Tag Archives: #scio11

ScienceOnline2011: dang I’m getting excited!!

ScienceOnline2011  begins Thursday evening and I’m getting more & more excited as the minutes tick away. The Keynote Lecture Thursday night is being given by Robert Krulwich, and is again being hosted at the RTP headquarters. I’ve gotten to sign up for a Friday tour at the RTP US Environmental Protection Agency. My whole family thinks that sounds cool & wants me to bring notes home on anything interesting that I learn. I’m looking forward to learning about some new databases that they develop – maybe I’ll get some cool tip ideas! :) After that I will attend two different workshops (‘Death to Obfuscation’ & Prezi), meet authors at the Casbah & dine in one of Durhams finest establishments. I’ve been so excited about these opening events, I haven’t begun to decide what Sat & Sunday sessions I’ll attend – other than my own OpenHelix demo on Sunday, of course :) – but I’m sure whatever session I join will be amazing. If you are drooling at my opportunity, fear not the conference sessions are being broadcast & you can participate online at  http://scienceonline2011.com/watch/ .

In my continued gathering of interesting articles on communication, information or other (that might be useful for some of the session discussions) here are a few more that I’ve found:

Great chemistry resource review (and minor personal rant)

In my continuing quest to be prepared for the upcoming ScienceOnline2011 conference I happened upon a great post by Antony Williams at ChemConnector. Apparently he has started a project with a number of other colleagues to compare and evaluate a variety of cheminformatics resources. Several people followed up with posts tweets or comments on his use of the word “trust”, but this is not the aspect of the post that I found most interesting.  Instead I was interested in 1) his project to compare resources, 2) his foresight to explain his initial assumptions, 3) and his actual (all be it fairly incomplete) findings. I also liked the list of resources tested because, like many others that he cites, there were some that I hadn’t run across before. (How wonderful, new sites to play with & learn… but that will be for another post.) His description of his assumptions as to which resources were “trustworthy” sometimes conflicting with his concrete data on its “trustworthiness” run parallel to some of my own experiences. As we (at OpenHelix) create trainings on resources we often find “unexpected gems” and occasionally find “limitation surprises” at well-known & respected resources.

He offers a chart of his findings from the first 10 “test” chemicals that he searched at each site. If you look across & up & down, you will notice that there are no “perfect” (check marks only) resources or chemicals. Looking in multiple resources for the same chemical by & large results in greater likelihood of correct & “complete” coverage & there are mistakes that can be found in even the best of resources. This reminds me of an NCBI talk given by Jim Ostell for the 25th anniversary of GenBank on the process of integrating data across 3 national databases – GenBank, EMBL and DDBJ – by comparing their data each database found errors that they had not been previously aware of & which they were then able to fix.

These chart results also display something that we here at OpenHelix try to stress as we teach researchers to use public resources – every resource has its own set of benefits and limitations. By understanding your specific research needs and having a basic understanding of what several different resources in your field offer, you can be the most efficient and effective in selecting & using the best resource & thereby in accomplishing your research. This is one reason that at OpenHelix we don’t just offer training on one variation database, but on over 10. We don’t just offer materials on one Genome browser but several. We create categories of tutorials as well as overview comparisons of one type or another. There are SO many amazingly useful databases and resources being created by expert, hard-working, well-meaning curators and developers. Always using the same “go to” resource is limiting & narrow minded…

Ooops, apparently I’ve wandered onto my soapbox again. I’ll step down (for today) and just suggest that you check out Antony’s post (and presumed future posts with additional comparison data) and the resources that he mentions, especially if you have an interest in cheminformatics, chemicals or chemistry – and who doesn’t? :).

ScienceOnline Warm-up: thinking about information and communication

Yet again this year I am lucky enough to be attending ScienceOnline unconference on science communication in January. I succeeded in registering in time – they were full up & adding people to the waiting list in less than one hour – & I’m so excited to be going that I already have gotten my hotel reservations & have begun ‘preparing’ (as requested by Anton & Bora) by specifically reading attendee blogs & thinking about various mechanisms for scientific communication. As I confessed in the past, I am by nature an introvert -social media and blogging do not flow naturally and abundantly from me. But in an effort to learn and grow I’ve been reading and dabbling more in social media outlets. I find the scope of venues and their ‘personalities’ really very interesting. I have begun to formulate the opinion that social media in general and scientific communication in specific are very similar to science careers – there really is an option out there that is perfect for anyone. The bugger is finding your perfect match and then using it efficiently & effectively. Below is an amorphous reporting on various things that  I (at least loosely) associate with the topics of communication & information:

