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November 08 2013

July 09 2013

Le code source de Seenthis est disponible -

Le code source de Seenthis est disponible -

Seenthis. Sous ce nom barbare se cache en fait un Twitter à la française ou plutôt un système de billets courts (« short-blogging »), sans limitation de caractères, mais avec un intérêt tout aussi important (et vous pouvez le déployer/gérer chez vous en ces périodes de #PRISM). La barrière des 140 caractères est ainsi franchie.

#Seenthis #opensource

Du coup : (car j’ai à l’origine trouvé l’info ici :

April 17 2013

Four short links: 17 April 2013

  1. Computer Software Archive (Jason Scott) — The Internet Archive is the largest collection of historical software online in the world. Find me someone bigger. Through these terabytes (!) of software, the whole of the software landscape of the last 50 years is settling in. (And documentation and magazines and …). Wow.
  2. 7 in 10 Doctors Have a Self-Tracking Patientthe most common ways of sharing data with a doctor, according to the physicians, were writing it out by hand or giving the doctor a paper printout. (via Richard MacManus)
  3. opsmezzo — open-sourced provisioning tools from the Nodejitsu team. (via Nuno Job)
  4. Hacking Secret Ciphers with Pythonteaches complete beginners how to program in the Python programming language. The book features the source code to several ciphers and hacking programs for these ciphers. The programs include the Caesar cipher, transposition cipher, simple substitution cipher, multiplicative & affine ciphers, Vigenere cipher, and hacking programs for each of these ciphers. The final chapters cover the modern RSA cipher and public key cryptography.

June 29 2012

UK Cabinet Office relaunches, releases open data white paper

The British government is doubling down on the notion that open data can be a catalyst for increased government transparency, civic utility and economic prosperity.

Yesterday, the United Kingdom's Cabinet Office hosted an event in London, England to highlight the release of a new white paper on "unleashing the potential of open data," linked at the bottom of the post, and the relaunch of a, the country's open data platform. The site now has over 9,000 data sets on it, according to the Cabinet Office.

In the video below, Francis Maude, minister for the Cabinet Office, talks about the white paper, which was the result of a public consultation over the last year.

"I think it's all good overall," commented author Dr. Ben Goldacre, via email.

"The UK government have been saying the right things about data for a long time: that it's the 21st century's raw material, that it has economic and social benefits, that privacy issues need caution, and so on. That in itself is reassuring, as governments can sometimes be completely clueless about this kind of stuff.

They also get the nerdy details: that standards matter, and so on. Also, all the stuff about building reciprocal relationships with developers, building coder capacity, two way relationships to improve datasets etc is all great. The star rating system for departments is neat, as one lesson from this whole area is simple structured public feedback often improves services.

The main concern is that the core reference data hasn't been released for free. The Postcode Address File allows developers to convert addresses into postcodes: this kind of dataset is like the road network of the digital domain, and it needs to be open with free movement so businesses and services can meet users. Our excellent Ordnance Survey maps are still locked up at the more detailed levels, which is problematic since a lot of geographical data from local government uses OS data too, so release of that is hindered. Companies House data is also still pay only.

The Cabinet Office seem to have been fighting hard for this stuff, which is great, but it's proving difficult to release."

The Guardian's Datablog published a smart, cogent analysis of the open data white paper and a spreadsheet of the government's commitments under it.

I strongly agree with Simon Rogers, the editor of the Datablog, that one of the most significant elements of the white paper is its acknowledgement of the need to engage developers and solicit their feedback on the quality and availability of open government data.

"Traditionally, government has almost ignored developers, even as prime users of its data," wrote Simon Rogers at the Guardian. "This commitment to take that community into account is probably the most striking part of this White Paper, which will allow users to ask government for specific datasets, feedback on how they've used them and, crucially, 'inform us when there are anomalies or mistakes in our data.'"

The past several years have shown such engagement is a critical aspect of building communities around open data. Directly engaging entrepreneurs, venture capitalists, industry and academia is, as US CTO Todd Park's success with stimulating innovation around open health data has demonstrated, necessary for downstream success. Publishing high quality open data online is, in that context, necessary but unsufficient for better downstream outcomes for citizens. In the context of the costs incurred through publishing open data, this investment of time and energy in community engagement can't be underemphasized - and the inclusion of this strategic element in the white paper is notable.

