Assembling a twitter following: people continue to be interested in genome assembly

Late in 2010, I was asked to help organise what would initially become The Assemblathon and then more formally Assemblathon 1. One of the very first things I did was to come up with the name itself — more here on naming bioinformatics projects — register the domain name, and secure the Twitter account @Assemblathon.

The original goal was to use the website and Twitter account to promote the contest and then share details of how the competition was unfolding. This is exactly what we did, all the way through to the publication of the Assemblathon 1 paper in late 2011. Around this time it seemed to make sense to also use the Twitter account to promote anything else related to the field of genome assembly and that is exactly what I did.

As well as tweeting a lot about Assemblathon 2 and a little bit about the aborted but oh-so-close-to-launching Assemblathon 3, I have found time to tweet (and retweet) several thousand links to many relevant publications and software tools.

It seems that people are finding this useful as the account keeps gaining a steady trickle of followers. The graph below shows data from when I started tracking the follower growth in early 2014:

All of which leaves me to make two concluding remarks:

  1. There can be tremendous utility in having an outlet — such as a Twitter account — to focus on a very niche subject (maybe some would say that genome assembly is no longer a niche field?).
  2. Although I am no longer working on the Assemblathon projects — I'm not even a researcher any more — I'm happy to keep posting to this account as long as people find it useful.

And the award for the most-retweeted-tweet-of-a-photo-of-a-slide-from-a-presentation-of-mine goes to…

On November 20th, on the last day of my employment at UC Davis, I gave an exit seminar. Jenna Gallegos, a PhD student at UC Davis — who works on the awesome Intron-Mediated Enhancement (IME) project under the supervision of Alan Rose — posted several tweets from my talk including this photo of one of my slides:

This tweet continued to generate interest (retweets, likes, and mentions) for most of the 20th November and for many subsequent days afterwards. The latest retweet of this tweet was today: 16 days after the original tweet! I find this amazing especially as the original slide deals with the topic of genome assembly. At the time of writing the tweet has had 369 retweets and 277 likes

I'm pleased that people have found my jigsaw analogy useful. Some people commented that this isn't the best possible analogy and pointed out various ways that it could be more technically accurate (including suggestions of shredding copies of books and trying to piece together the original).

While I accept that this isn't the most scientific way of depicting the many problems and challenges of genome assembly, it is hopefully an accessible way of illustrating the problem. Nearly everyone has tried putting a jigsaw together, but not everyone has tried reconstituting a shredded book. My exit seminar was aimed at a very broad audience and so I pitched this slide accordingly.

People can follow Jenna on twitter (@FoodBeerScience) and should, at the very least, check out her awesome twitter bio. If you want to know more about her work, here is a recent review of IME that she wrote:

Ewan Birney reflects on the use of twitter and blogging for science communication [Link] →

Worth reading. Ewan includes some comments regarding the growing use of pre-print platforms:

Blogging is nice, because it is accessible to a broader audience and allows for a more chatty, 'natural language' style – but if the main purpose is to communicate with scientists, pre-publication servers are a better way to go

Ewan singles out arXiv, bioRxiv, and F1000Research, but I think PeerJ are also worth a mention here. They also have their own pre-print server and they also encourage open peer review.

Additionally, I think figshare is another outlet that can be used for dissemination of science material that may not suitable for a peer reviewed publication. One cool thing about using figshare for posting preliminary data or commentary pieces is that articles are allocated a DataCite DOI and can therefore be cited.

3 important digital things all scientists should have nowadays

Good advice from Michael Koontz (@_mikoontz):

The second item on the list is something which I wrote about recently.

The top 10 #PLOSBuzzFeed tweets that will put a smile on your face

It all started so innocently. Nick Loman (@pathogenomenick) expressed his dissatisfaction with yet another PLOS Computational Biology article that uses the 10 Simple Rules… template:


There were two immediate responses from Kai Blin (@kaiblin) and Phil Spear (@Duke_of_neural):


I immediately saw the possibility that this could become a meme-worthy hashtag, so I simply retweeted Phil’s tweet, added the hashtag #PLOSBuzzFeed, and waited to see what would happen (as well making some of my own contributions).

