Highlights of the International Synthetic and Systems Biology Summer School 2014

sicily_etnaLast week I joined the International Synthetic and Systems Biology Summer School in Taormina, Italy and as the title describes it was all about Synthetic and Systems biology with some pretty cool speakers.  Weiss talked about the general principles of genetic circuits and the current limitations (record is currently 12 different synthetic promoters in 1 designed network). Sarpeshkar focused on the stochastic nature and the associated noise of cells, he showed how they can be simulated or mirrored using analog circuits. Paul Freemont took Ron Weiss’ design principles and showed how to apply them on different examples, he also elaborated on an efficient way of characterizing new circuits and parts. Tanja Kortemme, a former postdoc from the Baker lab, gave an introduction to the capabilities of computational protein design and using some neat examples showed the power (and limitations) of computational design. Below some highlights and the relevant links of the literature that was discussed.

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Setting up Syncthing for Raspberry Pi

Nowadays everything is apparently in the cloud. However the cloud comes in many different sizes and shapes. In my case primarily in the form of dropbox. However there are always downsides of “out sourcing” your data to an undefined cloud. Some popular alternatives include BitTorrent Sync (not open source and your data is still touched by a third party), ownCloud (an open source dropbox clone, however the performance on a Raspberry Pi is not very smooth) and since December 2013 Syncthing. The last one is a kind of open source implementation of BitTorrent Sync, so in contrast to Dropbox your data is distributed over your own computers and not at a distant server. In my setup I use a headless Raspberry Pi that is tucked a way in a cupboard as a node in the network, so this client is always online. Continue reading

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Papers of VizBi ’14 keynote by Jeff Heer

Screen Shot 2014-03-09 at 7.46.53 PMLast week I attended the Visualizing Biological Data (VizBi) conference in Heidelberg. According to the website the mission of the conference is to “ bring together scientists, illustrators, and designers actively using or developing computational visualization to study a diverse range of biological data.”. I can only say the organisers more than succeeded in this mission, it was indeed a very interdisciplinary, creative and interactive crowd. The first keynote of VizBi ’14 was presented by Jeffrey Heer from the University of Washington, since the papers he referred to are mostly published in non-PubMed journals I tried to collect links to the pdfs here. Update: Added two more references supplied by Heer.

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Getting you and your colleagues started with Illustrator

illustratorLast week I organised a small Adobe Illustrator bootcamp at my center with all the material sourced from Youtube. Youtube is great for the purpose because whenever it is unclear you can quickly pause and rewind. When a concept stays unclear the participants can collectively google for the solution stimulating the educational processes. Here a compilation of the tutorials we’ve been through, starting from the basics to more advanced Illustrator tools.

Terry White his 40 minute introduction:

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Book review: What Do You Care What Other People Think?

thinkWhat Do You Care What Other People Think? (1988) is ghost written by Ralph Leighton the son of Feynman’s Caltech collaborator Robert Leighton, who also collaborated with Feynman on writing Surely you must be joking (1985). One third of the 250 pages of the book consist of short, humorous, and easy reading stories. But some of them also contain intensely moving lessons, for example the chapters dealing about his wife who suffered from tuberculosis. These first 80 pages are already worth reading the book!

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The 9 reads for Christmas

logosA selection of some interesting papers of the past period. Unfortunately some are only accessible for subscribers. Some topics covered; protein folding and design, antibiotic resistance genes, RNA polymerase complex and a paper on choosing the right color for your data.

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Git for Scientists in 2 minutes

gitlogoSince the introduction of Git the world of version control went through a revelation. Currently Github is the biggest player in the field, offering a free place to host and collaborate on your open-source code. However Git is also very useful for a scientist to keep track of in silico experiments and it does not require any sophisticated or complicated tools. In this post a small tutorial on how to set Git up for your experiments. Continue reading

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Untangling the Hairball by O’Donoghue (ICSB13)

F1.largeToday Sean O’Donoghue talked at the 14th International Conference on Systems Biology (ICSB) in Copenhagen. O’Donoghue is affiliated with the Australia’s Commonwealth Scientific and Industrial Research Organization  (CSIRO) and the Garvan Institute of Medical Research both located in Sydney.  His talk was officially titled “Visual Analytics: A New Approach for Systems Biology” but he immediately after the start admitted it could better be named “Untangling the Hairball“. Using 6 guidelines he quickly showed the basic principles of data visualization for scientists. Since his talk contained quite some references to journal articles, webservers and online tools I thought it would be useful to put everything together in a post.

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Book review: The Double Helix

The Double Helix, book coverI recently came across a copy of “The Double Helix” by James Watson and will put forth some highlights in this post.

The book became quite famous for giving a glimpse of how science was done in the ’50. However it also generated a fair amount of controversy because of the harsh personal attacks especially towards Rosalind Franklin, who made essential contributions but was never acknowledged to the extend of Watson and Crick.

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Visualize your trail

Screen Shot 2013-07-23 at 12.50.45 PMCurrently I’m participating in the Quantified Self summer school at the CIID (Copenhagen Institute for Interaction Design). The focus lies on the visualisation of complex data sets, currently a hot topic in science. As workhorse the Java based environment Processing is used, which is widely known in the visualization community. (For some vivid examples check openprocessing.org).

To get a better grasp of Java in general and processing in particular I wrote a small package that visualizes all the places you have visited with the corresponding color mood (=the most prominent color in the pictures you took).

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