A programming language for biology

Antha is a high-level, open source language for specifying biological workflows.

Editor’s note: This is part of our investigation into synthetic biology and bioengineering. For more, download the new BioCoder Fall 2014 issue here.

OpenTronsOT_One

The OT.One liquid handling robot, photo courtesy of OpenTrons.

In a couple of recent posts, I’ve written about the need for a high-level programming language for biology. Now we have one. Antha is a high-level, open source language for specifying biological workflows (i.e., describing experiments). It’s available on Github.

A programming language for scientific experiments is important for many reasons. Most simply, a scientist in training spends many, many hours of time learning how to do lab work. That sounds impressive, but it really means moving very small amounts of liquid from one place to another. Thousands of times a day, thousands of days in preparation for a career. It’s boring, dull, and necessary work, and something that can be automated. Biologists should spend most of their time thinking about biology, designing experiments, and analyzing results — not handling liquids. Read more…

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Web by default

You're using the web even when you don't think you are.

InternetCities by Chris Harrison (ChrisHarrison.net), via Wikimedia Commons

With the rise of native apps and the Internet of Things (IoT), you might think we’re leaving the web behind.

We’re not. The web continues to be the easiest way for developers to connect people and computers. Whether you think you’re “on the web” or not, web tools power a huge chunk of communications and a vast number of interfaces. While HTML, CSS, and JavaScript are common, even in installable apps, even native apps and back-end systems use JSON, HTTP, and web services to communicate. IoT devices may not always use those protocols directly, but many of them have a web interface lurking somewhere.

Other languages and approaches absolutely have their place, especially in the many environments where constraints matter more than connection, but the web core is everywhere: in your phone, your apps, the kiosks you find in stores and museums. It lurks invisibly on corporate networks helping databases and messaging systems communicate.

That enormous set of web-related possibilities includes more than a set of technologies, though. Tools and techniques are great, but applying them yields a richer set of sometimes happy and sometimes controversial conversations.

I’ll be exploring a core set of nine key themes over the next few months, but I’ve started with brief explanations below. These short tellings set the stage for deeper explorations of the web’s potential for changing both computing and the broader world, as well as what you need to learn to join the fun.

Those pieces digging deeper will appear on this site, but you can also stay in the loop on our latest analysis and coverage through our weekly web platform newsletter.

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Designers can do anything

Jon Kolko on how empathy, theory, and tactical skills can put the next generation of designers on a path to success.

Design principles are being applied in all aspects of business today — they are no longer limited to graphic design, product design, web design, or even experience design. I recently spoke with Jon Kolko, vice president of consumer design at Blackboard, founder and director of Austin Center for Design, and author, about the skills designers need today and the curriculum formula to help them succeed.

In our conversation, Kolko talked about how a balance of process, empathy, theory, and tactical design skills can prepare designers for success in more traditional design roles and beyond. Kolko is a firm believer in an empathy-based, user-first approach to design. User-first is not unique, but Kolko advocates getting to know the user before even conceiving of the product:

“The switch to an empathy focus is actually really easy. You need to watch behavior, so that means actually watching people do things. We talk about watching people work, play, and live because sometimes the things they do are actually not that utility driven… So, depending on what your product is, you need to start to get to where people are actually doing things. It’s like a hair away from doing an interview, but that behavioral hair makes all the difference because when you conduct an interview, you get retrospective behavior anecdotes that tend to gloss over specifics; they make false estimates and generalizations, and they don’t have that rich nuance and outlier that you can start to build insights around. Those specific insights then go to drive your new product ideas.”

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Bitcoin’s road to democratization lies in decentralization

Conrad Barski on the bitcoin and blockchain landscape and how the technology will evolve over the next 10 years.

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Conrad Barski, a medical doctor, a cartoonist, programmer, and author of Land of Lisp, has been experimenting with bitcoin since 2011. In a recent interview, Barski talked about the bitcoin and blockchain landscape and noted the potential of decentralization:

“We’re heading into a world where things are becoming more decentralized. Most people already appreciate that because we all know about things like Airbnb and Uber. Of course, there’s kind of a paradox there because we think of Airbnb and Uber as being decentralized, but of course they’re these very centralized companies that run things…I think 10 years from now we’re going to see that these types of semi-decentralized companies are going to be replaced by fully decentralized companies, where the company itself just runs in an automated way on some kind of cryptocurrency. No one knows what cryptocurrency that will be, but there are folks from Ripple, from Counterparty, from Ethereum all trying to build an infrastructure that essentially let’s you run a company that isn’t controlled by any individual person. I think that’s really in the long term the most exciting part about bitcoin.”

What about bitcoin as a currency? In the short term, it’s an open question, said Barski, but he predicted an expansion similar to what we’ve seen with BitTorrent:

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Privacy is a concept, not a regime

In this O'Reilly Radar Podcast: Dr. Gilad Rosner talks about data privacy, and Alasdair Allan chats about the broken IoT.

In this podcast episode, I catch up with Dr. Gilad Rosner, a visiting researcher at the Horizon Digital Economy Research Institute in England. Rosner focuses on privacy, digital identity, and public policy, and is launching an Internet of Things Privacy Forum. We talk about personal data privacy in the age of the Internet of Things (IoT), privacy as a social characteristic, an emerging design ethos for technologists, and whether or not we actually own our personal data. Rosner characterizes personal data privacy as a social construct and addresses the notion that privacy is dead:

“Firstly, it’s important to recognize the idea that privacy is not a regime to control information. Privacy is a much larger concept than that. Regimes to control information are ways that we as a society preserve privacy, but privacy itself emerges from social needs and from individual human needs. The idea that privacy is dead comes from the vulnerability that people are feeling because they can see that it’s very difficult to maintain walls between their informational spheres, but that doesn’t mean that there aren’t countercurrents to that, and it doesn’t mean that there aren’t ways, as we go forward, to improve privacy preservation in the electronic spaces that we continue to move into.”

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As we move more and more into these electronic spaces and the Internet of Things becomes democratized, our notions of privacy are shifting on a cultural level beyond anything we’ve experienced as a society before. Read more…

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Bitcoin and blockchain use cases won’t be sexy, but will be essential

Tim Swanson on the blockchain's potential and what the future of crypto-coins might bring.

bitcoin_Antana_Flickr

Researcher and author Tim Swanson originally built bitcoin mining equipment in China a couple of years ago, but as he explained in a recent interview, he’s moved beyond the trading aspects of bitcoin and now focuses on research and use cases. Swanson, who also works in business development at Melotic, a digital asset exchange, expressed some skepticism about the future of bitcoin as a currency and noted that the greatest potential in the technology lies in the blockchain:

“I’m fairly skeptical that what [bitcoin] can and will do is probably either overstated or overhyped. I think most of the actual use cases, especially with blockchains in general, will be very mundane and will be related to proof of existence, so things like notary services.

“If anyone’s looking for a particular use case, I’d probably talk about one called CAT, Consolidated Audit Trail. It’s related to the SEC requiring traders to put together a way to find out when trades take place. On any given day, there’s about 48 billion trades that take place under their purview, and putting together a system for this, they want to make it centralized. Maybe you can use blockchains in some kind of decentralized fashion for this, but the idea — it’s not a very sexy, headline-getting use case — but it’s something that’s particularly needed to ensure their transparency within the trading aspect of these different financial instruments globally.”

Swanson will host a free webcast — The Continued Existence of Bitcoin, Altcoins, Appcoins, and Commodity Coins — on Tuesday, December 2, to talk about the various coins being created and the legal and technical challenges facing the developer community. Read more…

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