Mostrando entradas con la etiqueta Open Source. Mostrar todas las entradas
Mostrando entradas con la etiqueta Open Source. Mostrar todas las entradas

martes, 27 de septiembre de 2016

Yes, you really can make your own EpiPen for $30

Greg Friese/Flickr. 
Thank you, biohackers.

In the latest example of corporate greed in the pharmaceutical world, the US state of West Virginia announced today that it's investigating the makers of the EpiPen for Medicaid fraud - which means they think it's defrauded the US government healthcare system.

More specifically, it's accusing manufacturers Mylan of inflating the price of EpiPens by almost 500 percent since they purchased the life-saving device back in 2007

Since then, the cost of a single EpiPen has gone from around US$57 to $318 - a 461 percent increase. Which is pretty frustrating when you consider that many people with allergies need to keep the medication on them at all times in case of going into life-threatening anaphylaxis. Anaphylaxis can be triggered by anything from a bee sting to eating trace amounts of peanut.

In the face of the public backlash over their price rises, at the end of last month, Mylan announced they'd be releasing a generic version of the EpiPen that would cost only $150 per injection.

But industry insiders were quick to criticise this apparent act of goodwill, with pharmaceutical experts telling NBC News earlier this month that they estimated an EpiPen would only cost around $30 to make.

Now a bio-hacking collective called Four Thieves Vinegar has tested that claim out for themselves, and shown you really can engineer your own DIY EpiPen - which they called the "EpiPencil" - for around $35. And they claim it works as well as the $300 version - although we definitely don't recommend you try it at home.

The main difference between their version and the one you can buy at the pharmacy is that you have to measure out the correct dose of epinephrine before using the DIY version.

"We've gotten many requests to do something about the EpiPen, so we have,"says Michael Laufer, one of the founders of Four Thieves Vinegar, who has a PhD in mathematics from the City University of New York.

"We developed the EpiPencil, which is an epinephrine auto-injector built entirely from off-the-shelf parts, which can be assembled in a matter of minutes for just over $30."

EpiPens are designed as 'last resort' devices that are filled with epinephrine, an adrenaline drug that's more than 100 years old. The drug itself isn't patented, but what makes the EpiPen so attractive is the fact that its design lets pretty much anyone use it - which is handy in emergency situations.

So why haven't many other companies stepped up as competition and made an EpiPen equivalent to rival Mylan's? As Jamie Condliffe explains for MIT Technology Review, a big issue is the patent problem.

Mylan has the patent on the auto-injecting device up until 2025, and while it would be possible to build another type of model that does the same thing, it makes things a lot tricker.

"[There's] fear of creating a device that doesn’t work reliably, and a regulatory process that makes getting products to market incredibly difficult," writes Condliffe.

Four Thieves Vinegar has now published a video and fully downloadable instructions on how to make your own DIY EpiPencil at home. 

To be clear, we're definitely not recommending you go out and make your own EpiPen. The Four Thieves Vinegar version is not only totally unregulated, but it also hasn't been shown to reliably work for everyone - something that would require years of clinical trials and peer-reviewed papers.

"It's essential to remember that epinephrine auto-injectors are life-saving products, and it is critical that they are made to a high standard of quality so patients can rely on them to work safely and effectively," said US Food and Drug Administration spokesperson, Theresa Eisenman. 

But as an experiment to show that the EpiPen really can be created for around $30 - and with non-bulk parts at that - the Four Thieves Vinegar DIY version definitely makes its point. And hopefully it reminds people that they shouldn't have to pay ridiculous amounts for life-saving medicine.

"You know there are people who are just not buying an EpiPen because they can’t afford it," Laufer told The Parallax. "That’s unconscionable."


With West Virginia's new investigation and the public still pretty pissed off about the cost of EpiPens, it'll be interesting to see what happens next. Your move, Mylan.


Four Thieves Vinegar Biohacking Collective's Mantra: "Free Medicine for Everyone"



People are disenfranchised from access to medicine for various reasons. To circumvent these, we have developed a way for individuals to manufacture their own medications. We have designed an open-source automated lab reactor, which can be built with off-the-shelf parts, and can be set to synthesize different medications. This will save hundreds of thousands of lives.

The main reasons for people being disenfranchised from medicines are: price, legality, and lack of infrastructure. Medicines like Solvadi which costs $80,000 for a course of treatment, is beyond the reach of most people. Mifepristone and Misoprostal are unavailable in many places where abortion is illegal. Antiretroviral HIV treatments even when provided free, have no way of getting to remote locations in 3rd world countries.

The design will be published online, along with synthesis programs. The system will also have a forum system for users to communicate and contribute to the development of the system. With time, the system will become self-sustaining, much like other open source movements.

Original: Science Alert
FIONA MACDONALD
21 SEP 2016
Original: Four Thieves Vinegar.org

jueves, 26 de mayo de 2016

Inside OpenAI, Elon Musk's Wild Plan to Set Artificial Intelligence Free

 MICHAL CZERWONKA/REDUX
THE FRIDAY AFTERNOON news dump, a grand tradition observed by politicians and capitalists alike, is usually supposed to hide bad news. So it was a little weird that Elon Musk, founder of electric car maker Tesla, and Sam Altman, president of famed tech incubator Y Combinator, unveiled their new artificial intelligence company at the tail end of a weeklong AI conference in Montreal this past December.