All that being said, an actual strategy for developer engagement was not published in the white paper - stay tuned on that count.

Maude, Berners-Lee and Pollock on open data

Earlier this spring, I interviewed Francis Maude, the United Kingdom's minister for the Cabinet Office, about the responsibilities and opportunities for open government and transparency, including its relationship to prosperity and security. The video of our interview is embedded below:

The British government has also now officially adopted the "5 star" rubric of one of its most celebrated citizens, World Wide Web inventor Tim Berners-Lee, for evaluating the quality of open government data. Below, I've embedded my interview on open data with Berners-Lee, which remains relevant today:

For another view from civil society on what, exactly, open data is and why it matters, watch my interview with Rufus Pollock, the co-founder of the Open Knowledge Foundation, below. The Open Knowledge Foundation supports the, Comprehensive Knowledge Archive Network (CKAN), the open source open data platform software that underpins the site.

UK government white paper on open data

June 28 2012

Four short links: 28 June 2012

  1. Bogan Ipsum -- the Australian version of Loren Ipsum. (via Seb Chan)
  2. Microsoft BASIC for 6502 -- reverse-engineering magic, this person has RE'd the assembly language for various versions of the BASIC interpreter that shipped on microcomputers in the 80s. This page talks about the changes in each version, the easter eggs, and the hacks. This, kids, is how real programmers do it :)
  3. The Sudden Rise of Peer-to-Peer Commerce (Casey Research) -- Today, business are sprouting up around the world based on the idea of connecting individuals directly to each other to trade products and services. While the idea is very much in its infancy still, like the music business at the dawn of Napster, we're beginning to grasp the potential. Something we are tracking at O'Reilly as well.
  4. The Sensor/itive Side of Android (Luke Wroblewski) -- lots of details about sensors in Android, from a Google I/O talk. Sampling rates change between devices. The data has variance and static because it comes from cost-effective components for mobile phones not robust and industry-grade sensors.

June 27 2012

Four short links: 27 June 2012

  1. Turing Centenary Speech (Bruce Sterling) -- so many thoughtbombs, this repays rereading. We’re okay with certain people who “think different” to the extent of buying Apple iPads. We’re rather hostile toward people who “think so very differently” that their work will make no sense for thirty years — if ever. We’ll test them, and see if we can find some way to get them to generate wealth for us, but we’re not considerate of them as unusual, troubled entities wandering sideways through a world they never made. ... Cognition exists, and computation exists, but they’re not the same phenomenon with two different masks on. ... Explain to me, as an engineer, why it’s so important to aspire to build systems with “Artificial Intelligence,” and yet you’d scorn to build “Artificial Femininity.” What is that about? ... Every day I face all these unstable heaps of creative machinery. How do we judge art created with, by, and or through these devices? What is our proper role with them? [...] How do we judge what we’re doing? How do we distribute praise and blame, rewards and demerits, how do to guide it, how do we attribute meaning to it? ... oh just read the whole damn piece, it's the best thing you'll read this month.
  2. Handsontable -- Excel-like grid editing plugin for jQuery (MIT-licensed).
  3. Lumoback (Kickstarter) -- smart posture sensor which provides a gentle vibration when you slouch to remind you to sit or stand straight. It is worn on your lower back and designed to be slim, sleek and so comfortable that you barely feel it when you have it on. (via Tim O'Reilly)
  4. Robot Hand Beats You At Rock-Paper-Scissors (IEEE) -- tl;dr: computer vision and fast robotics means it chooses after you reveal, but it happens so quickly that you don't realize it's cheating. (via Hacker News)

June 26 2012

Four short links: 26 June 2012

  1. SnapItHD -- camera captures full 360-degree panorama and users select and zoom regions afterward. (via Idealog)
  2. Iago (GitHub) -- Twitter's load-generation tool.
  3. AutoCAD Worm Stealing Blueprints -- lovely, malware that targets inventions. The worm, known as ACAD/Medre.A, is spreading through infected AutoCAD templates and is sending tens of thousands of stolen documents to email addresses in China. This one has soured, but give the field time ... anything that can be stolen digitally, will be. (via Slashdot)
  4. Designing For and Against the Manufactured Normalcy Field (Greg Borenstein) -- Tim said this was one of his favourite sessions at this year's Foo Camp: breaking the artificial normality than we try to cast over new experiences so as to make them safe and comfortable.

