Tuesday, November 24, 2009

Interpreting a Promethease report

This new video helps to explain what is inside a Promethease report.

Thursday, November 5, 2009

Self Explorimentation

SNPedia is pleased to have contributed "Self Explorimentation" to the What ELSI is New series -- especially during the moment when it is generating such interesting blogosphere traffic about access to genomic data. Of course, Genomics Law Report has this well covered, but this is a topic close to my own heart.

As suggested by Anne Wojcicki of 23andMe and Eric Topol M.D. -- SNPedia is here for you. Whether you get your data from a DTC, Kaiser, or the melting curve analyzer in your garage, we can help you to understand your data, and you can help us.

People without their data have little interest in SNPedia. Expanding this access helps SNPedia become a better resource. For these reasons, I might be too inclined to rush towards this (seemingly) inevitable future. I'm grateful that Daniel, Anne and others are raising this issue. But I can understand why Kaiser might feel that releasing information compromises their original study design. Mostly I'm excited by a future where the next study of this sort will need to consider sharing data with patients.

Monday, September 14, 2009

SNPedia poikkeaa Suomeen

It is the day after the very enjoyable Human Genetic Variation conference in Tallinn, Estonia. Preparing for my talk motivated a new 'tag cloud' section in the Promethease reports as well as the new overview at http://www.snpedia.com/files/promethease/outputs/cloud.html. When reading it, bear in mind that the word "baldness" doesn't mean that Promethease is necessarily predicting baldness, merely that the report will be talking about baldness -- perhaps with decreased risk. This section is only supported in the paid Promethease reports. Unfortunately that feature, and all of Promethease are not (currently) supported on the recently released Mac OSX Snow Leopard. Such is the price of being an early adopter and Apple's fondness for 'shock and awe' marketing.

Tomorrow I'm off to Finnland to continue exploring my new European home and a presentation at the Helsinki Institute for Information Technology.

Wednesday, July 15, 2009


I'll also present SNPedia at HGV2009, the 11th International Meeting on Human Genome Variation and Complex Genome Analysis 11th - 13th September, 2009 in Tallinn, Estonia.

Monday, July 13, 2009

AM I? I AM . A MIA !

SNPedia will be presented at the American Medical Informatics Association Symposium 2009 November 14-18 in a favorite old home, San Francisco. I'm looking forward to seeing Mark Porter again. Email me if you're around the city by the bay.

I enjoyed ISMB and expect to be a next year's in Boston. Warm hellos to James Diggans, Aaron Darling, Michael Imelfort, Barend, Brian, Isabelle and a lot of other exciting scientists.

Monday, June 22, 2009

Promethease 0.1.68 video tutorial

Curious about Promethease? Now you can watch a full run.

Sunday, June 14, 2009


SNPedia will be presented at the European conference on Python for scientific July 25th and 26th in Leipzig, Germany.

I'll also be attending ISMB June 27 - July 2, 2009 in Stockholm, Sweden.

If you're near those areas and interested please say hello.

Sunday, May 24, 2009

Promethease 0.1.66 is out

As always there are many improvements since the last blog post, but these standout.

There is a new syntax for genosets. Older clients don't know how to read this, and will not be able to see these genosets. This is a good reason for you to upgrade to the latest version.

Since 0.1.50 it has been possible to pay $2 via Amazon.com and reduce the runtime to about 5 minutes. In doing so you're downloading a single compressed cachefile instead of making thousands of requests for individual pages. At the moment this cache file is updated approximately weekly, however in the future we expect to have this updated in realtime as the wiki is edited. There will be a new blog post when that works. Until then the $2 version is faster, but the free version uses slightly fresher data.

The upper right corner has a new button labeled 'Wizard'. Press this to use a simpler UI which walks you through setting up your run. If you pay the $2, not only will you get the cachefile for a faster run, but you'll also have access to 2 new features with this wizard. The first is the ability to only show pages which have been modified recently. This might be useful if you ran your report 2 months ago, and want to make a new report which only shows what is new since then.

The wizard also enables a highly experimental new kind of report. This report is based on loading multiple genotype files and predicting what is possible in the offspring. You might wish to use this if you have data for you and your spouse, and you'd like to see some possible genotypes in your children. Its really not quite ready for the general public, but it never will be unless it is released for wider testing. Most folks should just click 'Next' and move on to generate a traditional report.

Thursday, April 16, 2009

안녕, 서울, 한국에서

Greetings from Seoul, Korea home of User:Hongiiv and the KNIH/KCDC. In a previous blog post I asked about Singapore, but plans have changed for the better and now I am testing the rs671 status of my excellent hosts, Chang Bum Hong and Dong-Joon Kim.

I think Hongiiv says it best:
꼭 5시가 아니더라도 그 후에 넉넉한 시간에 오시면 되겠습니다.
But for those of you who do not read hangul, I think google's translation is nearly as eloquent:
After that it was not five cigars will come in early.

For the full story see either the Korean invite or English translation to join us for the Open Bioinformatics Korea meetup April 17 17:00.


Friday, February 27, 2009

Promethease 0.1.46 released

Promethease 0.1.46 is released. It is worth upgrading. The most visible change is in how the status window updates. Many other improvements are here too.

Tuesday, January 6, 2009