Crowdsourced biological science - edinburgh
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Insights and examples from crowdsourced biological sciences. Presented as part of a workshop at Edinburgh University.
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Crowdsourced biological science - edinburgh
- 1. Crowdsourcing biological science: examples & insights Cell slider Phylo Eyewire Dr Erinma Ochu Faculty of Life Sciences, University of Manchester
- 2. Overview •My background •Definitions: citizen science •Examples & insights •Considerations •Publications & Resources www.slideshare.net/erinmaochu
- 3. Wellcome Trust Engagement Fellows
- 4. Catalyst! Citizen-led social innovation tools for change # @catalystproj www.catalystproject.org.uk
- 6. Approach 1. Identify problems/define needs Consider ethics, failure, engagement & impact as innovation points 4. Mobilise knowledge 2. Pilot interdisciplinary policy & practice partnership solutions 3. Archive & evaluate journey & impact
- 7. Definitions/ Approaches • Citizen Science – Unpaid individuals & interest groups contributing to scientific experiments • Co-design (or extreme citizen science) – Public participate in setting research question(s), methods and/ or analysis to address social need • Crowdsourced science – Complex problem, wisdom & power of crowd to create, analyse, collect datasets – research benefits • DIYBIO – network of hobbyists & biohackers DIY, hack, open source ethos to labs, equipment, methods • Variations – Citizen Science with co-design & crowdsourcing elements
- 8. Large scale & complex Wisdom of problems the crowd
- 9. FOLDIT: http://fold.it/ Nature 2010 ;466 (7307); 756 - 60. Nature Biotechnology 2012; 30; 190 - 192 • Protein structure prediction computationally demanding • Competitive puzzles to better understand protein structures • 3D Tetris & Minecraft • Started as Rosetta@home – using computing power • Feedback between developers & users & lots of new puzzles • Compete against other players – leaderboard for each puzzle • See: http://www.youtube.com/watch?v=lGYJyur4FUA
- 10. Cell slider: http://www.cellslider.net/ • Cancer UK & Zooniverse ( https://www.zooniverse.org/#biology) • Identify cancerous breast cells donated from patients • Motivates by ‘joining the fight against cancer’
- 11. Phylo: http://phylo.cs.mcgill.ca/ • DNA puzzle game that contributes to mapping diseases within human DNA • Sheer size of genome makes it too expensive for computers • Relies on human pattern recognition • Visual tutorial • Leader boards (total, monthly & weekly) • Translated into 9 different languages
- 12. Eyewire: https://eyewire.org/ • Part of ‘Wired Differently’: http://wireddifferently.org which aims to map the connectome (connections between neurones) • EyeWire is an online community of “citizen neuroscientists” who map neural connections by playing a game.
- 13. CROWDSOURCED EXAMPLES • ADD to google doc: http://bit.ly/VidiGw • Join google+ communities: http://bit.ly/VhX7vy
- 15. Other considerations • Complex problem benefits from power & wisdom of the crowd to solve it collectively • Not solve-able by other means • Ethical considerations – patient data, samples • Simplicity of sign up & participation • Social software strategy: recognition & engagement • Clear instructions, guidance & accessibility • Feedback & evaluation • Partnerships
- 16. Partnerships • Biological Science Researchers • Other disciplines: IT, management, social science, communications, psychology? • Technology: platform & channels, database, architecture, server, instructional content, • Communication & marketing • Design: graphics, 3D modelling, website, game • Industry: scale-able problems? • Roles & Responsibilities, Budget, IP
- 17. Gamification • Applying game design techniques to encourage user adoption and participation. – Leader boards – Achievement badges – Achievement levels – Reward systems • Ensure your social software strategy includes ways of measuring and rewarding users for their participation.
- 18. Your idea – what’s the… • Problem/ Need? • Benefit & Impact? • Competition? • Approach: – Technology? – Instructional content? – Support, training, sharing findings? – Recognition, engagement & management? – Partners? • Ethical considerations?
- 19. Publications & Resources • Centre for Social Justice, Durham Ethical Guidance: http://www.dur.ac.uk/beacon/socialjustice/ethics_consultation/ • Guide to Citizen Science: http://www.ukeof.org.uk/documents/guide-to-citizen-science.pdf • Predicting protein structures with a multiplayer online game: http://www.ncbi.nlm.nih.gov/pubmed/20686574 • Exploring collective intelligence games with design: a citizen science case: http://crowston.syr.edu/system/files/designing %20citizen%20science%20games.pdf • Beyond research in the wild: citizen-led research as a model for innovation in the digital economy: http://www.de2012.org/sites/default/files/digitalfutures2012papers/P apers/Session1BTalesofEngagement/Whittle_etal_BeyondRitW.pdf
Editor's Notes
- Large scale and complex problems > bitesize solvable chunks > create large datasets, new insights & knowledge > new medicines, new discoveries Important bit – can’t be solved any other way
- http://www.americanscientist.org/science/pub/behind-the-scenes-of-foldit-pioneering-science-gamification Foldit – 2008 – University of Washington – David Baker and colleagues – Centre for games scientists Most of the players are from the United States, but there are a large number from Europe, Australia, New Zealand and other countries The game records the structure and the moves that the players do, and we get data that we use to improve the game in every aspect, from the quality of the scientific results that are coming back to how long people play the introductory levels that are supposed to teach the game. The whole game is like an ongoing, continuous experiment. We release updates every couple of weeks with new features. Every week, we publish a different set of puzzles. So we’re adapting the game to the players to make it the most effective scientific problem-solving tool that we can. We built the game using many different rewards or motivations. It's designed to encourage competition, because everyone is trying to fold their version of the protein better than everyone else to get the highest score. There are leaderboards overall for everyone, but there are also leaderboards for different types of puzzles, for individuals working alone and for groups working collaboratively. The game’s score is based on a proxy for how well the protein would work in the lab, whether that’s how well it catalyzes some reaction that the scientists are interested in, or how well this protein sticks to some part of a virus, or even in the case of the Symmetry puzzles, how well the protein sticks to itself. Then we take the solutions that players come up with and present those to scientists for analysis. Solutions that are promising are then synthesized in the lab. We’ve been doing this for a fair number of the puzzles that the players have completed now. “ The Cookbook,” which allows the players to script or code up their strategies in the game. You basically write up what we call a recipe , which is an automated tool that will run moves in Foldit that the players have written. Players can share and modify these recipes online.
- Cancer Research UK & Zooniverse
- Canadian. Move colour blocks horizontally to maximise colour alignment in columns
- EyeWire is a citizen science game that maps the 3D structure of neurons. By playing EyeWire, you contribute to neuroscience research at MIT. Like that it has General discussion forum, articles on the science behind it, bugs and feature requests (managing the crowd) The images from Max Planck Institute for Medical Research in Heidelberg, Germany, using a method known as serial block face scanning electron microscopy. EyeWire was made possible by financial support from the Howard Hughes Medical Institute and the Gatsby Charitable Foundation.