open source, health care, and the data commons

From his recent post for Strata Rx“Open Source software as a model for healthcare”Andy Oram with some important reminders and parallels. Do have a read.

“Open data is now a rallying cry for advocates of public information and more effective governments, but the lesson of the open source movement is that the mathematics and algorithms used to process data should be open as well. This applies to health care because data is inert in itself. Some kind of processing must be applied to extract useful information, and it this takes the form of open source code, many people can check it for accuracy, reuse it, and upgrade it.

It is this continuous activity of sharing and upgrading that drives and defines quality and value over time. In other words, the community is the purveyor of value.”

a supercomputing “driver’s license”

A smart approach from the folks at Software Carpentry and the Software Sustainability Institute – a means of assessing need before throwing resources at willing subjects. After witnessing first-hand through the discussions at the e-Infrastructure Leadership Council (I sit on the council as an industry representative), I cannot stress enough the importance of actually assessing a community’s level of awareness, skill and need before tossing them head first into serious hardware usage. A smart approach I hope gets extended beyond DiRAC.

a supercomputing “driver’s license”

GSK and their move to “open”

Fresh off the red eye back to London yesterday, the conversation about GlaxoSmithKline’s recent “open data” announcement had taken over my Twitter stream (as well as jtw’s, whom I’ll get to later).

There was coverage in The Guardian (as well as elsewhere), there was an event aptly timed at the Wellcome Trust that morning to further discuss the benefits of open, there were armfuls of open data friends taken aback (and rather curious) about a big pharmaceutical company going “open”. 

jtw goes into this in detail (and much more eloquently than I can) over on his blog. The GSK Malaria deposition came whilst we were both at CC, and was one of a number of discussions we were having with various big pharma neighbors in Boston and elsewhere about more open approaches. They were under tremendous financial pressures and looking for a way to breathe a bit of life into stale siloed approaches – and I have to say, it was by no means surprising, but refreshing nevertheless.

One of the companies I currently work with at Digital Science has been working in that space for a number of years now, offering more comprehensive, smarter search for chemical structures in patent documents (think, early-stage drug discovery). They’ve had to rethink their audience and design, as well, to be more open, allow for better integration amongst other open – and sometimes even closed – resources.

It’s an interesting time, but learned first hand in the aforementioned discussions … be mindful that not every “open” listing is truly open. We’re still dealing with disparities in the vernacular we use – and that’s OK. Just go in with open eyes. It’s still a step forward, but the devil is in the details.

Curious to see how this unfolds, but in the meantime, do give jtw’s post a read. 

february’s sameAs: education

Next Monday (Feb 21) Matt and I are back with our first in-person sameAs of 2011 (is it really mid-February already?). We’ve chosen education as our leitmotif, and have aligned a set of friends who really push the limits to how we think of formal education and learning.


We’re revisiting old stomping grounds, heading back to the Coach & Horses in Clerkenwell, and we hope you’ll join us. The night kicks off at 7 p.m.

We’re thrilled to welcome the following folks, who will each be sharing with us their innovative approaches to how we educate and interact with learning environments. In true sameAs spirit, they come from a diverse set of backgrounds and perspectives, from design, to life sciences and philosophy.

For this sameAs, we are pleased to welcome:

* Matthew Carlos – co-founder of MakeLab, Philosopher, Knowledge Architect. Matthew specialises in knowledge architecture and ethics with further experience in community regeneration, media & communication, and fine art. He’s been involved in the start-up of a number of social-benefit organisations, including most notably One Laptop Per Child, an effort tasked with providing inexpensive laptops as learning tools to children in the developing world. His current interest is the redesigning of civic institutions, particularly academies and libraries.

* Daniel Glaser – neuroscientist and Head of Special Projects at the Wellcome Trust. Daniel, among many other things, was responsible for getting kids in every primary school in Britain designing their own genetic experiments in celebration of the Darwin centenary year. He’s now working with schools on a project exploring physionomy pegged to the Olympics.

