GenoCAD has Moved!


GenoCAD has not been supported by an active research grant since 2013. As a result, the Virginia Bioinformatics Institute no longer has the resources necessary to maintain this free service to the community. Last we week we redirected the address to a new server available at This new infrastructure will be more suitable to support the […]

Stochastic modeling of the cell cycle goes on…

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A couple of weeks ago, we received the renewal of the NIH grant funding our collaboration with John Tyson to develop stochastic models of the regulatory network controlling the cell cycle in yeast. This is the third funding cycle of this project that started in 2006. This renewal did not as smoothly as we had […]

Funding of Open Source Software


This is a video shot in 2013 during the Bioinformatics Open Source Conference (BOSC). This round table was focused on strategies to fund the development and maintenance of open source software. The sound is not that great and the video quality marginal. I hope you still find that the four different perspectives on this hot […]

Database of biological parts

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Nucleic Acids Research just published a paper describing the results of our efforts to analyze the annotations of thousands of plasmids commonly used across many life science specialties. This effort allowed us to release a database of genetic parts and sequence features that will be useful in better annotating existing plasmids and develop new expression […]

Gen9 Launches Ordering Portal

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The gene synthesis company Gen9 recently announced a new online ordering portal powered by Benchling, a provider of cloud-based bioinformatics tools.  This is welcome news as the ordering of synthetic DNA has been a source of frustration for a long time. Clunky ordering systems create friction, opportunities for errors, and lack of transparency in pricing. […]

Twist Launches Alpha Program


TwistBiosciences reached a major milestone in its development. Emily LeProust, the company CEO,  announced the launch of the Alpha Access program at SynBioBeta in London. This program will allow select partners to get a taste of Twist new DNA manufacturing capability. Twist will accept applications to synthesize DNA fragments up to 1.8kb in length that […]

I Hate Science (not really)

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“People who have dedicated their lives to science.  People who made a decision when they were about 16 years old to focus on science, who went through four years of undergrad and an average 6 years of graduate school, and 4-10 more years of training.  People who’ve spent every moment since 2000 entirely dedicated to […]

DOIs for my Blogs

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The Winnower is a new service that academic bloggers have been waiting for. It is a platform that allow blogs to benefits from many of the services typically provided by regular journals. Academic bloggers can submit their posts for publication on the platform. The process is extremely simple. The software is even capable of retrieving […]

Why design DNA?

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I published a blog post entitled “Cloning forever” in which I show how biologists struggle with the notion of design applied to recombinant DNA. I hypothesize that most molecular biologists are still very focused on deriving new plasmids from existing ones using standard cloning techniques. Using a specific example, I explain the potential benefits of […]

Cloning forever


No design needed! Over the last six months, I spent considerable time and efforts trying to engage biologists in discussions about the design of expression vectors. My goal has been to better understand the design rules applicable in different domains and so that we can formalize them in GenoCAD. This effort has been an eye […]