Serious Games for Bioinformatics

EducationBenjamin 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 PopovićUniversity of WashingtonFoldit, 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 Attackhttp://ImmuneDefenseGame.com

High school studentsFirst person shooter gameSignificantly improves understanding of concepts in immunology

Finding educational bioinformatics games…

Educational gamesGame PurposeThe 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

MAX5Goal: 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. 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.

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.

MinusesVery high-level – shallow learning.

Bioinformatics education gamesGame PurposeFoldit Protein foldingPhylo, Fraxinus Multiple Sequence AlignmentEteRNA RNA structure designEyeWire Neuron image tracingMalariaSpot, MOLT

Blood cell phenotyping

Dizeez Gene-disease annotationGenes in Space Copy Number Variation detectionThe Cure Biomarker selection for breast

cancer survival prediction• All examples of gamifying tasks in

bioinformatics.• None built for the purpose of education!

Genes 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) http://tinyurl.com/talycureGoal: 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 tree4. Write essay about what you did

“Game”SoccerChessWorld of WarcraftHaloSuper Mario BrothersThe Game of LifeMonopoly

Angry BirdsPokerDoomPacmanThe SimsSporeCivilization

Game: defining traits

McGonigal J. Reality is broken : why games make us better and how they can change the world. New York: Penguin Press; 2011.

1. A goal2. Rules3. Feedback system4. Voluntary

participation

Games…?Running – no

Answering questions about programming – no

Programming – no

1. A goal2. Rules3. Feedback system4. Voluntary

participation

Nike+ Fuelband – yes

Stackoverflow – yes

TopCoder.com – yes

GamificationGoogle: “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.

Rosalind.info 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) http://gonuts.tamu.edu/wiki/index.php/Cacao_rules

CACAO participationSince 2010,

1000+ students15 universities2,800+ new, acceptable annotations

No empirical evidence that gamification helps, but anecdotally everyone likes it..

Example teams from 2013

Rosalind.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 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

FunBenefits: recruiting, engagement

Rosalind.infoCACAO

Gamified: badges, leaderboards, levels

Lecture course: Typically no game elements

Classroom

The CureFoldit

Phylo Max5

Game: you “play it”, learning more implicit, purposes aside from education

Genes in SpaceEteRNA

Holy 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 games

Genes in Space team – integration directly inside the context of “The Impossible Line” by ChilingoYako.io

http://yako.ioSystem for teachers to create lessons that move students through specified levels of multiple games.

Jerome Waldispuhl, McGill University, Phylo

AcknowledgementsJerome 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.orghttp://ImmuneDefenseGame.com

Funding

Andrew Su

Heroic 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!

BIOINFORMATICIAN

Finding educational bioinformatics games

http://www.sciencegamecenter.org/

Lists about 95 games related to science57 are tagged with “biology”2 with “computer science”None focus on bioinformatics learning objectives.

Melanie StegmanFederation of American Scientists

FunGoogle define:fun “enjoyment, amusement, or lighthearted pleasure”“Fun” from game design guru Raph Koster

“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”