* Tassos Stevens – co-director of Coney, an agency of play. He’ll be telling us about one of their recent developments involving a practice called “adventures-in-learning”, creating adventures in classrooms where the kids are the heroes, operated remotely over the digital wires and facilitated by their teacher. Tassos has also been involved with the development of such other games and experiences as SuperMe and Papa Sangre (for those of you who joined us for our November sameAs, this one may ring a bell … 😉 )

We hope to see you there. For more, visit our web site.

What I’m passionate about – sameAs

Cross-posting this from our sameAs blog, post entitled “This one’s for Jameson”. For anyone wondering how I ended up working in science and technology, here’s my story …

This month we are highlighting contributions from our sameAs friends around the world, each answering the question “what are you passionate about”. Over the course of the last few weeks, we’ve been lucky enough to be on the receiving end and hear your stories about what inspires you, be it the slightly dangerous hobby, pop music, or brain research. Thank you to each and every one of you whom have lent your voice and submitted (and keep ’em coming!)

The idea stemmed out of a conversation I had with Matt soon after I moved to London over a few pints – in some ways the first informal sameAs – where we shared our stories: how we came to work in this world of science and technology, what our hopes were, how we got our starts.

My passion, to answer the question that Matt and I posed earlier this month, is to make research more efficient. That aim transcends any work affiliation, paycheck, or hat I happen to be wearing on a given day. Let me tell you why.

I’ve never donned a lab coat, or run experiments – I don’t come from the sciences at all. My passion stems from two very important people in my life and a frustration, paired with a desire to help.

As a girl, I watched my grandfather waste away, suffering from a disease I didn’t understand, watching him in less than two years go from a very active man to one that could only blink to say hello. For a long time I was convinced it was ALS. It turned out to be something different – a progressive parasupranuclear palsy – a rare degenerative disease often mistakenly diagnosed as Parkinsons, that completely wore him down unexpectedly before our eyes. Even to this day, we don’t know how that came about, or why an accident spurred such rapid degradation of his body. You can read more about him in this post, written a few years ago.

The other person, Jameson, you’ll hear from below.

This post is for him, one of my oldest friends from my time in Boston, and the reason I decided to leave a career in print journalism to help fix what to me was a frustrating, slow, and unacceptable system. Jameson was diagnosed with Marfan Disease early in his days at Berklee College of Music, not long after we met waiting tables at a local restaurant. The doctors stumbled on the condition by accident, after he suffered a fall while rollerblading in the Back Bay, where they realised the connective tissue had begun to deteriorate around his knees. They then started to put the pieces together bit by bit – realising that his aches and pains weren’t just growing pains, that the 2-inch indentation the size of a fist over his heart was not a freak coincidence, that his chest pains were real.

Jameson let me in during some of the most difficult times in his time trying to understand this newfound burden, through the series of mini-heart attacks he would have throughout the night due to weakening of his heart, to days he could barely play piano – his passion – due to the pain in his hands. He was told by the doctors that he’d be in a wheelchair by his early thirties. Even more devastating, for the first time, his dream of being a professional musician was found hanging in the balance – with a threat of that time being cut short due to a failing body from a disease most didn’t understand, and one that was underfunded.

I remember trying to allay Jameson’s fears over the years, as any good friend would, by saying there had to be an answer (I can be a stubborn thing at times), that we’d find some way to get through this, that I’d play the piano for him should his hands fail – anything that I could do or say to offer him some peace of mind. He lives and breathes music – and taking that away from him would completely shake his core. I was determined to make sure that didn’t happen. He didn’t deserve it. No one does. I poured myself into research, as so many others do when a loved one is in trouble.

I told him I’d find a way to fix him.

