Greetings readers of the OpenHelix Blog.
You might have noticed a large change to the look and features of the OH blog. These are temporary. With the update of Word Press, some of the functionally of the old theme has become incompatible and unworkable. We are working on a new and better theme and appearance, but in the interim, we’ve reverted the blog to a default theme. Some of our old functions and features are temporarily missing, but the meat of the blog remains. You will still be able to read our posts, comment, etc.
If you do notice anything amiss or missing, please take the time to comment here or email us.
Just found this sign which cracked me up:
Via Sharon Astyk who linked to Buzzfeed’s best 100 signs.
Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours. Questions or problems asked on Thursday will be answered on Thursday to the best of our ability. You can leave questions on other days of the week, but the answer might not come that day.
We’d also like to invite resource providers to let us know if they have something new to talk about, or something they want to mention to the bioinformatics community. We’ve had some people email us because they weren’t sure if they should post something, and we want to say that’s fine.
So What’s Your Problem? And What’s Your Solution?
You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.
We are constantly on the look out for databases and resources. It’s a full time job. Our current search space includes about 500 databases and genomics resources. We have a masterlist of over 3,000 such genomics/biological, databases, but we’ve culled them to the top used and useful ones for the search. That’s not to say there aren’t extremely useful resources within the other 2,500 (phew), there definitely are!, but we had to start somewhere. We want the list to be highly useful and relevant, so we started with most highly useful and data rich. It will indeed grow over time, the blog here is one way to make note of many of these new databases and resources.
That said, here is a great comparison of a large number of immune databases. They have gathered a list of over 40 databases of immunological interest. I was directed to by this “researchblogging” post at Mystery Rays from Outer Space (love the name, love researchblogging).
If you are in need of immunological data, check out the paper.
IEDB, Immune Epitope Database
I got an email from Tadashi Imanishi about the upcoming Biocuration meeting occurring in Japan and I wanted to pass the news on. The conference details have changed slightly in that it will be occurring October 11th-14th in Tokyo, rather than Oct. 6-9th in Chiba:
The new dates and place for the Biocuration 2010 meeting will be as follows:
Date: October 11(Mon)-14(Thu), 2010
Place: Plaza HEISEI
-Address: 2-2-1 Aomi, Koto-ku, Tokyo 135-8630, Japan
#Some sessions may be held in other meeting rooms in nearby buildings.
I personally am very excited about the change – Chiba looked absolutely beautiful, but I can’t imagine a greater thrill than getting to experience Tokyo as a guest of colleagues from Tokyo! I have never been to Japan before, but have seen it featured on the travel channel many times – I’m usually ready to pack my bags before the end of the program. And attending the conference in a venue so close to the National Institute of Advanced Industrial Science and Technology (AIST) is just very cool. I’ve heard of so many cutting-edge experiments in curation from Japanese biocurators at past conferences & OpenHelix has so much respect for foundational scientific resources such as KEGG and H-InvDB, and others – well, getting to go there and learn sounds like an unimaginably cool opportunity.
Last year I was selected to give a talk at the Third International Biocuration Conference in Berlin. Since Berlin was on my husband’s ‘short list’ of places he’d like to visit, he came along too & we had a wonderful time with the city and the science. Well, guess what other city is on his short list – yep, Tokyo. I don’t know if we will be able to send everyone at OpenHelix who would like to attend this conference, but fingers crossed that I’ll be seeing you in Tokyo in October!
Stay tuned here for more details, and I’m sure information will be posted at the International Society for Biocuration (ISB) conference listing soon.
Provided without further comment….
For the full size version go to the source: http://xkcd.com/701/
Lots of people have already written lots of great posts about the ScienceOnline2010 unconference already – you can see a list of them from this post of Bora’s (Thanks, Bora, for collecting these!), with lots of good analysis and observation (including these: ). I know I am a bit slow, but I just can’t let something so special go by without trying to add to the discussion.
For anyone not familiar with ScienceOnline, it is an unconference for anyone interested in science communication. I’ve blogged about it in the past, but I think the best descriptions of it come in posts by some of its organizers, Anton Zuiker, here, and Bora Zivkovic, here.
As I tried to figure out what I could add, it occurred to me that OpenHelix might have a cool dichotomy of ScienceOnline experiences. You see, I am a less-experienced blogger and I attended in person. Mary is a savvy blogger & she attended virtually. We are going to collaborate on a series of posts that cover various collections of topics associated with the conference. I hope this series is informative, interesting, and inspires you to join the conversation too!