Engines of Gamification

After years of talking about games for science, I'm finally going to jump in and make one.  I've got an idea (which I will elaborate on soon) and now I'm trying to figure out how to go about implementing it.  The challenge right now is to decide which of the infinite options that I should use to make it happen.

My basic requirements are pretty simple:

1. the game should be accessible in most Web browsers
2. it should run happily on an iPad
3. it should have basic graphics (e.g. blocks and arrows) and sounds
4. it should talk to a server running Java that will perform some computations and keep track of the data
5. it should enable fast prototyping
6. I should be able to do the prototyping myself

I discussed this with Josh Peay, a longtime game engineer at Sony and recent founder of mobile gaming company South Bird Studios, and he advocated jumping right in and learning a full-fledged game development system called Unity3d.  So I had a look.. and was immediately intimidated by its complexity.  It turns out that building immersive interactive games in a 3d environment still takes quite a bit of work - and quite a bit of artistic support - even with a hulking (2GB application) gaming engine in the background.  Since I really haven't conceived of anything that would benefit substantially from the level of interactive control offered by Unity or its brethren I'm really hesitant to start climbing up its learning curve.

Flash seems like it would probably do the job pretty well, but see #2 above.

And that leads me towards some sort of javascript environment.  Though I have played a bit with javascript before, I'm really not very good at it.  This causes me concern for #5 and #6 above.  To reduce this concern I've started looking for library support.

Here is a year-old list of 66 game-related javascript libraries that clearly is an underrepresentation of what is out there.  One that isn't listed is a Google product called PlayN (formerly 'forplay') based on GWT.  PlayN is tempting for me because you write your code in Java (which I guess is appealing to those of us in their thirties or greater) and it can generate deployable games in HTML5, Flash, the desktop and there are rumors maybe someday for iOS.  Its also easy to distribute the games via the Chrome store.  It doesn't have a lot of the Unity3d bells and whistles but, like I said, I don't need to use it to build the next Call of Duty.  Still, PlayN is still alpha code and, as my colleagues enjoy reminding me, Java and other compiled languages are for old farts...

Which to choose????

Update The interested gamifier might also like to have a look at the following frameworks for creating computerized versions of board and card games:

1. Vassal
2. Battlegrounds
3. ZunTzu

I like that you have the basics of player/card/board/hand/deck etc. management taken care of, there are nice realtime communication features ready out of the box and that you are provided with what appears to be a pretty straightforward development environment.  I don't like that players would have to install the engine on their computers before they could play the game and that none of them would work on an iPad.

Interview with Results for Development Institute

A few days ago, Hassan Masum of the Results for Development Institute, asked me some questions about the Gene Wiki as a platform for collaboration and discovery in the health sciences.  The results of the interview were posted today on their blog as the first entry in what will be an ongoing series of interviews with people in the business of collaborative innovation.  It was fun talking with Hassan and I'm looking forward to seeing the rest of the interviews as they come out.

Results for Development looks like a really interesting kind of non-profit.  One of the many things that they do is to take really bright, creative people, like Hassan, and task them with identifying key avenues to accomplish major transformational change.  Their mission statement is:

"R4D's mission is to spark innovative ideas and catalyze high impact actions that reduce poverty and improve lives in developing countries."

Its very exciting to know that the Gene Wiki might play some very minor role in realizing a vision like that.

Sepublica 2012 deadline extended

Deadline extended: now March 18

http://sepublica.mywikipaper.org/ – the future of scholarly communication and scientific publishing

SePublica2012 an ESWC2012 Workshop.
May 27 or 28 (exact day to be announced), Heraklion, Greece.

At Sepublica we want to explore the FUTURE OF SCHOLARLY COMMUNICATION and SCIENTIFIC PUBLISHING. As we are going through a transition between print media and Web media, Sepublica aims to provide researchers with a venue in which this future can be shaped. Consider research publications: Data sets and code are essential elements of data intensive research, but these are absent when the research is recorded and preserved by way of a scholarly journal article. Or consider news reports: Governments increasingly make public sector information available on the Web, and reporters use it, but news reports very rarely contain fine-grained links to such data sources.  At Sepublica we will discuss and present new ways of publishing, sharing, linking, and analyzing such scientific resources as well as reasoning over the data to discover new links  and scientific insights.

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Community Intelligence session at ISMB 2012

Looking for something to do in Long Beach, California on the afternoon of Tuesday, July 17, 2012 ?  Stop by the special session on Community Intelligence in Bioinformatics at this year's conference on Intelligent Systems in Molecular Biology (ISMB)!

