Fuzzier Logic » Conference

Science Online London 2011

Simon — Thu, 08 Sep 2011 11:39:19 +0000

It is hard not to get carried away in a room full of people who seem mostly to want the same things. You come away from a conference like Science Online thinking that the open science revolution is inevitable, and there is nothing anyone can do to stop it. Then you get back to your day job and talk of REF and impact factors and get bought back to earth with a bump.

Word Cloud of #solo11 Tweets (tagxedo.com)

The take home message of the conference this year seemed to be this: for open science to work, long term, reward mechanisms within the profession have to change in a comprehensive and profound way. Do I think this is possible? Of course. Do I think this is inevitable? Not by a long chalk. There are too many parties with a vested interest in things remaining the same, some of whom were represented here, despite all of the talk being about openness.

NPG certainly don’t seem that interested in opening things up too far, as the breakout session on APIs demonstrated. Nothing outside of their paywall was discussed, even more broadly applicable tools, like Connotea, seem to be quietly dropped in the background. The research councils are still more interested in “impact” (whatever that means) than genuinely original thinking.

But for all this pessimism, there are interesting things happening, and a mainstream breakthrough becomes more likely as the volume of those agitating for change grows. MaryAnn Martone‘s keynote was genuinely inspiring, a clear case for breaking down the garden walls. Michael Nielsen made a compelling case for wholesale revolution (however unlikely I think this sort of change may be). We showed that in an afternoon, you can set up a collaborative blog and populate it with interesting scientific content, using freely available tools. The interest we always encounter for the Knowledgeblog project enthuses me, and encourages me that something similar will make hay someday soon (even if we don’t manage to be the people who make the breakthrough).

It may be difficult for me to get to SoLo12, but I will try very hard to return, because I always leave with a smile on my face.

Salbutamol promotes SMN2 expression

Simon — Mon, 05 Sep 2011 11:02:26 +0000

This is a cross-post from the Blogging for Science Online London group blog. During the Saturday workshop at Science Online London 2011, a bunch of us wrote content relating to Spinal Muscular Atrophy. My post was a short summary of a small scale drug trial, which shows promising results.

This is a summary of a paper that shows that Salbutamol promotes SMN2 expression in vivo (doi:10.1136/jmg.2010.080366) .

Patients with Spinal Muscular Atrophy (SMA) have no functioning copy of the gene SMN1. The SMN2 gene can theoretically function in its place, but a change in this gene means that only a small amount of functional protein is produced from the gene.

It is therefore suggested that any intervention that can increase the level of functional SMN2 transcript could well be effective as a treatment for SMA.

Salbutamol is a short acting beta-adrenergic agonist that is primarily used for treating asthma. A previous study (doi:10.1136/jmg.2007.051177) has shown that Salbutamol is effective in raising SMN2 full length (SMN2-fl) levels in cultured SMA fibroblasts.

In this study, the researchers administered Salbutamol to 12 patients with SMA, and measured the levels of SMN2-fl 3 times (0, 3 and 6 months). The levels of SMN2-fl were significantly increased in all but 3 patients after 3 months (average increase of 48.9%), and in all patients after 6 months (average increase of 91.8%). They also showed that patients with more copies of the SMN2 gene (some patients had 3 copies, some had 4) showed a larger response to Salbutamol treatment. This increase in expression cannot be explained by normal fluctuations over time in these patients, since studies have shown that levels of SMN2-fl are usually stable over time (doi:10.1212/01.wnl.0000252934.70676.ab) (doi:10.1038/ejhg.2009.116) . Clearly the big question now is whether this molecular response to the drug is reflected in a beneficial clinical response in the patient. This study does not address this question, but does propose that a full double-blind, placebo controlled trial should be carried out to ascertain whether or not this treatment is effective in treating the symptoms of SMA.

