On the relation between learning, teaching, science and games. Presentation for the course on simulation in medical pedagogy at Paris Descartes university.

1. Learning with games
@AntTaly #DIUP2015 #simulation
@iLumens

2. Learning with games?
1. Learning from games
[why do we learn from games?]
2. Teaching with games
[how/what can we teach with games?]
3. Scientific discovery games
[how can players contribute to build scientific
knowledge?]

3. 1. Learning from games
● a long story
● what is a game?
● how does it work?

4. A long story...
● Play found in nature, allowing
animals to learn
(i.e. selected by evolution)
● Games used for learning
historically
(e.g. war games in China)
Hillebrand Steve, U.S. Fish and Wildlife Service

5. Game definition
Following Gilles Brougère (“Jouer/Apprendre”, Economica/Anthropos):
○ second reality,
○ decisions (to enter the game and then during the
game),
○ rules (including goal and limits in time and space),
○ frivolity (no consequence)
○ uncertainty about the outcome
N.B.: serious games do not enter that definition...

6. How can learn from games?
● A game allows exploration
Alison Gopnik “Scientific Thinking in Young Children: Theoretical Advances, Empirical Research, and Policy
Implications” Science 2012: Vol. 337 no. 6102 pp. 1623-1627
● We learn from trial and error
→ We need a feedback loop… that is the core of games
● Uncertainty increase learning and motivation
http://link.springer.com/article/10.1007/s11251-008-9073-6#page-1
http://www.sciencedirect.com/science/article/pii/S0360131513000481
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0103640#pone-0103640-g004

7. Games effects on the brain have
been proposed:
● Increasing Speed of Processing With Action Video Games
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2871325/
● Gaming improves multitasking skills
http://www.nature.com/news/gaming-improves-multitasking-skills-1.13674
● Action Video Games Sharpen Vision
http://www.rochester.edu/news/show.php?id=2764
● “Real-Time Strategy Game Training: Emergence of a Cognitive Flexibility Trait”
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0070350

8. Can we learn useful things in a
game?
"I put my qualifications on my resume when I apply for jobs," Gillett said. "Here's my guild. Here's my
ranking. Here's my biggest online achievement. Some people look at it and say, 'What the hell is this?'
And others will be like, 'That's exactly what I'm looking for.'"
http://money.cnn.com/2014/06/19/technology/world-of-warcraft-resume/
Learning technical skills:
“TEENAGE GAMERS ARE BETTER AT VIRTUAL SURGERY THAN MDS”
http://www.popsci.com/gadgets/article/2012-11/teenage-gamers-are-better-virtual-surgery-medical-
professionals

9. 2. TEACHING WITH GAMES
● General exemples
● Bioinformatics at university [or focus]

10. 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.”

11. TEACHING WITH GAMES AT
SECONDARY SCHOOL
● Many examples of the use of games in
teaching
● Example of Dragon Box

12. A classical exemple: MinecraftEdu
Math,
Biology,
Geography,
etc...
MinecraftEdu

13. Teaching Medicine/health

14. Games allow to tackle difficult subjects
● Geopolitics
○ Romain republic
○ missile crisis in Cuba
○ initiation of WW1
“Jouer en classe en collège et en lycée” Dominique Natanson, Marc Berthou, éditions Fabert, 2013.
● Sex education
“The development approach of a pedagogically-driven serious game to support Relationship and Sex Education (RSE)
within a classroom setting” http://www.sciencedirect.com/science/article/pii/S0360131513001644
“seconde guerre Punique” shared via wikimedia by “Common Good”.

15. 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
Immune Attack
http://ImmuneDefenseGame.com
• High school students
• First person shooter
game
• Significantly improves
understanding of
concepts in immunology

16. Dragon Box is a good
exemple...
http://wewanttoknow.com/algebra/
@DragonBoxApp

17. … but that is not magical
Game alone does not work:
● need for be-briefing
● not enough room for error?
Yanjin Long, Vincent Aleven “Gamification of Joint Student/System Control over Problem Selection in a Linear Equation
Tutor” Intelligent Tutoring Systems, Lecture Notes in Computer Science Volume 8474, 2014, pp 378-387.
more general thougths: Learning Systems, Not Games JP Gee - Texas Education Review, 2013 - journals.tdl.org

18. Teaching with games at the
university
● Bioinformatics
● with serious games and scientific discovery
games

19. 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.

20. TBG – select a protein

21. TBG: fly around to hit the
next amino acid on your list

22. 4bases (Rostlab, masters
thesis)
Click the next base
in time as the
sequence scrolls by.
Introduces concept
of DNA sequencing
Click next
base

23. 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.

24. MAX5 starting screen 1

25. MAX5 starting screen 2

26. MAX5 “blasting” to detect what a
sample is infected with

27. MAX5 BLAST analysis

28. MAX5 alignment viewer

29. MAX5, TBG, 4Bases,…
Plusses
• Useful introductions.
• Useful for recruiting.
Minuses
• Very high-level –
shallow learning.

30. 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!

31. Genes in Space
• Fly a spaceship
• (oh by the way you are
helping cancer
research)
• 300,000 downloads 3
months..
• Cancer UK project.