We have four distinguished speakers lined up:

• Alex Bateman will discuss the use of Wikipedia in RFAM, PFAM and the rest of science.
• Alex Pico will tell us about the continued expansion of WikiPathways.
• Andrew Su will be on tap to discuss the latest and greatest breakthroughs in the Gene Wiki.
• Firas Khatib will tell us how his team managed to translate protein folding into a game (called Foldit) and that game into an expanding series of scientific discoveries.  

With nearly 7 billion people on the planet and a rapidly increasing number of them connected to the Web, it is time to figure out how to work together effectively, both to solve the problems that we are collectively causing and to solve the problems whose solutions will extend and enrich all of our lives.  Each of these talks will try to help answer the question of how we can translate the incredible scale, connectivity, and creativity of the world's population into scientific progress.  Hope to see you there.

Semantic Publishing workshop at ESWC in Greece

I'm helping to organize this exciting event, please consider submitting a manuscript and or attending.  From the official call for papers:

http://sepublica.mywikipaper.org/SePublica2012 an ESWC2012 Workshop.  May 27-31, Heraklion, Greece.
At Sepublica we want to explore the future of scholarly communication and scientific publishing. As we are going through a transition between print media and Web media, Sepublica aims to provide researchers with a venue in which this future can be shaped. Consider research publications: Data sets and code are essential elements of data intensive research, but these are absent when the research is recorded and preserved by way of a scholarly journal article. Or consider news reports: Governments increasingly make public sector information available on the Web, and reporters use it, but news reports very rarely contain fine-grained links to such data sources.  At Sepublica we will discuss and present new ways of publishing, sharing, linking, and analyzing such scientific resources as well as reasoning over the data to discover new links  and scientific insights. 

Workshop Format 

We are planning to have a full day workshop with two main sessions. During the first part of the workshop accepted papers will be presented; the second part of the workshop will address by means of focus groups two main questions, namely “what do we want the future of scholarly communication to be?”  and “how could data be preserved and delivered in an interactive manner over scholarly communications?”. These focus groups will be followed by a panel discussion. As an outcome of these activities we will have a communique that will be the editorial for the workshop proceedings,

Dates 

* workshop papers submission deadline: Feb 29
* workshop papers acceptance notification: April 1
* workshop papers camera ready: April 15 

Submission

 https://www.easychair.org/conferences/?conf=sepublica2012

Issues to be addressed

• Representation:
  • Formal representations of scientific data; ontologies for scientific information
  • What ontologies do we need for representing structural elements in a document?
  • How can we capture the semantics of rhetorical structures in scholarly communication, and of  hypotheses and scientific evidence?
  • Integration of quantitative and qualitative scientific information
  • How could RDF(a) and ontologies be used to represent the knowledge encoded in scientific documents and in general-interest media publications?
  • Connecting scientific publications with underlying research data sets

• Technological Foundations:
  • Ontology-based visualization of scientific data

• • Provenance, quality, privacy and trust of scientific information
  • Linked Data for dissemination and archiving of research results, for collaboration and research networks, and for research assessment

• • How could we realize a paper with an API?  How could we have a paper as a database, as a knowledge base?
  • How is the paper an interface, gateway, to the web of data? How could such and interface be delivered in a contextual manner?

Applications and Use Cases:

• Case studies on linked science, i.e., astronomy, biology, environmental and socio-economic impacts of global warming, statistics, environmental monitoring, cultural heritage, etc.
• Barriers to the acceptance of linked science solutions and strategies to address these
• Legal, ethical and economic aspects of Linked Data in science

Scientific Games in Genome Biology

Happy New year everyone! In case you are looking for some inspirational reading to start off 2012, Andrew and I wrote a Research Highlight for Genome Biology on Games With a Scientific Purpose.  Kudos to Andrew for convincing them to make it open access so you can actually read it...

Research highlight      Games with a scientific purpose Good BM, Su AI
Genome Biology 2011, 12:135 (28 December 2011)
[Abstract] [Full text] [PDF]

Gene Wiki on NAR database cover

The Gene Wiki Rainbow just got a little bit more famous.  Check it out on the cover of the 2012 Nucleic Acids Database issue.  Thanks again Martin K.!

The Gene Wiki on the cover of NAR

Mining the Gene Wiki

Our article about mining ontology-based gene annotations from the text of the Gene Wiki just came out at BMC Genomics.  Yay!

