Twitter coverage of the Australian Bioinformatics & Computational Biology Society Conference 2017

You know the drill by now. Grab the tweets. Generate the report using RMarkdown. Push to Github. Publish to RPubs.

This time it’s the Australian Bioinformatics & Computational Biology Society Conference 2017, including the COMBINE symposium. Looks like a good time was had by all in Adelaide.

A couple of quirks this time around. First, the rtweet package went through a brief phase of returning lists instead of nice data frames. I hope that’s been discarded as a bad idea :) There also seem to be additional columns, new column names and list-columns in the output from the latest search_tweets(), so there goes my previous code…

Second, given that most Twitter users have had 280 characters since about November 7, is this reflected in the conference tweets?

With thanks to Andrew Lonsdale for clearing up my confusion and pointing me to Twitter extended mode, the answer is “yes, somewhat”. Plenty of tweets are still hitting the 140 limit though: time to update those clients?

Twitter Coverage of the ISMB/ECCB Conference 2017

Search all the hashtags

ISMB (Intelligent Systems for Molecular Biology – which sounds rather old-fashioned now, doesn’t it?) is the largest conference for bioinformatics and computational biology. It is held annually and, when in Europe, jointly with the European Conference on Computational Biology (ECCB).

I’ve had the good fortune to attend twice: in Brisbane 2003 (very enjoyable early in my bioinformatics career, but unfortunately the seed for the “no more southern hemisphere meetings” decision), and in Toronto 2008. The latter was notable for its online coverage and for me, the pleasure of finally meeting in person many members of the online bioinformatics community.

The 2017 meeting (and its satellite meetings) were covered quite extensively on Twitter. My search using a variety of hashtags based on “ismb”, “eccb”, “17” and “2017” retrieved 9052 tweets, which form the basis of this summary at RPubs. Code and raw data can be found at Github.

Usually I just let these reports speak for themselves but in this case, I thought it was worth noting a few points:
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Twitter Coverage of the Bioinformatics Open Source Conference 2017

count-words-1July 21-22 saw the 18th incarnation of the Bioinformatics Open Source Conference, which generally precedes the ISMB meeting. I had the great pleasure of attending BOSC way back in 2003 and delivering a short presentation on Bioperl. I knew almost nothing in those days, but everyone was very kind and appreciative.

My trusty R code for Twitter conference hashtags pulled out 3268 tweets and without further ado here is:

The ISMB/ECCB meeting wraps today and analysis of Twitter coverage for that meeting will appear here in due course.

Visualising Twitter coverage of recent bioinformatics conferences

Back in February, I wrote some R code to analyse tweets covering the 2017 Lorne Genome conference. It worked pretty well. So I reused the code for two recent bioinformatics meetings held in Sydney: the Sydney Bioinformatics Research Symposium and the VIZBI 2017 meeting.

So without further ado, here are the reports in markdown format, which display quite nicely when pushed to Github:

and you can dig around in the repository for the Rmarkdown, HTML and image files, if you like.

Update: also available as published reports at RPubs:

Twitter Coverage of the Lorne Genome Conference 2017

Things to know about Lorne in the state of Victoria, Australia.

  • It’s situated on the Great Ocean Road, a major visitor attraction and a great way to see the scenic coastline of the region
  • It’s home to a number of life science conferences including Lorne Genome 2017

tweets-by-day-hour-1This week’s project then: use R to analyse coverage of the 2017 meeting on Twitter. I last did something similar for the ISMB meeting in 2012. How things have changed. Back then I prepared PDF reports using Sweave, retrieved tweets using the twitteR package and struggled with dates and time when plotting timelines. This time around I wrote RMarkdown in RStudio, tried out the newer rtweet package and, thanks to packages such as dplyr and lubridate, the data munging is all so much cleaner and simpler.

So without further ado here are:

The presentation examines several aspects of the conference coverage under the broad headings of timeline, users, networks, retweets, favourites, quotes, media and text. Make sure to click in the title page, then you can navigate using your arrow keys. The latest version will always be at Github; you can simply download that and open in a browser.

Presentations online for Bioinformatics FOAM 2015

Off to Melbourne tomorrow for perhaps my favourite annual work event: the Bioinformatics FOAM (Focus on Analytical Methods) meeting, organised by CSIRO.

Unfortunately, but for good reasons, it’s an internal event this year, but I’m putting my presentations online. I’ll be speaking twice; the first for Thursday is called “Online bioinformatics forums: why do we keep asking the same questions?” It’s an informal, subjective survey of the questions that come up again and again at bioinformatics Q&A forums such as Biostars and my attempt to understand why this is the case. Of course one simple answer might be selection bias – we don’t observe the users who came, found that their question already had an answer and so did not ask it again. I’ll also try to articulate my concern that many people view bioinformatics as a collection of recipe-style solutions to specific tasks, rather than a philosophy of how to do biological data analysis.

My second talk on Friday is called “Should I be dead? a very personal genomics.” It’s a more practical talk, outlining how I converted my own 23andMe raw data to VCF format, for use with the Ensembl Variant Effect Predictor. The question for the end – which I’ve left open – is this: as personal genomics becomes commonplace, we’re going to need simple but effective reporting tools that patients and their clinicians can use. What are those tools going to look like?

Looking forward to spending some time in Melbourne and hopefully catching up with this awesome lady.

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.