Two years ago, when the Autodesk Molecule Viewer was still in it’s infancy, we dreamed at how incredible it would be when we can finally open up a web browser to see the entire machinery inside a cell, with billions of molecules at our fingertips. Proof here. Well, the future seems to be close. Ray Stevens and the Bridge Institute at USC launched a program that brings together scientists (computational biologists, structural biologists, pharmacologists), engineers, and cinematic artists in an effort to visualize an entire human cell. Leveraging the expertise of students and professions across these domains, they...

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by Daniela Quaglia, PhD Paul Jaschke is a newly appointed Assistant Professor at Macquarie University in synthetic biology. Before landing in Australia, Paul studied and worked for years in North America. His story? Well, it hits close to home for Autodesk Research. Autodesk has a program called Artists in Residence thanks to which they allow artists from around the world to come and work at their facilities with state of the art equipment to imagine, design, and make anything. Based on this program, Paul was accepted at Autodesk as the first Scientist in Residence where had the opportunity...

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by Charlotte Evans, MaRS Discovery District Last month, MaRS hosted an event with Eli Groban, a senior manager at Autodesk’s BioNano group. The focus of his discussion was cloud-based software for biological design. Eli has worked for a number of biotech companies, but he quickly realized that the tools he created were shielded by IP, meaning they weren’t shared outside of specific organizations. He wanted to evolve this system, so he started talking to Autodesk. In the past, Autodesk projects focused on the non-living world, for example the expansion of the Panama Canal. Large, complicated projects formed its...

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If you conduct a google image search for "plasmid map" 99% of the results will show a circular map. And that is also what I would expect - but why is that so? Throughout my scientific career I have been trained to expect the virtual expectation to match the nanoscale - plasmids are circular structures of DNA - so we depict them as such. But is that the best way? To me this seems inaccurate and inefficient to me in many ways by now. First, if I could actually look at my plasmid it would likely be coiled...

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On the BioNano team at Autodesk Research, running molecular analysis in the cloud is something we already enable scientists to do with ease.  Our Molecular Design Toolkit gives users access to this power in a web interface with a Python backend.  But what if we wanted to scrap the network lag and run some analysis directly in the browser? Molecular Design Toolkit calculating the orbitals of butene in an iPython notebook With the Web Assembly browser preview recently landing in V8, I got curious about what it would take to use it to run some of these computations....

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PhD's and undergraduates spend countless hours designing plasmids. Between debating about which cloning strategy to use, designing primers, and copy-pasting thousands of base pairs, you probably spend more time designing than physically assembling your construct. This is bearable if you only have a handful of designs - but it creates a huge bottleneck if you want to analyze hundreds or thousands of assemblies at a time, not to mention it’s highly error prone. Genetic Constructor and GSL are addressing this problem - together they are the dynamic duo for synthetic biology: elegant visualization paired with powerful design abstraction....

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