32. The Cure game
Alternate turns
picking a gene
from a “board”
of 25
Your
hand
Opponent
s hand

33. 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

34. Use of games/gamification in
bioinformatics education
Expressivity: Number and depth of learnable concepts
Fun
Benefits:
recruiting,
Rosalind.info
CACAO
Gamified: badges,
leaderboards, levelsLecture
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
Holy Grail
?
Cost $$
Cost $$

35. 3. SCIENTIFIC DISCOVERY GAMES
● FOLDIT
● THE CURE
● PHYLO

36. GAMES WITH A PURPOSE
The Cure
MOLT

37. FOLDIT
A Key exemple:
● pioneering work
● scientific results published in peer reviewed journals
● deep analysis of players inputs

38. Started with grid computing
● ROSETTA@HOME

39. Foldit

40. Seth Cooper, Firas Khatib, Adrien Treuille, Janos Barbero, Jeehyung Lee, Michael Beenen, Andrew Leaver-Fay, David Baker, Zoran Popović, Foldit players (2010).
Predicting protein structures with a multiplayer online game. Nature 446 p. 756-760, 05 August 2010.
How do players do etter than the
computer?

41. What makes the players good?
→ strategy
Seth Cooper, Firas Khatib, Adrien Treuille, Janos Barbero, Jeehyung Lee, Michael Beenen, Andrew Leaver-Fay, David Baker, Zoran Popović, Foldit players (2010).
Predicting protein structures with a multiplayer online game. Nature 446 p. 756-760, 05 August 2010.

42. What makes the players good?
→ strategy
Seth Cooper, Firas Khatib, Adrien Treuille, Janos Barbero, Jeehyung Lee, Michael Beenen, Andrew Leaver-Fay, David Baker, Zoran Popović, Foldit players (2010).
Predicting protein structures with a multiplayer online game. Nature 446 p. 756-760, 05 August 2010.

43. 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.

44. THE CURE

46. PLAY = GENE SELECTION
Alternate turns
picking a gene from
a “board” of 25
Your
hand
Opponents
hand

47. SCORING
Cure Server
Score reflects accuracy of
decision tree created with
just the selected genes on
real training data

48. PLAY WITH KNOWLEDGE: GENE ONTOLOGY

49. PLAY WITH KNOWLEDGE: GENE RIFS

50. YOU WIN!

51. GENE SET OVERLAPS, SOME BUT NOT MUCH
http://bioinformatics.psb.ugent.be/webtools/Venn/
“Expert Gene Set”

52. CLASSIFIER PERFORMANCE WITH DIFFERENT
GENE GROUPS, DIFFERENT DATASETS
X-axis Test Set performance
Griffith 2013 data
Y-axis Test Set performance
Metabric training Oslo Test
Only difference between points,
are the genes used to build SVM
classifier
10 year survival
Yes
No
“Expert Gene Set”

53. PLAYERS http://io9.com/
these-cool-games-let-you-do-real-life-science-486173006
1,077 Players registered (one year)
Sage DREAM7
challenge, game
announcement

54. PLAYER DEMOGRAPHICS

55. PHYLO

56. Players of Phylo compare the genome sequences of many animals to find genetic segments that are similar.
Mark Schrope PNAS 2013;110:7104-7106
©2013 by National Academy of Sciences

57. Figure 3. Statistics on the performance of players as a function of the number of sequence in the puzzle.
Kawrykow A, Roumanis G, Kam A, Kwak D, Leung C, et al. (2012) Phylo: A Citizen Science Approach for Improving Multiple Sequence
Alignment. PLoS ONE 7(3): e31362. doi:10.1371/journal.pone.0031362
http://127.0.0.1:8081/plosone/article?id=info:doi/10.1371/journal.pone.0031362

58. Open-Phylo crowd-computing system. (1) Scientists upload their sequences to the database, validate the alignment puzzles built by the
system (See green box in the data administration interface), or select new ones. (2) The same users monitor the progress of the crowd in
improving their alignments, close puzzles, open new puzzles and finally (3) download the best solutions. The crowd-computing engine is powered
by (a) many casual gamers playing classic puzzles and (b) a smaller number of experienced players, who have access to larger and more difficult
puzzles. Kwak et al. Genome Biology 2013 14:R116 doi:10.1186/gb-2013-14-10-r116
Open Phylo

59. Open Phylo
Performance of Open-Phylo using the casual or expert version of the Phylo video game. Ratio of puzzles improved by Open-Phylo for the scoring functions
Ancestor (top left), MUSCLE (top right), GUIDANCE (bottom right) and T-Coffee (bottom left). The alignment program used to calculate the initial MSAs is indicated
on the axis of the radar charts: Multiz (north), MUSCLE (west), PRANK (south) and T-Coffee (east). The area surrounded by a blue line corresponds to the
performance achieved with the casual puzzles only, while the area surrounded by a red line indicates the performance of the expert version only. The area
surrounded by a dashed green line shows the ratio of alignments improved by either the classic or expert version. Kwak et al. Genome Biology 2013 14:R116 doi:
10.1186/gb-2013-14-10-r116

60. More scientific discovery games in
medicine?

61. Acknowledgments
● Ben Good for many interactions and slides (slides with black background):
http://fr.slideshare.net/goodb/serious-games-for-bioinformatics-education-ismb-2014-education-workshop
http://fr.slideshare.net/goodb/good-ben-rocky2013games
● Students at FDV who tested the use of games in class