Sifting through my website stats, I realised that bioinformaticians are reading more posts discussing "how to do bioinformatics" than the ones with a strict scientific content. Is this a feature of this blog, or does it reflect a common problem with working habits? Drawing some conclusions after two years of atcgeek After almost a couple … Continue reading Is "how to do bioinformatics" the major topic in bioinformaticians online reading habits?
It was a cold November morning, year 2011. Sapienza University has a huge campus next to the city centre of Rome, where the main faculties are stored in huge buildings in the rationalist style. Yet, the faculty of Biochemistry has a detached site in the neighboured flanking the campus, San Lorenzo. I was crossing the streets of … Continue reading The four most stupid things I have ever done in bioinformatics.
It was the early eighties, a day like any other at the MIT. And a printer was not working. The Artificial Intelligence Laboratory programmer Richard Stallman did his best to fetch the source code of the driver from the manufacturer to fix it, but there was no chance. The code was closed, and this was … Continue reading Happy birthday mr. GNU
Yesterday I have found an amazing audio comment on Nature's Arts and Books blog that was discussing a possible influence of music on the development of modern science. Among the many connections we may find between science and music, the one I am going to propose today turns out quite unexpected. I understand that pipeline development is … Continue reading Tune up your pipeline with Luigi, the Python module to manage workflow used in Spotify.
We could agree that a bioinformatician is basically a naked, starving castaway who's trying to survive in a desert island. As in one of those realities that run on tv, or in the movie starring Tom Hanks, he is provided with a knife, quite a few clothes, and a good dose of motivation. In this allegory, … Continue reading Project Rosalind: learn bioinformatics and programming through problem solving
The paper I am going to explore today introduces MethylMix, an R package designed to identify DNA methylation-driven genes. DNA methylation is one of the processes that are more extensively studied in biomedicine, since it has been found as a principal mechanism of gene regulation in many diseases. Although high-throughput methods are able to produce … Continue reading MethylMix: an R package for identifying DNA methylation-driven genes
We already had the chance to discuss about the importance of reproduciblity in computational research, and to comment some good practices to improve it. As we read the Ten Simple Rules that Sandve and co-workers proposed the last October, we cannot help but underline the importance of pipelines. A correct pipeline- based approach will prevent researchers from potentially harmful manual interventions … Continue reading Software for pipeline creation with Python.