But there was a reason they revealed OpenAI at that late hour. It wasn’t that no one was looking. It was that everyone was looking. When some of Silicon Valley’s most powerful companies caught wind of the project, they began offering tremendous amounts of money to OpenAI’s freshly assembled cadre of artificial intelligence researchers, intent on keeping these big thinkers for themselves. The last-minute offers—some made at the conference itself—were large enough to force Musk and Altman to delay the announcement of the new startup. “The amount of money was borderline crazy,” says Wojciech Zaremba, a researcher who was joining OpenAI after internships at both Google and Facebook and was among those who received big offers at the eleventh hour.
How many dollars is “borderline crazy”? 
Two years ago, as the market for the latest machine learning technology really started to heat up, Microsoft Research vice president Peter Lee said that the cost of a top AI researcher had eclipsed the cost of a top quarterback prospect in the National Football League—and he meant under regular circumstances, not when two of the most famous entrepreneurs in Silicon Valley were trying to poach your top talent. Zaremba says that as OpenAI was coming together, he was offered two or three times his market value.

OpenAI didn’t match those offers. But it offered something else: the chance to explore research aimed solely at the future instead of products and quarterly earnings, and to eventually share most—if not all—of this research with anyone who wants it. That’s right: Musk, Altman, and company aim to give away what may become the 21st century’s most transformative technology—and give it away for free.

Ilya Sutskever.
CHRISTIE HEMM KLOK/WIRED
Zaremba says those borderline crazy offers actually turned him off—despite his enormous respect for companies like Google and Facebook. He felt like the money was at least as much of an effort to prevent the creation of OpenAI as a play to win his services, and it pushed him even further towards the startup’s magnanimous mission. “I realized,” Zaremba says, “that OpenAI was the best place to be.”

That’s the irony at the heart of this story: even as the world’s biggest tech companies try to hold onto their researchers with the same fierceness that NFL teams try to hold onto their star quarterbacks, the researchers themselves just want to share. In the rarefied world of AI research, the brightest minds aren’t driven by—or at least not only by—the next product cycle or profit margin. They want to make AI better, and making AI better doesn’t happen when you keep your latest findings to yourself.

OpenAI is a billion-dollar effort to push AI as far as it will go.

This morning, OpenAI will release its first batch of AI software, a toolkit for building artificially intelligent systems by way of a technology called reinforcement learning—one of the key technologies that, among other things, drove the creation of AlphaGo, the Google AI that shocked the world by mastering the ancient game of Go. With this toolkit, you can build systems that simulate a new breed of robot, play Atari games, and, yes, master the game of Go.

But game-playing is just the beginning. OpenAI is a billion-dollar effort to push AI as far as it will go. In both how the company came together and what it plans to do, you can see the next great wave of innovation forming. We’re a long way from knowing whether OpenAI itself becomes the main agent for that change. But the forces that drove the creation of this rather unusual startup show that the new breed of AI will not only remake technology, but remake the way we build technology.

AI Everywhere
Silicon Valley is not exactly averse to hyperbole. It’s always wise to meet bold-sounding claims with skepticism. But in the field of AI, the change is real. Inside places like Google and Facebook, a technology called deep learning is already helping Internet services identify faces in photos, recognize commands spoken into smartphones, and respond to Internet search queries. And this same technology can drive so many other tasks of the future. It can help machines understand natural language—the natural way that we humans talk and write. It can create a new breed of robot, giving automatons the power to not only perform tasks but learn them on the fly. And some believe it can eventually give machines something close to common sense—the ability to truly think like a human.

But along with such promise comes deep anxiety. Musk and Altman worry that if people can build AI that can do great things, then they can build AI that can do awful things, too. They’re not alone in their fear of robot overlords, but perhaps counterintuitively, Musk and Altman also think that the best way to battle malicious AI is not to restrict access to artificial intelligence but expand it. That’s part of what has attracted a team of young, hyper-intelligent idealists to their new project.

OpenAI began one evening last summer in a private room at Silicon Valley’s Rosewood Hotel—an upscale, urban, ranch-style hotel that sits, literally, at the center of the venture capital world along Sand Hill Road in Menlo Park, California. Elon Musk was having dinner with Ilya Sutskever, who was then working on the Google Brain, the company’s sweeping effort to build deep neural networks—artificially intelligent systems that can learn to perform tasks by analyzing massive amounts of digital data, including everything from recognizing photos to writing email messages to, well, carrying on a conversation. Sutskever was one of the top thinkers on the project. But even bigger ideas were in play.

Sam Altman, whose Y Combinator helped bootstrap companies like Airbnb, Dropbox, and Coinbase, had brokered the meeting, bringing together several AI researchers and a young but experienced company builder named Greg Brockman, previously the chief technology officer at high-profile Silicon Valley digital payments startup called Stripe, another Y Combinator company. It was an eclectic group. But they all shared a goal: to create a new kind of AI lab, one that would operate outside the control not only of Google, but of anyone else. “The best thing that I could imagine doing,” Brockman says, “was moving humanity closer to building real AI in a safe way.”

