Sriram Kosuri/blog

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Hello all, This is the beginnings of my blog on OWW... We'll see how it goes. Already we need better software :-) --Sri Kosuri (talk) 01:32, 5 March 2007 (EST)

Human Genome Editing

How would you genetically improve humans? The Scientist asks several academics how we could make our lives longer and more healthy by editing our genomes. See the article here.

--Sri Kosuri (talk) 18:54, 5 March 2007 (EST)


Austin Che was kind enough to implement OpenID on OpenWetWare so we can interface with some of our other wiki projects. It's pretty slick, and now we can authenticate OpenWetWare users for other wiki projects. It's quite sad their there is no science resource for managing identity, and linking that to OpenID. In general,, run by a company called JanRain, seems to be the company that is getting the most traction of being an OpenID central repository. I don't know if it makes sense for OWW to interface with them until they get some major backers. For now, it's just frustrating to wait for something that obviously makes sense to appear.

--Sri Kosuri (talk) 01:32, 5 March 2007 (EST)

E. coli Wiki

Jim Hu at Texas A&M is involved with the E. coli reannotation efforts and is leading up the wiki parts.

The wiki is still exerimental, but it's pretty cool. For example, check out everyone's favorite gene, lacI.

--Sri Kosuri (talk) 01:32, 5 March 2007 (EST)

As a follow-up... check out ... Same idea, different approach

Protein Fabrication automation

A new paper from the Hellinga lab on robust automated construction of ORFs. They combine using ION PCR (inside out PCR, where middle primers are at higher concentrations than later primers) to construct ~500 bp fragments, and then stitch those together using SOE (splice overlap extension) PCR. Finally, they fuse them to the coding domain of tetracycline resistance gene to select against single base deletions. They find 28% of clones to be correct without selection, and 82% with selection.

There is a lot of detailed work here, and would probably be informative to anyone doing automized synthesis using liquid handling robots.

  1. Cox JC, Lape J, Sayed MA, and Hellinga HW. Protein fabrication automation. Protein Sci. 2007 Mar;16(3):379-90. DOI:10.1110/ps.062591607 | PubMed ID:17242375 | HubMed [hellinga]

--Sri Kosuri (talk) 01:32, 5 March 2007 (EST)

The New Science of Sharing

An article on from BusinessWeek... there is a favorable mention of OpenWetWare somewhere on the second page:

As large-scale scientific collaborations become the norm, scientists will rely increasingly on distributed methods of collecting data, verifying discoveries, and testing hypotheses not only to speed things up but to improve the veracity of scientific knowledge itself. For example, rapid, iterative, and open-access publishing will engage a much greater proportion of the scientific community in the peer-review process. Conventional paper-based scientific journals, meanwhile, will be augmented by dynamic publishing tools such as blogs, wikis, Web-enabled RSS feeds, and podcasts that turn scientific publications into living documents. Projects such as MIT's OpenWetWare are already doing this.

Apparently, we are again an "MIT" project... Apologies to those of you who are not.

--Sri Kosuri (talk) 01:32, 5 March 2007 (EST)