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Serious games for bioinformatics education. ISMB 2014 education workshop

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This presentation surveys the current state of games in bioinformatics education.

Text of Serious games for bioinformatics education. ISMB 2014 education workshop

  • Serious Games for Bioinformatics Education Benjamin Good The Scripps Research Institute @bgood
  • Why games? Attention!!!
  • is useful for: 1.Recruiting getting their attention 2.Engaging holding their attention Attention
  • Recruiting bioinformaticians We're hopefully going to change the way science is done, and who it's done by Zoran Popovi University of Washington Foldit, a game for protein folding
  • 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.
  • 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.
  • Games can be used to teach 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. Immune Attack High school students First person shooter game Significantly improves understanding of concepts in immunology
  • Finding educational bioinformatics games
  • Educational games Game Purpose The DAS game Teaching data integration in bioinformatics (in person, not online) The Bioinformatics Game Introducing protein sequence and structure (mobile) 4bases Introduce DNA sequencing (mobile) MAX5 Introduction to sequence comparisons with BLAST, concepts in distributed computing. High school.
  • TBG select a protein
  • TBG: fly around to hit the next amino acid on your list
  • 4bases (Rostlab, masters thesis) Click the next base in time as the sequence scrolls by. Introduces concept of DNA sequencing Click next base
  • 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. 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.
  • MAX5 starting screen 1
  • MAX5 starting screen 2
  • MAX5 blasting to detect what a sample is infected with
  • MAX5 BLAST analysis
  • MAX5 alignment viewer
  • MAX5 sample hunting
  • MAX5 parallel computing
  • MAX5, TBG, 4Bases, Plusses Useful introductions. Useful for recruiting. Minuses Very high-level shallow learning.
  • Bioinformatics education games Game Purpose Foldit Protein folding Phylo, Fraxinus Multiple Sequence Alignment EteRNA RNA structure design EyeWire Neuron image tracing MalariaSpot, MOLT Blood cell phenotyping Dizeez Gene-disease annotation Genes in Space Copy Number Variation detection The Cure Biomarker selection for breast cancer survival prediction All examples of gamifying tasks in bioinformatics. None built for the purpose of education!
  • Genes in Space Fly a spaceship (oh by the way you are helping cancer research) 300,000 downloads 3 months.. Cancer UK project.
  • The Cure game Alternate turns picking a gene from a board of 25 Your hand Opponents hand
  • Classroom uses The Cure story (Antoine Taly) Goal: understand the concept of Biomarkers 1. Watch short video 2. Play The Cure game (involves picking genes useful for predicting breast cancer survival) 3. Create custom predictive decision tree 4. Write essay about what you did
  • Game Soccer Chess World of Warcraft Halo Super Mario Brothers The Game of Life Monopoly Angry Birds Poker Doom Pacman The Sims Spore Civilization
  • Game: defining traits McGonigal J. Reality is broken : why games make us better and how they can change the world. New York: Penguin 1. A goal 2. Rules 3. Feedback system 4. Voluntary participation
  • Games? Running no Answering questions about programming no Programming no 1. A goal 2. Rules 3. Feedback system 4. Voluntary participation Nike+ Fuelband yes Stackoverflow yes yes
  • Gamification Google: the application of typical elements of game playing to other areas of activity
  • Gamified education. Sort of games Gamified learning environment Purpose CACAO Teach Gene Ontology annotation. Collect new annotations. Undergraduate. Teaching bioinformatics algorithms ranging from DNA- >Amino Acid translation to genome assembly
  • CACAO Rules Students form teams In each of a series of innings: 1. They are presented with (or find themselves) lists of proteins 2. They look up articles about them and try to create GO annotations. 3. The team gets points for complete, correct annotations 4. 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)
  • CACAO participation Since 2010, 1000+ students 15 universities 2,800+ new, acceptable annotations No empirical evidence that gamification helps, but anecdotally everyone likes it.. Example teams from 2013
  • Rosalind is a platform for learning bioinformatics and programming through problem solving. Python Village (learn programming) Bioinformatics Stronghold (learn algorithms) Bioinformatics Armory (learn tools) Textbook exercises
  • Storm the bioinformatics stronghold now!
  • Problems: 228 (total), users: 18194, attempts: 296869, correct: 172873
  • Rosalind user profile
  • Rosalind leaderboard
  • Use of games/gamification in bioinformatics education Expressivity: Number and depth of learnable concepts Fun Benefits: recruiting, engagement CACAO Gamified: badges, leaderboards, levels Lecture course: Typically no game elements Classroom The Cure Foldit Phylo Max5 Game: you play it, learning more implicit, purposes aside from education Genes in Space EteRNA ? Cost $$ Cost $$
  • 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
  • System for teachers to create lessons that move students through specified levels of multiple games. Jerome Waldispuhl, McGill University, Phylo
  • 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 Funding Andrew Su
  • Heroic Purpose Biology and medicine provide a heroic purpose not unlike the more standar