Greg's blog

Nodalpoint: USA

Just a short note if you're interested in meeting up: I'll be in the US over the next two weeks. I'll be attending Discovery 2 Diagnostics in Philadelphia from Monday the 17th until Wednesday, after which I'll be in New York until Friday morning. I plan to stay over the weekend in LA, and then from Monday until Wednesday I'll be in San Fransisco. The whole trip will be sponsored by my company, but evenings will be free, so if you're in the area, have some time and would like me to buy you a beer then get in touch:

If you publish in OA journals, you're publishing communism!

Open Source Communism: Open Source CommunismOpen Source Communism: Open Source CommunismI don't participate much in the OA Debate, largely because I see the outcome as a foregone conclusion. What we are seeing now is the reaction of publishers with an established business model (read license to print money) being threatened by change. Given that OA will not be going away, in my opinion what publishers should be doing is thinking creatively and developing new business models for scientific publishing. Update: It gets better according to Cognitive Daily, apparently the the images used on the PRISM website were in violation of copyright law. Blog around the clock has the definitive roundup post for more reactions.

Site Maintenance Shortly

I plan to do some site maintenance (including the wiki), starting in about 20 min or so and I expect it will talk an hour (probably less). So if you're planning to post or edit something (unlikely) hold off for a while. I'll be on IRC (, #nodalpoint) if you're interested to know what's going on in real time.

Update: Both the Drupal and wiki upgrades are complete. Read on for details...

ISMB 2007 highlights

First up, meet-up(s) details are still being worked out, Roland will be attending tomorrow and David Aanensen has suggested getting together after the cocktail reception this evening, meet at the exit after the event. I'll try and update via email or this post before I leave tonight.

This year the SIG ticket was open so, I drifted into talks on on biopathways, alternative splicing, and bioontologies, here-in, a few of my picks:

Greetings from Vienna

Greetings from Vienna ISMB 2007, the weather is nice and our tribe is out in force for the two day SIGs. I'm currently sitting in on BOSC waiting to hear about the latest AJAX genome browser developments. I don't plan to 'live-blog' any of the talks, instead I will keep notes and post some of the highlights at the end of the day.

If any nodalpoint readers attending ISMB would like to meet up for a beer drop me a note at greg[dot]tyrelle[at]gmail[dot]com.

Freebase invitations

I have a couple of Freebase invitations to give away. If you're interested, send an email to greg[dot]tyrelle[at]gmail[dot]com. For more information on Freebase see Pierre's posts. Update: they're gone. I waited for 24hrs (timezone issues) and then chose three names from the six requests randomly. Apparently all current users received five invitations, so there should be more invitations out there.

Ninth Edition of Bio::Blogs

Bio::BlogsBio::BlogsUpdate: Pedro posts on blog round-ups (aka carnivals), morphing into blog journals.

Just in case you have been busy like me or maybe just new to Bio::Blogs, Pedro has once again done some sterling editorial work and posted the Ninth Edition of Bio::Blogs. Apart from this months edition, the are a few good comments on the last edition regarding relevance of blogs and blog carnivals to bioinformatics. I don't want to see Bio::Blogs (and all Pedro's hard work) vanish into the aether, so I'm happy to see nodalpoint become a semi-permanent host of a monthly blog round up under the Bio::Blogs banner. Any further thoughts on the future Bio::Blogs ?

Advice to a young computational biologist

Just when I though Bosco was posting too much poetry, he comes out with this truly excellent post on advice for young computational biologists. Bosco has managed to distill his 10 years of experience into eleven succinct points that are relevant to not only those just starting out in computational biology, but experienced hackers as well. This post is a must read, I highly recommend his advice in point four on using configuration files. It is a simple way of adding value to scripts, by extracting out the parameters into a config file and then writing another script to iterate over different values. Python has a default module for this, with many other third party options. And of course point eight, using command line plotting software, my current favorite is Ploticus.

Wiki Reviews

Finding high quality up to date reviews on the current literature is always a little hit and miss. Jason Kelly has started a new page on the OpenWetWare wiki for WikiReviews (via Pedro and Depak). As Pedro points out, Writing a review on the progress of a field could be the most obvious use of collaborative efforts. The reviews could be continually updated and periodic versions could be frozen and submitted to a more conventional repository.

New Recommended Reading List

Update: I won't bother with a vote since there hasn't been a great deal of active editing of the wiki list. I've started to add the links to a 'links directory' on the main website. The suggestion to pull random links into the side bar works (thanks Alf) and should be up shortly.

Update 2: Done. The Recommended Reading block to the right should now show a random selection of links (10) each time the page is loaded. Currently there are 32 sites in the database.

Now that the site is reasonably stable, it is time to finish off the house cleaning (at least a little bit more of it). I'm inviting everyone to help reorganize the recommended reading list. I have a new candidate list up on the wiki here. Please go and have a look, add any blogs that I have missed or add comments to the ones that are there.

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