The presentation of my PhD defence

That’s it! Last week I defended my PhD thesis!! I have gone through it, and survived to tell!

I don’t feel very different from before, apart from being relieved :-). Now the future is possibly more difficult than before, because I have to look for a job position and finish a lot of things.

While I was preparing the slideshow, I realized that there are not many examples of presentations for a PhD defence online. This is bad, because you need all forms of help to prepare this presentation.The PhD defence is the last thing that you do as a PhD student, so you want to do it perfectly. It is also the moment when you describe many years of your work to the your colleagues and family. Thus, it is bad that there are few examples of slideshows for PhD defence online.

Here is the presentation that I have prepared for my defence. I hope that it will be useful to other people as an example for their defences.

I think that, for this type of presentation, the first slide to make is the “summary of the talk” slide, like the “Topics” slide I have. Usually I don’t like to have such summary slides in my presentation, but for the Thesis defence it is very important, because it gives you a feeling of security when you present. Having a well defined structure allows you to know when you can stop to drink some water or to check if everybody is following, and to know exactly what to say in each slide of the talk.

Introduction to Unix systems for Evolutionary Biologists – slides online

Here are the slides of the “Introduction to Unix-like systems” lecture I gave last Saturday at the “Programming for Evolutionary Biology” workshop in Leipzig.

In these slides, I did my best to communicate to the students what is philosophy behind the Unix systems and why they have been so important in the past. The Unix philosophy is in reality an approach to data analysis and programming: I am happy if I have been able to convince the students that, by studying how the first programmers have approached the problem of data analysis, they will be able to learn good programming practices, and avoid mistakes that have already been surpassed many years ago.

I would like to thank my colleague Brandon Invergo and my supervisor Hafid Laayouni for suggestions on how to improve the slides. Enjoy!

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Programming for Evolutionary Biology Course – Leipzig 2012

This year I will teach in a two-week Introductory course to Programming and Bioinformatics, aimed at PhD students and Post-Docs working in Evolutionary Biology. This is a course designed for researchers that have little or no experience with programming, and it will teach them the basics of Bash, Perl, R Programming along with popular tools used in Evolutionary Biology.

The deadline for application is January 31st 2012, and the course will be held in Leipzig (Germany) in the last two weeks of March 2012. Please check the home page of the course for details on how to apply:

We tried to keep the cost of the course as low as possible, and thanks to a contribution from the Volkswagen foundation we have been able to keep it at only 300 euros for person. Plus, we have some fellowships available.

Here it is the programme, that you can also find in the home page of the course:

  • Introduction to Linux (Giovanni Marco Dall’Olio, University Pompeu Fabra, Barcelona, Spain)
  • Introduction to R (Katja Nowick, University Leipzig, Germany)
  • Analysis of next generation sequencing data (Tomas Marques-Bonet, University Pompeu Fabra, Barcelona, Spain)
  • Analysis of structural variants (Tomas Marques-Bonet, University Pompeu Fabra, Barcelona, Spain)
  • Analysis of expression data (Katja Nowick, University Leipzig, Germany)
  • Promoter evolution (Annalisa Marsico, Max-Planck-Institute for Molecular Genetics, Berlin, Germany)
  • Statistics & Inference (Stuart Baird, University Porto, Portugal)
  • Introduction to Perl (Sofia Robb, University of California Riverside, USA)
  • Phylogenomics (Rui Faria, University Porto, Portugal)
  • Ensembl API (Bert Overduin, EMBL – European Bioinformatics Institute, Hinxton, Cambridge, UK)
  • Introduction to databases (Jan Aerts, Leuven University, Belgium)
  • Visualization of scientific data (Jan Aerts, Leuven University, Belgium)

Invited speakers:

  • Evolution of behavior (Sarah London, University of Chicago, USA)
  • Evolutionary ecology (Claudia Acquisti, Westfälische Wilhelms-University Münster, Germany)
  • Phylogenomics (Rasmus Nielsen, University of California, Berkeley, USA)

second part of the slideshow on HG for bioinformatics

I gave the second part of the talk on Version Control and hg for my group (check the first part). Here you have the slides:

I am working in collaboration with some of my colleagues to write a pipeline for calculating some tests for our projects.

The idea is to use hg to coordinate the writing of these scripts. We will have a reference version of the scripts on a private bitbucket.org repository; then, everybody will synchronize its local copy of the scripts from there, uploading new changes to the same place.

Some of my colleagues told me that hg is much easier than what they thought. I am very happy of this because I was worried about it being too difficult to use. It is really a long time that I want to convince my colleagues to adopt some version control tools, and it seems that it was easier than what I expected.