Serious Games for Bioinformatics Education

1. Serious Games for Bioinformatics Education Benjamin Good The Scripps Research Institute @bgood

2. Why games? Attention!!!

3. Attention is useful for: • Recruiting • getting their attention • Engaging • holding their attention

4. Recruiting bioinformaticians “We're hopefully going to change the way science is done, and who it's done by” ZoranPopović University of Washington Foldit, a game for protein folding

5. Foldit players come from many backgrounds Top 50 players Busn/finance/legal largest group.. Majority have no training in biochemistry Cooper, Seth, et al. "Predicting protein structures with a multiplayer online game." Nature 466.7307 (2010): 756-760.

6. Teaching with games “The use of educational games within learning environments raises motivation, increases interest in the subject matter, intensifies information retention, encourages collaboration, and improves problem-solving skills.” • Schneider, Maria Victoria, and Rafael C. Jimenez. "Teaching the fundamentals of biological data integration using classroom games." PLoS computational biology 8.12 (2012) • Quoting: Michael D, Chen S (2006) Serious games: games that educate, train and inform. Boston: Thomson Course Technology.”

7. Games can be used to teach • High school students • First person shooter game • Significantly improves understanding of concepts in immunology • Immune Attack • http://ImmuneDefenseGame.com Stegman, Melanie. "Immune Attack players perform better on a test of cellular immunology and self confidence than their classmates who play a control video game." Faraday Discuss 169 (2014): 1-20.

8. Finding educational bioinformatics games…

9. Educational games

10. TBG – select a protein

11. TBG: fly around to hit the next amino acid on your list

12. 4bases (Rostlab, masters thesis) Click the next base in time as the sequence scrolls by. Introduces concept of DNA sequencing Click next base

13. MAX5 • Goal: introduce the concepts and purposes of DNA sequence comparisons (BLAST) and distributed computing to high school students • First person game set in 3-d world beset by an influenza pandemic. • http://gamestem.com/portfolio/max5-storyline-1/ Perry, Daniel, et al. "Human centered game design for bioinformatics and cyberinfrastructure learning." Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery. ACM, 2013.

14. MAX5 starting screen 1

15. MAX5 starting screen 2

16. MAX5 “blasting” to detect what a sample is infected with

17. MAX5 BLAST analysis

18. MAX5 alignment viewer

19. MAX5 sample hunting

20. MAX5 parallel computing

21. MAX5, TBG, 4Bases,… Plusses • Useful introductions. • Useful for recruiting. Minuses • Very high-level – shallow learning.

22. Bioinformatics education games • All examples of gamifying tasks in bioinformatics. • None built for the purpose of education!

23. Genes in Space • Fly a spaceship • (oh by the way you are helping cancer research) • 300,000 downloads 3 months.. • Cancer UK project.

24. The Cure game Opponents hand Alternate turns picking a gene from a “board” of 25 Your hand

25. Classroom uses • The Cure story (Antoine Taly) http://tinyurl.com/talycure • Goal: understand the concept of Biomarkers • Watch short video • Play The Cure game (involves picking genes useful for predicting breast cancer survival) • Create custom predictive decision tree • Write essay about what you did

26. “Game” • Soccer • Chess • World of Warcraft • Halo • Super Mario Brothers • The Game of Life • Monopoly • Angry Birds • Poker • Doom • Pacman • The Sims • Spore • Civilization

27. Game: defining traits • A goal • Rules • Feedback system • Voluntary participation McGonigalJ. Reality is broken : why games make us better and how they can change the world. New York: Penguin Press; 2011.

28. Games…? • Running – no • Answering questions about programming – no • Programming – no • A goal • Rules • Feedback system • Voluntary participation • Nike+ Fuelband – yes • Stackoverflow – yes • TopCoder.com – yes

29. Gamification • Google: “the application of typical elements of game playing to other areas of activity…”

30. Gamified education. • Sort of games…

31. CACAO Rules • Students form teams • In each of a series of “innings”: • They are presented with (or find themselves) lists of proteins • They look up articles about them and try to create GO annotations. • The team gets points for complete, correct annotations • At the end of the inning they can “challenge” the annotations of other teams and steal their points. (Like Scrabble!!) Jim Hu, Texas A&M (TAMU) http://gonuts.tamu.edu/wiki/index.php/Cacao_rules

32. CACAO participation Example teams from 2013 • Since 2010, • 1000+ students • 15 universities • 2,800+ new, acceptable annotations • No empirical evidence that gamification helps, but anecdotally everyone likes it..

33. Rosalind.info • Rosalind is a platform for learning bioinformatics and programming through problem solving. Python Village (learn programming) Bioinformatics Armory (learn tools) Textbook exercises Bioinformatics Stronghold (learn algorithms)

34. “Storm the bioinformatics stronghold now!”

35. Problems: 228 (total), users: 18194, attempts: 296869, correct: 172873

36. Rosalind user profile

37. Rosalind leaderboard

38. Use of games/gamification in bioinformatics education Cost $$ Expressivity: Number and depth of learnable concepts Holy Grail ? Gamified: badges, leaderboards, levels Classroom Rosalind.info Game: you “play it”, learning more implicit, purposes aside from education Lecture course: Typically no game elements CACAO The Cure Foldit EteRNA Phylo Max5 Genes in Space Cost $$ Fun Benefits: recruiting, engagement

39. Future Directions • Slowly pushing towards the holy grail(s) • Example: ‘Cyclo6’ will attempt to teach advanced organic chemistry – to be released on the app store this fall. • Removing boundaries that divide scientific games from each other and from other games • Genes in Space team – integration directly inside the context of “The Impossible Line” by Chilingo • Yako.io

40. http://yako.io System for teachers to create lessons that move students through specified levels of multiple games. Jerome Waldispuhl, McGill University, Phylo

41. Acknowledgements • Jerome Waldispuhl (Phylo) • Daniel Perry (MAX5) • Antoine Taly (pioneering the use of games (Foldit, Phylo, The Cure) in his courses) • Julia Winter (Cyclo6) • Jim Hu (CACAO) • Melanie Stegman • http://www.sciencegamecenter.org • http://ImmuneDefenseGame.com Andrew Su Funding

43. Heroic Purpose • Biology and medicine provide a heroic purpose – not unlike the more standard purpose of saving the world from aliens. • There are great games to be made and great bioinformaticians to be discovered! BIOINFORMATICIAN

44. Finding educational bioinformatics games • http://www.sciencegamecenter.org/ • Lists about 95 games related to science • 57 are tagged with “biology” • 2 with “computer science” • None focus on bioinformatics learning objectives. Melanie Stegman Federation of American Scientists

45. Fun • Google define:fun “enjoyment, amusement, or lighthearted pleasure” • “Fun” from game design guru RaphKoster • “the act of mastering a problem mentally” • “the feedback the brain gives us when we are absorbing patterns for learning purposes” • “fun is about learning in a context where there is no pressure, and that is why games matter”