Tiziano, F., Lomastro, R., Pinto, A., Messina, S., D’Amico, A., Fiori, S., Angelozzi, C., Pane, M., Mercuri, E., Bertini, E., Neri, G., & Brahe, C. (2010). Salbutamol increases survival motor neuron (SMN) transcript levels in leucocytes of spinal muscular atrophy (SMA) patients: relevance for clinical trial design Journal of Medical Genetics, 47 (12), 856-858 DOI: 10.1136/jmg.2010.080366

Bibliography

Science Online London 2010

Simon — Thu, 09 Sep 2010 21:26:29 +0000

It’s nearly a week since Science Online London 2010 finished, and there’s been plenty of perspectives of the event posted already, neatly summed up by this post on ‘Of Schemes and Memes‘ on Nature Network. I wanted to add my own voice to the crowd, since this was an event dominated by discussions of the dissemination of science, in one way or another – so might as well do some disseminating. So here’s my own, rather disjointed, overview of proceedings.

This was a very different conference to those I usually attend, and if it weren’t for my participation in Knowledge Blog this year I’d probably have been following coverage from my desk again, rather than being at the British Library. I am very glad I got to go though, Science Online is a much warmer affair than your standard scientific conference. The reception for every talk I attended was much more positive than for your average ISMB talk, or even keynote. Obviously I’ve not been in previous years where it was a smaller event, but I’m not sure that this atmosphere could be maintained if it grew much larger next year.

There were many highlights, but the biggest for me was the first. Martin Rees’ keynote really was an excellent way to kick things off. Here was one of the most respected scientists working today, very firmly an establishement figure – President of the Royal Society and the Astronomer Royal – lambasting the publishing industry, and later the University sector, for failing to move with the times. Praising projects such as Galaxy Zoo and Folding@home. It was inspiring, and refreshing. There were many gems amongst his keynote, but the best quote, for me, was (with a certain degree of paraphrasing):

“scientific information and ideas should be absolutely and freely available to everyone, regardless of academic affiliation”

Now, I know he was largely preaching to the choir with this one, but surely this is an ideal worth aiming for?

Having listened to David Allen Green‘s wise words about libel and science writing (“You can incur legal liability in 140 characters” – eep), it’s a wonder that anyone writes anything at all on the subject, but the majority of Science Online was taken up with discussions of it. Blogging, journalism and traditional publishing were all covered to varying degrees and much of the conversation was introspecitve and self-critical. Are we doing a good enough job? How can we do better? Engage more? Make scientists seem less monstrous? I’m not sure you’d find any other group of bloggers discussing their craft in quite the same way. Do Guido Fawkes and Michael White sit around worrying whether they give the public the right impression of politicians? I somehow doubt it.

David McCandless showed how to make science engaging and accessible, and many of his visualisation are stunning, though not all of his content is scientifically rigorous. I find it amusing that he was given a stern examination by this particular audience, with a number of flaws being pointed out in his parade of attractive slides.

I think more discussions of the business of doing science online, rather than just talking about it, would have been welcome. My inner geek felt a little deprived by the end of Saturday, and unforunate clashes meant I missed the sessions most likely to have sated it. Though the fact these sessions did exist among all the dynamic bloggers talking about community engagment gives me heart. Maybe they’ll survive and grow for future years.

I’ve written before about the energising effects of a really good conference, Science Online did not let me down in this regard. Finding time for my blog is always going to be problematic, but a few more evenings like this one, attempting to bash out some words, will be most welcome.

People love a word cloud

Simon — Mon, 06 Sep 2010 13:56:46 +0000

I haven’t seen one yet, so I took a few minutes to generate a Wordle from the #solo10 tweets over the last few days:

Tweets were pulled using the search API, and I dumped the text to a file. Then I filtered out all the hashtags and usernames (along with all instances of “RT”), because otherwise they obfuscate the interesting stuff.

This is a reasonably simple representation of the word cloud, if anyone would like to funky it up a bit, the corpus of text can be downloaded.

