2. Challenges
data
designdeployment
trial & error
time management
debugging
iterative design
complexity
manual error
standardization
sharing
automation
integration
specification
high throughput
initial research
verification
speed
accuracy
3. Apply engineering principles to synthetic
biology by utilizing user-centered design to
build software tools that foster collaborative
problem solving, support complex system
design, and enable automation in the lab.
BU-Wellesley Software 2011
Our Vision
6. Preliminary User Studies
Position #
PIs 9
Postdocs 6
Industry Researchers 2
Student Researchers 12
Research Assistant 2
Master Student 1
Total 32
Goal
Design requirements for
synthetic biologists
Interview
Procedure
1 hour interviews in
laboratories
Interview
Questions
Procedure walk-through
Research goals
Work practices
Computational tools
Future of the field
Data
collection
Video
Voice recordings
Screenshots
Observations
Qualitative
Methods
• Affinity diagrams
• Iterative coding
Institutions
• Boston University
• Harvard Medical School
• MIT
• WellesleyCollege
• Wyss Institute
8. Findings: User Study Results
Alleviate Data Explosion
IntegrateWorkflow
Provide Multiple Forms of Evidence
Support from Novice to Expert
Facilitate Collaboration
BU-Wellesley Software 2011
9. Findings: User Study Results
Alleviate Data Explosion
IntegrateWorkflow
Provide Multiple Forms of Evidence
Support from Novice to Expert
Facilitate Collaboration
BU-Wellesley Software 2011
10. “ ”
By taking into account the collaborative process,
tabletop software can help novices learn from
experts, making an invaluable impact on
synthetic biology
-Natalie Kuldell, SynBERC
18. G-nome Surfer Pro reduces subjective workload,
improves collaboration, encourages reflection,
and facilitates intuitive interaction.
Findings
BU-Wellesley Software 2011
19. Using Gnome Surfer in the Lab
Gnome Surfer Pro
Pubmed research onTuberculosis
Gene selection fromTB genome
Sequence analysis Tuberculosis Genes
Rv2324
Rv3574
Rv3574 promoter
Rv0324
Other genes
Smeg6038
Smeg6042
Cre
Dre
Flp
20. Designing Primers
Optimus Primer
Designed primers to amplifyTB genes and generate BioBricks
A subset of our primers is listed below
Genes Forward Primers Reverse Primers
RV2324 CGGCCGCTTCTAGATGGACCGCCTGGATGACACC CGGCCTACTAGTACTAGGGCGGCATGCGGTCG
Smeg6038 CGCCCGCTTCTAGAGCGGGGTGACCCTTTCTCTTC CCGCTACTAGTATGAATTGCCTCCCGGATCG
RV3574 GGCCGCTTCTAGAGCTTGCAGACCTCCGCGTCGA GGCCGCTACTAGTATTTCATGACCGCGCGAGGTG
RV0324 CGCGCGCTTCTAGATGGCTGGACAGTCCGATCG CGCCTGTAGATTCGCCGATGCCGTGGATA
RV3574 CGCCCGCTTCTAGATGGCGGTACTTGCCGAGTC TCGATGCGGCTGAACTCCCGACCCAGCGCCGAC
Smeg_6042 CGCGCTTCTAGATGACCAACGTGGCGGTTCTC CGATGCGTTCGAACTCGCGTCCGAGTGCCGAG
21. BU-Wellesley Software 2011
Synbio: General outlook
• Biology is...
• Want to investigate complex interactions between genes
• Avoid large number of constructs
• Create sophisticated genetic circuits
• Generate a large state space
22. BU-Wellesley Software 2011
Trumpet: Configurable constructs
• Can we build a configurable biological construct?
• Prior work
• Ham et al. five-state machine (2009)
• Friedland et al. three-state counter (2008)
• Our goal: a fully permutable construct
• Results:
• Two algorithms for designing such constructs
24. Trumpet: Configurable constructs
• Two design algorithms:
• Pancake and Linksort
• Pancake operations
• Bring to head (BtH)
• Push into place (PiP)
• Complexity
• invertases, operations
• Implemented with nested
invertase sites
• BtH: One site per part
• PiP: N sites per part
28. Invertase –sites
Flp – frt
Dre – rox
Cre – lox
Trumpet
Generated a reconfigurable circuit with 2TB genes and 3 invertase sites
Generating a Circuit Design with
Trumpet
29. PuppetShow:
• 10 part BioBrick using current
software:
•200 lines of code
• 10 part Biobrickusing
PuppetShow:
•~ 20 lines
BU-Wellesley Software 2011
Define protocols Call function Robot moves
30. PuppetShow: features
BU-Wellesley Software 2011
• Define protocols and assembly programs
• Generates Puppeteer code automatically
• Optimizes labware allocation
• Saves samples and protocol history to
database
• Maintains Puppeteer Protocol Repository
34. Assembling DNA with
PuppetShow
Puppet Show
Run protocols for the DNA
assembly of the genetic circuit
using a liquid handling robot
Manual LabWork
Do the protocols manually
to build the genetic circuit
M: MW Ladder
1: Uncut BioBrick
2: Manual trial
3-5: Robot trials
36. Impact
• Feasible to streamline experimental process through a suite of tools
• Facilitates collaborative learning support of novice users
• Developed and automated 2 different algorithms which place invertase sites
through Clotho.
• Created user-friendly interface for automating protocols to a robot
• Successfully tested in the wet lab
BU-Wellesley Software 2011
The user interface is limiting in many fields. Designing
software for synthetic biology with collaborative and
educational capabilities will help attract new blood to the field
and provide those in the field with vital new design
perspectives.
-George M. Church,
Harvard Medical School
“ ”
37. Acknowledgements
BU: Daniel Dwyer, Jim Collins, and the Collins Lab, Andrew Krueger, James Galagan, and the Galagan Lab, Gretchen
Fougere, Assistant Dean of Outreach and Diversity
BBNTechnologies: Aaron Aadler
JBEI: Josh Gilmore
JHU: Jef Boeke, NoahYoung
MIT: Jonathan Babb and theWeiss Lab,Tiffany Huang, Louis Lamia and the MIT iGEMTeam, Joy, Leanna, Paul,
Shawn, and Shirley of the MIT iGEM team of 2010
Somerville High School: Chris Angelli
UC Berkeley: J. Christopher Anderson
WellesleyCollege: Catherine Summa,Wellesley College ScienceCenter Summer Research,Yui Suzuki and the
Suzuki Lab
Wyss Institute: Avi Robinson-Mosher
40. Evaluating Problem Solving
• Quantitative measures
– Number and value of
insights
– time per activity
– subjective workload
– attitude
– physical and verbal
participation
– equality of participation
• Qualitative indicators
– collaboration style
– problem-solving strategy
– nature of discussion
BU-Wellesley Software 2011
41. Feedback from Users
BU-Wellesley Software 2011
Our discussions were
able to get further with
the help of the G-nome
Surfer.
G-nome Surfer contributed most to my satisfaction because while I usually
prefer to work alone, the teamwork felt effortless, natural, and fun.
G-nome Surfer really helped in examining the strengths and
weaknesses of your own hypothesis with those of others in the group.
Being able to see and compare researched data side-by-side was
particularly useful.
It was very helpful in the sense
that information was very easy
to find and could be organized
into places that are easily seen
and used.
