Tip of the Week: Twitter in Bioinformatics

So let’s talk about Twitter. Some voted against it in the poll–but the folks who were interested in seeing how I use Twitter carried the day 80% to 20%. If you were the one of the ones who voted against this–join us next week instead :)  But if you are wondering how this tool might be of use in this arena, you can watch as I introduce my strategy for gaining useful bioinformatics tidbits from this source.

I suppose if you are very new to this you need some vocabulary. Twitter is the provider of the platform that enables people to send short (140 character) text messages around. The individual messages are referred to as tweets. And although it may not seem like 140 characters is of much utility, there are some really useful things that can be conveyed in that much text.  Here’s a sample tweet from the NCBI. They would be referred to as @NCBI in the twittersphere.

You don’t have to have a twitter account to see tweets from NCBI. You could just go to the NCBI twitter page and look at them. Or you can do what I do–I use another kind of software tool to organize and monitor the tweets I’m interested in.

I use TweetDeck, a free interface for twitter management. I have no relationship with them. It’s just the one I started using. There may be other tools for this other people will recommend–feel free to tell us your favorite. I have it on my desktop, and on my iPhone.

Here’s a sample of my TweetDeck interface (click for larger size). It sits on my desktop, and  sort of trills when a new message comes in. You can change the settings for the notifications if that drives you nuts, though. And if you share an office–turn the sound off.

I have it set up to do a standing search for keywords, and to show me things that people or projects that I am “following” have sent out. I have a column for the keywords genome/genomics/etc, one for bioinformatics, and then the OpenHelix follow set on the right. (I also have my friends and personal tweets off to the left; you’d have to scroll over to see those columns). So items flow in all day that meet my search criteria, or are from professional sources I’m interested in following, and not shown are notes from my friends–some of whom are e-friends and some I know IRL (in real life).

You could stop at this point and just watch things come to you if that’s all you need. Some people, though, may want to share things–items they’ve read and liked, questions for others, announcements they have, etc. For that part you need a Twitter account to send messages.

The message sending part is at the top of the TweetDeck. It tells you how many characters you have left, and turns red if you are over the limit of 140. A couple of things about messages:

  1. Consider sending less than 140 sometimes, if you want people to re-tweet your message. The re-tweet would carry your twitter name and eat up more characters. So retweets of something we send would begin: RT @openhelix…. costing an additional 13 characters for the next person. Sometimes in a re-tweet people will have to edit, and those might be designated as MT or Modified Tweet.
  2. Use a URL shortening service to make small links rather than long ones that use up your characters. I use http://bit.ly, but others are available. You can set up your TweetDeck to automatically convert them too.
  3. Use a hashtag for key terms–which you can add in addition to your text. For example, you may see examples like #genomics or #bioinformatics in there. #GWAS is a common one. In the movie I show the hashtag for the Pacific Symposium for Biocomputing 2011 conference, #PSB2011. People at the conference can tweet stuff with that tag, and if you have a column set up for that it will feed to that. Or you can use it as a search term. Hashtags have also become a means of joking around on twitter. Such as #PeopleAreInsane, #itswetoutthere, or #Aflockalypse was big around the Arkansas bird death news.

{One quick additional item about links: we have a service that stores all the links we tweet in one place. It’s a handy place to look for things that you know were sent, but can’t remember exactly. Our list is here: http://trunk.ly/openhelix/ }




You may not be convinced that Twitter is of any use for you from this. And that’s fine. But people are using it for networking, outreach, sharing science, asking questions, and many people find it has utility for them. I love to get updates from NCBI, Cytoscape, and other database and software providers about new features and updates. People share cool papers and new useful sites. There really are some gems out there. And we will forward interesting items, or send out information when we have cool blog posts or new tutorials or other sorts of stuff. So we use it for outreach as well.

Twitter use may even contribute to the world knowledge. I found a recent paper in PLoS that analyzed tweets associated with the H1N1 flu epidemic. And they found a lot of good information was being generated. And they were also able to find some that was bad information–peak misinformation when some of the cranks at Natural News published an article of some fiction. So it certainly is a mixed bag. (It was the first scientific paper I ever read that referred to Harry Potter, Twitter, and the flu.) PubMed currently has 66 articles that contain the search term “twitter” (one seems to be about actual birds….). I’m sure there will be more.

In a recent interview, Ed Yong the science writer describes his perspective on the use of twitter for his work. As I was writing this up, Ed provided a funny tidbit for a Friday afternoon:

edyong209 Codswallop. You, sir, are a cad and blackguard, wot wot. RT @b0yle : Are you tweeting with an accent? http://on.msnbc.com/gU3Tc6

If you start watching it, you’ll catch on to the etiquette and the common abbreviations–apparently some of the local variants, too. You can look for helpful stuff all around the web.

Twitter is not for everyone. But like most technology–if used properly, you can get something valuable out of it. And the #bioinformatics community is pretty good about using it well, I would say.

Follow us if you want to: http://twitter.com/openhelix Oh–and if you manage the twitter feed for a project or database or type of tool that we’d be interested in, drop us a comment and we’ll start following you. It would be neat to link up more of the projects with this mechanism for outreach.


Chew, C., & Eysenbach, G. (2010). Pandemics in the Age of Twitter: Content Analysis of Tweets during the 2009 H1N1 Outbreak PLoS ONE, 5 (11) DOI: 10.1371/journal.pone.0014118

10 thoughts on “Tip of the Week: Twitter in Bioinformatics

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  4. Linda McMahan

    Hi Mary,

    After reading “twitter in bioinformatics”, I downloaded and installed TweetDeck on my Mac desktop and was unable to add people I follow. To add a person, e.g. http://twitter.com/#!/mndoci, I follow on twitter to TweetDeck, I (1) clicked on the + icon at the top left hand side of he TweetDeck screen, (2) clicked on the ‘create a new group’ under the ‘add full news feed column for:’ header, (3) named ‘people I follow’ for ‘name your new full news feed group’, (4) past ‘http://twitter.com/#!/mndoci’ for ‘add group members’, and (5) clicked the ‘Finish’ button – And nothing happened. Very much appreciate on any suggestions on how I should go about to get this work.

    Also, how do you have TweetDeck set up to do a standing search for keywords?

    Thanks for your help.

    TweetDeck newbie

  5. Mary Post author

    Hi Linda–I’m on a PC, so I’ll defer to Trey on the details. But my follow column editing looks like this:

    Here I have to select someone from my account, use the arrow to move them over, and then save at the bottom. On the next window you have to use the bottom button to save again.

    I’ll do another reply on the standing column.

  6. Mary Post author

    To add a standing column, my steps are:

    1. Click the + thing at the top:

    2. Then in the new dialog window, put your search term. Here’s my sample:

    Then click “search”. It creates a new column over to the right of my existing one. I have to scroll to see it.

    Again, this is the PC view. Yours might be a bit different.

  7. Linda McMahan

    Hi Mary,

    Thank you very much for your prompt assistance. I now have a working TweetDeck interface to my social networks.


  8. Mary Post author

    Oh, terrific Linda. I’m sure I don’t know everything about it–I’m apparently the last person who isn’t on facebook, but I see there are ways to set it up to do even more.

    I just wanted to introduce the basics to get people started.

    And I know there are other interfaces out there, and I haven’t used them. People will probably have others they like.

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