Musk is one of the loudest voices warning that we humans could one day lose control of systems powerful enough to learn on their own.

Musk was there because he’s an old friend of Altman’s—and because AI is crucial to the future of his various businesses and, well, the future as a whole. Tesla needs AI for its inevitable self-driving cars. SpaceX, Musk’s other company, will need it to put people in space and keep them alive once they’re there. But Musk is also one of the loudest voices warning that we humans could one day lose control of systems powerful enough to learn on their own.

The trouble was: so many of the people most qualified to solve all those problems were already working for Google (and Facebook and Microsoft and Baidu and Twitter). And no one at the dinner was quite sure that these thinkers could be lured to a new startup, even if Musk and Altman were behind it. But one key player was at least open to the idea of jumping ship. “I felt there were risks involved,” Sutskever says. “But I also felt it would be a very interesting thing to try.”

Breaking the Cycle
Emboldened by the conversation with Musk, Altman, and others at the Rosewood, Brockman soon resolved to build the lab they all envisioned. Taking on the project full-time, he approached Yoshua Bengio, a computer scientist at the University of Montreal and one of founding fathers of the deep learning movement. The field’s other two pioneers—Geoff Hinton and Yann LeCun—are now at Google and Facebook, respectively, but Bengio is committed to life in the world of academia, largely outside the aims of industry. He drew up a list of the best researchers in the field, and over the next several weeks, Brockman reached out to as many on the list as he could, along with several others.

Greg Brockman,
one of OpenAI’s founding fathers and
its chief technology officer.
CHRISTIE HEMM KLOK/WIRED
Many of these researchers liked the idea, but they were also wary of making the leap. In an effort to break the cycle, Brockman picked the ten researchers he wanted the most and invited them to spend a Saturday getting wined, dined, and cajoled at a winery in Napa Valley. For Brockman, even the drive into Napa served as a catalyst for the project. “An underrated way to bring people together are these times where there is no way to speed up getting to where you’re going,” he says. “You have to get there, and you have to talk.” And once they reached the wine country, that vibe remained. “It was one of those days where you could tell the chemistry was there,” Brockman says. Or as Sutskever puts it: “the wine was secondary to the talk.”

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By the end of the day, Brockman asked all ten researchers to join the lab, and he gave them three weeks to think about it. By the deadline, nine of them were in. And they stayed in, despite those big offers from the giants of Silicon Valley. “They did make it very compelling for me to stay, so it wasn’t an easy decision,” Sutskever says of Google, his former employer. “But in the end, I decided to go with OpenAI, partly of because of the very strong group of people and, to a very large extent, because of its mission.”

The deep learning movement began with academics. It’s only recently that companies like Google and Facebook and Microsoft have pushed into the field, as advances in raw computing power have made deep neural networks a reality, not just a theoretical possibility. People like Hinton and LeCun left academia for Google and Facebook because of the enormous resources inside these companies. But they remain intent on collaborating with other thinkers. Indeed, as LeCun explains, deep learning research requires this free flow of ideas. “When you do research in secret,” he says, “you fall behind.”

As a result, big companies now share a lot of their AI research. That’s a real change, especially for Google, which has long kept the tech at the heart of its online empiresecret. Recently, Google open sourced the software engine that drives its neural networks. But it still retains the inside track in the race to the future. Brockman, Altman, and Musk aim to push the notion of openness further still, saying they don’t want one or two large corporations controlling the future of artificial intelligence.
The Limits of Openness

All of which sounds great. But for all of OpenAI’s idealism, the researchers may find themselves facing some of the same compromises they had to make at their old jobs. Openness has its limits. And the long-term vision for AI isn’t the only interest in play. OpenAI is not a charity. Musk’s companies that could benefit greatly the startup’s work, and so could many of the companies backed by Altman’s Y Combinator. “There are certainly some competing objectives,” LeCun says. “It’s a non-profit, but then there is a very close link with Y Combinator. And people are paid as if they are working in the industry.”

According to Brockman, the lab doesn’t pay the same astronomical salaries that AI researchers are now getting at places like Google and Facebook. But he says the lab does want to “pay them well,” and it’s offering to compensate researchers with stock options, first in Y Combinator and perhaps later in SpaceX (which, unlike Tesla, is still a private company).

Brockman insists that OpenAI won't give special treatment to its sister companies.
Nonetheless, Brockman insists that OpenAI won’t give special treatment to its sister companies. OpenAI is a research outfit, he says, not a consulting firm. But when pressed, he acknowledges that OpenAI’s idealistic vision has its limits. The company may not open source everything it produces, though it will aim to share most of its research eventually, either through research papers or Internet services. “Doing all your research in the open is not necessarily the best way to go. You want to nurture an idea, see where it goes, and then publish it,” Brockman says. “We will produce lot of open source code. But we will also have a lot of stuff that we are not quite ready to release.”

