Category Archives: Uncategorized

Exploring the Harvard Personal Genome Project Dataset with Untap

Recently, my co-worker Abram Connelly scraped the phenotypes in the Harvard Personal Genome Project and made it available in a small SQLite database, publicly available for anyone to download. He made a small webapp around the database where people can play around with the data directly in their browser.

Webapp (first page has link to gzip of the database): curoverse.link/22d61dd43786c65cd175b04ad6954af0+3119/html/index.html 

dataset

The dataset consists of people who have completed the enrollment process and were free to upload their own data for public release and also answer the surveys online (but not necessarily people who have donated samples, had the samples sequence, or had the samples released publicly).

To put it concretely, there are around 4000 people enrolled, and around 200 people with whole genome sequences that were  sequenced, interpreted, and returned by Harvard PGP as of August 2015 (though keep your ears open for upcoming news). (Participants may have whole genomes sequenced independently and then elect to upload and donate the data to the Harvard PGP).

webapp

Returning to the webapp, there are a few default tabs, where you can do things like explore what year PGP participants were born, where you can see that our population is mostly young folks…

“Summary” Pre-Packaged View of Allergies of Participants

…or with two clicks see what allergies are most common in PGP participants. Note that this is a quick scrape of the Tapestry database and no clean-up has been done, so you’ll notice allergies being listed twice with different spellings.

SQL Queries for Participants with “Oak” Allergies

On the “queries” tab, you can query the sql database and see the results in neat table form in your browser.

Additionally, there are some pre-packaged but interactive visualizations, where you can edit the text and have the graph update to reflect your changes / newly requested data.

For instance, here’s a display of the participant gender ratio at different ages which I modify to display information about the allergies at different age buckets

before, displaying gender of participants

and after, displaying penicillin and house dust allergies

Obligatory cat statistics

Although one could hope that this graph shows that PGP participants are not more likely to develop allergies to cats as they grow older, we have a lot more younger participants and this is absolute and not percent frequency, so we might have to say the data points to the opposite. Sad!

(Disclaimer: Just for fun, no real thought put into this analysis :] )

Conclusion

Ever wanted a public genotype + phenotype dataset? The Harvard PGP has you covered!

We have phenotype surveys galore (including a recently released one that includes blood type and eye color), with responses available in CSV form. The questions on the survey forms are available on github for now.

I hope you all enjoy! Untap is on github

https://github.com/abeconnelly/untap

and Abram welcomes feature requests / issue reporting. We hope this is beneficial to the GA4GH working groups specifically and other researchers in general.

Enabling Multi-touch Gestures on Lenovo Thinkpad 2nd gen x1 with Ubuntu 14.04

I recently set-up multi-touch on my lenovo x1 2nd gen and got it to work (pinch and zoom, one-finger drag) on Chrome and Chromium, although not the (sadly less-featured right now) Firefox.

My  post on askubuntu.com follows.

Touchegg  (sudo apt-get install touchegg)  works for me — however apparently not on Firefox or Chrome, only on Chromium, do the multi-touch gestures work for me (out-of-the-box).

On Chromium, I can one-finger drag (on-screen touch, not touchpad), two finger scroll (touchpad), pinch and zoom (on-screen touch).

See: Firefox bug, http://askubuntu.com/a/664898/67349

To fix chrome, I had to follow both answers at Chrome + Touchscreen + Unity (14.04)

First,

  • Navigate to chrome://flags/#touch-events and
  • set Enable touch events Mac, Windows, Linux, Chrome OS to enabled.
  • I also set “Enable pinch scale. Windows, Linux, Chrome OS” to enabled (instead of default).

Second, I needed to start google chrome and tell it which device.

$ xinput list
⎡ Virtual core pointer                      id=2    [master pointer  (3)]
⎜   ↳ ELAN Touchscreen                          id=9    [slave  pointer  (2)]
$ google chrome --touch-devices=2

My Setup

  • ubuntu 14.04
  • lenovo 2nd gen x1.
  • Chromium: Version 43.0.2357.130 Ubuntu 14.04 (64-bit)
  • Chrome: Version 43.0.2357.134 (64-bit)
  • Firefox: 40.0

My ~/.config/touchegg/touchegg.conf if it’s useful: http://pastebin.com/qGexA1gB

Rainbow!~ heart cookies (pt1)

I really like rainbow things. This has entailed baking an increasing amount of rainbow things. Here’s a brief blog, pt1, about rainbow heart cookies. pt2 is about challah, and pt3 about asian chiffon cake.

Update 9/4/15: Added pictures from webcam, which detail missing parts of the process

1) Rainbow Heart Cookies

Following these instructions ‘Eugenie Kitchen Rainbow Heart Cookies”: https://www.youtube.com/watch?v=I2yW_VONWco

The ideal

eugeniekitchencom

Ours didn’t turn out as pretty, but then again we didn’t use a ruler.

final cookie! missing a few colors, so it goes
final cookie! missing a few colors, so it goes

Full gallery: https://goo.gl/photos/yvgARo9pxZYsZwD26

2) Rainbow Challah

To be continued in the next post, pt 2!