My impressions of it? There’s a lot of positive words in there, and many of the obvious memes of the conference are represented (although, surprisingly, I don’t see any representation for kittens). Also, as always with these things, it can get a little meta, with ‘Twitter’, ‘Tweet’, ‘hashtag’ and so on all featuring prominently (though another surprise is no ‘wifi’, which almost always makes an appearance in conference word clouds).

The two URLs that are represented are, perhaps unsurprisingly, for the conference program, and the live stream.

I will post more complete impressions from the conference when I have the time to write it up.

EDIT – Ed Yong pointed out on the Flickr page of the image that kittens are there, sandwiched between like and twitter, on the left of the picture.

Summary of the BBSRC Systems Biology Grant Holders’ Workshop 2010

Simon — Thu, 14 Jan 2010 17:42:20 +0000

You could be forgiven for thinking that this meeting was doomed from the outset, heavy snow across the UK making travel very difficult, even for those already in Edinburgh. Those of us in Newcastle just about managed to arrive on time, but there were plenty that didn’t. Despite this, a high proportion of posters still made it, and all but one talk was delivered, though admittedly not by the intended speaker in all cases. Indeed, the first day was like an extended and cruel session of Powerpoint karaoke at one point, with people delivering talks having never seen the slides.

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.

An Ondex dataset for in silico drug discovery

View more presentations from Simon Cockell.

Posted via email from Simon’s posterous

Now that’s what I call microblogging

Simon — Mon, 29 Jun 2009 10:29:03 +0000

As noted previously, ISMB is underway, and the FriendFeeders present are working hard to keep the rest of us updated on what’s going on.

I just wanted to highlight the coverage of this morning’s keynote, which was absolutely exemplary.

ISMB – attending without travelling

Simon — Thu, 25 Jun 2009 20:52:23 +0000

It’s ISMB time again, and as colleagues jet off to Stockholm, I can’t help but feel that twinge of envy. Lucky then, that the conference organisers have a fantastic attitude towards live- and micro-bloggers, and after the success of last year’s efforts (see the FriendFeed room, and the paper), they are positively encouraging more of the same this year. There’s a FriendFeed room again, where a new thread will be posted 10 minutes before each talk, and with a number of dedicated FFers present, there’s sure to be some fantastic live coverage. I’ll be following along.

IET BioSysBio 2009

Simon — Fri, 27 Mar 2009 16:17:23 +0000

Frank and Dan have already blogged about this year’s BioSysBio conference in Cambridge (23rd-25th March). I just thought I’d add my thoughts to theirs.

I don’t get to go to many conferences. The nature of my work doesn’t really demand it, but about once a year it does me good to reconnect with some cutting edge science, and get a good idea of developments in the field as a whole.

Before now, ISMB has been the conference of choice, as the largest gathering of bioinformatics types, it certainly was the obvious one. But in recent years it has become a cumbersome beast. Multi-tracked and vast, hard to pin down stuff you want to hear, often disappointing when you do find something. So this year we cast about for something smaller and fresher. We had heard good things about BioSysBio last year, and it certainly looked promising, so we made our decision.

And boy, was it the right decision. Small enough to be single track, there were very few choices to make in terms of what talks to attend (actually there were none, there was only really one parallel session, workshops on the Tuesday afternoon, and I was obliged to be at the ONDEX one, since I was helping out). This meant that instead of skipping between halls, missing bits and pieces of talks, and sometimes not bothering at all, I sat in one place, pretty much for 3 days straight, and listened to everything.

Highlights were the ethics and biosecurity debate, with a fabulously engaging talk from Drew Endy; showcases of the importance of transcription initiation and elongation from Marko Djordjevic and Andre Riberio; an excellent Synthetic Biology talk from a man apparently inspired by the iGEM competition, Philip LoCascio; and a couple of excellent videos of lab robots hard at work (Adam the Robot Scientist, and another in the final paper talk of the conference by T Ben Yehezkel).

