Technical Note

The quality of the recordings wasn’t great. I finally managed to get something watchable without too much effort with help of the following tools:

• TMPGEnc XPress was used to extract the videos from the DVDs on which we got them, clean up and boost the audio signal, and encode the result as DivX movies.
• Audacity was used to clean up the audio of the keynote speech (which was so bad that TMPGEnc XPress failed).
• VirtualDubMod was used to boost the audio level of all talks further (TMPGEnc XPress can only do 500%), merge back the audio of the keynote speech, and to trim some movies. All of this could be done very fast as VirtualDubMod does not need to re-encode the movies for such operations.

The reason for choosing Google Video over the more popular YouTube or the more specialized DnaTube site was that it didn’t have their upload limitations (max file size 100MB). The main drawback of Google Video is that it doesn’t allow you to create sets of movies that belong together — it seems you can’t even link to e.g. all movies from a specific publisher! But of course this is less of a problem than not being able to even upload your movies…

Prior to the main conference I attended BOSC where I gave a “lightning talk” titled beta.uniprot.org — 5 Lessons Learned. (I had submitted an abstract for a full-length talk but that was eaten by the conference organizer’s spam filter, oh well…) There isn’t much you can say in five minutes, so the purpose of this talk was simply to let people know that there is this new site that may be worth a look in case they hadn’t noticed yet. I did get some people interested, but not interested enough to do a proper workshop afterwards, as I had hoped. Other than that there were some moderately interesting talks such as the usual Bio* project updates. I learned about two interesting projects that I had been unaware of: Galaxy (a simple to set up and use workflow system) and E-Cell 3D (don’t know if this is of any use, but it’s cool). There was also a lot of talk about software development practices etc. Yawn.

The biggest event for me at the main conference was doing a demo of the new UniProt web site. I ended up being one of the few people doing an actual demo (versa just showing a bunch of slides). Fortunately everything worked well — though I had to make use of a copy of the web site I had on a USB drive as there was no Internet connection in the demo room… I also presented a poster on the same topic. Despite the large number of posters I had quite a few people stopping by — need to remember to attach some flyers or something next time I present a poster!

Spent a lot of time at the booths of companies that provide access to UniProt data somewhere in one of their products, looking at how they did so and asking and answering some technical questions. This was most productive with vendors such as CLC Bio and Biomax who seemed to have some actual developers on place.

The “Web Services (SOAP, REST) in bioinformatics” “Birds of a Feather” session was sort of a follow-up meeting to a recent EMBRACE meeting in Geneva where we had committed ourselves to producing a paper on said topic. This will be an interesting experiment as the authors of this paper take opposing views on what the most appropriate way to support programmatic access to bioinformatics data and services is… In any case the BoF session didn’t progress the discussion any as we didn’t stray into controversial waters: We agreed that services ought to be documented. Say what!

Finally, I met quite a few people I had been in contact with but had never — or not for a long time — met face to face. Some would say that’s the main purpose of such conferences! Wearing a UniProt t-shirt (printed just prior to the conference) turned out to be a good idea: I was frequently approached with various questions about UniProt. The two boxes of UniProt pens that had brought along also disappeared quite quickly…

If you have some experience with coding Java, have a strong interest in science and the technologies we use, thrive in chaotic open environments, and would like to work in one of the world’s best cities to live, here are the instructions for applying.

You can meet me at BOSC and ISMB next month. If you have any questions, contact me!

Here are the slides that I showed along with the demo I gave:

The workshop (which was really more of a series of normal talks than a real workshop) ended with a SOAP vs REST debate. The SOAP camp felt that their technology would in some unspecified way address interoperability issues. The REST camp on the other hand had plenty of war stories that showed that SOAP helped little with that but introduced a lot of problems. Of course no consensus was reached, but some of the participants volunteered to write a review paper that explains the different positions… Let’s see what comes out of that.

Using aria2 — a command line download client that supports the Metalink standard — you can do:

aria2c ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/rdf/RELEASE.metalink

This will retrieve the data from all available mirrors in parallel, piece the files together, and verify the transferred data with checksums.

If you prefer graphical user interfaces, there is another tool called wxDownload Fast. Be sure to use the latest version (0.5.5) — previous versions wouldn’t do parallel downloads from some servers due to a small bug.

This gadget is fairly basic (see source) as all it does is provide an input form for submitting a sequence similarity search to some server. Note however that the form is customizable with two parameters…

In most cases normal web searches work fine. But sometimes you have terms that are frequently used in other contexts, e.g. hedgehog or ada…

Google’s custom search engines are based on lists of URLs (or URL patterns) of sites that should be included. I suppose that behind the scene Google runs a normal web search, but filters out sites that are not included in the list.

The initial list of sites for the life sciences search engine was based on a file that lists all sites that are referenced from a popular, well-linked life sciences database.

grep ^Server dbxref.txt | perl -lne 'print $1 if m{http://(.+?)/}' | sort | uniq

If you’d like to add any sites, let me know (you can also request to participate in this search engine via Google).