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Monthly Archives: March 2008

Biohacker logo

Despite all negative associations I still like word “biohacker” and I sympathize with people thinking about all kinds of bioengineering. We have already tools and data to “biohack” in silico (just to mention 17-years old developing model for identyfing cancer patients), while technology for home-based experiments will knock to our doors very soon.

Hackers have already an emblem, which actually I incorporated in the biohacker logo. However, I thought that it would be nice to have our own, just to indicate in which area we “hack” stuff. So, by displaying this logo one would express a sympathy with hackers’ attitide:

The world is full of fascinating problems waiting to be solved.
No problem should ever have to be solved twice.
Boredom and drudgery are evil.
Freedom is good.
Attitude is no substitute for competence.

applied to a bioengineering field.

If you like the idea, maybe we can together write “How to become a biohacker” guide?

2 Comments

Posted by Pawel Szczesny on March 21, 2008 in Biological engineering, Community

Tags: bioengineering, biohacker, biohacking, logo

Semi-automated workflows – Taverna Interaction Service

12 Mar

I was still thinking about recent Neil’s wondering about possibility of automating every scientific workflow, when I saw this (Bioinformatics Advance Access abstract):

The Taverna Interaction Service: enabling manual interaction in workflows by Anders Lanzén and Tom Oinn

Taverna is an application that eases the integration of tools and databases for life science research by the construction of workflows. The Taverna Interaction Service extends the functionality of Taverna by defining human interaction within a workflow and acting as a mediation layer between the automated workflow engine and one or more users.

I have not tried it yet but this Taverna plugin is very likely an answer to doubts I often have when automation of bioinformatics workflows is discussed: we shouldn’t always remove ourselves from the workflow, as interaction with software can be often critical in making a discovery. For example conscious decision about which sequences should go in during PSI-BLAST search can dramatically influence quality of resulting profile. So I agree with Neil that not every workflow can be automated, but more importantly not every workflow should be. Possibility of wrapping one’s mind around a problem is gone when there’s no feedback loop on the process.

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Posted by Pawel Szczesny on March 12, 2008 in bioinformatics, Papers, PubMed

Tags: bioinformatics, Research, Taverna

Mining PubMed – another tools available

05 Mar

There are two new tools available that mine semantically PubMed abstracts, e-LiSe and Anne O’Tate. First one was made by my colleagues from Institute of Biochemistry and Biophysics in Warsaw, while the second is from University of Illinois, Chicago. Female-sounding names is not the only thing that makes them look similar, they both provide analogous functionality, like keywords or author names associated with user query.

There’s quite a lot of third party interfaces to PubMed (see David Rothman’s excellent list), so I couldn’t resist to run few queries on both servers and compare them to GoPubmed, which currently wins hands down in terms of features and interface. I wasn’t surprised to see that results overlap significantly, although not completely. Each of servers found valuable keywords other two did not have – that’s understandable, they use different algorithms. I wonder if we will see a meta-server of PubMed data-miners, like there are for protein structure prediction (for example meta.bioinfo.pl). In theory, exhaustive search for meaningful keywords by different methods and then their classification and analysis should work better than any single method, but this is just a guess.

5 Comments

Posted by Pawel Szczesny on March 5, 2008 in bioinformatics, Data mining, PubMed

Tags: bioinformatics, Data mining, literature search, PubMed

Life of a freelancing scientist – few observations

03 Mar

This post is mainly to indicate that I’m alive and blogging plus I wanted to share a few observations from my two month long freelancing scientist life:

1. If you are unemployed, but affiliated with an academic institution, applying for grants is OK, but getting an award for young and (possibly) smart is most of the time not possible (formal employment is usually required)

2. It takes very little time to sink in new projects (it’s me right now), after you’ve announced that you go freelance. That usually means:

3. It can take little time to go from no-salary to almost-a-salary-from-several-grants. Count grant turnover times in.

4. You have a lot (I mean really a lot) of skills that can be useful outside the academia. So useful that others may want to pay for them (I’ll let you know in a few months). And I’m not talking about programming.

5. You can switch the field in no time. It’s like going for a postdoc, sinking in projects and after few weeks deciding that after all it’s not that interesting. Although I keep in mind that I need to settle to have anything done.

3 Comments

Posted by Pawel Szczesny on March 3, 2008 in Career

Tags: Career, freelancing, scientific life