In the article, we discuss the results of what I think might be the simplest text-mining strategy that could possibly work.  Based on the premise that each Gene Wiki article is fundamentally about one particular gene, we make the simplifying assumption that all of the concepts detectable in the article are descriptors of what that gene does.  With those assumptions in place, we use the NCBO annotator to detect concepts from the Gene Ontology (GO) and the Human Disease Ontology (DO) in the text of articles about genes.  Each detected occurrence thus produces a candidate annotation for the gene.  From the article:

For example, we identified the GO term ‘embryonic development (GO:0009790)’ in the text of the article on the DAX1 gene: “DAX1 controls the activity of certain genes in the cells that form these tissues during embryonic development”.  From this occurrence, our system proposed the structured annotation ‘DAX1 participates in the biological process of embryonic development’.  Following the same pattern, we found a potential annotation to the DO term ‘Congenital Adrenal Hypoplasia’ (DOID:10492) in the sentence: “Mutations in this gene result in both X-linked congenital adrenal hypoplasia and hypogonadotropic
hypogonadism”.

We found that, in terms of precision, this simple approach worked pretty well on detecting gene-disease  annotations (90-93%) but not nearly as well at detecting gene-function (GO) annotations (48-64%).  As you might expect, the recall equation worked in the opposite direction with many more potential GO annotations discovered (11,022) then DO annotations (2,983).  Though there was some overlap, the majority of the predicted annotations did not have any match in existing annotation databases, showing that the Gene Wiki contains some knowledge that centralized resources like the Gene Ontology Annotation database do not yet represent and that basic text mining provides a way to access that knowledge computationally.

But, you say, that precision for the GO is really low, what use is this really?  For applications that require 100% accuracy, like a curated database, well you would need to curate the predicted results and that might be quite a lot faster than searching through PubMed to find them all from scratch.  As it turns out, there are also other kinds of applications that can take advantage of data like this that has noise in it.  As long as there is a strong signal within the noise, probabilistic techniques, like enrichment analysis, can work.  This is possible because, although many of the individual annotations might turn out to be incorrect, as a group they are far far from random.

For more details, read the paper ;).

Grain of Sand Quote - stolen!

I was amused to see an article come out today that used the same introductory quote as we did six years ago.  The paper from today is called "A world in a grain of sand: human history from genetic data" and is available from Genome Biology.  I would tell you what its about, but neither I nor the Scripps Research Institute where I work has paid for access to it.  You can however access our very cool paper called "Sand DNA-a genetic library of life at the water's edge" for free!  Oh yes, the quote is:

‘To see a world in a grain of sand,

and heaven in a wild flower,

Hold Infinity in the palm of your hand,

and eternity in an hour.’

—William Blake from Auguries of Innocence

While I can't say which is the better manuscript, I'd wager that we win for most appropriate use of that quote in the intro. 

Quotes from Reality is Broken

I'm currently supposed to be writing an article about scientific discovery games in biology, but I have writer's block.  So instead, I'm writing here.. which is much easier!  The article I am not currently writing will discuss recent successes like "Algorithm discovery by protein folding game players" by Firas Khatib and others.  In preparing to write this article (i.e. more not-writing), I assembled some inspiring quotes from the fantastic book "Reality is Broken" by Jane McGonigal.  I share them here below because, well they made me think a little bit and perhaps they will do the same for some else, and this allows me to push back my real work by another 5 minutes..

“It is games that give us something to do when there is nothing to do.  We thus call games “pastimes” and regard them as trifling fillers of the interstices of our lives.  But they are much more important than that.  They are clues to the future.  And their serious cultivation now is perhaps our only salvation” -  quote that opens McGonigal’s book - from Bernard Suits

“Games aren’t leading to the downfall of human civilization.  They’re leading to its reinvention” (p354)

“Game developers know better than anyone else how to inspire extreme effort and reward hard work.  They know how to facilitate cooperation and collaboration at previously unimaginable scales.  and they are continuously innovating new ways to stick with harder challenges, for longer, and in much bigger groups.” (p13)

“Game design isn’t just technological craft.  It’s a twenty-first-century way of thinking and leading.  And gameplay isn’t just a pastime.  Its a twenty-first-century way of working together to accomplish real change.” (p13).

“Anything else you think you know about games, forget it for now.  All the good that comes out of games-every single way that games can make us happier in our everyday lives and helps us change the world-stems from their ability to organize us around a voluntary obstacle” (p34)

“Compared with games, reality is unproductive.  Games give us clearer missions and more satisfying, hands-on work.” (p55)

“If you were able to focus the attention of the entire planet on a single goal, even just for one day, and even if it just involved dispatching aliens in a video game, it would be a truly awe-inspiring occasion.  It would give the whole earth goose bumps.” (p112)