Technology and Research Mendeley Masterclass

©Tom Atkinson 2013 - www.r3digital.co.uk
©Tom Atkinson 2013

Last month we saw another edition of the global extravaganza that is Social Media Week. This time around there were over 1000 events and 25,000 attendees in 8 cities around the globe. The theme for this year was “Open & Connected” which is pretty much a perfect fit for the Mendeley philosophy. So we thought it would be great to host an event in the London SMW Hub about how technology is changing the way we conduct and fund research, how researchers interact, discover content and share their findings, as well as how the non-academic public can get involved and make a real different through citizen science initiatives.

Our Masterclass was streamed live and proved to be one of the most popular events of the week, with hundreds of people tuning in and sending their own questions.

Mendeley Co-founder and President Jan Reichelt kicked off the series of lightning presentations by explaining how Mendeley can help researchers organise their papers, but also how it went far beyond that. “Research is an inherently social activity, and Mendeley is an environment starting with productivity going over into collaboration, and that also crucially captures the social context going on around that research.”

Rachel Greene from JoVE challenged researchers to “stop reading and start watching,” explaining how the majority of the time scientists failed to accurately replicate the findings of key studies. She believes that technologies such as the one used in their peer-reviewed Journal of Visualized Experiments are much more suited for that purpose than traditional print, and can therefore dramatically increase reproducibility and the pace of scientific discovery.

“In the past everything was recorded on paper, but current science is very digital,” says IJsbrand Jan Aalbersberg from Elsevier’s Article of the Future project, which aims to improve scientific communication in all its rich facets. “All the records are digital, all the capturing of scientific data is digital, and the communication of that information of course is also digital. However the traditional publishers have not yet adapted to that, what they usually do is flatten the multidimensional, rich research that an author has created into a two-dimensional paper of text and images.” He gave insight into some tantalizing possibilities, including the ability to run variations of some experiments – in computer science for example – within the parameters of the article itself, making it a living, evolving piece of collaborative research.

Nicolai Humphreys from The Lancet told of how the meaning of the journal’s name came from the fact that “A lancet can be an arched window to let light in and can also be a sharp surgical instrument to cut out the dross” and upon founding the journal in 1823 Thomas Wakley stated his intention that the publication should serve both those functions. Fast-forward nearly 200 years and Nicolai is part of the team that is using technology to cut out the dross and make academic publishing more dynamic and cutting edge.

Emma Cooper described the journey that took their digital amusements company Team Cooper to developing a Facebook game in conjunction with The Sainsbury Laboratory to help harness the brainpower of citizen scientists to tackle Ash Dieback disease. Quoting Dr Dan MacLean, who approached them about building the game with their data, “humans are smart and humorous, and we love games.” The key to the success of Fraxinus is the human ability to recognise patterns, and this proved really addictive with players (over 38,000 in the first month), who spend 20 minutes on average playing the game, where the average tends to be around 5-10 minutes.

That is what Robert Simpson from citizen science web portal Zooniverse calls “cognitive surplus,” which describes the vast amount of time that we collectively spend on activities such as watching TV. “The human race spends 16 years every hour playing Angry Birds every hour. There’s a lot of brainpower out there and what we try to do is take that brainpower and make it more useful to researchers.” The team at Zooniverse works with researchers to design sites that take their data and presents it into a format that will let the crowd help them to achieve their objectives. In the case of Snapshot Serengeti, for example, this meant classifying the millions of pictures taken over 2 years by camera traps in Tanzania to provide new insight into wildlife dynamics.

“These days with modern technology Citizen Science is becoming a fresh new hot subject in science,” says Margaret Gold of Citizen Cyberlab, which is leveraging the web, mobile phones and other tools and platforms to enable crowd-sourced scientific research. “We give people across the globe an interactive means to either help with the collection of data or the processing of data, pattern recognition and so forth, and all this makes a very genuine contribution towards science.”