The November 5th issue of Science has an article “Open mHealth Architecture: An Engine for Health Care Innovation”  (available here without a subscription) describing a health care delivery system using mobile communication devises – mHealth. The entire article makes a lot of sense, describing how ‘stovepipe’ mHealth apps mean duplicated patient efforts and information blockades for health care provides. It suggests a public-private partnership to create an “open” architecture and standards similar to the internet where apps use standard formats and can all feed data into and retrieve data from the same central “data vaults”. I find little to argue with in the article, but also few details on how this could practically be accomplished or who could/would lead the effort. The article’s authors are associated with UCLA and UCSF, and are also listed as contacts for the Open mHealth organization (not strictly pointed out  in the article).

Another interesting concept in health care is offered in the article “When Facebook is your Medical Record“. As implied by the title of the post, it will be interesting to see what’s developed & what’s been dropped as techniques in health care. From my own Facebook experiences I wonder how easy it is to find large numbers of patients and search their posts for health information. Any thoughts on this would be appreciated.

The next item that has caught my attention is the Nature article on biohackers entitled “Garage biotech: Life hackers“. This may not seem like science communication, but the amateur biologists had to gain excitement about science from somewhere before wanting to go out & convert their garage/basement into a lab. I’ve been hearing about DIYbio.org for at least a couple of years now, and recently found a ‘pre DIYbio blog‘, though it seems to be  inactive of late.

And for those of you with a subscription to Science, here’s an interesting article: “Reducing the Gender Achievement Gap in College Science: A Classroom Study of Values Affirmation“, which I found through a LinkedIn discussion. It describes a short, affirmative writing exercise performed off and on throughout the course of an intro physics class. The researchers report increased grades & class success for women in the affirmation group over women in the control group. Men did not show a difference. I’m not sure if writing about my core values would have been able to affirm me enough to raise my Physics grades – I wasn’t so much buying into the stereotype that men were better at Physics, more the fact that Physics just wasn’t my bag of tea. And the authors are quick to state that the intervention is only one tool, not a silver bullet, to solving the complex issue of gender inequity in science.

I’ll update this post with my continuingly random finds. Feel free to add your thoughts & finds here too…

ScienceOnline2011 is coming…

…and requests any help you can provide to organize this great event. We are slated to brain storm on ways that we here at OpenHelix might be able to help, but I also wanted to post the plea in hopes that some of our readers will also pick up the cause. So with no further delay:

We’re looking forward to ScienceOnline2011, the fifth and, we hope, biggest and best conference yet.

But, we need your help….So, we’re appealing to the community, and hoping for some crowdsourced assistance. Here are 10 ways to help us:

  1. Fix the logo. The ScienceOnline2010 logo looked great, but had a serious flaw — the fancy atom couldn’t print on a non-white background. We need someone with Photoshop or Illustrator expertise to rebuild the logo and customize it for  ScienceOnline2011 (notice we’ve reduced the size and placement of the atom).
  2. Design the T-shirt — be creative — and arrange for printing and delivery (and maybe help find a sponsor to underwrite the costs).
  3. Be the webmaster for this site, and help us make it more compelling.
  4. Be the webmaster for the planning wiki, and help us get the look and feel there to match this site. Also on the wiki, add your program ideas and tell us if you’d like to be a session discussion leader.
  5. Find a sponsor. Download the ScienceOnline2011 info sheet and share with companies, organizations, institutions and individuals who might be willing to become a sponsor of the conference — have them contact me (zuiker@gmail.com). While you’re at it, visit the ScienceOnline2010 sponsors (logos linked here) and share your appreciation for their past support.
  6. Find a donor willing to help us order lots of Flip video cameras. At ScienceOnline2010, we were able to give out a couple dozen cameras in exchange for short videos of conference participants (see this post, for example, and more examples here). Or, donate your gently used Flip cameras.
  7. Find a North Carolina organization willing to be our institutional partner (meaning our checkbook — accept sponsorship checks, write a few dozen checks to pay our bills, earn our admiration and gratitude).
  8. Offer another way to help. Use the Contact form to let us know about your talents, interests and experiences, and how we can put those to use in planning the conference.
  9. Help someone in your community learn to blog, tweet or make use of social networking tools (Facebook, LinkedIn, Flickr). Why? ScienceOnline2011 is a BlogTogether event, and we want the spirit of conversation to spread (read this essay for background).
  10. Sign up for updates so you can be the first to know when registration opens. Tweet, blog and tell your friends, too.

You can read the full original post here.