Stack Overflow reached critical mass a few months ago now. The site gets upwards of 6 million unique visitors a month. The chances are, if you write code, you know it exists, and you’ve received some sort of help there, whether directly or by proxy. In its wake, Stack Overflow has spawned Stack Exchange, a question and answer platform that anyone can buy into, and set up a site. So there’s now Stack Overflow type sites for any number of topics.

• Not enough users, no critical mass achieved.
  • The site seems to be gaining some traction, and getting more active by the day.
• Not enough questions, no reason for users to keep coming back.
  • This does remain an area for concern, but is also starting to pick up a little.
• No financial backing, the site may disappear after the test period comes to an end.
  • Stack Exchange is not a cheap platform, and a site like this will need funding to continue. However, the administrator, Istvan Albert, has insisted on the Google Group, set up for ‘meta’ discussion surrounding the site, that the site is funded for a year at least.

Posted via email from Simon’s posterous

via news.bbc.co.uk

The winner of the Wildlife Photographer of the Year award has been disqualified after judges ruled that the featured wolf was probably a “model”.

It is tough to imagine how you would go about getting this photo of a wild animal. The story given by the photographer on winning the prize was reasonably convincing, however.

Posted via web from Simon’s posterous

What emerged was a healthy picture of a vibrant systems biology community in the UK, although one tinged by an uncertainty lurking in the not too distant future. Talks from the Centres for Integrated Systems Biology (CISB) directors on the first afternoon gave a flavour of the kind of research being done, and more detailed talks over the following day and a half filled in the picture.

Talks of note (to me at least)
I really enjoyed the keynote, from Peter Smith, of the University of Aberdeen. He is certainly doing systems biology, but not in the way most people first think of it. The ’system’ he is concerned with is not a cell, an organ, or even a whole organism – it’s a whole ecosystem, or sometimes maybe even larger than that. Systems biology on a continental scale. He painted a very interesting picture of how taking biological factors into account in warming models can make a real difference to predictions. There was also an interesting story of using ecological models to predict bioenergy crop yield, and how this can feed into efforts to introduce certain traits into plants, in order to increase their yields in desirable parts of the globe.

The MCISB talk was great, a really good example of how modelling and ‘omics technologies can dovetail really nicely in a properly integrated project. They’re studying metabolism in yeast, looking at metabolite flux and the reactions that best control it. Flux Balance Analysis, metabolomics, proteomics and ‘traditional’ bioinformatics all combine nicely to illuminate different parts of the process, with data being deposited in many public repositories along the way.

The talk from the PRESTA project was also very impressive. Using lots of microarrays in interesting ways to investigate the stress response of Arabadopsis . Examining at more than just the changing expression of genes in isolation, but looking for patterns of genes that change together in interesting ways, in opposition, or a subset that react to the change in another subset, etc.

The BBSRC systems biology initiative is coming to an end. It was intended to kickstart large-scale systems biology research in the UK through a number of large grant awards, including the CISBs and the Systems Approach to Biological Research (SABR) projects. It was clear from some of the discussions at the workshop that some people are concerned that the winding up of these big grants, coupled with the looming shadow of considerable cuts, means that there is little future for the posse of systems biologists who have been produced over the last few years. ‘Too generalist’ was the major complaint, suggesting that systems biologists are jacks of all trades but masters of none. I would disagree. Systems biologists are masters of systems biology (I know this sounds rather obvious, but bear with me). Traditional biologists tend to be scared by maths, and modelling, and don’t really know where it fits in with what they do. Mathematicians and computing scientists tend to not know anything about biology. There is a large cohort here that knows a great deal of both. Mathematicians who are biology literate, and biologists who aren’t afraid of mathematics and computers. These are skill sets to be prized, not shunned. Systems biology is a discipline in its own right now, and I would be shocked to discover that these researchers do not have a life beyond their Centres.

P.S. I took a poster along, as a part of my role on the Ondex project, it’s on SlideShare, and I’ve embedded it here.

Posted via email from Simon’s posterous

The top visualization project of the year, according to FlowingData, is a project by Ben Fry, which shows changes to the theory of evolution over time. The project takes advantage of the publication of the full works of Darwin online to trace changes in the text of On the Origin of Species over time.
A deserved winner, and very apt, considering the batch of anniversaries that have gone by this year.

Posted via web from Simon’s posterous

“Beautiful Data”, “Coders at Work” and “xkcd volume 0″

Posted via web from Simon’s posterous

We are happy to announce that AppJet Inc. has been acquired by Google. The EtherPad team will continue its work on realtime collaboration by joining the Google Wave team.

[...]

The EtherPad site will stay online through March 2010 with some restrictions.

[...]

No new free public pads may be created. Your pads will no longer be accessible after March 31, 2010, at which time your pads and any associated personally identifiable information will be deleted.

[...]

Etherpad was a nice little tool, very effective at what it offered, I’m sure the guys who developed it will bring a lot to the Wave party. But seriously, Wave is nowhere near functional yet, it’s confusing, and glacially slow. So is there a decent alternative to Etherpad that is usable – right now?

Posted via web from Simon’s posterous

Option 1 is basically an impossibility, given our current understanding of the laws of physics. That leaves option 2.

So I’m going to try cross-posting the content of my Posterous blog to my main site. I generate more posts at Posterous, mainly because it is recycled content, and the barrier to creating posts is so low, I just send an email, or use the bookmarklet that grabs content right from webpages.

Step 1 – stop auto-posting Posterous content to Friendfeed. I’ll let my blog propagate there, and not double-post.

Step 2 – enable XMLRPC posting on my Wordpress site.

Step 3 – Turn on Wordpress cross-posting on Posterous.

Step 4 – Write this post, and see if it propagates properly.

Posted via web from Simon’s posterous

Recently, a three step method has been proposed for determining the absolute quantities of proteins in the cell, on a proteome scale. Step one is isoelectric focussing of tryptic digests of whole cell extracts. Step two, calculating the absolute abundance of a small group of proteins by Selective Reaction Monitoring (SRM). SRM uses spike in, isotopically labelled peptides of known concentration as references to calculate the actual abundance of peptides of interest. Finally, step three uses these abundances as reference points to calculate the abundance of all proteins in the sample, using the median intensities from the 3 most intense peptides for each protein.

Leptospira interrogans (Wikimedia Commons)

Using this methodology, the abundances of >50% of the proteome of a human parasite (Leptospira interrogans) have been determined to an accuracy of ~2-fold. These abundance measurements were confirmed by almost literally counting the number of flagellar proteins present in a cell by cryo-electron tomography.

Although current hardware probably limits this technique to a few thousand proteins, that is still a big step forward on what was previously possible. If whole proteome scale absolute abundance measurements become an achievable reality, maybe proteomics can finally take on microarrays as the dominant technique in the post genomics world.

Malmström, J., Beck, M., Schmidt, A., Lange, V., Deutsch, E., & Aebersold, R. (2009). Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans Nature, 460 (7256), 762-765 DOI: 10.1038/nature08184