My day out at #osddmalaria

Finally, I get around to telling you that…
…on Friday 24th February, I took a day out from my regular job to attend a meeting on Open Source Drug Discovery for Malaria. I should state straight away that whilst drug discovery and chem(o)informatics are topics that I find very interesting, I have no professional experience or connections in either area. However, it was an opportunity to learn more, listen to some great speakers, think about what bioinformaticians might be able to bring to the table and of course, finally meet Mat Todd in person. Mat, if you don’t know, is one of the few people on the planet who really does science online, as opposed to talking about science online.

Here’s what I learned – with just a little analysis using R later in the post, hence the statistics/R category.
Read the rest…

ISMB coverage on Twitter? It’s possible there was…

Peter writes:

I wonder if part of the drop off is live bloggers moving to platforms like Twitter? I can tell you it seemed like there were almost as many tweets for one SIG (#bosc2011) as for the whole of #ISMB / #ECCB2011, and I personally didn’t post anything to FriendFeed but posted lots on Twitter.

Well, there’s a problem with using Twitter for analysis of conference coverage. Let’s try searching for ISMB-related tweets using the twitteR package:

library(twitteR)
ismb <- searchTwitter("ismb", 1000)
length(ismb)
# [1] 30

oldertweets

If we can't archive, how can anyone else?

30? Are we using twitteR properly? Running the same search at the Twitter website gives roughly the same results, plus this unhelpful message.

I like Twitter – as a real-time communication tool. As a data archive? Forget it.

I can’t resist a word cloud: now using R!

wcloud

Top 1000 words in FriendFeed comments, ISMB 2008-2011

The wordcloud package is word clouds for R with a difference: they look great.

Of course, having just analysed online coverage of the ISMB conference, I had to run all 6 906 comments from the 2008-2011 meetings through some code. If you followed along via the Sweave code, I went as far as generating the data frame of comments, ismb.comments, then pulled the comment text into a new data frame using:

data.frame(ismb.comments$body)

It was then simply a case of following along with the excellent example code from the post Word Cloud in R, over at One R Tip A Day, limiting myself to the 1000 most-used words. Watch out, the TermDocumentMatrix() function from the tm package uses quite a lot of memory.

Result shown at right: click image for full-size version. I think that word in the centre says it all.

ISMB/ECCB 2009 reports

Great to see more reports describing the use of online tools to cover scientific meetings. Here are the publications, from PLoS Computational Biology:

Live Coverage of Scientific Conferences Using Web Technologies.
doi:10.1371/journal.pcbi.1000563

Live Coverage of Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2009.
doi:10.1371/journal.pcbi.1000640

And here’s Ally a.k.a the robo-blogger on Social Networking and Guidelines for Life Science Conferences.

Looks like we’ve started a trend, long may it continue at future meetings.

Our ISMB 2008 conference report

In a nutshell: we went to ISMB 2008, had a great time and live-blogged the meeting using this FriendFeed room. The nice people at ISCB were so impressed that they asked us to write up a report.

So here it is. FriendFeed life scientists might recognise some (or all) of the author names.

Saunders, N., Beltrão, P., Jensen, LJ, Jurczak, D., Krause, R., Kuhn, M. and Wu, S. (2009).
Microblogging the ISMB: A New Approach to Conference Reporting.
PLoS Comput Biol 5(1): e1000263
doi:10.1371/journal.pcbi.1000263

This is a highlight of my career to date. Thanks are due: to the authors (especially Roland who got it all started); to everyone who contributed at the ISMB 2008 room; and to BJ Morrison and Phil Bourne for their support in making this happen.