Bio::Blogs #7

A Happy New Year to you all!

This time I have got the privilege of hosting an edition of Bio::Blogs on my blog Biohacking. Well, I start with a little disappointing news (at least for me) that Wikipedia has deleted the article on Biohacking. They claim that it is a pseudo-scientific term and it’s not acceptable to the scientific community. To add credibility to their claim, they say that since there is no journal named Biohacking, so the article should not persist in Wikipedia. “What the heck”, I say. I never claimed that Biohacking is a scientific term and, moreover, Wikipedia is not just for science. Nevertheless, Biohacking (as a term) will persist. Neologism is not that bad. πŸ™‚


Suddenly my interest in biomathematics has peaked up due to my research internship at National Center for Biological Sciences, Bangalore under Dr. Mukund Thattai during December 2006. As we were brainstorming for a particular project, I was mesmerized by his approach to science. He was using mathematical concepts to describe real biological entities and manipulating those entities in his head. The biological entities are just an instance, the real power of mathematics lies in ability to describe any arbitrary concept. Also, even though we were able to describe equations for our system easily, so, we could have easily simulated the system, but he insisted on cracking the system analytically as it yields exact answers and is much faster than simulating the system. I believe that biomathematics (or mathematical biology) has traditionally been ignored by the computational biology community. For them, insistence is usually on simulations, which of course look cool but are not the only way towards the solutions. Now for the starter links on biomathematics, see this excellent set of lectures. And this is the web page of the Society for Mathematical Biology. Although I haven’t read it for myself, I would recommend this textbook for an introduction. Of course there is the bible for mathematical biology by J.D. Murray.

How about using your expertise in bioinformatics to earn easy money by taking a plunge into risk ladden world of entrepreneurship? Jokes apart, I, myself, am little ambivalent on this whole issue of entrepreneurship in bioinformatics. With the extent of hype around this field (in India) one would almost want to jump into it immediately. But, a little research will show that most bioinformatics companies are perishing. So, unless you have a really good business model, don’t think about starting your venture in bioinformatics for its own sake. A company can’t really survive on breakthrough research unless it makes it marketable.

Regarding conferences, there was one which I attended in Bangalore called Computational Insights into Biological Systems. It was actually a satellite meeting of the International Conference in Bioinformatics 2006. The CIBS06 had great talks from well known people in this field such as Sarah Teichmann, Ravi Iyengar and Rama Ranganathan. Apart from the talks, the free lunch there was nice too.. πŸ™‚

Synthetic Biology
Here are some links (chosen randomly) for the blogs (on synthetic biology) which I like to read. Biohackery discusses some cool topics on biology. The Greythumb blog takes a very unconventional approach to the “intersection between biology and technology”. Omics Omics is also an informative blog. The Synthesis Blog discusses topics mainly related to Synthetic Biology. Also see DigitalBio @ Biomedical Computation Review is not a blog but an excellent magazine; make sure you don’t miss checking it out.

Links from the fellow bloggers
Pierre discusses about the features of Java 1.6 from a bioinformatics point of view. He thinks that the new integrated db engine is cool enough and he also uses the new scripting engine for making a little awk-like tool.

Pedro Beltrao discusses the exciting possibility of extracting (or mining, i must say) useful biological information from social bookmarking sites such as Connotea.

Sandra Porter has been writing a series on DNA sequencing on her blog. First she discusses the basics. Then she moves on to explain Sequencing strategies, Reads and chromats and How many reads does it take?. At the time of writing this post, the fifth part of the series has also been released – and the sixth one also coming out soon.

Finally, Neil has interesting posts on “computing tips and tricks”. Check out his posts on Automated SRS using Perl and LWP and Running a background process in PHP.

The End
That was all from the (first ever, i hope) Indian edition of Bio::Blogs. The bioinformatics field is very hot in my country as large number of so-called students are getting trained in it. But they don’t really have the real sense of doing bioinformatics. From what I have observed, the majority of them just know Perl & Blast and have programmed a DNA to Protein sequence translator once in their life. And they claim to be bioinformaticians. Bioinformatics is much more than mere programming. Enjoy. πŸ˜‰

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