New Communication Channels for Biology
San Deigo, CA June 26-27, 2008
I just returned from a small conference in La Jolla on “New Communication Channels for Biology”. I was invited based on our work with WikiPathways (wikis being a perfect example of a “new communication channel”). I didn’t know what to expect, but it turned out to be a profound experience. While the topics are fresh in my mind, I wanted to dump them on you guys. Feel free to follow-up with me on any particular topics/tools you find interesting. And if you are already using tools like this that you find helpful, please add them to the list!
STATEMENTS – a.k.a. new convictions following the conference:
- Everyone working in biology today (wetlab and informatics) should be using one or more of these tools.
- Participation in the communities formed by these tools will become an important measure of your career, rivaling that of your publication record. If you are a grad student now, your tenure committee will likely take into consideration such participation.
- Expanding and enriching your contacts beyond your immediate lab mates will help your research today, and help you get a job later down the road.
- Using these tools will make you a better, broader scientist, especially in terms of being able to communicate your work with colleagues, grant review sections, and students.
NATURE OF THE TOOLS:
The “new communication channels” are referring to wikis, blogs, forums, podcasts, social bookmarking, open-access models, and multimedia presentations of your work. These are moving targets, but now is a great time to start tracking them and getting familiar with them. Though a lot of tools have catered to bioinformatics and computational biology in the past, many are now much broader and geared towards wetlab topics.
TOOLS WORTH HIGHLIGHTING:
1. OPENWETWARE
This is a lab-oriented wiki (like the one we started for GICD), but for the world. This is where you want to put profiles, protocols, etc that you want to share. This is also where you want to go to learn about or compare protocols. And it’s for more than just protocols. Of all the science wikis out there, this one is by far getting the most traffic and is clearly taking off.
Idea: One could have a lab wiki or website that cross-links with their lab presence on OpenWetWare to split private and public content.
http://openwetware.org/wiki/Labs
http://openwetware.org/wiki/Protocols
2. SCIVEE
This is a really cool site that lets you augment your papers beyond supplemental figures and movies. You can add video providing subtle details of a protocol or providing more conceptual background. They call them pubcasts = publication broadcasts. This can help to bump citations for you paper (they had compelling numbers demonstrating the “scivee bump”). You can, of course, also look up publications from others to get more out of their story. You can transform a poster into a short video using really easy-to-use editing tools in just a matter of minutes, and then “publish” the poster online and send the url to colleagues. Obviously this is great for teaching as well.
Idea: This could be a great way to push papers using some of our pathway visualization tools, like GenMAPP, Cytoscape and WikiPathway.
3. NATURE PRECEDINGS
A preprint server for posting papers, presentations, documentation, etc, prior to (or in lieu of) publishing. For topics where you don’t think you’ll get immediately scooped, you can post an early draft of a paper here before sending it for review. This also can help the citation rate of the final paper. You can also post items you don’t want to take the time to formally publish, items not worth publishing, ideas you want to stake an early claim on, or items like presentations and posters.
Idea: We should post some of our presentations here.
Note: we found out about the work in Chris Evelo’s group from a powerpoint presentation posted online!
http://precedings.nature.com/
Note: some journals don’t allow preprints before publishing. Make sure to check the policy per journal.
4. TOPSAN and PROTEOPEDIA
These are for those interested in protein structure. These sites support community annotation of structure, plus provide a host of visualization and analysis tools that are very easy to use. Proteopedia allows you to make little 3D movies of proteins, highlighting regions or residues and it supports hyperlinks to the movies within the text. Topsan is poised to completely change how folks work with PDBs. They’ve got all the content and good momentum.
Idea: Contribute to pages for your favorite structures to recruit new ideas from the structure community.
http://www.topsan.org/
http://www.proteopedia.org/wiki/index.php/Main_Page
5. LINKEDIN
I think everyone knows about this already. But if you don’t, sign up now!
6. DELICIOUS and CITEULIKE
These are social bookmarking and biobliography tools. The idea is that your collection of bookmarks and citations can themselves be a powerful way to connect to colleagues. Both tools have a dead-easy way to add content. E.g., for citeulike, you can click a link whenever you are looking at a pubmed abstract and it’ll add all the info. Citeulike then provides you with all the formats for citing the paper and let’s you tag the paper to organize your citations. Most importantly, it tells you who else was interested in this paper. You can then go and browse the citations that they have already collected! This is way more efficient than cold pubmed searches. Delicious does the same thing, but for web page bookmarks.
Idea: This is a great way to share citations and links with colleagues without even having to email or post them anywhere. For example, I found all of Thomas’ “pathwayanalysis” citiations without him even having to contact me. So it’d be even easier to share papers within a lab than posting them to the wiki!
http://www.citeulike.org/user/AlexanderPico
http://del.icio.us/AlexanderPico/pathways