June 21 2012

Clinician, researcher, and patients working together: progress aired at Indivo conference

While thousands of health care professionals were flocking to the BIO International Convention this week, I spent Monday in a small library at the Harvard Medical School listening to a discussion of the Indivo patient health record and related open source projects with about 80 intensely committed followers. Lead Indivo architect Daniel Haas, whom I interviewed a year ago, succeeded in getting the historical 2.0 release of Indivo out on the day of the conference. This article explains the significance of the release in the health care field and the promise of the work being done at Harvard Medical School and its collaborators.

Although still at the early adoption stages, Indivo and the related SMART and i2b2 projects merit attention and have received impressive backing. The Office of the National Coordinator funded SMART, and NIH funded i2b2. National Coordinator Farzad Mostashari was scheduled to attend Monday's conference (although he ended up having to speak over a video hookup). Indivo inspired both Microsoft HealthVault and Google Health, and a good deal of its code underlies HealthVault. Australia has taken a nationwide PHR initiative inspired by Indivo. A Partners HealthCare representative spoke at the conference, as did someone from the MIT Media Lab. Clayton M. Christensen et al. cited Indivo as a good model in The Innovator's Prescription: A Disruptive Solution for Health Care. Let's take a look at what makes the combination so powerful.

Platform and reference implementation

The philosophy underlying this distributed open source initiative is to get clinicians, health researchers, and patients to share data and work together. Today, patient data is locked up in thousands of individual doctors or hospital repositories; whether they're paper or electronic hardly makes a difference because they can't be combined or queried. The patient usually can't see his own data, as I described in an earlier posting, much less offer it to researchers. Dr. Kenneth Mandl, opening the conference, pointed out that currently, an innovative company in the field of health data will die on the vine because they can't get data without making deals with each individual institution and supporting its proprietary EHR.

The starting point for changing all that, so far as this conference goes, is the SMART platform. It simply provides data models for storing data and APIs to retrieve it. If an electronic health record can translate data into a simple RDF model and support the RESTful API, any other program or EHR that supports SMART can access the data. OAuth supports security and patient control over access.

Indivo is a patient health record (or, to use the term preferred by the conference speakers, a personally controlled health record). It used to have its own API, and the big significance of Monday's 2.0 release is that it now supports SMART. The RESTful interface will make Indivo easy to extend beyond its current Java and Python interfaces. So there's a far-reaching platform now for giving patients access to data and working seemlessly with other cooperating institutions.

The big missing piece is apps, and a hackathon on Tuesday (which I couldn't attend) was aimed at jump-starting a few. Already, a number of researchers are using SMART to coordinate data sharing and computation through the i2b2 platform developed by Partners. Ultimately, the SMART and Indivo developers hope to create an app store, inspired by Apple's, where a whole marketplace can develop. Any app written to the SMART standard can run in Indivo or any other system supporting SMART. But the concept of an app in SMART and Indivo is different from a consumer market, though. The administrator of the EHR or PHR would choose apps, vetting them for quality and safety, and then a doctor, researcher, or patient could use one of the chosen apps.

Shawn Murphy of Partners described the use of i2b2 to choose appropriate patients for a clinical study. Instead of having to manually check many different data repositories manually for patients meeting the requirements (genetic, etc.), a researcher could issue automated queries over SMART to the databases. The standard also supports teamwork across institutions. Currently, 60 different children's hospitals' registries talk to each other through i2b2.

It should be noted i2b2 does not write into a vendor's EHR system (which the ONC and many others call an important requirement for health information exchange) because putting data back into a silo isn't disruptive innovation. It's better to give patients a SMART-compatible PHR such as Indivo.

Regarding Tuesday's hackathon, Haas wrote me, "By the end of the day, we had several interesting projects in the works, including an app to do contextualized search based on a patient's Problems list (integration with and MedlinePlus), and app integration with BodyTrack, which displays Indivo labs data in time-series form alongside data from several other open API inputs, such as Fitbit and Zeo devices."

