30 November 2011 by Jason Hoyt

We, along with PLoS, have been overwhelmed by the huge response that academics and the developer community have given to open up science. When we announced this contest to develop science applications on top of the Mendeley and PLoS platforms last March, we were not totally sure that anyone would even be interested. Boy, were we wrong!

Tim O’Reilly, Founder and CEO of O’Reilly Media and one of five all-star judges, said this about the Binary Battle –

“I always tell developers to work on stuff that matters. It’s time to stretch beyond the consumer internet, and what better place to focus than on furthering the cutting edges of science?”

Mendeley launched the API platform in April of 2010 with the hope that it would 1) spur innovation in the science ecosystem and 2) send a signal to others that opening up data benefits everyone. To date, more than 1000 developers have applied for API keys to build on top of that data. With the Binary Battle announcement, we hoped to carry open science further and by all accounts we did.

Today we announce the winners of the 2011 Mendeley-PLoS Binary Battle. We narrowed the Binary Battle entries down to the Top 10+1, and then handed the voting over to our list of expert judges (Werner Vogels, Juan Enriquez, Tim O’Reilly, James Powell, and John Wilbanks. We also opened the vote up to the public to count as 1/6 and combined with the judges. It was great to see that both the public voting and the judges voting correlated very well. It was so close for many of the apps, but one stood out to both the judges and the public….

Winners

Grand prize

events 2 design research tools  Winners of the first Binary Battle Apps for Science Contest

The overall grand prize of the 2011 Mendeley-PLoS Binary Battle, receiving $10,001 and $1,000 of Amazon AWS credits, goes to openSNP!

With openSNP (pronounced “open snip“), you can share your personal genome from 23andMe or deCODEme to find the latest relevant research and let scientists discover new genetic associations.

Werner Vogels, Amazon CTO and one of our star judges said this, “OpenSNP is cool. I have uploaded my genotype, and it is interesting to see it at work.”

We did a brief interview today with openSNP to find out more about the project, so check below for that.

Runner up

events 2 design research tools  Winners of the first Binary Battle Apps for Science Contest

And Runner Up, receiving $5,000 and $500 of Amazon AWS credits, goes to PaperCritic!

PaperCritic allows for post-publication peer review in an open environment. Rate papers, write critical reviews or read those from others.

Second Runner Up for making use of both Mendeley and PLoS APIs

events 2 design research tools  Winners of the first Binary Battle Apps for Science Contest

We wanted to give an extra prize for the top voted app that used both sets of APIs (openSNP uses both as well). The winner receives $1,000 and the best prize of all, a Parrot AR Drone Quadricopter. That prize goes to rOpenSci!

rOpenSci provides R-based tools to facilitate Open Science; including R packages for both Mendeley and PLoS.

The other Binary Battle contenders

The judges had a difficult time, because of the quality of the 11 finalists. These are all great apps in their own right, so once again, here are the other finalists in alphabetical order (also see our finalists page for more info):

Collabgraph
Droideley
KLEENK
PLoS Impact Explorer
ReaderMeter
ScienceCard
TiNYARM
Total-Impact

Although the above were not overall winners, as said, it was a tight battle and they are all helping to make an impact on opening up science. So, congratulations to all of you from everyone at Mendeley and PLoS. Science is better off because of your efforts, and we hope that you’ll receive recognition for that going forward.

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Interview with openSNP team

This morning we asked one of the founders of openSNP, Bastian Greshake, a few questions after letting them know that they had won the Binary Battle.

What problem is openSNP trying to solve?

There is a trend that more and more people get themselves genotyped by Direct-To-Consumer Genetic testing companies. 23andMe and other companies also use this data of consenting customers for scientific research. Some customers already liberate their data and make it available to the public by uploading it to the internet. But genetic information without any phenotypic information is not that useful.

So we try to be a community-driven platform for people who are willing to share phenotypic and genetic information for the public. We hope that this will enable crowdsourced genome wide association studies in the future.

Who is on the openSNP team?

There is Philipp Bayer, who currently studies Computer Science in Australia. As we speak he is working on his master thesis (which also includes working with SNPs). Much of the code is written by him.

Fabian Zimmer, who currently does his master thesis in Germany, is a great help and provides design-stuff and expertise in server management.

Helge Rausch is a web developer here in Germany, he does a great job on testing the application and killing bugs.

I’m [Bastian] also doing my master studies right now, here in Germany about Ecology & Evolution. I’m also involved in the code-writing and besides this do user support and the social networking-stuff.

Why did you choose to enter the Binary Battle?

We chose to implement PLoS and Mendeley early on in the development of openSNP as both are a great resources to find the latest publications on SNPs.

This enables users to get in touch with the primary literature and to see the latest information we have about the SNPs that get screened.

So entering the binary battle seemed like the obvious thing to do.

Any words of advice for others wanting to develop an app for science?

Make use of open data, the APIs of Mendeley and PLoS and all submissions in the Binary Battle have shown how creative people can re-use the data in many ways.

So don’t only make use of open data but also be open yourself: Use open licenses like Creative Commons and make it easy for others to re-use your application.

What is next for openSNP?

We are trying to get some funding through the WissensWert-contest of the german WikiMedia ,in order to get some more people genotyped. This would not only benefit openSNP but everyone who is looking for free-to-use genetic data sets.

On the technical side we are working on implementing the Distributed Annotation System-Protocol, which is widely used in Genetics. As soon as we have added this it will get even simpler to re-use the data (for example in genome browsers) that users upload to openSNP. We are also trying to extent the phenotype-information and are looking for a standardised way of providing the phenotypic information for bulk downloading.



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And that’s it! We’ll highlight interviews with the other winning apps in upcoming blog posts. Thank you to everyone for making Apps for Opening up Science a huge success, and special thanks to our judges and PLoS for joining us in the Binary Battle.

Jason Hoyt is Chief Scientist & VP of R&D at Mendeley. Follow him on Twitter @jasonHoyt

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2 Responses to “Winners of the first Binary Battle Apps for Science Contest”

  1. Daniel Says:

    For the contestants that did not receive a stipend, consider posting a project profile on FundaGeek. FundaGeek is the new crowdfunding platform expressly for scientific research. Looking for a new funding paradigm? Try FundaGeek. Visit: http://www.fundageek.com to learn more.

  2. Sean P Fullerton Says:

    Big congratulations to the guys involved with openSNP. It’s an excellent achievement and a very interesting concept (albeit a little over my head if I’m honest!). Best of luck with your future endeavours.