At the time of writing — about 10 hours later — there have been several hundred tweets using this hashtag. Presented in reverse order, here are the most ‘popular’ tweets from today (as judged by summing retweets and favorites):

Why I twitter →

I cannot sit on the fence. I like twitter and what it offers. I have learned things I never would, built genuine relationships with international people who I would have perhaps have only met over a quick coffee at a conference. And I have changed the way I speak about science.

This post by Mark Brandon sets out nine great reasons as to why he finds Twitter so useful, many of which relate to science communication.

I believe twitter is a strong positive for science, and it is a worthwhile investment of your time.

I completely agree with just about everything he has to say. It's a good list.

Real bioinformaticians and old bioinformaticians

A passing mention of the phrase 'real bioinformaticians' by Michael Hoffman (@michaelhoffman) yesterday, prompted me to elevate the concept to be worthy of its own hashtag. This is what happened next:

You will notice that Sara G's response (@sargoshoe) humorously introduced the concept of #oldbioinformaticians, and this in turn spawned an even longer set of tweets (see below). I think that many of the more — how shall we put this — wise and distinguished members of the bioinformatics community, enjoyed the chance for a trip down memory lane.

Can Twitter help us find out the gender ratio of bioinformaticians?

I'm still collecting survey results to try to understand the extent of gender bias in bioinformatics. I plan to publish an analysis of these results next week and I'll also share all of the the raw survey results via Figshare (in case anyone else wants to dive deeper).

One thing that is hard to accurately know is just what the gender ratio is across everyone who identifies themselves as a bioinformatician. A survey that is trying to ask something about gender bias no doubt introduces its own bias in the types of people who would be interested in completing such a survey.

But maybe Twitter can be of use in trying to determine a 'background' gender ratio among bioinformaticians. The evidence is hardly conclusive, but there are some data that suggests that more women use twitter than men. There's also data that there are comparable numbers of male/female users. In any case, numbers of users doesn't tell the whole story. Other research shows that, on average, men have  15% more followers than women, and a tool called Twee-Q that tries to identify the likely gender of twitter users, finds that men tend to be retweeted almost twice as often as women.

Despite gender biases in how people use twitter, it might still be useful to see what the gender ratio is of people who follow bioinformatics-type accounts. This is something that twitter can show you at analytics.twitter.com. However, this only seems to be enabled on accounts that have a certain number of followers. Here is what the results looks like for the @assemblathon twitter account (click to enlarge):

So twitter identifies — presumably using some sort of gender-guessing-algorithm — that 82% of  the followers are male. I'd love to see what other results look like for other bioinformatics twitter accounts. However, I think it is a better test if the accounts in question are themselves gender-neutral. I.e. affiliated to a resource or institution. If you run a bioinformatics-related twitter account that is gender-neutral, and if you can access analytics.twitter.com, I'd love it you could share your results with me (via comments below or on twitter @kbradnam).

Top twitter talent: UC Davis genome scientists lead the way

The Next Gen Seq website has just published its 2013 list of the Top N Genome Scientists to Follow on Twitter. Over 10% of this International list of scientists are all staff or Faculty here at UC Davis, which says a lot about the quality of genomics talent here on campus:

It is also worth mentioning that there are so many other people at UC Davis who work in genomics and bioinformatics and who use twitter to effectively communicate their research and engage with the community. E.g.

  • @dr_bik - Holly Bik (Postdoc in Jon Eisen's lab)
  • @ryneches - Russel Neches  (Grad student in Jon Eisen's lab)
  • @theladybeck - Kristen Beck (Grad student in Ian Korf's lab)
  • @sudogenes - Gina Turco (Grad student in Siobhan Brady's lab...and winner of best twitter account name)

Great to see UC Davis recognized like this.

 

Update

Updated at 9:09 am to reflect that Next Gen Seq have now added Vince Buffalo to the list (he was apparently meant to be on the list anyway).