cpauvert/bioinformatics-master-degree-report

A two-year apprenticeship in computational biology condensed.

Bioinformatics Master Degree Report

Thesis sources are provided to whom is interested in TikZ figures and biofinformatics.

Have a glance at report-cpauvert-2016.pdf!

This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

## Compilation usage

For the complete report

$ make all

To compile only a chapter, say introduction:

$ make introduction.pdf

Preview TikZ figures

Use the dedicated script preview to compile only specific TikZ figures:

$ ./preview figures/fig-mixture-model.tex

## Figures TikZ

Figures can be drawn in TikZ using knitr engine with a modified template: template-tikz2pdf.tex Chunks needs to be configured with the following options:

engine="tikz",engine.opts=list(template="template-tikz2pdf.tex"),echo=FALSE,fig.cap=""

Technical specifications

### Number of pages

Page number estimation from last year report.

• *-doc : report page number according to master degree recommendations.
• *-real : actual report page number.

Type	#M2.1-doc	Ratio	#M2.2-doc	#M2.1-real	#M2.2-real	#ALA
Introduction	4	0.14	6.90	7	11.3	13-15
Materials	6	0.21	10.34	7	11.3	7
Results	10	0.34	17.24	14	22.6	22.6
Discussion	6	0.21	10.34	-	-	-
Conclusion	3	0.10	5.17	3	4.8	4.8
Total	29	-	50	32	50	50

Spell-checking

In order to correctly write in English.

$ aspell --lang=en_GB -c FILE

Vim customisation

Interesting note: don't forget to add the following lines to ~/.vimrc to prevent from autocompleting pdf files in command line.

set wildignore+=*.pdf,*.o,*.obj,*.jpg,*.png

bioinformatics-master-degree-report's Issues

Cheese samples used

The following cheeses were used. Note that the surface of the cheese was sampled for every cheese.

• Epoisses
• Gorgonzola bon
• Munster
• Roquefort
• Saint-Nectaire laitier
• Saint-Nectaire fermier
• Salers
• Tome des Bauges
• Toscanello

Reference genome used: Psychrobacter aquimaris

Foreign abbreviations

According to my English teacher, foreign abbreviations needs to be written in the language of origin.
They can be followed by a dash and an English explanation.