Wordle of #biosysbio tweets

Next year I would happily micro-blog the conference again. This was my first conference since I joined Twitter and FriendFeed, and I was unsure about how I (and my followers) would feel about really going hard at the live updating of the conference experience. I think, though, that those of us who Tweeted provided an idea of the content being presented to those who could not attend, and the feeling I got from the feedback we received, and the fact that not a single person unfollowed me in the three days, is that we were providing a useful service. It has also provided me with a useful resource, a set of notes on the event produced by a crowd, not just me. Search for #biosysbio to see what I mean. Oh, and no review of this conference would be complete without a mention of Ally’s blogging, in which she chronicled pretty much every single talk, except her own (I did that one!)

I do think that for future events I would create threads on FriendFeed for each talk, and group my thoughts about it there, then tweet the URL of the FriendFeed post – this might make things a little less noisy.

Coming back from a conference feeling exactly how you should feel, refreshed, invigorated and excited to get on with your own work, is a great thing. For this feeling alone I will be returning to BioSysBio next year.

Saint: A lightweight SBML annotation integration environment

Simon — Wed, 25 Mar 2009 10:35:59 +0000

Allyson Lister

CISBAN, Newcastle University

This post is an homage to Ally’s own herculean note taking style, since she can’t blog her own talk.

Saint has been developed to help modellers get information into their SBML models really quickly. Ally shows a picture of a model describing neuromuscular junctions (standard biomodel). This model contains terms which are descriptions, and the mathematical model. The maths doesn’t know anything about the underlying biology. For example, actin is just a label, there is no implicit knowledge contained in that label (ie actin is a protein, invoved in the cytoskeleton etc).

Short intro to SBML: SBML is a standard format, which is widely used. it stores the maths and enables linking to the underlying biology.

So what do we know about actin -

its a protein (UniProt)
interactions? (Pathway Commons, STRING)
reactions and parameters (SABIO-RK, BRENDA, KEGG)
vocab (SBO, GO)

Now we can use the MIRIAM standard to annotate the model with the above information.

When building a model, you need to add info to things like species, name, reaction, compartment
Annotation and SBO term sit between the model and the biology information – these can be used to retrieve the information from the databases. This has to be done manually currently, this is hard and is often not done exhausively, or even at all.

Saint enables automation of this procedure. It already links to a number of data sources – MIRIAM, UniProt, STRING, SBO, Pathway Commons. Reduces effort on the part of the modeller. Saint is lightweight and easy-to-use. Useful as a first pass annotation tool, or to add annotation to an existing model.

How Saint works:

import SBML into Saint
Saint then searches for appropriate annotation
and presents this annotation, and allows to to accept or reject the changes

Ally is using a model produced by Carole Proctor in CISBAN as an example run-through of Saint.

Saint does some validation via libsbml on import of an SBML model. The tool then presents a list of species found in the model, these can be hidden if you don’t want to retrieve information on them. Zoom into ‘Ctelo’ for an example – a plus next to the name of the species shows the annotation already available in the SBML model (‘known’ information). So we can se that Ctelo is a Capped Telomere. You can decide which species you want to annotate, and which datasources you want to retrieve that annotation from.

Queries are made from datasources by a Master Asynchronous Query Service – once information becomes available, it is immediately visible in the UI (as an ‘inferred’ tab), and you see a ‘New Annotation found’ message. Once Saint has retrieved annotation, the user can choose which annotation he wants to keep, and how this information links to the species in the model (is, part etc – MIRIAM terms)

CDC13 = polypeptide chain, nuclear telomere cap complex, protein binding, single-stranded telomeric DNA binding, telomerase inhibitor activity.

Future work – more data sources, use of species type, better support for non-systematic names, adding software source attribution, incorporation of SBGN (Systems Biology Graphical Notation) for better display.

Personal comments – good job Ally – hope I did it justice!

http://friendfeed.com/rooms/biosysbio

http://conferences.theiet.org/biosysbio

Ally’s standard disclaimer:

Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else’s. I’m happy to correct any errors you may spot – just let me know!