Skip to main content

Freely-Speaking: Biology and Big Data

Computational sciences at the interface of a hard science are gaining in importance as shown by the recent Nobel Price in chemistry awarded this year. I also recently read two more commentaries that appeared in Nature and Nature Biotechnology that I found interesting.

 The first article [1] talked about the need to develop systems that can handle "Big Data" in Biology. Despite the need, a widely-adopted system has not emerged yet. The author credits this to two problems:
  • Biological data exists in a variety of changing formats.
  • Commercial systems may impose steps that are unintuitive to the way data is recorded, the workflow of the scientist or add additional steps for converting data from one format to another - arguably to prevent scientists from using rival systems.
  • A lot of home-grown solutions were not written in a robust way and are badly annotated which makes modifications difficult.
In response to the increasing discrepancy between data generation, and the capturing, storing, annotation, and retrieval of biological information across different systems, the second article [2] was a commentary on interviews that Nature Biotechnology did with  writers of successful computational biology software.

In their summary, the article described that there appears to be a gap in communication between dry and wet-bench biology: Wet-bench biologists often under-appreciate aspects of computation and the craft of software engineering. On the other hand, computational scientists often are oblivious to the need to make their tools more accessible and comprehensible to the wider biology audience.

Both articles seem to suggest that a change in mentality on both sides and closer collaboration between the different sides will be both necessary and helpful in coming up with successful software solutions that address big data problems in biology. These articles describe really well the experiences I have obtained over the last two years myself. And the solutions suggested seem mostly in light with what I think ought to be the solutions. I feel happy to be able to work towards solutions in this space together with my team.

Literature Cited:

[1] Boyle J. "Biology must develop its own big-data systems". Nature 499, 7 (04 July 2013). Last visited: 2013-10-13. Link.
[2] "In need of an updgrade". Nature Biotechnology 31, 837 (2013). Last visited: 2013-10-13. Link.

Popular posts from this blog

Focus on Algae - Part I: Bioremediation

After spending the last few blog posts on different aspects of dissimilatory bacteria, I want to switch the focus to a different class of organisms I have been interested in for a long time now. These are the algae. Algae comprise a large diversity of "sea weeds" and an even larger variety of single-celled organisms that mostly are capable of doing photosynthesis. They include the ordinary sea-weed, and make up a portion of the green slime found around the edges and the bottom of a pond. More exotic types of algae can live symbiotically - that is together with another organism in a mutually beneficial way. Lichens are an example of symbiotic relationship between algae and fungi. More information about the evolution and lineage of algae can be found in this wiki article.
Image via Wikipedia
Typically, these organisms are either not mentioned at all or only in conjunction with toxic algal blooms. But lately, algae, of course, have been in the news recently because of the promi…

Journal Club:”Direct Exchange of Electrons Within Aggregates of an Evolved Syntrophic Coculture of Anaerobic Bacteria” - OR: How Bacteria Hook up to Share Energy

Another curious observation made the science rounds the past week: wired, electric bacteria. Reading this article reminded me of a review article on dissimilatory bacteria I read before, and one of the most interesting talks I ever attended in my life titled "Eavesdropping on Bacterial Conversations".

What did they do?

Summers, who is Microbiologist working in the Lovley lab at the University of Massachusetts, was studying Fe(III) reducing bacteria in the soil. They wondered what would happen when Fe(III) reducing bacteria would deplete Fe(III) available in the soil. In order to study this question, the research group co-cultured two strains of geobacter bacteria: Geobacter metallireducens and Geobacter sulfurreducens. The research team thought that combining the former bacteria that can oxidize ethanol in order to obtain energy, but normally must pass obtained electrons onto Fe(III) which was not present in the solution, with the latter strain which cannot metabolize, but c…