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

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Games that teach, Games that learn:

Serious Games for Bioinformatics Education

Benjamin GoodThe Scripps Research Institute@bgoodWhy games?Attention!!! is useful for:Recruiting getting their attentionEngaging holding their attentionAttention Recruiting bioinformaticiansWe're hopefully going to change the way science is done, and who it's done by

Zoran PopoviUniversity of WashingtonFoldit, a game for protein foldingSpeaking in a UW press release

Games are mechanism to draw new populations to participate. These might be people from different fields (Foldit) or people from under-represented sociocultural backgrounds (MAX5). Games get peoples attention and encourage them to play with new concepts.4Foldit players come from many backgrounds

Top 50 players Busn/finance/legal largest group..

Majority have no training in biochemistryCooper, Seth, et al. "Predicting protein structures with a multiplayer online game." Nature 466.7307 (2010): 756-760.Teaching with gamesThe 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 teachStegman, 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 studentsFirst person shooter gameSignificantly improves understanding of concepts in immunology

Finding educational bioinformatics games

Educational gamesGamePurposeThe DAS gameTeaching data integration in bioinformatics (in person, not online)The Bioinformatics GameIntroducing protein sequence and structure (mobile)4basesIntroduce DNA sequencing (mobile)MAX5Introduction to sequence comparisons with BLAST, concepts in distributed computing. High school.Biostar ?9TBG 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 sequencingClick next baseMAX5Goal: introduce the concepts and purposes of DNA sequence comparisons (BLAST) and distributed computing to high school studentsFirst person game set in 3-d world beset by an influenza pandemic., 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,PlussesUseful introductions.Useful for recruiting.MinusesVery high-level shallow learning.Bioinformatics education gamesGamePurposeFolditProtein foldingPhylo, FraxinusMultiple Sequence AlignmentEteRNARNA structure designEyeWireNeuron image tracingMalariaSpot, MOLTBlood cell phenotypingDizeezGene-disease annotationGenes in SpaceCopy Number Variation detectionThe CureBiomarker selection for breast cancer survival predictionAll examples of gamifying tasks in bioinformatics.None built for the purpose of education!

Biostar ?22Genes in SpaceFly 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 usesThe Cure story (Antoine Taly) 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 treeWrite essay about what you did

Similarly structured lessons that use Foldit and Phylo25GameSoccerChessWorld of WarcraftHaloSuper Mario BrothersThe Game of LifeMonopolyAngry BirdsPokerDoomPacmanThe SimsSporeCivilization

Given those excellent reasons for looking at games for education, lets step back and try to understand what games are so that we can think about how to create them and use them effectively. If you look at all of these examples, they are all clearly recognizable as games, yet they vary dramatically from one to the other. What unifies the?26Game: defining traitsMcGonigal J. Reality is broken : why games make us better and how they can change the world. New York: Penguin Press; 2011.

A goalRulesFeedback systemVoluntary participationThese four features provide a framework for understanding games. They provide key areas to look at when attempting to build or improve a game. In addition, they provide a lens through which many things in the world start to look like games. By examining aspects of real world challenges as games, we can adapt them to make us happier, better and to make the world a better place.

If you take nothing else away from this talk, take the recommendation to go read this book.27Games?Running no

Answering questions about programming no

Programming no

A goalRulesFeedback systemVoluntary participationNike+ Fuelband yes

Stackoverflow yes yes

All of these systems meet McGonigals criteria and can be discussed and thought about as games. Doing so sheds light on why they are designed the way they are and why they are effective.So, as we think about games, I want to take a broad view that encompasses systems like these. Another term that applies to this group is gamification.

@widdowquinn: Academia gamified: citation counts, medals, tenure; meaning implicit, purposes apart from learning ;)

28GamificationGoogle: the application of typical elements of game playing to other areas of activityGamified education. Sort of gamesGamified learning environmentPurposeCACAOTeach Gene Ontology annotation. Collect new annotations. Undergraduate.Rosalind.infoTeaching bioinformatics algorithms ranging from DNA->Amino Acid translation to genome assemblyCACAO RulesStudents form teamsIn each of a series of innings:They are presented with (or find themselves) lists of proteinsThey look up articles about them and try to create GO annotations. The team gets points for complete, correct annotationsAt 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) terms of benefits and disadvantages, we've never done the control of not doing it as a competition. But you will see in the annotations/user analysis, that there's a long tail of users who have made lots of annotations. I don't think there would be that many if we didn't have that incentive to go past the top end of the grading rubric, which is 20 acceptable annotations either made directly or via correction by challenges.31CACAO participationSince 2010, 1000+ students15 universities2,800+ new, acceptable annotations No empirical evidence that gamification helps, but anecdotally everyone likes it..

Example teams from 2013Rosalind.infoRosalind is a platform for learning bioinformatics and programming through problem solving.

Python Village(learn programming)

Bioinformatics Stronghold(learn algorithms)

Bioinformatics Armory(learn tools)

Textbook exercisesStorm the bioinformatics stronghold now!

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

As of July 9, 201435Rosalind user profile

Rosalind leaderboard

Use of games/gamification in bioinformatics educationExpressivity: Number and depth of learnable conceptsFunBenefits: recruiting, engagementRosalind.infoCACAOGamified: badges, leaderboards, levelsLecture course: Typically no game elementsClassroomThe CureFolditPhyloMax5Game: you play it, learning more implicit, purposes aside from educationGenes in SpaceEteRNAHoly Grail?Cost $$Cost $$Future DirectionsSlowly 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 gamesGenes in Space team integration directly inside the context of The Impossible Line by ChilingoYako.io

System for teachers to create lessons that move students through specified levels of multiple games.

Jerome Waldispuhl, McGill University, PhyloAcknowledgementsJerome 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


Andrew Su41Heroic PurposeBiology 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!

BIOINFORMATICIANFinding educational bioinformatics games about 95 games related to science57 are tagged with biology2 with computer scienceNone focus on bioinformatics learning objectives.Melanie StegmanFederation of American ScientistsFunGoogle define:fun enjoyment, amusement, or lighthearted pleasureFun from game design guru Raph Kosterthe act of mastering a problem mentallythe feedback the brain gives us when we are absorbing patterns for learning purposesfun is about learning in a context where there is no pressure, and that is why games matter


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