bioinformaticsCore

HiSeq Lego model

2011-04-16T15:30:00.001-07:00

I created this model when I first heard that BGI ordered 128 HiSeq machines. Would that be great if I have one of them? Since it costs 3/4 $million dollars, I can only afford to build a Lego version.

All copyright reserved by Dawei Lin, 2010-2011

A perfect enclosure

2011-03-11T14:06:00.000-08:00

The Lego DNA model I designed fit perfectly in a 4" transparent tube. It may not be just a pure luck. :-)

DNA Hat

2011-03-11T14:03:00.000-08:00

My mother and wife have been very creative on putting double strand on hat. It is for winter. I had a chance to wear it a little bit. Will do more in the coming winder.

A close-up picture of my Lego DNA

2010-09-23T18:32:00.000-07:00

An actionable LEGO DNA model

2010-03-24T10:35:00.000-07:00

How to make a DNA model that children like to play instead just looking cool is a question that I have been thinking for the past year. I built one using magnet pieces last month that really got my 6 years old daughter interested in. It is a good start.

Some new designs of my LegoDNA fun endeavour

2010-03-24T10:29:00.000-07:00

Some new designs of DNA double helix model using 100% LEGO pieces.

Virus Model as a Maker Faire Landmark

2010-03-24T10:22:00.000-07:00

I built a T4 Phage model. Phage is a virus that "eats" bacteria. Because the big size of it, I often heard people saying "My booth is near the Virus model".

Learned from the Education day experiences, I want to add some LED lights to the virus model to make it more attractive to children.

Maker Faire 2009

2010-03-24T10:15:00.000-07:00

It was a great fun last year at Maker Faire. That was the second time for me to exhibit my models. It was satisfying to see how people from small children to adults enjoyed interacting with my models.

Origami

2009-12-31T09:54:00.000-08:00

I began to show interest in Origami after I watched Robert Lang's talk at TED.com. This is the first complex origami animal model I folded. It is also the first time I used foil paper. I am thinking to make some more DNA models using origami.

Display Wall with 50M pixel resolution

2009-12-31T09:48:00.000-08:00

My group built a high resolution display wall using commodity computers. It has 12 30" monitors and 7 Dell computers. It can display high resolution pictures up to 50M pixels. It should be the higher "monitor" in Sacramento area so far.

Lunch Box

2009-12-31T09:45:00.001-08:00

Inspired by a story in New York Times, I made several Bento boxes for my daughter. She liked the designs but not all the food.

T4 Phage Model

2009-12-31T09:32:00.001-08:00

This is a T4 Phage model I created using PVC pipes. I intended to built it to hang up my mother's knitting DNA model, but It turned to a separate project by itself. It was displayed at Maker Faire Bay Area 2009 as "I am a Virus". Because its big size, it became of a land mark of the faire. "Where is your booth?" "My booth is near the Virus model?"

Bloxes in my office

2009-04-01T16:13:00.000-07:00

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

2009-04-01T16:07:00.000-07:00

"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

2009-04-01T16:04:00.000-07:00

Attempt on next gen sequencing

2008-06-17T09:58:00.000-07:00

This is a prototype to demonstrate sequence clusters on flow cell

DNA lego model

2008-03-19T17:52:00.000-07:00

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

2007-06-24T06:48:00.001-07:00

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

2007-04-04T13:45:00.000-07:00

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

Fink is not as easy as it sounds like

2007-03-26T18:17:00.000-07:00

I did not realize that in MacOS there are still lot of things that you can not do easily.

Such as fink. If you can not find fink in a stable list ( I am trying to do it for unstable list), it is not trival to install a packages. Because a lot of time, a package may have dependencies. It is tedious to install them manually one by one.

I am trying to find a way to look for unstable packages (unstable does not means bad, it refers sometimes to "not enough tested" in fink.

First attempt to find "fink list" only has mysql4, but after fink selfupdate and select rsync, it did update the list to use mysql5. But I still can not install biopython, which is in unstable package list.

Things needs to be careful:

1. After default fink install even from the latest version, it still needs to run
fink selfupdate, so the package can udpate by itself.