Both Sutskever and Brockman also add that OpenAI could go so far as to patent some of its work. “We won’t patent anything in the near term,” Brockman says. “But we’re open to changing tactics in the long term, if we find it’s the best thing for the world.” For instance, he says, OpenAI could engage in pre-emptive patenting, a tactic that seeks to prevent others from securing patents.

But to some, patents suggest a profit motive—or at least a weaker commitment to open source than OpenAI’s founders have espoused. “That’s what the patent system is about,” says Oren Etzioni, head of the Allen Institute for Artificial Intelligence. “This makes me wonder where they’re really going.”

The Super-Intelligence Problem
When Musk and Altman unveiled OpenAI, they also painted the project as a way to neutralize the threat of a malicious artificial super-intelligence. Of course, that super-intelligence could arise out of the tech OpenAI creates, but they insist that any threat would be mitigated because the technology would be usable by everyone. “We think its far more likely that many, many AIs will work to stop the occasional bad actors,” Altman says.

But not everyone in the field buys this. Nick Bostrom, the Oxford philosopher who, like Musk, has warned against the dangers of AI, points out that if you share research without restriction, bad actors could grab it before anyone has ensured that it’s safe. “If you have a button that could do bad things to the world,” Bostrom says, “you don’t want to give it to everyone.” If, on the other hand, OpenAI decides to hold back research to keep it from the bad guys, Bostrom wonders how it’s different from a Google or a Facebook.

If you share research without restriction, bad actors could grab it before anyone has ensured that it's safe.

He does say that the not-for-profit status of OpenAI could change things—though not necessarily. The real power of the project, he says, is that it can indeed provide a check for the likes of Google and Facebook. “It can reduce the probability that super-intelligence would be monopolized,” he says. “It can remove one possible reason why some entity or group would have radically better AI than everyone else.”

But as the philosopher explains in a new paper, the primary effect of an outfit like OpenAI—an outfit intent on freely sharing its work—is that it accelerates the progress of artificial intelligence, at least in the short term. And it may speed progress in the long term as well, provided that it, for altruistic reasons, “opts for a higher level of openness than would be commercially optimal.”

“It might still be plausible that a philanthropically motivated R&D funder would speed progress more by pursuing open science,” he says.

Like Xerox PARC
In early January, Brockman’s nine AI researchers met up at his apartment in San Francisco’s Mission District. The project was so new that they didn’t even have white boards. (Can you imagine?) They bought a few that day and got down to work.

Brockman says OpenAI will begin by exploring reinforcement learning, a way for machines to learn tasks by repeating them over and over again and tracking which methods produce the best results. But the other primary goal is what’s called unsupervised learning—creating machines that can truly learn on their own, without a human hand to guide them. Today, deep learning is driven by carefully labeled data. If you want to teach a neural network to recognize cat photos, you must feed it a certain number of examples—and these examples must be labeled as cat photos. The learning is supervised by human labelers. But like many others researchers, OpenAI aims to create neural nets that can learn without carefully labeled data.

“If you have really good unsupervised learning, machines would be able to learn from all this knowledge on the Internet—just like humans learn by looking around—or reading books,” Brockman says.

He envisions OpenAI as the modern incarnation of Xerox PARC, the tech research lab that thrived in the 1970s. Just as PARC’s largely open and unfettered research gave rise to everything from the graphical user interface to the laser printer to object-oriented programing, Brockman and crew seek to delve even deeper into what we once considered science fiction. PARC was owned by, yes, Xerox, but it fed so many other companies, most notably Apple, because people like Steve Jobs were privy to its research. At OpenAI, Brockman wants to make everyone privy to its research.

This month, hoping to push this dynamic as far as it will go, Brockman and company snagged several other notable researchers, including Ian Goodfellow, another former senior researcher on the Google Brain team. “The thing that was really special about PARC is that they got a bunch of smart people together and let them go where they want,” Brockman says. “You want a shared vision, without central control.”

Giving up control is the essence of the open source ideal. If enough people apply themselves to a collective goal, the end result will trounce anything you concoct in secret. But if AI becomes as powerful as promised, the equation changes. We’ll have to ensure that new AIs adhere to the same egalitarian ideals that led to their creation in the first place. Musk, Altman, and Brockman are placing their faith in the wisdom of the crowd. But if they’re right, one day that crowd won’t be entirely human.

ORIGINAL: Wired
CADE METZ BUSINESS 
04.27.16 

miércoles, 9 de diciembre de 2015

Here’s What Developers Are Doing with Google’s AI Brain

Researchers outside Google are testing the software that the company uses to add artificial intelligence to many of its products.

WHY IT MATTERS
Tech companies are racing to set the standard for machine learning, and to attract technical talent.
Jeff Dean speaks at a Google event in 2007. Credit: Photo by Niall Kennedy / CC BY-NC 2.0
An artificial intelligence engine that Google uses in many of its products, and that it made freely available last month, is now being used by others to perform some neat tricks, including 
  • translating English into Chinese, 
  • reading handwritten text, and 
  • even generating original artwork.
The AI software, called Tensor Flow, provides a straightforward way for users to train computers to perform tasks by feeding them large amounts of data. The software incorporates various methods for efficiently building and training simulated “deep learning” neural networks across different computer hardware.