Standards keep things simple

All the projects mentioned are low-budget efforts, so they all borrow and repurpose whatever open source tools they can. As Mostashari said in his video keynote, they believe in "using what you've got." I have already mentioned SMART's dependence on standards, and Indivo is just as behold to other projects, particularly Django. For instance, Indivo allows data to be stored in Django's data models (Python structures that represent basic relational tables). Indivo also provides an even simpler JSON-based data model.

The format of data is just as important as the exchange protocol, if interoperability is to success. The SMART team chose to implement several "best-of-breed" standards that would cover 80% of use cases: for instance, SNOMED for medical conditions, RxNORM for medications, and LOINC for labs. Customers using other terminologies will have to translate them into the supported standards, so SMART contains Provenance fields indicating the data source.

The software is also rigorously designed to be modular, so both the original developers and other adopters can replace pieces as desired. Indivo already has plenty of fields about patient data and about context (provider names, etc.), but more can be added ad infinitum to support any health app that comes along. Indivo 2.0 includes pluggable data models, which allow a site to customize every step from taking in data to removing it. It also supports new schemas for data of any chosen type.

The simplicity of Indivo, SMART, and i2b2--so much in contrast with most existing health information exchanges--is reminiscent of Blue Button. Mandl suggested that a Blue Button app would be easy to write. But the difference is that Blue Button aimed to be user-friendly whereas the projects at this conference are developer-friendly. That means that can add some simple structure and leave it up to app developers to present the data to users in a friendly manner.

The last hurdle

Because SMART and Indivo ultimately want the patient to control access to data, trust is a prerequisite. OAuth is widely used by Twitter apps and other sites across the Web, but hasn't been extensively tested in a health care environment. We'll need more experience with OAuth to see whether the user experience and their sense of security are adequate. And after that, trust is up to the institutions adopting Indivo or SMART. A couple speakers pointed out that huge numbers of people trust with their passwords to financial accounts, so when they learn the benefits of access to patient records they should adopt Indivo as well. An Indivo study found that 84% of people are willing to share data with social networks for research and learning.

SMART, Indivo, and i2b2 make data sharing easier than ever. but as many have pointed out, none of this will get very far until patients, government, and others demand that institutions open up. Mandl suggested that one of the major reasons Google Health failed was that it could never get enough data to gain traction--the health providers just wouldn't work with the PHR. At least the open source standards take away some of the technical excuses they have used up to now.

June 15 2012

Four short links: 15 June 2012

  1. In Flawed, Epic Anonymous Book, the Abyss Gazes Back (Wired) -- Quinn Norton's review of a book about Anonymous is an excellent introduction to Anonymous. Anonymous made us, its mediafags, masters of hedging language. The bombastic claims and hyperbolic declarations must be reported from their mouths, not from our publications. And yet still we make mistakes and publish lies and assumptions that slip through. There is some of this in all of journalism, but in a world where nothing is true and everything is permitted, it’s a constant existential slog. It’s why there’s not many of us on this beat.
  2. Titan (GitHub) -- Apache2-licensed distributed graph database optimized for storing and processing large-scale graphs within a multi-machine cluster. Cassandra and HBase backends, implements the Blueprints graph API. (via Hacker News)
  3. Extra Second This June -- we're getting a leap second this year: there'll be 2012 June 30, 23h 59m 60s. Calendars are fun.
  4. On Creativity (Beta Knowledge) -- I wanted to create a game where even the developers couldn’t see what was coming. Of course I wasn’t thinking about debugging at this point. The people who did the debugging asked me what was a bug. I could not answer that. — Keita Takahashi, game designer (Katamari Damacy, Noby Noby Boy). Awesome quote.

June 11 2012

Four short links: 11 June 2012

  1. When Code Can Kill or Cure (The Economist) -- I've linked to the dangers of closed source devices before, but this caught my eye: "In the 1990s we developed an excellent radiation-therapy treatment-planning system and tried to give it away to other clinics," says Dr Mackie. "But when we were told by the FDA that we should get our software approved, the hospital wasn't willing to fund it." He formed a spin-off firm specifically to get FDA approval. It took four years and cost millions of dollars. The software was subsequently sold as a traditional, closed-source product.
  2. Gut Fungus (Wired) -- the microbiome of bacteria in your body is being studied, but now researchers have scoured the poop of different species and found different mycological populations in each, and linked them to diseases.
  3. Evaluating the Harm from Closed Source (Eric Raymond) -- whether or not you argue with his ethics, you will appreciate the clear description of the things you're trading off when you choose to use closed source software.
  4. PyBossa -- a free, open-source, platform for creating and running crowd-sourcing applications that utilise online assistance in performing tasks that require human cognition, knowledge or intelligence such as image classification, transcription, geocoding and more! (via The Open Knowledge Foundation)