Dr Rayna Stamboliyska, a Research Fellow and Digital Content Coordinator at the Centre for Research and Interdisciplinarity in Paris, believes that technology can be used to bring research into primary schools, and that “we can change the world many kids at a time.” In these programs, PhD fellows work with school children to develop research projects, leveraging and incorporating various technologies and social media. “This not only engages them in the STEM curricula at a young age, but it’s a really gender neutral policy, so we’re addressing the problem of having so few women in science.”

But ground-breaking research often comes across the stumbling block that is lack of funding, and this is where Liz Wald from Indiegogo believes that crowdfunding can help scientists. “it’s really about getting rid of gatekeepers, knocking down barriers and taking ideas right to the crowd,” she said as she went through a few of the projects that were crowdfunded through Indiegogo, such as Kite Patch (a patch that lets people avoid mosquito bites) and uBiome (where you sent off swabs of your bacteria to them so that they could let you know more about yourself and also help the wider project to sequence the Microbiome). The message was that people will not only fund cool and useful gadgets, but all forms of science as long as you tell a good story.

If you missed it on the day don’t worry, all the presentations are on the Mendeley YouTube Channel, so you can watch them any time and let us know what you think! There are also some cool pictures of the day available on our Flickr page, we had a great time and thanks again to all our speakers and community!

 

 

 

Facebook Game Uses Crowdsourcing to Tackle Ash Die Back Disease

Fraxinus

Britain’s estimated 80 million ash trees are under threat, with scientists fearing that the Chalara fungus – known ash ash die back disease – could prove as deadly to the UK’s woodlands as Dutch elm disease was in the 1970s, killing millions of trees. In Denmark, the impact of ash die back was devastating, with between 60 and 90 per cent of all its ash trees being lost.

But there is hope… In the unexpected form of a Facebook game. Researchers sequenced the DNA from many infected trees and re-assembled them as closely as possible so they can identify variations that determine how susceptible the trees are to this disease. The human brain is uniquely adept at seeing patterns more quickly and adeptly than computers, and it’s that ability that the developers of Fraxinus (from the ash tree’s Latin name, Fraxinus Excelsior) are harnessing. The hope is that by identifying those patters through gameplay, players will provide potentially vital clues as to how the disease works on a genetic level.

“Every organism, whether human, tree of fungus has a genome virtually identical to the rest of the species but with tiny variations,” the game’s introductory screen explains. Players are challenged to manipulate and match up sequences of coloured leaves representing strings of genetic information from ash trees (both vulnerable ones from the UK and resistant strains taken from Denmark) and the Chalara fungus. Scientists will then look to use that data to cross-breed trees resistant to the disease.

Matching sequences closely earns high scores, and lets players claim patterns for their collection. However, these patterns can be stolen from under their noses by other players who use the same pattern to achieve a higher score. The competitive element adds to the addictiveness of the game and keeps players engaged for longer in order to build up and maintain their collections. The advantage for the database is that each pattern theft also serves to make the data even more accurate.

The game was envisaged by Dr Dan MacLean, head of bioinformatics at The Sainsbury Laboratory in Norfolk and designed by Bafta-nominated game developers Team Cooper. The unique challenge, say the developers, was to design a game that was engaging and addictive in its own right, but also managed to produce valid scientific results. These results are now being gathered and will be published as an open source supply for scientific research.

Dr MacLean told BBC News: ‘how we get the most out of it is if people want to come back to it and play it with their friends. That it’s for a good cause is a bonus.’

Apart from the lovely feeling of helping to save millions of trees, those who top the game’s leaderboard will actually be credited on articles as having helped with the research. Lead Developer for Team Cooper Russell Stearman said that it was a unique move for players to both contribute meaningful data to the Open Ash Die Back Project and be officially recognised in scientific papers.

Whiling away the hours on Facebook might not be everyone’s idea of advancing science and protecting the environment, but citizen science projects have used gamification to tap into the power of crowds with great success. The scientists behind this project believe that crowdsourcing this social media hive mentality could bring forward the production of disease-resistant trees by over 40 years, which is certainly an impressive claim. But what are the wider implications for science, and does this mean that social media gaming is coming of age? Let us know what you think!