I still tell him that to this day, over eight years later. And in some way or another, be it through working directly with rare and neglected disease research groups or advocating better knowledge sharing practices, working in open science or even now through tool development, I’m working towards that each and every day. Jameson is the reason I believe in what I do. Not all of us are fortunate enough to work in a field that we’re truly passionate about – but I am. And I’ve been fortunate enough to come to know others such as Sharon Terry of Genetic Alliance and Josh Sommer of the Chordoma Foundation – two astonishing individuals that share similar passions (each stemming from their own stories). It’s reassuring to know people like those two are out there, pushing the envelope and asking the hard questions.

Jameson currently has the Marfans at bay and is currently a professional musician – a brilliant pianist and rockstar in Florida. I’m thrilled to be able to say that he’s living his dream and still doing what he’s passionate about: writing and playing music.

And I’m still here working to make sure he can do that as long as possible, in some way or another. That’s my passion. Every little step forward helps.

Jameson was kind enough to submit his own video (with his own music, as well 🙂 ) for this month’s sameAs. He’s a remarkable musician, but even more so a remarkable human being and inspiration, and I’m thrilled to be able to tell my story, his story, and have him be a part of this month’s sameAs. Jamie, this one’s for you.

science online, sameAs and #solo11

I’m still recovering from this past week / weekend’s Science Online ’11 in the Research Triangle – the 5th annual event on science and the Web. A massive thanks again to the organisers, Bora and Anton, for putting together a marvelous and rich event from start to finish. It’s not an easy task (speaking from experience), and they did an absolute brilliant job.

Saturday was when the event kicked into high gear, with a day of truly thought provoking discussion sessions. I joined the fun, leading a discussion on technology and infrastructure in science. The slides below were meant to seed the conversation with a few starting points, as well as set some of the context about the science in the information age. Many thanks to the audience for their insightful commentary, questions and participation, especially Heather Piwowar, Jean-Claude Bradley, Jan and Jason from Mendeley, Carl Boettinger, Walter Jessen and Ana Nelson. I’m most certainly leaving people off that list, so my apologies in advance for that. More to come on that session in the coming days. But thank you all.

On to sameAs (see the video above) – we have 2 more weeks left in January for submissions, and are elated/excited/inspired by the ones we’ve received thus far. This month we’re turning the mic around and asking the community to tell us what you’re passionate about, just as a fun user-contribution, virtual exercise. We all have something that we’re passionate about, something that inspires us, gets us excited. Or, if nothing comes to mind, what better time than the start of a new year to reflect on what may drive you to do what you do. You can participate by sending us short video clips, images / audio files, or even tweets (do mark them with #sameAs so we can collate, please and thank you). We’ll be featuring the contributions on our shiny new sameAs blog, as well, so stay tuned. Help us spread the word and make this a truly global event. We want to hear from you (and #scio11 folks, note the friendly challenge posed in the video above 😉 )

Speaking of Science Online, I’m delighted to join Lou Woodley (of NPG) and Martin Fenner (Hannover Medical School) on the organising team for the London-based event this year (#solo11). Sponsored by Digital Science (my day-job) and NPG, Science Online London will be taking place at the British Library again this year, just after my birthday on Sept 2-3. Stay tuned for more in the coming months as planning progresses. We hope you all can make it.

And here are those slides, as promised. Off to Beyond the PDF in San Diego tomorrow – the next stop on the US tour. More to come.

I hope you all will help lend your voice to this month’s sameAs. Passion is something that can be a powerful driver in what we do, not only in keeping us inspired, but helping to inspire others. We hope to hear from you. 🙂

jumping on the ‘new year’ bandwagon

It’s a new year, and at the risk of sounding a bit trite, I’ve set some goals for 2011. They’re slightly different than the go-to-the-gym, travel-more, quit-smoking variety. 2010 was monumental, particularly the last 6 months of it. I left my perch at Creative Commons after 4+ years working with incredible folks on the science side of things. I joined a team of heavy hitters to help get a new technology company off the ground, involving a move to London. With the help of a dear friend, we launched a side project that provides us with an outlet for exceptionally geeky and tremendously fun conversation with brilliant folks day in and day out, allowing us to put our own stamp on the London meetup scene. There are no complaints on this end. But, there’s always room for improvement … so for the sake of transparency and knowledge sharing, here are a few things I hope to work on in the new year.

