Andrew Scheidecker's Website

Personal Genome Explorer 1.2

andrew — Mon, 28 Jan 2008 01:57:16 +0000

I’ve updated Personal Genome Explorer to version 1.2 (install, source). If you installed the previous version, it should offer to automatically update itself to the new version the next time you run it.

Changes:

SNPs are grouped by the trait they affect.
Importing from 23andme’s official download-able data format is supported; this has replaced the “screen scraping” data path.
Importing from deCODEme’s official download-able data format is supported.
Genotypes are appropriately oriented on the reference human genome, which makes the cross-referencing between personal genome data and SNPedia more accurate and complete.
Some miscellaneous UI polish.

Screenshot

Genome data available from 23andme and deCODEme

andrew — Tue, 22 Jan 2008 07:00:28 +0000

It looks like 23andme and deCODEme have both started to allow users to download their raw genome data.

I’ll try to update Personal Genome Explorer to import the data ASAP, but I may not have the time to put together a new release until next weekend.

Personal Genome Explorer 1.1

andrew — Mon, 21 Jan 2008 00:21:31 +0000

I’ve posted version 1.1 of Personal Genome Explorer; both source and binaries are available.

Features

23andme data import
Encrypted file format
Export to CSV
SNP database import from SNPedia
Comes with pre-imported data from SNPedia
Analysis of genome based on SNPedia metadata
Random genome generation based on population frequency data

The new version brings together the 23andme data import from version 1.0 with a new SNPedia metadata importer. It cross-references the 23andme genome data with the SNP information from SNPedia to display the traits associated with the genome.

For my personal genome data from 23andme and the default SNPedia data included with the binary download, it can find about 150 traits. There are 800 additional SNP associations it finds in SNPedia that don’t have information about the effects of the different alleles of the SNP. As more information is added to SNPedia, Personal Genome Explorer will be able to show more traits.

Andromeda is big

andrew — Sun, 13 Jan 2008 17:59:47 +0000

From 2.5 million light years away, the Andromeda galaxy’s angular diameter is 7 times larger than the full moon’s in Earth’s sky; but only the galactic core is bright enough to be seen by the naked eye.

SNPedia

andrew — Sun, 13 Jan 2008 03:29:07 +0000

I found a great Wiki about human genetics: SNPedia

Hello

andrew — Sat, 12 Jan 2008 23:58:53 +0000

Welcome to my blog. You can read a little bit about me here.

I’ve just posted the first source release of Personal Genome Explorer. It features data import from 23andme, an encrypted file format, and a basic analysis UI framework. However, there aren’t any real analyses yet; I’m just releasing this for those who would like to download their personal genome data from 23andme, and get started hacking. Enjoy!