Deep learning is an extremely effective technique for training computers to recognize patterns in images or audio, enabling machines to perform with human-like competence useful tasks such as recognizing faces or objects in images. Recently, deep learning also has shown significant promise for parsing natural language, by enabling machines to respond to spoken or written queries in meaningful ways.

Speaking at the Neural Information Processing Society (NIPS) conference in Montreal this week, Jeff Dean, the computer scientist at Google who leads the Tensor Flow effort, said that the software is being used for a growing number of experimental projects outside the company.

These include software that generates captions for images and code that translates the documentation for Tensor Flow into Chinese. Another project uses Tensor Flow to generate artificial artwork. “It’s still pretty early,” Dean said after the talk. “People are trying to understand what it’s best at.”

Tensor Flow grew out of a project at Google, called Google Brain, aimed at applying various kinds of neural network machine learning to products and services across the company. The reach of Google Brain has grown dramatically in recent years. Dean said that the number of projects at Google that involve Google Brain has grown from a handful in early 2014 to more than 600 today.

Most recently, the Google Brain helped develop Smart Reply, a system that automatically recommends a quick response to messages in Gmail after it scans the text of an incoming message. The neural network technique used to develop Smart Reply was presented by Google researchers at the NIPS conference last year.

Dean expects deep learning and machine learning to have a similar impact on many other companies. “There is a vast array of ways in which machine learning is influencing lots of different products and industries,” he said. For example, the technique is being tested in many industries that try to make predictions from large amounts of data, ranging from retail to insurance.

Google was able to give away the code for Tensor Flow because the data it owns is a far more valuable asset for building a powerful AI engine. The company hopes that the open-source code will help it establish itself as a leader in machine learning and foster relationships with collaborators and future employees. Tensor Flow “gives us a common language to speak, in some sense,” Dean said. “We get benefits from having people we hire who have been using Tensor Flow. It’s not like it’s completely altruistic.”

A neural network consists of layers of virtual neurons that fire in a cascade in response to input. A network “learns” as the sensitivity of these neurons is tuned to match particular input and output, and having many layers makes it possible to recognize more abstract features, such as a face in a photograph.

Tensor Flow is now one of several open-source deep learning software libraries, and its performance currently lags behind some other libraries for certain tasks. However, it is designed to be easy to use, and it can easily be ported between different hardware. And Dean says his team is hard at work trying to improve its performance.

In the race to dominate machine learning and attract the best talent, however, other companies may release competing AI engines of their own.

December 8, 2015

miércoles, 25 de noviembre de 2015

IBM's SystemML machine learning system becomes Apache Incubator project

There's a race between tech giants to open source machine learning systems and become a dominant platform. Apache SystemML has clear enterprise spin.


IBM on Monday said its machine learning system, dubbed SystemML, has been accepted as an open source project by the Apache Incubator.
SPECIAL FEATURE

Machine learning, task automation and robotics are already widely used in business. These and other AI technologies are about to multiply, and we look at how organizations can best take advantage of them.
The Apache Incubator is an entry to becoming a project of The Apache Software Foundation. The general idea behind the incubator is to ensure code donations adhere to Apache's legal guidelines and communities follow guiding principles.

IBM said it would donate SystemML as an open source project in June.

What's notable about IBM's SystemML milestone is that open sourcing machine learning systems is becoming a trend. To wit:
For enterprises, the upshot is that there will be a bevy of open source machine learning code bases to consider. Google TensorFlow and Facebook Torch are tools to train neural networks. SystemML is aimed a broadening the ecosystem to business use.

Why are tech giants going open source with their machine learning tools? 
The machine learning platform that gets the most data will learn faster and then become more powerful. That cycle will just result in more data to ingest. IBM is looking to work the enterprise angle on machine learning. Microsoft may be another entry on the enterprise side, but may not go the Apache route.

In addition, there are precedents to how open sourcing big analytics ideas can pay off. MapReduce and Hadoop started as open source projects and would be a cousin of whatever Apache machine learning system wins out.

IBM's SystemML, which is now Apache SystemML, is used to create industry specific machine learning algorithms for enterprise data analysis. IBM created SystemML so it could write one codebase that could apply to multiple industries and platforms. If SystemML can scale, IBM's Apache move could provide a gateway to its other analytics wares.

The Apache SystemML project has included more than 320 patches for everything from APIs, data ingestion and documentation, more than 90 contributions to Apache Spark and 15 additional organizations adding to the SystemML engine.

Here's the full definition of the Apache SystemML project:
SystemML provides declarative large-scale machine learning (ML) that aims at flexible specification of ML algorithms and automatic generation of hybrid runtime plans ranging from single node, in-memory computations, to distributed computations on Apache Hadoop and Apache Spark. ML algorithms are expressed in a R or Python syntax, that includes linear algebra primitives, statistical functions, and ML-specific constructs. This high-level language significantly increases the productivity of data scientists as it provides (1) full flexibility in expressing custom analytics, and (2) data independence from the underlying input formats and physical data representations. Automatic optimization according to data characteristics such as distribution on the disk file system, and sparsity as well as processing characteristics in the distributed environment like number of nodes, CPU, memory per node, ensures both efficiency and scalability.

