Bioinformatics

How to be a Biohacker


Biohackers embrace fully the philosophy of hackers: love for freedom, veneration of competence and utter curiosity for how things work. How does one become a biohacker? Usually biohackers cannot tell if they are really one of them until someone else says so. However, it is not enough to be competent in the mastery of programming or being a computer wiz. You need IT skills that suit computational biology research and familiarity with the biology itself, which in the end is the problem one has to solve.

A big attitude to the biohacker philosophy is that you do not only need love to solve technical problems for their own sake; you need to think of living organisms as an extension of the information systems you work with. Biological concepts may be then abstracted into objects whose hierarchical organization reflect the different levels of order in living things. Computer languages thus become the perfect analogy for understanding the complex information flows in living systems.

True to hackerdom culture, Unix, Perl and MySQL are programming skills that you need to master (I can think of people who would also say Java, Javascript, CSS, etc.). The best way to master the art of programming is to spend as much time as possible reading and writing source code. Some people think Perl is doomed. This is not true in the biohackers world. In part due to legacy and in part to the flexibility it provides, Perl is still the language of choice for many biohackers. Perl is used to construct 1) the back end of web applications, 2) pipelines and workflows and 3) quick and dirty scripts for parsing and calling other programs.

You will also need to be familiar with projects like R and Bioconductor, since a lot of the work will involve providing the computational infrastructure for analyzing data. In addition, you’ll need to know about data formats (fasta, sbml, mmcif…), software toolkits and libraries (Paup, Phylip, EMBOSS, BioPerl…), databases (Ensembl, InterPro, PDB, KEGG…), webservers and portals (Pubmed, ISCB).

Finally keep in mind best practices. Some of them I have written about elsewhere (like refraining from reinventing the wheel), but above all, give yourself the time to enjoy the learning process. Getting to the top usually takes longer than staying at the top; so what’s the point if you haven’t enjoyed the trip?

4 replies »

  1. Cool thank you. I am developer and I wanna hack with bio, that was informative but can you provide more e.g. links, tools, books anything at all. Thanks.

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    • George, have a look at the Computational Biology Wikiproject in Wikipedia. There you can have some general pointers.
      Manuel

      Like

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