Bioinformatics Infrastructure

2007-03-25T19:43:00.000-07:00

1. LIMS
I have already listed in a post before

2. Web Interface for customize Program release
We need a web system to allow biologist to access the program we develop through a Web interface. This is to avoid programer to install on different platform. The advanges is that the program can be used easily by other people.
Most of the programs in this category will need input file from users and get result back.
Things need to be done:
a. Web interface
b. Backend data processing
c. Privacy protection.

PISE package is a good starting point: http://www.pasteur.fr/recherche/unites/sis/Pise/

3. Computation Pipelines
a. EST Clustering and analysis
b. Sequence calling and assembly (Phred/Phrap/Consid)
c. Association Studies
d. Data Integration (iProtein)
e. Network and Pathway analysis
f. Structure prediciton and modelling
g. Data submition to public databases (NCBI, PDB, GEO)
h. SNP analysis
i. Workflow (Keppler)

4. Local databases
a. NCBI
b. SRS
c. Human Genome Browser

5. Software tools
a. GeneString (microarray analysis)
b. Spotfire (Multi-dimentional data analysis and visualization)
c. Matlab
d. Mathmatica

6. Project managment tools, Time Management and tracking, CRM

7. Cluster Computing Infrastructure
a. open source software in cluster environment (some of them from ROCK distribution)
b. local databases

8. Computing infrastructure

a. Servers
b. Development environment (Test, Develop, production environment)

9. IT infrastructure
a. Network (DNS, DHCP)
b. Security (Kerberos, Firewall)

Configure My MacPro Book

2007-03-25T11:23:00.000-07:00

I was trying to install biopython releated module into my Mac. I am still new to MacOX.

I found Fink to install think. From the first tried, I failed to install bioperl. So it is not as easy as I expected.
I also need to install Apple developer package which require a free registration.

So far I experienced MacOS:

1. Wireless connection is good: reliable but somehow I felt the connection speed is slow.
2. The mouse is hard to click, very rigid.
3. Multi-media is good. Once put a CD in, it can automatically recoginzed it. Same things for DV camera. I tried this on Windows, after install required software, it is still hard to do.
4. The screen is bright, expecially good to work outside
5. No developer program installed by default. Xcode, fink needed
6. Dash board is handy, especially the dictionary
7. I can not use Kingword, which is a English-Chinese dictionary that use mouse to capture the work from screen can translate into Chinese automatically
8. Sound is good.
9. Not every program is available on MacOS. such as camtaria
10. Powerbutton is too obvious. It is not good to have little kids around. My son, 1 year old contantly cause me trouble
11. Email program Entourage is slow

template LIMS thoughts

2007-03-21T05:10:00.000-07:00

It is apparant that various forms of Laboratory Informaion Management System are needed by different people in UCD campus. It has to be Web based. So I am thinking to estiblish some template systems for different purposes.

Wikipedia defined LIMS as:

A Laboratory Information Management System (LIMS) is computer software that is used in the laboratory for the management of samples, laboratory users, instruments, standards and other laboratory functions such as invoicing, plate management, and work flow automation. A LIMS and a Laboratory Information System (LIS) perform similar functions. The primary difference is that LIMS are generally targeted toward environmental, research or commercial analysis, such as pharmaceutical or petrochemical, and LIS are targeted toward the clinical market (hospitals and other clinical labs).

I found one nice blog about several Web based systems at

http://labsoftnews.typepad.com/lab_soft_news/2006/03/the_first_brows.html

There is also a website has a lot of discussions (http://www.limsfinder.com/)

Most existing system especially commercial ones are for pharmacedutical or biotech to track chemicals and data high throughput instruments. They are not only expensive, but also not what most genomics based biologists.

There are some open source solutions too, like:

Bika: A South Africa company. A system developed on Plone and Python
Website: www.bikalabs.com/

Halx: A system developed for Structural Genomics activities. I like the way they develop their design that seperate presentation and data model.
Website: http://halx.genomics.eu.org/

BASE: It is for Microarray.
Website: http://base.thep.lu.se/

My idea is to see if we can develop different modules that can simplify the process of building customized system. For example:

User admination: User authentication and authorization modules
Data and File management: Data upload and download
Billing
Communications
Report
Visulization
Backend bulk upload