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Democratizing biotech research

The O'Reilly Radar Podcast: DJ Kleinbaum on lab automation, virtual lab services, and tackling the challenges of reproducibility.

The convergence of software and hardware, and the growing ubiquitousness of the Internet of Things is affecting industry across the board, and biotech labs are no exception. For this Radar Podcast episode, I chatted with DJ Kleinbaum, co-founder of Emerald Therapeutics, about lab automation, the launch of Emerald Cloud Laboratory, and the problem of reproducibility.

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Kleinbaum and his co-founder Brian Frezza started Emerald Therapeutics to research cures for persistent viral infections. They didn’t set out to spin up a second company, but their efforts to automate their own lab processes proved so fruitful, they decided to launch a virtual lab-as-a-service business, Emerald Cloud Laboratory. Kleinbaum explained:

“When Brian and I started the company right out of graduate school, we had this platform anti-viral technology, which the company is still working on, but because we were two freshly minted nobody Ph.D.s, we were not going to be able to raise the traditional $20 or $30 million that platform plays raise in the biotech space.

“We knew that we had to be much more efficient with the money we were able to raise. Brian and I both have backgrounds in computer science. So, from the beginning, we were trying to automate every experiment that our scientists ran, such that every experiment was just push a button, walk away. It was all done with process automation and robotics. That way, our scientists would be able to be much more efficient than your average bench chemist or biologist at a biotech company.

“After building that system internally for three years, we looked at it and realized that every aspect of a life sciences laboratory had been encapsulated in both hardware and software, and that that was too valuable a tool to just keep internally at Emerald for our own research efforts. Around this time last year, we decided that we wanted to offer that as a service, that other scientists, companies, and researchers could use to run their experiments as well.” Read more…

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A bigger and different way of looking at the IoT

Tim O’Reilly’s Solid Conference keynote highlights the capabilities that will let us shape the physical world.

Tim O’Reilly has recently focused on the connection between humans and the Internet of Things (IoT). It’s a topic he’s written about and talked about, and it’s also at the heart of our explorations into interaction design and connected devices and experience design and the Internet of Things.

O’Reilly’s keynote address at the Solid Conference in 2014 explored the human-IoT link. The talk expanded the scope of the IoT, making it clear this isn’t just about individual devices and software — we’re creating “networks of intelligence” that will shape how people work and live.

The talk has become an essential resource for us as we’ve investigated the blurring of the physical and virtual worlds. That’s why we decided to put together a text-friendly version of the presentation that’s easy to scan and reference. And since we think it’s so useful, we’ve made the text version publicly available.

You can download your free copy of “Software Above the Level of a Single Device: The Implications” here. Read more…

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Network structure and dynamics in online social systems

Understanding information cascades, viral content, and significant relationships.

weave_911_Joel_Ormsby_Flickr

I rarely work with social network data, but I’m familiar with the standard problems confronting data scientists who work in this area. These include questions pertaining to network structure, viral content, and the dynamics of information cascades.

At last year’s Strata + Hadoop World NYC, Cornell Professor and Nevanlinna Prize Winner Jon Kleinberg walked the audience through a series of examples from social network analysis, looking at the content of shared photos and text, as well as the structures of the networks. It was a truly memorable presentation from one of the foremost experts in network analysis. Each of the problems he discussed would be of interest to marketing professionals, and the analytic techniques he described were accessible to many data scientists. What struck me is that while these topics are easy to describe, framing the right question requires quite a bit of experience with the underlying data.

Predicting whether an information cascade will double in size

Can you predict if a piece of information (say a photo) will be shared only a few times or hundreds (if not thousands) of times? Large cascades are very rare, making the task of predicting eventual size difficult. You either default to a pathological answer (after all most pieces of information are shared only once), or you create a balanced data set (comprised of an equal number of small and large cascades) and end up solving an artificial task.

