The OpenHelix Blog

Today’s tip of the week is introducing dbRIP, a database of Retrotransposon Insertion Polymorphisms in Humans. The dbRIP database, as you can tell from the title, is a focused resource on one subject: Retrotransposons in humans. Though focuses, retrotransposons are an important aspect of the human genome comprising 40% of it. They have an effect and a useful branch of study. This databases uses a local installation of the UCSC Genome Browser annotated with the RIP data. The tip movie (click the graphic to start) introduces you to the database. If it is something that interests you, you can learn more about how to use this database from the free UCSC Genome Browser tutorials at OpenHelix, since this database uses the same software.

It’s not ground breaking and you probably hadn’t noticed it yet, but it looks like something that could add some more, possibly useful, info to your PubMed searches. Last week, Pubmed announced on their technical bulletin that they’ve added a column to the right of the PubMed search summary which will contain results from other resources based on your search. Think of it as kind of an Amazon’s “you might also like” feature.

You might be forgiven for missing it because unless you are searching for one of the 200 drugs they’ve added this feature for (or read their technical bulletin), like “lovastatin,” you won’t see the column and links to the other resource. This other resource is the “Clinical Q&A” for the first implementation of this feature. It will be interesting to see how that develops and grows over time.

Still enjoying the ICSB meeting, and it is a gorgeous fallish morning in Göteborg. What a great city and terrific people here. Not entirely sure I want to come home….

My brain is approaching “full” already, and there are still several days to go. I’ll have a lot of tools to talk about in the coming weeks as I check more of them out. But I wanted to talk about a couple of neat tools that I have heard about so far. First–CellDesigner 4.0, that I mentioned the other day, was a good choice of tutorials to attend for sure. You can access their tutorial material here. Turns out they are also about to release a web-based version of this that will be a collaborative community editing tool for networks and pathways. It is called Payao–which I’m told means a type of “fish-aggregating device” according to their poster. I was unable to catch the poster authors so far to discuss it further, but it looked like a neat tool. I can’t find a release on the web yet and there was no URL on the poster. I’ll try to track them down again today.

Update: Found it here http://celldesigner.org/payao/payaopreview.html

Another fun tool (which I haven’t had a chance to use much yet) is BioMyn. The idea behind BioMyn is that it is something like a Google search for systems biology and other relevant biological data types. It aggregates a lot tools into a single search, here’s a partial list: ensembl, MINT, GAD, HPRD, Corum, InterPro, PDB, OMIM, GO, Reactome, KEGG, UniProt, HiMap, IntAct, GNF, and DIP. I spoke to Fidel Ramirez, the creator, about this tool and he was very eager to have users and feedback on this new beta phase. He was saying that people have suggested the results link should be re-organized a bit. If you do a search you get a list of results and some context. The link at the top goes to your “best” resource hit–leaving BioMyn. But if you click the link at the bottom of the result ( View all annotations for …) you go to the aggregated results in BioMyn. Organized into a collection of data in tabs, you can find a wealth of information on this gene. You can find gene links, of course, but also diseases, pathways, interactions, GO terms, and on and on. Anyway–check it out. And keep in mind it is beta. Feel free to offer feedback here and I will pass it along to the developers–they don’t have a feedback link on the site yet. But they do have a blog, I suppose you could put comments over there. In fact, I’ll suggest that to the team today if I see them.

I’m in Göteborg today, at the ICSB International Conference on Systems Biology. I’m taking a couple of the tutorials today. My first one is on the Edinburgh Pathway Editor or EPE (description of this can be found in this PDF of the session). They have made available a 2.0 version for the attendees here. I’m eager to learn more about this.

The next session I signed up for is CellDesigner 4.0. You can learn more about it from the session PDF here.

Both of these tools require downloading and installation. We usually focus more on web-based software, but these systems biology tools often require you to install and run it locally. You can get the software directly from these sites:

Edinburgh Pathway Editor: http://www.bioinformatics.ed.ac.uk/epe/index.shtml

CellDesigner: http://celldesigner.org/

Have fun! I expect I’ll post more thoughts on them after I have had a chance to dive in and swim around some.

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.

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.

