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

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

2. Why games?
Attention!!!

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

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. 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
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. Finding educational
bioinformatics games…

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. 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
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. 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
Alternate turns
picking a gene
from a “board” of
25
Your
hand
Opponents
hand

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

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. 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. 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. 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. “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
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. 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
Funding
Andrew Su

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!

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 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”