Bloxes in my office

I bought some bloxes for my programmers. We plan to use it to build tables, whiteboard holders. But most of the uses for now are some geeky art.

my model was featured at Illumina newsletter

"A Unique View of DNA
Dr. Dawei Lin at the Genome Center, University of California, Davis uses Illumina BeadChips and LEGO bricks to bring DNA to life for a recent "Bring Your Child to Work Day" event."

http://www.illumina.com/icommunity/Sep2008/

A new model picture taken by Simon Willison

Attempt on next gen sequencing

This is a prototype to demonstrate sequence clusters on flow cell

DNA lego model

Inspired by the simple DNA model by Eric Harshbarger (http://www.ericharshbarger.org/lego/mini_dna.html), I decided to build one with my daughter. This is also to prepare for the upcoming "Bring your daughters and sons to work day".

Because of the simpleness, Eric's model can not demonstrate the difference between G-C and A-T pairs. This is a major complain that my wife had who is also a biologist. That triggered me to build a more complicated DNA model. While preserve the beauty of Eric's model, I wanted more information to be added. After tried and errors to about 2:00am. I thought one solution. Here it is. The middle one is what I built. The right one is Eric's model. My one is bigger. It has more room between double helix. So I can put three or two hydrogen bonds in.





My mother also got involve. I found one site talk about knitting. She followed the instruction and knitted one.



Some models created by Affymetrix Chips







Some pictures of a model made by Illumina Genechips and Lego

Illumina data analysis

I am working on the first dataset from Charlie to pilot the analysis of Illumina data analysis.

Lumi is a package to use. Initial problems I had:

1. Different version of BeadStudio have different format. Charlie is using BeadStudio 3.0.14. One interesting thing is current version give STD_ERR. Early version gave STD_DEV.
2. Annotation package should use lumiMouseV1. This is for mouse chip v1.1
3. The output file directly generated by BeadStudio did not put \t for rows that do not have data at the end of the row. So each row have different number of columns. For example, some has 50 columns (including DEFINATION, SYNONYM), but others that do not have those data at the last several columns may only have 48 columns or less. The way to solve this problem is to modify read.table like the following:
read.table("pmt1_all.txt", sep = "\t", fill = TRUE, header = TRUE, skip =8)

4. The pmt1_all.txt is too big. When I read into my laptop with 1.5G memory. It can only read in 3817 lines. I have to trim most of the columns to read in all the data.



R Script:

1. Generate a summary table

for(i in 1:542) {
tid = upTargetIDAB[[i]]
ABresults[i,1] = pmt1[which(pmt1$TargetID == tid),2]
}

Plone as a website template

I am thinking about to use Plone to do the website management. For UC Genome Website, it might be a better choice. There will be some non-programming people to edit the content of the Website.

One advantage Plone over Wiki is that it does not require to enter any HTML or wiki code.

Need more thinking on that