Category Archives: meetings

On the road: CSS and eResearch Conference 2014

Next week I’ll be in Melbourne for one of my favourite meetings, the annual Computational and Simulation Sciences and eResearch Conference.

The main reason for my visit is the Bioinformatics FOAM workshop. Day 1 (March 27) is not advertised since it is an internal CSIRO day, but I’ll be presenting a talk titled “SQL, noSQL or no database at all? Are databases still a core skill?“. Day 2 (March 28) is open to all and I’ll be talking about “Learning from complete strangers: social networking for bioinformaticians“.

I imagine these and other talks will appear on Slideshare soon, at both my account and that of the Australian Bioinformatics Network.

I’m also excited to see that Victoria Stodden is presenting a keynote at the main CSS meeting (PDF) on “Reproducibility in Computational Science: Opportunities and Challenges”.

Hope to see some of you there.

Git for bioinformaticians at the Bioinformatics FOAM meeting

Last week, I attended the annual Computational and Simulation Sciences and eResearch Conference, hosted by CSIRO in Melbourne. The meeting includes a workshop that we call Bioinformatics FOAM (Focus On Analytical Methods). This year it was run over 2.5 days (up from the previous 1.5 by popular request); one day for internal CSIRO stuff and the rest open to external participants.

I had the pleasure of giving a brief presentation on the use of Git in bioinformatics. Nothing startling; aimed squarely at bioinformaticians who may have heard of version control in general and Git in particular but who are yet to employ either. I’m excited because for once I am free to share, resulting in my first upload to Slideshare in almost 4.5 years. You can view it here, or at the Australian Bioinformatics Network Slideshare, or in the embed below.

See the slides…

ISMB 2012 on Twitter: here today, gone tomorrow

In previous years, when FriendFeed was used as the micro-blogging platform for the annual ISMB meeting, I’ve written a post describing some statistical analysis of the conference coverage. Here’s my post from last year.

This year, it appears that the majority of the conference coverage happened at Twitter, using the #ISMB hashtag. Here’s what happened on July 18th when I used the R package twitteR to retrieve ISMB-related tweets for July 13/14:

library(twitteR)
ismb1 <- searchTwitter("#ISMB", since = "2012-07-13", until = "2012-07-14")
length(ismb1)
# [1] 383

383 tweets. Here’s what happened when I ran the same query today:

library(twitteR)
ismb1 <- searchTwitter("#ISMB", since = "2012-07-13", until = "2012-07-14")
length(ismb1)
# [1] 0

Zero tweets. Indeed, run the same query via the Twitter web interface and you’ll see only a very few tweets with the message “Older Tweet results for #ismb are unavailable.”

So far as Twitter is concerned, ISMB 2012 never happened. Or if it did, the data are buried away in a data centre, inaccessible to the likes of you and I. Did you ever hear anything more about that plan to archive every Tweet at the Library of Congress? Neither did I. I very much doubt that it’s going to happen.

I think Twitter is great – for broadcasting short pieces of information, such as useful URLs, in near real-time. For conference coverage which benefits from threaded conversation, longer comments and archiving, I think it’s rubbish.

On July 18 I did manage to retrieve 3162 Tweets for ISMB 2012, created between July 13 and July 17. I’ll write about them in a forthcoming post. All I’ll say for now is – lucky I was able to grab them when I did.

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.

Analysis of ISMB coverage at FriendFeed: 2008 – 2011

ISMB/ECCB 2011 was held between July 15-19 this year and as in previous years, FriendFeed was used to cover the meeting.

Last year, I wrote a post about how to use R to analyse the coverage. I was planning something similar for 2011 when I thought: we have 4 years of ISMB at FriendFeed now – why not look at all of them?

So I did. Read on for the details.
Read the rest…

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.