ORIGINAL: ZDNet
November 23, 2015

sábado, 21 de noviembre de 2015

How will the children of the future learn about science?

Image by :  opensource.com
From the advent of the printing press to the emergence of the Internet, knowledge has become increasingly abundant and accessible. But as we move into the future, I ponder
  • how accessible, interactive, and understandable knowledge will be as more and more individuals are connected to the Internet and as computing technologies advance. 
  • How will the techniques by which we share knowledge change? 
  • How will the children of the future learn about science? 
  • How will the scientists of the future expand our thinking? 
I think the answer is Jupyter Notebooks.

Jupyter Notebooks are interactive web applications that allow users to create and share documents that contain live code, equations, visualizations, and explanatory text. Project Jupyter is an open source project that develops the Notebook and other components that relate to it. But what excites me most about the project is not 
  • the technology, or 
  • the fantastic development team, or 
  • the extremely open nature of the community, 
rather 
  • its potential to change the way that millions of people understand science. 
Originally a Python-only project called IPython, Project Jupyter is an effort to expand the project to allow interactive notebooks to be written in other languages as well.

A Jupyter Notebook rendered as a webpage. CC BY-SA 4.0.

As our understanding of the world expands, it is important to ensure that that knowledge is equally accessible by all members of our society. This is vital to the progress of humanity. This philosophy, which is shared by the open source software movement, is not new; it has been around since the 1600s when the first academic journals were published for public reading. The Jupyter Notebook hints at what the academic journals of tomorrow will look like and paints a promising picture. They will be 
  • interactive, 
  • visualization-focused, 
  • user-friendly, and 
  • include code and data as first-class citizens. 
I believe that these unique characteristics will go a long way toward bridging the gap of understanding between the scientific community and the general public through both narrative and code—a gap that, when bridged, will have a significant impact on our society.

But the work that has been completed thus far is only the beginning for the project. In a grant proposal that was recently submitted to several nonprofit organizations, Fernando Perez and Brian Granger outline several bold visions for the project that will allow the development of software that is as collaborative and rigorous as the scientific community itself. I believe that with our dedicated and passionate core team, our willingness to grow as an open source project, and our ambitious visions, the project is set to accomplish these goals and many more.

If you'd like to experiment with a Jupyter Notebook, please visit our demo page. If you are interested in contributing to the project (and to the future of open science), please visit our GitHub organization to explore the projects that we maintain. If you are interested in joining the discussion around Jupyter, feel free to join our mailing list.

Project Jupyter is financially sponsored by the Helmsley Charitable Trust, the Alfred P. Sloan Foundation, the Gordon and Betty Moore Foundation, and various corporate sponsors. The project is part of the 501(c)3 NumFOCUS Foundation, a nonprofit that supports the development of open source computing tools for scientific computing and data science. The development of the project is supported by several full-time and volunteer developers, and we are always looking for individuals and organizations with which to collaborate.

ORIGINAL: OpenSource
18 Nov 2015

domingo, 2 de noviembre de 2014

Lego-like modular components make building 3-D 'labs-on-a-chip' a snap


Modular fluidic and instrumentation components developed by researchers at the University of Southern California Viterbi School of Engineering. Credit: USC Viterbi School of Engineering

Thanks to new LEGO-like components developed by researchers at the USC Viterbi School of Engineering, it is now possible to build a 3-D microfluidic system quickly and cheaply by simply snapping together small modules by hand.

Microfluidic systems are used in many fields including engineering, chemistry and biotechnology to precisely manipulate small volumes of fluids for use in applications such as 
  • enzymatic or DNA analysis, 
  • pathogen detection, 
  • clinical diagnostic testing, and 
  • synthetic chemistry. 
Traditionally, microfluidic devices are built in a cleanroom on a two-dimensional surface using the same technology developed to produce integrated circuits for the electronics industry.

Though tiny, designing, assembling and testing a new microfluidics system can take a lot of time and money. Building a single device can often require multiple iterations, each of which can take up to two weeks and several thousand dollars to manufacture. And the more complex the system, the higher the number of iterations needed.

"You test your device and it never works the first time," said Krisna Bhargava, materials science graduate student at the USC Viterbi School of Engineering. "If you've grown up to be an engineer or scientist, you've probably been influenced by LEGO at some point in your childhood. I think every scientist has a secret fantasy that whatever they're building will be as simple to assemble."

Frustrated that reproducing a simple microfluidic circuit could cost him so much time and money, Bhargava set out simplify the construction process. First, he identified the primitive elements commonly used in microfluidic systems, much like how circuitry is broken down in electrical engineering. Basic microfluidic functions would be separated into standardized modular components, not an entirely revolutionary concept. But then, he abandoned the two-dimensional method of building microfluidic devices altogether.

