VISIBLE NEWS : Software modeling of cells in the Covert Lab

July 19, 2012

Stanford researchers produce first complete computer model of an organism

A mammoth effort has produced a complete computational model of the bacterium Mycoplasma genitalium, opening the door for biological computer-aided design.




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The simulation of the complete life cycle of the pathogen was described in the journal Cell, you can find the article here.

Occasional Hotspot : Abbas El Gamal and Advanced Mesh Networking

I have admired the work of Abbas El Gamal, the Hitachi American Professor in the School of Engineering at Stanford University, since he co-founded Pixim a decade ago to commercialize the technology developed under the programmable digital camera program.  I wondered what was new in his lab? 

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Looking at the widget, the Digital Camera Project has spun many of derivatives over time.  Dr El Gamal has been Director of the Information Systems Laboratory from 2004 to 2009.  Dr El Gamal's latest collaboration is with the DARPA/ITMANET : FLoWS (Fundamental Limits of Wireless Systems) project with Andrea Goldsmith, head-PI.  This 5 year multi-campus project is  developing a more powerful information theory for mobile wireless networks, one can imagine a wide variety of applications.

Optical sensors combined with mobile ad-hoc networked platforms and advanced algorithms seems compelling.  But then again so is the collaboration with Mark Schnitzer on Optical Imaging for Neuroscience.

We've updated the Visible Legacy Overview Presentation, please have a look.

We've made several improvements to the Visible Legacy widget, please check out the demo.  These updates will appear automatically in embedded widgets.

• Improved navigation
• Modified filters
• Improved clustering

We have been working away on implementation and have been a bit quiet on the blog.  We have just posted an updated website at www.visiblelegacy.com, which has an interactive demo and a look at the updated interfaces.

The new site has a registration mechanism, behind which you will find more information about our invited alpha offerings.

Tracing innovation : Agilent to Solazyme

I've posted on YouTube a video screen capture of my experiments using Visible Legacy to explore the collaboration between Agilent Technologies and Stanford University's professor Fritz Prinz.  This interesting activity is a research program designed to explore a new class of nanoscale devices using a combination of the scanning probe microscope and atomic layer deposition.  Interestingly, I also found papers from within Professor Prinz's lab describing the search for electrical current stemming from plants, and that a couple of co-authors are part of an emerging firm in San Francisco named Solazyme that is developing fuels from algae.  Solazyme's strategic advisory board includes Donald Kennedy, Bing Professor of Environmental Science and President Emeritus of Stanford, and former Commissioner of the Food and Drug Administration.  I believe there are several hotspots of innovation to be found in Professor Prinz's lab!

posted by Will Snow

Mapping an illustrious career : the Roger Summit collection

Visible Legacy can be used as a way to navigate through the career of an illustrious luminary as a case study for teaching and learning.  This short informal screencast walks through the profile for Roger K Summit, pioneer in the information retrieval industry.  It shows in particular how his published and unpublished papers can be viewed in the context of projects and collaborators.

posted by Will Snow