Marine ecology – a kind of research where you do loads of field work like tagging whales, go fishing and dive among corals? Well, not quite. Of course most of these activities are included into my job description, however they make up maybe 2% of my time (together!).
At the beginning of each project (after getting grants, planning and convincing colleagues) is getting the biological samples. In my case I filter liters of seawater on small filters, count bacteria in the microscope or grow microbes in the labs under certain environments. Mostly I extract their genomic material (DNA or RNA) to see their potential or which genes they express at which times to get to know their function in the marine food-web.We prepare the DNA and send it for sequencing, this means to encode the information saved in DNA molecules.
Here, my problems normally start. How do I know which information are encoded in the DNA sequences that I am interested in and which programs can I use to get out the information? In order to get more insights into how to compute and decode DNA, I now attend a workshop on genomics. The genomics workshop takes place in beautiful Cesky Krumlov where 84 participants and me are trained by experts in the field. We have a couple of hours lectures in the morning, followed by 2 breaks and six hours computing until 10pm. Today, we try to encode the E.coli genome. More information and updates during the course can be found here. Back to coding…