Thinking of a social network as an information transport layer, Kleinberg and his colleagues instead set out to track the evolution of cascades. In the process, they framed an interesting balanced algorithmic prediction problem: given a cascade of size k, predict whether it will reach size 2k (it turns out 2k is roughly the median size of a cascade conditional on whether it reaches size k). Read more…

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Four short links: 5 February 2015

Four short links: 5 February 2015

Mobile Supply Chain, Regulating the Interwebs, Meh MOOCs, and Security School

  1. The Home and the Mobile Supply Chain (Benedict Evans) — the small hardware start-up, and the cool new gizmos from drones to wearables, are possible because of the low price of components built at the scale required for Apple and other mobile device makers. (via Matt Webb)
  2. FCC Chairman Wheeler Proposes New Rules for Protecting the Open Internet (PDF) — America may yet have freedom. No blocking, no throttling, no paid prioritisation.
  3. The Future of College (Bill Gates) — The MOOC, by itself, doesn’t really change things, except for the very most motivated student. HALLELUJAH!
  4. Breaker 101 — 12-week online security course. $1,750 (cue eyes water). Putting the hacker back in hacker schools …
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There is room for global thinking in IoT data privacy matters

The best of European and American data privacy initiatives can come together for the betterment of all.

Editor’s note: This is part of a series of posts exploring privacy and security issues in the Internet of Things. The series will culminate in a free webcast by the series author Dr. Gilad Rosner: Privacy and Security Issues in the Internet of Things will happen on February 11, 2015 — reserve your spot today.

Please_Josh_Hallett_FlickrAs devices become more intelligent and networked, the makers and vendors of those devices gain access to greater amounts of personal data. In the extreme case of the washing machine, the kind of data — who uses cold versus warm water — is of little importance. But when the device collects biophysical information, location data, movement patterns, and other sensitive information, data collectors have both greater risk and responsibility in safeguarding it. The advantages of every company becoming a software company — enhanced customer analytics, streamlined processes, improved view of resources and impact — will be accompanied by new privacy challenges.

A key question emerges from the increasing intelligence of and monitoring by devices: will the commercial practices that evolved in the web be transferred to the Internet of Things? The amount of control users have over data about them is limited. The ubiquitous end-user license agreement tells people what will and won’t happen to their data, but there is little choice. In most situations, you can either consent to have your data used or you can take a hike. We do not get to pick and choose how our data is used, except in some blunt cases where you can opt out of certain activities (which is often a condition forced by regulators). If you don’t like how your data will be used, you can simply elect not to use the service. But what of the emerging world of ubiquitous sensors and physical devices? Will such a take-it-or-leave it attitude prevail? Read more…

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Power of the platforms

Uncertainty is a feature, not a bug.

Image: CC BY 2.0 NASA's Earth Observatory via Wikimedia Commons  http://commons.wikimedia.org/wiki/File:Southern_Lights.jpg#mediaviewer/File:Southern_Lights.jpg

After decades of work on programming, we finally got a development environment with massive reach and tremendous power. Somehow, though, the web isn’t centered on a comprehensive programming environment. The web succeeded with a (severely) lowest-common denominator, specification-driven approach that let it grow with time, technology, and multiple communities, across multiple platforms.

Almost two decades ago, I was all excited about Java. Write applets once, run anywhere, with libraries to make sure it all came out the same wherever anywhere might be. Java is still a powerhouse, but it all worked out differently than I expected. Even in Java’s early years, before the Java news was filled with security bulletins, applets felt like a strange mix with their surrounding web pages. Creating an applet demanded programmers to build every detail. Even with Java’s ever-improving libraries, creating a Java applet that did much was an intense experience focused on programming.

Java wasn’t the only comprehensive way to build web apps, of course. Flash demanded programming, but its values always incorporated design, action, and well, flash, in ways that meshed well with the way people built sites. Flash kept growing and growing before its ecosystem took a fatal hit from the iPhone as HTML5 offered replacements for some of its key strengths. I mostly notice Flash these days because it asks me to update it regularly and because pages tell me when it’s crashed.

Compared to either of those rich environments, web technology is a tangled mess. The early web was functional but unstyled, with no behavior beyond navigating among pages. That? That would dominate client-side computing? Read more…

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