I have just uploaded my first paper to arXiv. The title is “Human Genome Variation and the concept of Genotype Networks“, and presents a first, preliminary application of the concept of Genotype Networks to human sequencing data. I know that the title may sound a bit pretentious, but we wanted to pay a tribute to a great article by John Maynard Smith, to which the work presented is inspired.
Nevertheless, in this blog post I am not going to discuss the contents of the paper, but only on how I did this work. This was a project that I did in my last year of my PhD, and I have made an extra effort in trying to follow every best practice rules I knew.
I started my PhD in the pre-bedtools and pre-vcftools era of bioinformatics, and I saw the evolution of this field, from a spare group of people in nodalpoint to the rise of Biostar and Seqanswers. During this time, I have read and followed a lot of discussions about “what is the best way to do bioinformatics”, from whether to use source control, to testing, and much more. For the last project as a PhD student, I wanted to apply all the practices that I had learn, to determine if it was really worth to spend time learning them.
Premise: dates and times of the project
My PhD fellowship supports a three months stay in another laboratory in Europe. I decided to do it in prof. Andreas Wagner’s group in Zurich.
The decision to go to Wagner’s group was motivated by a book that he had recently published, entitled “The Origins of Evolutionary Innovations”. Previous to the start of this project I had read some articles by Andreas Wagner, and found them very interesting, so the opportunity to stay in his lab was very exciting. However, in light of what I learned during this time, I have admit that before December 2011, I didn’t understand most of the concepts present in the book. Thus, we can say that for this project, I started from zero.
I started thinking of this project in December 2011. I did the first practical implementation in the three months of the stay in Zurich, from May to August 2012. The first preliminary results came in January 2013, and the first manuscript in April 2013. We submitted to ArXiv in August 2013. During this period of time, I have also worked on three other projects, wrote my thesis, and taught at the Programming for Evolutionary Biology workshop in Leipzig.
Note: this blog article is very long, you may want to download as PDF and read it more comfortably.