The "Hack your Genome" idea, which is the one I spent most time on,
was inspired by frustration with lack of visualization tools for
23andMe genotype data. 23andMe itself doesn't even bother showing you
how the SNPs on its chip are related to the genes they affect. At the
other extreme of the spectrum, you have professional genome browsers
liek GBrowse built into the HapMap website. Very dense in information,
but it's also a 20-year old interface design, and completely user-
unfriendly.
We didn't quite get as far as we wanted with this one, but we were
able to display the gene structures, and neighboring SNPs, with rare
SNP variants highlighted. We also wanted to color each SNP with a
magnitude of its effect by combining data from SNPedia, OMIM, GWAS etc
where available.
My original plan was also to show associations with related genes or
correlated SNPs as well, by showing additional DNA strands in the
background. I think that would pose some interesting visualization
challenges and opportunities, but we never got that far.
We did wind up implementing a rudimentary genome browser from scratch
in just a little over 24 hours, which is no mean feat!
On Nov 17, 8:58 am, Cathal Garvey <cathalgar...@gmail.com> wrote:
> Hey all,
> If you (like me) weren't attending the SF-SciHackday, then you might
> like to peruse the list of hacks/projects to see what people got up to.
> Looks like a lot of fun was had, and there are a bunch of familiar names
> there!http://sciencehackday.pbworks.com/w/page/47743279/sfhacks2011
>
> A few particularly DIYbio projects to look out for:
>
> "Save the Cardinal!", Software to assist an ornithology citizen science
> project:http://sciencehackday.pbworks.com/w/page/47743279/sfhacks2011#hack_3
>
> "Homebrew Microscope", a sub-micron DIY microscope using plumbing parts
> and a camera:http://sciencehackday.pbworks.com/w/page/47743279/sfhacks2011#hack_9
>
> "HIV/AIDS: Meaningful Indicators?", using machine-learning to seek out
> cryptic cues in UNAIDS data that could inform better epidemiology:http://sciencehackday.pbworks.com/w/page/47743279/sfhacks2011#hack_10
>
> "EpiCell", mapping cell phone usage versus healthcare availability to
> determine areas where cell-based epidemiology would be most effectively
> applied:http://sciencehackday.pbworks.com/w/page/47743279/sfhacks2011#hack_13
>
> "Hack Your Genome", a code project to visualise and explore 23andMe data:http://sciencehackday.pbworks.com/w/page/47743279/sfhacks2011#hack_22
>
> A project to search for semantic cues in research papers indicating that
> the author has a lot of confidence or excitement about his work, to mine
> for early publications worth reading:http://sciencehackday.pbworks.com/w/page/47743279/sfhacks2011#hack_23
>
> "DNAquiri", a Surfacant-free DNA extraction for DNA-cocktails:http://sciencehackday.pbworks.com/w/page/47743279/sfhacks2011#hack_15
>
> Can't wait to get me to a hackday sometime soon. Any Euro-Hackdays planned?
>
> Cathal
>
> --www.indiebiotech.com
> twitter.com/onetruecathal
> joindiaspora.com/u/cathalgarvey
> PGP Public Key:http://bit.ly/CathalGKey
--
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To post to this group, send email to diybio@googlegroups.com.
To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/diybio?hl=en.
0 comments:
Post a Comment