June 07 2012

Four short links: 7 June 2012

  1. Electric Imp -- yet another group working on the necessary middleware for ubiquitous networked devices.
  2. How Big Data Transformed the Dairy Industry (The Atlantic) -- cutting-edge genomics company Illumina has precisely one applied market: animal science. They make a chip that measures 50,000 markers on the cow genome for attributes that control the economically important functions of those animals.
  3. The Curious Case of Internet Privacy (Cory Doctorow) -- I'm with Cory on the perniciousness of privacy-digesting deals between free sites and users, but I'm increasingly becoming convinced that privacy is built into business models and not technology.
  4. Chronoline (Github) -- Javascript to make a horizontal timeline out of a list of events.

June 01 2012

Four short links: 1 June 2012

  1. BeWell App (Google Play) -- continuously tracks user behaviors along three key health dimensions without requiring any user input — the user simply downloads the app and uses the phone as usual. Finally, someone tracking my behaviour for my own good.
  2. Met 3D -- the Metropolitan Museum of Art hosts its first 3d printing and scanning hackathon. [O]n June 1 and 2, approximately twenty-five digital artists and programmers will gather at the Met to experiment with the latest 3-D scanning and replicating technologies. Their aim will be to use the Museum's vast encyclopedic collections as a departure point for the creation of new work. THIS. IS. AWESOME. (via Alison Marigold)
  3. The Perfected Self (The Atlantic) -- everything you knew about B. F. Skinner was wrong, and you should know about him because you're using his techniques to lose weight, stop smoking, and do your homework. (via Erica Lloyd)
  4. Google Blockly -- (Google Code) A web-based, graphical programming language. Users can drag blocks together to build an application. No typing required. Open sourced.

May 31 2012

Nominations open for the O'Reilly Open Source Awards 2012

The 8th Annual O'Reilly Open Source Awards will be hosted this July at OSCON 2012 in Portland, OR. These annual awards recognize individual contributors who have demonstrated exceptional leadership, creativity, and collaboration in the development of open source software.

Past recipients include Karen Sandler, Brian Aker, Deborah Bryant, Ryan Dahl, Angela Byron, Brad Fitzpatrick, Karl Fogel, Pamela Jones, Bruce Momjian, Chris Messina, David Recordon, and Andrew Tridgell.

The nomination form is open to the entire open source community. The nomination period closes on July 1, 2011.

Nominations should include the name of the recipient, any associated project or organization, and a description of why you are nominating the individual.

O'Reilly employees cannot be nominated.

OSCON 2012 — Join the world's open source pioneers, builders, and innovators July 16-20 in Portland, Oregon. Learn about open development, challenge your assumptions, and fire up your brain.

Save 20% on registration with the code RADAR

May 30 2012

May 25 2012

Four short links: 25 May 2012

  1. Meet The New Boss, Worse Than The Old Boss -- transcript of a thoughtful music industry insider considering the effect of the net on the business. The other problem? I’ve been expecting for years now to see aggregate revenue flowing to artist increase. Disintermediation promised us this. It hasn’t happened. Everywhere I look artists seem to be working more for less money. And every time I come across aggregate data that is positive it turns out to have a black cloud inside. Example: Touring revenues up since 1999. Because more bands are touring, staying on the road longer and playing for fewer people. Surely you all can see Malthusian trajectory?
  2. Kottke on Quarterly -- I eyed TED's book club and thought "hmm, interesting business model: you like my taste, sign up and I'll send you things". Quarterly is a "my taste as a service" service. (via Sacha Judd)
  3. Pipe Viewer -- clever little command-line utility to show progress of pipes.
  4. Sheryl Sandberg's HBS Class Day Speech -- two things stood out, beyond the honesty of the talk: If you’re offered a seat on a rocket ship, don’t ask what seat (that's her quoting Eric Schmidt) and [careers] are not a ladder; they’re a jungle gym (her quoting Facebook's head of HR). (via Sacha Judd)

