by Gorodkin et al. [1] should be reimplemented. Then, a new idea should be tried out that visualizes the structural matrix entries by means of arcs in different width, style, and color. Finally, a mixture of these and possibly new ideas that might have come up during the first phase should be proposed and implemented.

All implementations should be run on different, meaningful input. The thesis should describe all efforts in a sound, scientific way and document the computational results properly.

Literature

[1] J. Gorodkin, L. J. Heyer, S. Brunak and G. D. Stormo. Displaying the information contents of structural RNA alignments: the structure logos. Comput. Appl. Biosci., Vol. 13, no. 6 pp 583-586, 1997.

Time table

week 1	read [1], get acquainted with LiSA: compile and start a first test program
week 2-4	plan and implement the initial visualizations
week 5	propose final visualization, run experiments, start writing thesis
week 6	run experiments, write thesis
week 7	write thesis
week 8	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.