(Also, stay tuned for more on the new company – long overdue – and exciting news about our January sameAs. Coming soon.)

So, here goes:

Write / blog more. Well, off to a good start, at least … //pats self on the back. On to number two.

Learn a new language, or at least give it the old college try. I thought I’d spice things up this year a bit and try to tackle two in this category. Oddly enough, I think I may have better luck with the latter listed.

(1) French – Or at least brushing up on my vocabulary. Thanks to Polyglot for streamlining that into my online activity. Such a smart little Chrome plug in.

(2) Ruby – Yep, you heard me. With my brand new PickAxe by my side and a slew of wacky tutorials involving zombies and cartoon foxes, I’ve taken the plunge. I’m determined to be able to do more than basic arithmetic and page changes. This also means certain male friends of mine will be pestered more with n00b programming questions. They still think it’s charming. They’ll learn soon enough 🙂

Getting better at clearing out my browser windows (current tab count is low, at 34). I think I need to come up with a term for this. Any suggestions? Tabular-info-filter-failure? Tab-ulitis?  And this isn’t even touching on the RSS Reader that’s chock full of unread goodies. I’m determined to make my way through it, but in the meantime,  some recent links of interest:

Tim O’Reilly on the Maker Revolution, and how DIY has affected various aspects of our life.

Clive Thompson on how tweets are stimulating deeper analysis, rather than shortening our attention span / information consumption threshholds.

Death by Irony: How the Librarians Killed the Academic Library … and more on the differences between (and increase of the former) “Born Digital” and “Born Again” publisher playbooks.

* Why Linked Data is not enough for scientists – Dave de Roure hitting it out of the park again.

* Statistical Zombies – A look at the top 10 mistakes in day-to-day reporting of numerical and statistical info (with a catchy title to get in on the zombie craze. Can’t blame him, really)

And to round it out, some predictions for the New Year. Instead of adding to the deluge of NY related information out there on teh interwebs, here’s a smattering of posts I particularly liked, looking forward to the year ahead.

* 2011: the Year of the Exome

* Jim Hendler with his Semantic Web flavored New Year’s Resolutions

* On a broader scale, what to look for in 2011. Sadly, bacon was on the 2010 list … M’mm bacon.

* The Guardian’s take on New Year’s Resolutions and how to be a better person in 2011. This one may surprise you …

* And last but not least, Nico Adams reads the data and technology tea leaves for 2011, taking a stab at some predictions of his own. Ones that I happen to believe wholeheartedly with. Bravo.

That wraps it up for now. There’s much more to write, but the jetlag is kicking in again … Stay tuned. And here’s to 2011.

some holiday sci/tech themed geekery

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It’s the perfect stocking stuffer, really.

This past Monday, Matt and I hosted our first sameAs pub quiz – a night of science / tech / design brain benders, laughs, pints and general geekery goodness. We were fortunate to have a number of sameAs friends make the trek in despite a less than reliable transit network for some pre-holiday fun. And of course, plenty of new faces in the crowd, each embarking on a night of trivia.

Many thanks to Matt Brown of the Londonist for lending us his brain and drafting the quiz for us. I now have a new appreciation for not only his knowledge of London and its inner workings, but nerdery as well.

Miss Monday night’s fun? Don’t fret. The questions have been posted on Nature Network, available for all of you to give a try. See how many you can answer without using the googles (or Yahoo – do they still exist? 😉 ). First installment here,second here.

Thanks to Aaron Dey for snapping some shots of the night’s fun, as well. It’s been an incredible year for sameAs, but only the beginning. We hope you stay tuned for what the new year can bring. I hear it may even involve the Internets. 😉

Happy holidays, from both of us.