May 22 2012

Four short links: 22 May 2012

  1. New Zealand Government Budget App -- when the NZ budget is announced, it'll go live on iOS and Android apps. Tablet users get details, mobile users get talking points and speeches. Half-political, but an interesting approach to reaching out to voters with political actions.
  2. Health Care Data Dump (Washington Post) -- 5B health insurance claims (attempted anonymized) to be released. Researchers will be able to access that data, largely using it to probe a critical question: What makes health care so expensive?
  3. Perl 5.16.0 Out -- two epic things here: 590k lines of changes, and announcement quote from Auden. Auden is my favourite poet, Perl my favourite programming language.
  4. WYSIHTML5 (GitHub) -- wysihtml5 is an open source rich text editor based on HTML5 technology and the progressive-enhancement approach. It uses a sophisticated security concept and aims to generate fully valid HTML5 markup by preventing unmaintainable tag soups and inline styles.

May 17 2012

Four short links: 17 May 2012

  1. The Mythology of Big Data (PDF) -- slides from a Strata keynote by Mark R. Madsen. A lovely explanation of the social impediments to the rational use of data. (via Hamish MacEwan)
  2. Scamworld -- amazing deconstruction of the online "get rich quick" scam business. (via Andy Baio)
  3. Ceres: Solving Complex Problems with Computing Muscle -- Johnny Lee Chung explains the (computer vision) uses of the open source Ceres Non-Linear Least Squares Solver library from Google.
  4. How to Start a Think Tank (Guardian) -- The answer to the looming crisis of legitimacy we're facing is greater openness - not just regarding who met who at what Christmas party, but on the substance of policy. The best way to re-engage people in politics is to change how politics works - in the case of our project, to develop a more direct way for the people who use and provide public and voluntary services to create better social policy. Hear, hear. People seize on the little stuff because you haven't given them a way to focus something big with you.

May 04 2012

Four short links: 4 May 2012

  1. Common Statistical Fallacies (Flowing Data) -- once you know to look for them, you see them everywhere. Or is that confirmation bias?
  2. Project Hijack -- Hijacking power and bandwidth from the mobile phone's audio interface. Creating a cubic-inch peripheral sensor ecosystem for the mobile phone.
  3. Peak Plastic -- Deb Chachra points out that if we’re running out of oil, that also means that we’re running out of plastic. Compared to fuel and agriculture, plastic is small potatoes. Even though plastics are made on a massive industrial scale, they still account for less than 10% of the world’s oil consumption. So recycling plastic saves plastic and reduces its impact on the environment, but it certainly isn’t going to save us from the end of oil. Peak oil means peak plastic. And that means that much of the physical world around us will have to change. I hadn't pondered plastics in medicine before. (via BoingBoing)
  4. web.go (GitHub) -- web framework for the Go programming language.

May 02 2012

Recombinant Research: Breaking open rewards and incentives

In the previous articles in this series I've looked at problems in current medical research, and at the legal and technical solutions proposed by Sage Bionetworks. Pilot projects have shown encouraging results but to move from a hothouse environment of experimentation to the mainstream of one of the world's most lucrative and tradition-bound industries, Sage Bionetworks must aim for its nucleus: rewards and incentives.

Previous article in the series: Sage Congress plans for patient engagement.

Think about the publication system, that wretchedly inadequate medium for transferring information about experiments. Getting the data on which a study was based is incredibly hard; getting the actual samples or access to patients is usually impossible. Just as boiling vegetables drains most of their nutrients into the water, publishing results of an experiment throws away what is most valuable.

But the publication system has been built into the foundation of employment and funding over the centuries. A massive industry provides distribution of published results to libraries and research institutions around the world, and maintains iron control over access to that network through peer review and editorial discretion. Even more important, funding grants require publication (but the data behind the study only very recently). And of course, advancement in one's field requires publication.

Lawrence Lessig, in his keynote, castigated for-profit journals for restricting access to knowledge in order to puff up profits. A chart in his talk showed skyrocketing prices for for-profit journals in comparison to non-profit journals. Lessig is not out on the radical fringe in this regard; Harvard Library is calling the current pricing situation "untenable" in a move toward open access echoed by many in academia.

