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PGP Forum and Wiki

December 14, 2012

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This is a guest blog post from James M. Turner, a Boston-area software engineer, freelance journalist, author, and PGP-65. James recently created a forum and wiki for discussion of topics related to the Personal Genome Project. While our staff isn’t responsible for these sites, we plan to contribute to them and hope they provide an additional place for PGP participants to find useful information and answers to their questions.

When I was 8, I read “The Andromeda Strain”, by Michael Crichton (yes, the geek force was strong in this one, even at a young age.) The book left a strong impression on me about the future of genetics, to the degree that I was writing programs in high school to convert DNA sequences to amino acids. Mind you, this was in the late 1970s, when you had to walk uphill both ways to school to save your BASIC programs on paper tape, but tell that to the kids today, I tell you…

For a while, I was sure that my future would be in the biosciences, perhaps as a geneticist. Unfortunately (or perhaps fortunately) for the biosciences, I was distracted from base pairs by the other up and coming technology of the time, computers. Although I continued to avidly follow the life sciences, I fell in love with software and have spent the last 35 years making hardware jump through hoops with clever code.

But a funny thing happened on the way to 2013. Genomics, and the obscenely steep slope of the $/genome price slide, has created another example of what trendy geeks like to call ‘Big Data.’ Big data is a challenge, because it strains the computational and storage limits of computers to analyze, but it’s also an opportunity to correlate and draw new insights from datasets that used to live in their own private silos. The PGP, microbiome atlases, health data, exercise records, phenotypic traits, diet and much more are now digital and starting to hang around in the same neighborhoods. Between the years of 8 and 50, my two passions became “two great tastes, that taste great together.”

I first became aware of the new field of personal genomics when I researched 23andMe and deCODEme for an article I wrote in 2009. As part of the research for the piece, I got my Single Nucleotide Polymorphism (SNP) data from 23andMe, while my wife tried out deCODEme. As anyone who has used the SNP services knows, there’s interesting data to be looked at, but it’s just a tiny fraction of what goes on in the entire genome. I had experienced a taste of my genome, now I wanted the real deal.

That’s what led me to the PGP, drooling into test tubes, hanging out at GET 2012, and finally receiving my whole genome sequence a few months ago. Once I had all those lovely base pairs to play with, it immediately became clear that there’s not a really good user manual for the data, a “Genome Interpretation for Dummies.” I’m a pretty tech-savvy guy, and know enough about biology to be dangerous, but I quickly found myself dealing with the subtleties of GFF vs GTF vs BED format, comparison shopping genome browsers, and coming to the realization that a “whole” genome has small holes scattered throughout it (this must be why they call it shotgun sequencing…)

One of the things I know well from software is that crowdsourcing works. That’s the entire model behind GET-Evidence, many eyes and fingers building up a larger and more useful database of gene to phenotype relationships, so that eventually a newcomer will have a wealth of information about their genome. But what’s missing right now is a place to talk about the process, learn from each other, and share what works and what doesn’t.

I started talking to the folks at the PGP a few months ago about the idea of setting up a forum and Wiki for PGP participants (and researchers, and anyone else who wants to join in) to share information, look for help, or just chat. For a number of reasons, it was decided that it would be better to have them hosted and administered outside of the formal PGP organization, and I was asked if I was interested in setting them up. I was, and have.

At http://forum.personal-genome.org/, you’ll find the Personal Genome Project Forum. It’s a place to introduce yourself, discuss the PGP, GET-Evidence, genomics, and anything else that you want to. The PGP is a community as much as a project, and people in a community should have a town square to mill around and chat.

For more formalized knowledge transfer, there’s also http://wiki.personal-genome.org/, the PGP Wiki. Hopefully, this will grow into a fount of information about the how and why of genomes. I expect there will be a fair amount of cross-pollination between the Wiki and the forums, with forum discussions turning into Wiki articles, and people discussing wiki topics on the forums. There aren’t a lot of rules at the moment (beyond the obvious about spam and privacy and civility), so the personality of the fraternal sites will evolve as people use them.

So, they’re there, they’re open for business, and with this blog posting, they’re announced. A good first start would be to drop by the forum, register as a user, and put up an introduction in the appropriate topic. There’s only two posts there right now, and it’s a little lonely. We could also really use some articles on the basics of genomic data in the Wiki, I’m going to try to contribute as I have time, and some of the PGP staff have indicated there’s stuff they’d like to write, but the more the merrier!

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