I've updated the Links and Books sections to be more relevant.
Be sure to check out MIT's Registry of Biological Parts. It's a great idea.
I've also linked the research site of Yiannis Kaznessis, my advisor. In addition to synthetic biology, my group also performs docking calculations for protein-protein pairs and protein-DNA pairs as well as bioinformatics techniques to analyze microarray data. One obstacle to designing synthetic bio systems is the lack of the necessary 'parts'. Part of our integrative approach is to use computational design of proteins/DNA sequences to predict which modifications should be made to provide the needed parts for a particular design.
My (soon to be) published papers are in the list of publications. The first one is available in PDF form and should be published soon (we've corrected the galleys already, but they've been dragging their feet on this 'special' issue of theirs. It's taken a year after acceptance for us to get back the galleys!).
Very interesting...
Since I'm accustomed to, as you mentioned in an earlier post, cartoonish diagrams, I had supposed genetic switches to be more deterministic.
And the math was more accessible than I'd feared...
Posted by: rob at October 23, 2004 05:39 PMYep, the concepts behind the math aren't difficult to understand. Markov processes can be a very tactile subject with lots of real-life examples. The two books I listed on the sideline are very applied. I've read through some very theoretical stochastic process books and they can be very..unaccessible. They usually start with measure theory, which is often explained very badly. And then it just gets worse from there.
It's amazing how big the difference between a good and bad math book can be. I read the monograph of Milstein, a renowned mathematician studying SDEs, and it covers the Ito-Taylor expansion, the Milstein method, and a lot of other topics. It blew my brain away. Then I picked up a book by Kloeden and Platen (listed on the left) and it explains the same topics and theory, but it is so well written that I understood it on the first pass. I think it helps if the author comes from a background of deterministic numerical methods and then has moved into stochastic ones. I think they more understand what connections exist between stochastic and deterministic numerical methods and are better able to translate those connections into a textbook for non-mathematicians.
Kloeden and Milstein recently published a paper on balanced implicit SDE numerical methods. There's also a duo named Burrage and Burrage (Australians) who have published quite a few papers on implicit or adaptive SDE numerical methods. It's an exciting new field.
Posted by: Howard at October 23, 2004 06:49 PMCould u please tell me the resources to learn " the success stories on synthetic Biology'?
please mail me.
Im a post graduate student in India.
Have fun !
bye
Posted by: Gangadhar at August 5, 2005 08:42 AM