Lawrence Lessig keynote at Sage Congress
Lawrence Lessig keynote at Sage Congress.

How do we open up this system that seemed to serve science so well for so long, but is now becoming a drag on it? One approach is to expand the notion of publication. This is what Sage Bionetworks is doing with Science Translational Medicine in publishing validated biological models, as mentioned in an earlier article. An even more extensive reset of the publication model is found in Open Network Biology (ONB), an online journal. The publishers require that an article be accompanied by the biological model, the data and code used to produce the model, a description of the algorithm, and a platform to aid in reproducing results.

But neither of these worthy projects changes the external conditions that prop up the current publication system.

When one tries to design a reward system that gives deserved credit to other things besides the final results of an experiment, as some participants did at Sage Congress, great unknowns loom up. Is normalizing and cleaning data an activity worth praise and recognition? How about combining data sets from many different projects, as a Synapse researcher did for the TCGA? How much credit do you assign researchers at each step of the necessary procedure for a successful experiment?

Let's turn to the case of free software to look at an example of success in open sharing. It's clear that free software has swept the computer world. Most web sites use free software ranging from the server on which they run to the language compilers that deliver their code. Everybody knows that the most popular mobile platform, Android, is based on Linux, although fewer realize that the next most popular mobile platforms, Apple's iPhones and iPads, run on a modified version of the open BSD operating system. We could go on and on citing ways in which free and open source software have changed the field.

The mechanism by which free and open source software staked out its dominance in so many areas has not been authoritatively established, but I think many programmers agree on a few key points:

  • Computer professionals encountered free software early in their careers, particularly as students or tinkerers, and brought their predilection for it into jobs they took at stodgier institutions such as banks and government agencies. Their managers deferred to them on choices for programming tools, and the rest is history.

  • Of course, computer professionals would not have chosen the free tools had they not been fit for the job (and often best for the job). Why is free software so good? Probably because the people creating it have complete jurisdiction over what to produce and how much time to spend producing it, unlike in commercial ventures with requirements established through marketing surveys and deadlines set unreasonably by management.

  • Different pieces of free software are easy to hook up, because one can alter their interfaces as necessary. Free software developers tend to look for other tools and platforms that could work with their own, and provide hooks into them (Apache, free database engines such as MySQL, and other such platforms are often accommodated.) Customers of proprietary software, in contrast, experience constant frustration when they try to introduce a new component or change components, because the software vendors are hostile to outside code (except when they are eager to fill a niche left by a competitor with market dominance). Formal standards cannot overcome vendor recalcitrance--a painful truth particularly obvious in health care with quasi-standards such as HL7.

  • Free software scales. Programmers work on it tirelessly until it's as efficient as it needs to be, and when one solution just can't scale any more, programmers can create new components such as Cassandra, CouchDB, or Redis that meet new needs.

Are there lessons we can take from this success story? Biological research doesn't fit the circumstances that made open source software a success. For instance, researchers start out low on the totem pole in very proprietary-minded institutions, and don't get to choose new ways of working. But the cleverer ones are beginning to break out and try more collaboration. Software and Internet connections help.

Researchers tend to choose formats and procedures on an ad hoc, project by project basis. They haven't paid enough attention to making their procedures and data sets work with those produced by other teams. This has got to change, and Sage Bionetworks is working hard on it.

Research is labor-intensive. It needs desperately to scale, as I have pointed out throughout this article, but to do so it needs entire new paradigms for thinking about biological models, workflow, and teamwork. This too is part of Sage Bionetworks' mission.

Certain problems are particularly resistant in research:

  • Conditions that affect small populations have trouble raising funds for research. The Sage Congress initiatives can lower research costs by pooling data from the affected population and helping researchers work more closely with patients.

  • Computation and statistical methods are very difficult fields, and biological research is competing with every other industry for the rare individuals who know these well. All we can do is bolster educational programs for both computer scientists and biologists to get more of these people.

  • There's a long lag time before one knows the effects of treatments. As Heywood's keynote suggested, this is partly solved by collecting longitudinal data on many patients and letting them talk among themselves.

Another process change has revolutionized the computer field: agile programming. That paradigm stresses close collaboration with the end-users whom the software is supposed to benefit, and a willingness to throw out old models and experiment. BRIDGE and other patient initiatives hold out the hope of a similar shift in medical research.

