Games can be used for learning, teaching, and scientific discovery. For learning, games allow exploration and feedback which facilitates learning. Teaching with games increases student motivation and problem solving skills. Scientific discovery games leverage large numbers of players to solve problems or analyze data, resulting in real scientific contributions. Examples include Foldit for protein structure prediction and Phylo for genome sequence alignment.

1. Learning with games
@AntTaly #DIUP2016 #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. Need for a debriefing
©Le Lombard 2015, tous droits réservés.

7. 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

8. 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

9. 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:
“Systematic video game training in surgical novices improves performance in virtual reality endoscopic surgical simulators: a prospective
randomized study.” Schlickum MK, Hedman L, Enochsson L, Kjellin A, Felländer-Tsai L. http://www.ncbi.nlm.nih.gov/pubmed/19649553
“Will the Playstation generation become better endoscopic surgeons?” Koen W. van Dongen, Egbert-Jan M. M. Verleisdonk, Marlies P.
Schijven, Ivo A. M. J. Broeders Surgical Endoscopy 2011, 25:2275. http://link.springer.com/article/10.1007%2Fs00464-010-1548-2.
“Virtual reality laparoscopy: which potential trainee starts with a higher proficiency level?” M. Paschold , M. Schröder, D. W. Kauff, T.
Gorbauch, M. Herzer, H. Lang, W. Kneist; International Journal of Computer Assisted Radiology and Surgery; 2011, 6(5), pp 653-662 http:
//link.springer.com/journal/11548/6/5/page/1

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

11. 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.”

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

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

14. Teaching Medicine/health

15. 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”.

16. 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

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

18. … 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.
● Or need for a de-briefing
Kluge, Anders, and Jan Dolonen. "USING MOBILE GAMES IN THE CLASSROOM." Mobile Learning and Mathematics (2015): 106.
more general thougths: Learning Systems, Not Games JP Gee - Texas Education Review, 2013 - journals.tdl.org

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

20. 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.

21. TBG – select a protein

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

23. 4bases (Rostlab, masters
thesis)
Click the next base
in time as the
sequence scrolls by.
Introduces concept
of DNA sequencing
Click next
base

24. 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.

25. MAX5 starting screen 1

26. MAX5 starting screen 2

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

28. MAX5 BLAST analysis

29. MAX5 alignment viewer

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

31. 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!

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

33. What does scientific discovery
games so interesting?
● simulation
● rules of interaction possibility to build on
others’ contributions
● large number of participants/data
● open ended
→ emergent properties, including collective
intelligence

34. GAMES WITH A PURPOSE
The Cure
MOLT

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

36. Started with grid computing
● ROSETTA@HOME

37. Foldit

38. 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?

39. 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.

40. 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.

41. 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.

42. THE CURE

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

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

46. PLAY WITH KNOWLEDGE: GENE ONTOLOGY

47. PLAY WITH KNOWLEDGE: GENE RIFS

48. YOU WIN!

49. 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”

50. PHYLO

51. 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

52. 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

53. More Scientific Discovery Games
around Biology/Medicine
Dementia:
http://www.seaheroquest.com/fr

54. More Scientific Discovery Games
around Biology/Medicine
remote medical image diagnosis
http://biogames.ee.ucla.edu/

55. More Scientific Discovery Games
around Biology/Medicine
Malaria
http://malariaspot.org/game/

56. More scientific discovery games in
medicine?

57. 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