"The founders of the microfluidics field took the same approach as the semiconductor industry: to try to pack in as much integrated structure as possible into a single chip," explained Bhargava. "In electronics, this is important because a high density of transistors has many direct and indirect benefits for computation and signal processing. In microfluidics, our concerns are not with bits and symbolic representations, but rather with the way fluidics are routed, combined, mixed, and analyzed; there's no need to stick with continuing to integrate more and more complex devices."

Borrowing an approach from the electronics industry, which uses prototype boards to build circuits, Bhargava conceived of three-dimensional modular components that encapsulated the common elements of microfluidic systems, as well as a connector that could join the separate components together. Inspired by recent advancements in micron-scale 3D-printing, he and a USC Viterbi research team that included chemical engineering and materials science professor Noah Malmstadt and biomedical engineering graduate student Bryant Thompson, designed computer models for eight modular fluidic and instrumentation components (MFICs, pronounced "em-fix") that would each perform a simple operation. Examples are a "helix" component that can mix two fluid streams and a component that contains an integrated optical sensor for measuring the size of small droplets. The components constructed for this study are approximately 1 cm3, slightly smaller than a standard 6-sided die.

The team's development of these MFICs represents the first attempt to break a device into separate components that can be assembled, disassembled and re-assembled over and over.


viernes, 15 de agosto de 2014

Building Mind-Controlled Gadgets Just Got Easier

A new brain-computer interface lets DIYers access their brain waves
Photo: Chip AudetteEngineer Chip Audette used the OpenBCI system to control a robot spider with his mind.

The guys who decided to make a mind-reading tool for the masses are not neuroscientists. In fact, they’re artists who met at Parsons the New School for Design, in New York City. In this day and age, you don’t have to be a neuroscientist to muck around with brain signals.

With Friday’s launch of an online store selling their brain-computer interface (BCI) gear, Joel Murphy and Conor Russomanno hope to unleash a wave of neurotech creativity. Their system enables DIYers to use brain waves to control anything they can hack—a video game, a robot, you name it. “It feels like there’s going to be a surge,” says Russomanno. “The floodgates are about to open.” And since their technology is open source, the creators hope hackers will also help improve the BCI itself.
Photo: OpenBCI The OpenBCI board takes in data from up to eight electrodes.

Their OpenBCI system makes sense of an electroencephalograph (EEG), signal, a general measure of electrical activity in the brain captured via electrodes on the scalp. The fundamental hardware component is a relatively new chip from Texas Instruments, which takes in analog data from up to eight electrodes and converts it to a digital signal. Russomanno and Murphy used the chip and an Arduino board to create OpenBCI, which essentially amplifies the brain signal and sends it via Bluetooth to a computer for processing. “The big issue is getting the data off the chip and making it accessible,” Murphy says. Once it’s accessible, Murphy expects makers to build things he hasn’t even imagined yet.

The project got its start in 2011, when Russomanno was a student in Murphy’s physical computing class at Parsons and told his professor he wanted to hack an EEG toy made by Mattel. The toy’s EEG-enabled headset supposedly registered the user’s concentrated attention (which in the game activated a fan that made a ball float upward). But the technology didn’t seem very reliable, and since it wasn’t open source, Russomanno couldn’t study the game’s method of collecting and analyzing the EEG data. He decided that an open-source alternative was necessary if he wanted to have any real fun.

Happily, Russomanno and his professor soon connected with engineer Chip Audette, of the New Hampshire R&D firm Creare, who already had a grant from the U.S. Defense Advanced Research Projects Agency (DARPA) to develop a low-cost, high-quality EEG system for “nontraditional users.” Once the team had cobbled together a prototype of their OpenBCI system, they decided to offer their gear to the world with a Kickstarter campaign, which ended in January and raised more than twice the goal of US $100,000.

Murphy and Russomanno soon found that production would be more difficult and take longer than expected (as is the case with so many Kickstarter projects), so they had to push back their shipping date by several months. Now, though, they’re in business—and Russomanno says that shipping a product is only the beginning. “We don’t just want to sell something; we want to teach people how to use it and also develop a community,” he says. OpenBCI wants to be an online portal where experimenters can swap tips and post research projects.


So once a person’s brain-wave data is streaming into a computer, what is to be done with it? OpenBCI will make some simple software available, but mostly Russomanno and Murphy plan to watch as inventors come up with new applications for BCIs.

Audette, the engineer from Creare, is already hacking robotic “battle spiders” that are typically steered by remote control. Audette used an OpenBCI prototype to identify three distinct brain-wave patterns that he can reproduce at will, and he sent those signals to a battle spider to command it to turn left or right or to walk straight ahead. “The first time you get something to move with your brain, the satisfaction is pretty amazing,” Audette says. “It’s like, ‘I am king of the world because I got this robot to move.’ ”

In Los Angeles, a group is using another prototype to give a paralyzed graffiti artist the ability to practice his craft again. The artist, Tempt One, was diagnosed with Lou Gehrig’s disease in 2003 and gradually progressed to the nightmarish “locked in” state. By 2010 he couldn’t move or speak and lay inert in a hospital bed—but with unimpaired consciousness, intellect, and creativity trapped inside his skull. Now his supporters are developing a system called the BrainWriter: They’re using OpenBCI to record the artist’s brain waves and are devising ways to use those brain waves to control the computer cursor so Tempt can sketch his designs on the screen.

