Category Archives: Uncategorized

Don’t mind the dust

building_under_constructionGreetings 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.

Thank you!

What’s Your Problem? Open Thread

wyp_q_mark2_thumbnail1Welcome 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.

Immune Databases

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

Update on Biocuration 2010 Meeting

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
-HP: http://www.tiec.jasso.go.jp/plaza/index_e.html
-Map: http://www.tiec.jasso.go.jp/info/map_e.html
==========
#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.  

What’s Your Problem? Open Thread

wyp_q_mark2_thumbnail1Welcome 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.

NEW FEATURE: 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.

OpenHelix Collaborative Conversations on ScienceOnline2010

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!

All I Want for Christmas Is a Personal Genome Sequence.

Santa's giftAll I Want for Christmas Is a Personal Genome Sequence.   If that seems like too much to ask from Santa, then I just want to say up front that I am not asking for my own genome sequence, only my husband’s. Not more that 7 or 8 years ago this type of “present” would have cost upwards of $3 billion. It’s hard to believe that it can now be free. That’s because we signed him up as a volunteer for the Personal Genome Project, or PGP. So we will have to wait and see if Santa delivers – and it looks like it may not be this Christmas!

This all began several months ago when Mary and I attended a lecture series in Boston celebrating the retirement of Temple Smith (of the Smith-Waterman algorithm). Mary highlighted this meeting on the blog here. Among the distinguished list of speakers was George Church, a Harvard Medical School genetics professor, and a founder of PGP. After hearing him speak in detail about this project I thought how neat it would be to volunteer. They are aiming to enroll 100,000 volunteers now. The PGP website provides a nice outline of the volunteering process, and also presents the data for the 10 volunteers who have already gone through the entire process (including George Church and several other prominent local professors, i.e. the PGP-10). You can look through all of the information that the PGP-10 volunteers have provided by viewing their public profiles on the PGP website. So much detail is there – vital signs, medications, entire medical history, age, major traits, ancestry, and more. Upon viewing all of these details I decided I was not quite brave enough to volunteer yet (particularly after buy viagra seeing the enlarged facial pictures of the volunteers from a variety of angles), yet my husband jumped at the prospect. I am altruistic, but it just seemed that this would be a good thing for him to try first.

So we began the PGP enrollment process several months ago. This is not an easy or quick process at all. There are a ton of consent/disclaimer-type forms, very involved medical and family history questions to answer, and general trait profiles. In addition, there are a series of tests that you must take (and pass) in order to prove that you are familiar with the process that is going to take place, as well as to demonstrate a basic knowledge of genetics. And let me just say that a Ph.D. in molecular biology didn’t seem to be enough to breeze through their “basic” tests. Eventually we did pass. And they do provide study guides so you really need to just swallow your ego – the phraseology and questioning is very unusual on their tests. They also have a neat testing method that certainly wasn’t around when I was in graduate school. You can keep resubmitting your answers until they are correct. They don’t tell you which answers are wrong, only that you didn’t get the entire test right, but with some patience anyone can pass all of the individual tests (there may have been about 10). We then continued on to another series of forms, tests and waiting periods. Currently, we are in one of the several 2-4 week waiting periods, and could still be rejected at any point. It would be quite frustrating to be rejected now because it really is a reasonable amount of work to enroll in this.

My main concern now is that the folks at PGP will reject my husband on the basis of him being a rather boring genetic specimen. They freely admit to giving preference to older individuals, people with an exome already, “under-represented categories”, and those with known common or rare genetic conditions. Check out the eligibility/selection criteria. :( The most exciting – and only – genetic issues we could come up with for him were allergies and eczema. And his demographic (early forties, white male) probably won’t help either. I imagine that to be one of the most highly populated groups of applicants. My only hope is that his 100% Italian heritage may add some genetic interest, but we shall see.

For any of you who would like to read more about this, George Church just published an article in Newsweek entitled The Genome Generation, the case for having your genes sequenced. In it he really makes a strong case for having your genome sequenced, as well as for being totally open with all of your medical and genetic background information. Probably volunteers are pouring into PGP now. My favorite part of this article is his quote that the message is not “Here’s your destiny. Get used to it! Instead it’s here’s your destiny and you can do something about it.”

What a Christmas present a genome sequence would be…maybe next year.

Merry Christmas and Happy New Year to all of you!

What’s Your Problem? Open Thread

wyp_q_mark2_thumbnail1Welcome 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.

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.