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Monthly Archives: September 2008

Future of Science on the (ZuiPrezi) map

I’ve just stumbled across map of predictions about global science and innovation created at a recent IFTF workshop in Singapore (the interface is a novel service for online presentation called ZuiPrezi – it looks very promising and I’m waiting for it to come out of private beta). The map contains a few points that resonate with my own scientific interests:

bioelectricity, microbial fuel cells and self-assembly for molecular electronics were for me areas where synthetic biology comes into play
scientific publications changing from journals to articles and proposal to make an institute for free exchange of ideas looked like indications that Science 2.0 memes are spreading very well
and finally, I’m happy to see more people believing that real-time, non-invasive and possibly 3D sensing of biological processes (aka “how is my cholesterol level building up?”) will be available sooner than in 50 years

As usuall with such predictions, I feel like many of them are quite conservative – or even schematic. Only very few were completely new to me, but that’s not necessarily a bad thing. It means that actually most of these predictions will turn out to be true in some time. I would like to see something that would immediately blow me away, but on the other hand it’s all relative :).

Crowdsourcing the future: Can alternate reality game Superstruct help save the world?

1 Comment

Posted by Pawel Szczesny on September 30, 2008 in Comments, Research

Tags: Energy, Institute for the Future, Microbial fuel cell, Synthetic biology, Technology

Skyrails and STRING

09 Sep

Of course I couldn’t resist not to play a little bit with Skyrails after I saw it at Flowing Data blog. Skyrails is a graph visualization system that was designed with expandability and awesome look in mind. All menus can be programmed in odd-looking, but quite easy to learn language, which helps in writing customized interface to particular data.

My quick attempt was to take some sample data from STRING, feed it into Skyrails and see if that makes any sense. My choice was #1 example from STRING main page, which was trpA protein from E. coli K12. The main graph on the trpA interactions page looks as follows:

The same graph in Skyrails:

Of course Skyrails has a 3D representation, is fully interactive, with a little work one can filter some of the connections out, put images of structures instead of green dots, etc. etc. It doesn’t look as clear as STRING, because it wasn’t optimized for such use – in practice it’s much clearer. The video below shows the basic interactions with this dataset.

Is it useful? At the moment, not really. It has already lots of features that more mature programs lack (completely programmable menus are great idea), but usage is still crude and in some cases the flashy effects are disturbing. However, it’s worth to keep an eye on Skyrails. First, development is pretty much guaranteed, as the author said he starts a PhD on this project. Second, the basic roadmap includes features that again aren’t present anywhere else, like client-server architecture (so you can talk to Skyrails system from external application – dynamic, time-aware visualization?). And third – it’s the most cool-looking visualization system I’ve found so far (will it make into a movie, like Genome Valence from Ben Fry did?).

2 Comments

Posted by Pawel Szczesny on September 9, 2008 in Software, Visualization

Tags: Graph, Information Visualization, Skyrails, STRING, Visualization

Data from Bioinformatics Career Survey posted

02 Sep

Data analysis of Bioinformatics Career Survey

Michael Barton did a great job of collecting and cleaning data for First Bioinformatics Career Survey. Raw results are available at Github and please read also details on the analysis and sharing results over at OWW page.

Michael encouraged to go wild with an analysis, so here’s my quick look at the data. On the image above you can see a scatter plot of salary vs years in the field (top), histogram of salaries (bottom left), histogram of planned years in the field and histogram of positions (bottom right). All plots are colored according to the positions.

There some obvious things in these graphs, such as correlations between position and salary or between years in the field and position (see also the video below). But what strikes me is the plot showing estimated number of years in the field. There are some local maxima at around 5, 20 and 30 years, but its very interesting to see that ca. half of the people see themselves in bioinformatics for another 25-30 years and longer, and there’s no clear correlation between positions of these people and these predictions (other than senior/PI-level staff doesn’t like an idea of working for another 30-40 years). The reason I find it interesting is that I have no idea how bioinformatics will look like in these 20-30 years (and that was the reason I’ve put conservative 5 years in this field). Do you know? Do you have an idea how bioinformatics will look like so much time ahead?