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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 Popović...
Foldit players come
from many backgrounds
Top 50 players
Busn/finance/legal
largest group..
Majority have no training in b...
Teaching with games
“The use of educational games within learning
environments raises motivation, increases
interest in th...
Games can be used to
teach
Stegman, Melanie. "Immune Attack players perform better on a test
of cellular immunology and se...
Finding educational
bioinformatics games…
Educational games
Game Purpose
The DAS game Teaching data integration in bioinformatics
(in person, not online)
The
Bioinf...
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 sequenc...
MAX5
Goal: introduce the concepts and purposes of DNA
sequence comparisons (BLAST) and distributed
computing to high schoo...
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 ...
Genes in Space
Fly a spaceship
(oh by the way you are
helping cancer
research)
300,000 downloads 3
months..
Cancer UK proj...
The Cure game
Alternate turns
picking a gene
from a “board” of
25
Your
hand
Opponents
hand
Classroom uses
The Cure story (Antoine Taly)
http://tinyurl.com/talycure
Goal: understand the concept of
Biomarkers
1. Wat...
“Game”
Soccer
Chess
World of Warcraft
Halo
Super Mario Brothers
The Game of Life
Monopoly
Angry Birds
Poker
Doom
Pacman
Th...
Game: defining traits
McGonigal J. Reality is broken : why games make us better
and how they can change the world. New Yor...
Games…?
Running – no
Answering questions about
programming – no
Programming – no
1. A goal
2. Rules
3. Feedback system
4. ...
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...
CACAO Rules
• Students form teams
• In each of a series of “innings”:
1. They are presented with (or find themselves) list...
CACAO participation
Since 2010,
1000+ students
15 universities
2,800+ new, acceptable
annotations
No empirical evidence th...
Rosalind.info
Rosalind is a platform for learning
bioinformatics and programming
through problem solving.
Python Village
(...
“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: r...
Future Directions
Slowly pushing towards the holy grail(s)
Example: ‘Cyclo6’ will attempt to teach advanced organic
chemis...
http://yako.io
System for teachers to create
lessons that move students
through specified levels of multiple
games.
Jerome...
Acknowledgements
Jerome Waldispuhl (Phylo)
Daniel Perry (MAX5)
Antoine Taly (pioneering the use of games
(Foldit, Phylo, T...
Heroic Purpose
Biology and medicine provide
a heroic purpose – not unlike
the more standard purpose of
saving the world fr...
Finding educational
bioinformatics games
http://www.sciencegamecenter.org/
Lists about 95 games related to science
57 are ...
Fun
Google define:fun “enjoyment, amusement, or lighthearted
pleasure”
“Fun” from game design guru Raph Koster
“the act of...
Serious games for bioinformatics education.  ISMB 2014 education workshop
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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.

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  • As of July 9, 2014
  • Transcript of "Serious games for bioinformatics education. ISMB 2014 education workshop"

    1. 1. Serious Games for Bioinformatics Education Benjamin Good The Scripps Research Institute @bgood
    2. 2. Why games? Attention!!!
    3. 3. is useful for: 1.Recruiting • getting their attention 2.Engaging • holding their attention Attention
    4. 4. Recruiting bioinformaticians “We're hopefully going to change the way science is done, and who it's done by” Zoran Popović University of Washington Foldit, a game for protein folding
    5. 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. 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. 7. 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 http://ImmuneDefenseGame.com High school students First person shooter game Significantly improves understanding of concepts in immunology
    8. 8. Finding educational bioinformatics games…
    9. 9. 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.
    10. 10. TBG – select a protein
    11. 11. TBG: fly around to hit the next amino acid on your list
    12. 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. 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. 14. MAX5 starting screen 1
    15. 15. MAX5 starting screen 2
    16. 16. MAX5 “blasting” to detect what a sample is infected with
    17. 17. MAX5 BLAST analysis
    18. 18. MAX5 alignment viewer
    19. 19. MAX5 sample hunting
    20. 20. MAX5 parallel computing
    21. 21. MAX5, TBG, 4Bases,… Plusses Useful introductions. Useful for recruiting. Minuses Very high-level – shallow learning.
    22. 22. 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!
    23. 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. 24. The Cure game Alternate turns picking a gene from a “board” of 25 Your hand Opponents hand
    25. 25. Classroom uses The Cure story (Antoine Taly) http://tinyurl.com/talycure 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
    26. 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. 27. 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
    28. 28. 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 TopCoder.com – yes
    29. 29. Gamification Google: “the application of typical elements of game playing to other areas of activity…”
    30. 30. 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
    31. 31. 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
    32. 32. 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
    33. 33. Rosalind.info 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
    34. 34. “Storm the bioinformatics stronghold now!”
    35. 35. Problems: 228 (total), users: 18194, attempts: 296869, correct: 172873
    36. 36. Rosalind user profile
    37. 37. Rosalind leaderboard
    38. 38. Use of games/gamification in bioinformatics education Expressivity: Number and depth of learnable concepts Fun Benefits: recruiting, engagement Rosalind.info 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 $$ Cost $$
    39. 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. 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. 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 Funding Andrew Su
    42. 42. 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!
    43. 43. 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
    44. 44. Fun Google 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”
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