Another early collaborator thinks that OpenBCI will be useful in mainstream medicine. David Putrino, director of telemedicine and virtual rehabilitation at the Burke Rehabilitation Center, in White Plains, N.Y., says he’s comparing the open-source system to the $60,000 clinic-grade EEG devices he typically works with. He calls the OpenBCI system robust and solid, saying, “There’s no reason why it shouldn’t be producing good signal.”

Putrino hopes to use OpenBCI to build a low-cost EEG system that patients can take home from the hospital, and he imagines a host of applications. Stroke patients, for example, could use it to determine when their brains are most receptive to physical therapy, and Parkinson’s patients could use it to find the optimal time to take their medications. “I’ve been playing around with these ideas for a decade,” Putrino says, “but they kept failing because the technology wasn’t quite there.” Now, he says, it’s time to start building.


ORIGINAL: IEEE Spectrum
By Eliza Strickland
11 Aug 2014

martes, 10 de diciembre de 2013

Opinion: Science Counterculture. On taking DIYbio to the next level

FLICKR, ADONOFRIO
Open-source software paved the way for a new, community-driven development model by providing a product that was free to use and modify. This in turn fostered a business culture that was driven by support-services. That open-source principles could also herald a new era in biology was demonstrated by the successful completion of the publicly funded Human Genome Project more than a decade ago. Today, that same open, community-driven mindset continues to drive much research in the life sciences.

Soon after the human genome sequence was published, biohackers and do-it-yourself biology (DIYbio) groups came onto the scene. Among the first to demonstrate the feasibility of garage biology was Meredith Patterson, who created glow-in-the-dark yogurt by transfecting green fluorescent protein DNA into Lactobacillus. Rob Carlson, who in 2005 was among the first to spot this new development and start his own garage lab, opined in The Scientist in 2011 that garage innovation would be as important for technological advancements in biology as it was in IT. Since then, some biohackers have organized themselves into low-cost, community-based labs providing both lab space and training. However, unleashing their true technological potential will call for greater networking between these groups and borrowing concepts from business incubator models and the open-source hardware movement.

DIYbio groups—such as BioCurious, CounterCulture Labs, Genspace, Bioartlab, and Biogarage—have sprung up in many cities across North America, Europe, Asia, and Oceania. While many have demonstrated that simple experiments like isolating DNA or creating recombinant microbes are easily replicated outside the traditional lab, more promising, low-cost, open-source tools are also being developed. These include Biocurious’s bioprinter, OpenFuge, and the Kickstarter-backed OpenPCR. Of these, the latter two are already available, and at a fraction of the cost of the cheapest commercial models.

To grow, the DIYbio community must have access to inexpensive lab equipment and consumables. A number of companies, which include Open Biotechnology, IORodeo, and Chai Biotechnologies, are offering open-source products ranging from mammalian cell lines, electrophoresis kits, and power packs to thermal cyclers for PCR. While this list is by no means exhaustive, partnering with these and other similar startups could satisfy DIYbio’s thirst for machines and reagents, and help create innovative technologies.

And then there are the open-source hardware companies, such as SparkFun, Adafruit Industries, and MakerBot, as well as initiatives like RepRap, which are well positioned to serve the DIYbio community. SparkFun and Adafruit manufacture hardware components for DIY projects, such as Arduino microcontroller boards, printed circuit boards, and other accessories. MakerBot produces the Replicator 2 series of 3-D printers and RepRap is a community-based initiative for building self-replicating 3-D printers. Writing in Science, Michigan Technological University’s Joshua Pearce noted that Arduino-controlled research equipment fabricated on 3-D printers could soon become a reality. Members of Joseph DeRisi’s lab at the University of California, San Francisco, have already taken the first steps by 3-D printing lab consumables and equipment such gel electrophoresis combs, gel trays, and rotors for bench-top centrifuges.

While the ability of DIYbio to drive technological innovation is fairly obvious, its ability to spur basic research innovation is less clear. For this to happen, equipment and operating costs must be brought down. Technological innovation may well fuel research advances in the long run, but for now, DIYbio groups could focus on community outreach programs and targeting high school and university participation. Community labs that are up and running could invite students to volunteer. They could expand community outreach online by posting videos or providing links to educational sites. Networking among DIYbio groups to develop shared goals and invest in shared equipment could be one way out of the resource crunch. Another would be to borrow from the business incubator model by asking for a small percentage of equity in exchange for assistance in developing a successful product and bringing it to market.

Countercultural movements are evidence of a society’s diversity and vitality. Many of the biggest advances in science have come from people outside or on the fringes of the science establishment. The emerging DIYbio community could become the incubator that nurtures the next generation’s technologies and public scientists. For this to happen, DIY biologists will need to band together to gain the critical mass necessary to support the open-source development of biological techniques, equipment, and experimental methods.

ORIGINAL: The Scientist
By Usha Nair
December 9, 2013 

Usha Nair is a research associate in the department of biology at the University of Saskatchewan, where her research focuses on the structure determination of proteins associated with bacterial virulence.