The question we probably hear the most from researchers is…what can I do with a giant list of genes to figure out what’s going on in there? And about once every 6 months this question comes across the Gene Ontology mailing list. This is followed by a flurry of developers who offer their cool tools for analysis purposes. There are actually quite a few different tools with different strategies out there–and they are designed for different purposes, and in this tip I’m going to use the Gene Ontology consortium’s GO Term Enrichment tool as a primary example, but I’ll also point you to a list of other tools to try out.

From Kaisernetwork.org, this web seminar on Wednesday 8/20 1ET (tomorrow):

View a live webcast of the Kaiser Family Foundation’s series, Today’s Topics In Health Disparities, which will discuss the potential of race-based medical solutions for improving healthcare and reducing racial/ethnic health disparities. The webcast will take a closer look at efforts to study the interaction between race, genetics and health.

Panelists will discuss the efforts underway to develop medications to treat diseases that disproportionately affect certain racial and ethnic groups, as well as the benefits and drawbacks of using genetic markers for race in medical decisions. Other topics covered include which genetic factors are being used to personalize medicine and what pharmaceutical companies are doing to target the drugs and treatments they offer to certain groups.

Details about the technology and setup are here: Today’s Topics In Health Disparities - Race and Genetics: The Future of Personalized Medicine

I’m not sure how research-oriented it will be. But if you are interested in the future directions of personal genomics this is an area that might be worth learning more about. A new focus at NIH includes the NICGHD, that we talked about here.

As genome-wide association studies (GWAS) become much more widespread and useful, the genome browsers are finding ways to incorporate these data and to allow you to view the published data or your own.

The UCSC team has already developed a useful interface in their “Genome Graphs” tool which allows you to view and compare disease studies (9 diseases so far), browse regions in the genome browser, sort genes and more. It also allows you to import your own GWAS data.

The Ensembl blog has just announced that Ensembl too has now incorporated genome-wide association studies into their database (7 so far). You can access these in the DAS Sources menu  in the ContigView (in detailed view section as shown here, click to enlarge) and CytoView pages. These are listed as “WTCCC” and then disease initials (BD, CAD, CD, HT, RA, T1D, T2D) in the menu. I don’t yet see a way to easily upload and view your own data, but I’ll double check as I play around with it.

I see a blog post and  tip-of-the-week comparing these two in more detail coming! For now, just letting you know they are there.

The second edition of the blog carnival called The Giant’s Shoulders is up, hosted by The Lay Scientist blog. It is a collection of science blogging about classic papers in science, or other older papers that are interesting or curious for some reason. I did an entry for the inaugural edition, and it was so much fun to re-visit that old paper. I have another one percolating, but haven’t managed to get very far with it yet.

Giant’s Shoulders #2: http://layscience.net/node/164

Giant’s Shoulders #1: http://scienceblogs.com/clock/2008/07/the_giants_shoulders_1.php

This was all started by Skulls in the Stars as a challenge to science bloggers, and is now also monitored at: http://ontheshouldersofgiants.wordpress.com/

Consider doing one of your favorite antique papers. C’mon, you know you have one…and submit to the next carnival. Details on the subsequent hosts will be available at The Giant’s Shoulders blog.

The Jackson Lab courses are really terrific–I took a couple of them while I was up there for my post-doc. This announcement just came over the mailing list and I thought I would pass it along. I’m thinking a lot about systems biology and the tools for it right now (more details on that later), and so I’m going to need more people generating data so I can play with the tools. And September in Maine is a nice time, btw:

Applications continue to be accepted for the Short Course on Systems Genetics being held September 23-29, 2008 at The Jackson Laboratory in Bar Harbor, Maine.

This one-week course will cover computational and experimental approaches to genetic studies that utilize the whole genome approaches. Lectures and computer workshops are designed to accommodate students with a wide variety of backgrounds. Biologists seeking to gain a deeper understanding of statistical and computational methods as well as quantitative scientists desiring exposure to biological problems are welcome. Topics to be covered include genetic mapping, gene expression microarray analysis and computational modeling of complex systems.

For more information, including the course schedule and application instructions, please visit http://courses.jax.org/2008/systemgenetics08.html

The tourists are mostly gone at this point, and the town is still running. Good time to visit Bah Hahbah.

http://courses.jax.org/2008/systemgenetics08.html