After finishing the first rotation project at the Sanger Institute, we (all the 1st years) had some courses to attend, but there was also some free time. Mainly I used it to start a new private software project called MiniPauker, to meet friends and to work on “Espresso” research.

A bit more specific:

1. MiniPauker: It will be a J2ME product, related to the “real” Pauker. Well, I want to use the same file format and the same concept, except that it works for mobile devices. A prototype already works, but it’s a hack to test J2ME and get a feeling for this kind of programming. Currently I am working on a “clean” version which will go to Sourceforge at some point (approx. February 2006).

2. Friends: I met Flo, Bene, Tom, Pete & Steph for some coffees in various coffee shops. I mostly like the atmosphere (it can be done better though) but the actual coffee quality is bad to medium. Therefore the idea of opening a own “Coffee geek” coffee shop with Tom rose, but we are not sure whether we mean it serious or not :)

3. This leads me to the last point. I have to know how to brew perfect coffee and espresso. Well – I did not expect that it is actually a kind of research and art and NOT easy to learn. Becoming a real “Barista” takes months to years. Getting all the parameters right is the most important and complicated thing. Currently I am learning, reading, practicing …

A couple of countries (including Germany) want a biometric RFID tagged passport, which is a clear threat to both privacy and personal safety (Some references: The blog of security expert Bruce Schneier for serious background information and a nice story of Richard Stallman who brings together a RFID tag and an entire roll of aluminum foil – but read yourself – highly recommended!).

Today the great news of data retention! Wow! What is the benefit of collecting even more private data? Will this solve our problems? Sure :) I think the terror guys already won! Our “free” life is more and more controlled and regulated (having in mind Orwell’s 1984)

Where does all this lead to? I had a discussion today with Henning, and both of us think that even encryption like GnuPG will be illegal at some point – but as it works for most things right now … STEP BY STEP … so citizens are NOT AWARE of what is happening … so it won’t be right now :)

For background reading I recommend this website:

Citation of this website – for more click the logo above …

What’s wrong with data retention? The proposal to retain traffic data will reveal who has been calling and e-mailing whom, what websites people have visited and even where they were with their mobile phones. Telephone companies and internet services providers would be ordered to store all traffic data of their customers. Police and intelligence agencies in Europe would be granted access the traffic data. Various, competing proposals in Brussels mention retention periods from 6 months up to four years.

Data retention is an invasive tool that interferes with the private lives of all 450 million people in the European Union. Data retention is a policy that expands powers of surveillance in an unprecedented manner. It simultaneously revokes many of the safeguards in European human rights instruments, such as the Data Protection Directives and the European Convention on Human Rights.

The last 2 weeks were quite busy. Our first year PhD rotation projects here at the Sanger Institute are only 2 months each, which is not much time for a small project, including a new working field, a new place, new people and a lot of new experiences …

And then there is Murphy’s law, which seems to be a natural phenomenon. It is always like that, but in the end one can mostly finish on time :) It was extremely interesting and a wonderful project to combine web-lab with computer science. I have worked through the whole pipeline of an protein profiling experiment – ranging from sample preparation including “wet fingers” to the more advanced data analysis which is obviously more “theoretical”. There is a great chance, that I’ll come back to mass spectrometry for my PhD project. It is an extremely interesting and diverse field!

The project was very dynamical and I followed some side tracks, especially for the data analysis, which resulted in new ideas and approaches. Here’s a small abstract of my work:

Abstract: Since many genomes are fully sequenced, research focus is shifting towards genome function.
This relies on genome annotation which remains one of the major challenges. Mass
spectrometry can provide experimental evidence of peptides which can be mapped back onto
the genome for annotation purposes. We have established a mass spectrometry (MS) data
analysis pipeline for peptide identification and genome annotation, which can be used to verify
and elucidate novel gene products.

Now I have to catch up some sleep over the weekend :)