All these things are needed to rescue the study of genetics. It's a lot to do all at once. Progress on some fronts were more apparent than others at this year's Sage Congress. But as more people get drawn in, and sometimes fumbling experiments produce maps for changing direction, we may start to see real outcomes from the efforts in upcoming years.

All articles in this series, and others I've written about Sage Congress, are available through a bundle.

OSCON 2012 — Join the world's open source pioneers, builders, and innovators July 16-20 in Portland, Oregon. Learn about open development, challenge your assumptions, and fire up your brain.

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The UK's battle for open standards

Many of you are probably not aware, but there is an ongoing battle within the U.K. that will shape the future of the U.K. tech industry. It's all about open standards.

Last year, the Cabinet Office ran a consultation on open standards covering 970 CIOs and academics. The result of this consultation was a policy (PDF) in favour of royalty-free (RF) open standards in the U.K. I'm not going to go through the benefits of open standards in this space, other than to note that they are essential for the U.K.'s future competitive position, for spurring on innovation and creating a level playing field within the tech field. For those who wish to read more on this subject, Mark Thompson, the only academic I know to have published a paper on open standards in a quality peer reviewed journal, has provided an excellent overview.

Normally, I put these battles into an historical context, and I certainly have a plethora of examples of past industries attempting to lobby against future change. However, to keep this short I'll simply note that the incumbent industry has reacted to the Cabinet Office policy with attempts to redefine open standards to include non-open FRAND (fair, reasonable and non discriminatory) licenses and portray some sort of legitimate debate of RF versus FRAND, which doesn't exist.

Whilst this is clearly wrong and underhanded, there's another story I wish to focus on. It relates to the accusations that the meetings have been filled with "spokespeople for big vendors to argue in favour of paid-for software, specifically giving advocates of FRAND the chance to argue that free software on RF terms would be a bad thing" as reported by TechWeek Europe.

The back story is that since the Government policy on open standards was put in place, the Cabinet Office was pressured into a u-turn and running another consultation by various standards bodies and other vested interests. The arguments used were either fortuitous misunderstandings of the policy or willful misinformation in favour of current business interests. The Cabinet Office then appeared to relent to the pressure and undertake a second set of consultations. What happened next shows the sorry behaviour of lobbyists in our industry.

"Software patent heavyweights piled into the first public meeting," filling the room with unrepresentative views backed up by vendors flying in senior individuals from the U.S. It apparently seems that the chair of the roundtable was himself a paid lobbyist working on behalf of those vested interests, a fact that he forgot to mention to the Cabinet Office. Microsoft has now been "accused of trying to secretly influence government consultation."

What's surprising is that the majority of this had been uncovered by two journalists — Mark Ballard at Computer Weekly and Glyn Moody — who work mainly outside the mainstream media. In fact, the mainstream media has remained silent on the issue, with the notable exception of The Guardian.

The end result of the work of these two journalists is that the Cabinet Office has had to extend the consultation and, as noted by The Guardian, "rerun one of its discussion roundtables after it found that an independent facilitator of one of its discussions was simultaneously advising Microsoft on the consultation."

So, we have two plucky journalists who stand alone uncovering large corporations that are bullying Government to protect profits worth hundreds of millions. Our heroes' journey uncovers gerrymandering, skullduggery, rampant conflicts of interests, dubious ethics and a host of other sordid details and ... hold on, this sounds like a Hollywood script, not real life. Why on earth isn't mainstream media all over this, especially given the leaked Bell Pottinger memo on exploiting citizen initiatives?

The silence makes me wonder whether investigative journalism into things that might matter and might make a positive difference doesn't sell much advertising? Would it help if the open standards battle had celebrity endorsement? Alas, that's not the case and the battle for open standards might have been extended, but it is still ongoing. This issue is as important to the U.K. as SOPA / PIPA were to the U.S., but rather than fighting against a Government trying to do something that harms the growth of future industry, we are fighting with a Government trying to do the right thing and benefit a nation.

If you're too busy to help, that's understandable, but don't ever grumble about why the U.K. Government doesn't do more to support open standards and open source. The U.K. Government is trying to make a difference. It's trying to fight a good fight against a huge and well-funded lobby, but it needs you to turn up.

The battle for open standards needs help, so get involved.


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