Presented in the Synthetic Biology & Gene Editing strand of the 4Bio Summit. For more information, visit:
www.global-engage.com
Integration of omics data and systems biology models should optimise knowledge gain from synthetic biology experimentation. However, data is not leveraged effectively, due to a lack of readily available tools. In this presentation, Niko Sonnenschein from the Novo Nordisk Foundation describes a project which aims to make omics data useful to biotechnology and life science research by integrating systems biology with design in one platform.
3. What we do …
• Construct cell factories!
• Determine the spectrum of molecules
that can be produced biologically
(basic research).
• Shortening the strain design and
development process (translational
research).
• Develop new technologies and transfer
knowledge to industry for the benefit
of society.
• Train the future workforce of a bio-
based economy.
4. Commercial:
Product titre > 10–100 g/L
25–50 FTE for 5–10 years
Cost $50M–$250M
Death valley
Valley of Death
Academic:
Product titre < 1 g/L
1–2 FTE for 2–3 years
Cost < $1M
5. Commercial:
Product titre > 10-100 g/L
< 2 years
Cost <$20M
Bridging the valley of death
Omics
Lab automation
Valley of Death
Systems biology
guided design
Academic:
Product titre < 1 g/L
1–2 FTE for 2–3 years
Cost < $1M
6. Computer Aided Metabolic Engineering and
Optimization of Cell Factories
http://cameo.bio
http://www.biorxiv.org/content/early/2017/06/09/147199 =>
https://tinyurl.com/cameo-biorxiv
16. Data-Driven Design of Cell Factories and Communities
http://dd-decaf.eu/
The project has received funding from the
European Union’s Horizon 2020 research
and innovation programme under grant
agreement No 686070
17. Data-Driven Design of Cell Factories and Communities
Pathways Cells CommunitiesEnzymes
Health AgricultureIndustrial biotech Environment
Fluxome(Meta)genome Transcriptome Proteome Metabolome
OmicsDesignApplications
23. Next steps
• Registration via Google, Twitter, Github,
Facebook, ORCID, …
• BYOM: Bring your own models
• Mine (meta)genomic data for enzymes
• Support more types of omics data
• Add community modeling
Models Enzymes
Omics data
AGTGG AGTT AA TC TC T
TATT GG AG ATT AA GA
GTT ATC TC TT GAA TT G
TATGG AC TT GC TT ATT
GATC TC GTT AA GAGTT
AA TC TT GG AG ATGC TT
ATT GATT GTAGAGTT A
TT
27. Automate all the things
High-level strain design
“Delete native genes A, B, C, and D. Add foreign
genes X, Y,Z. Increase flux through reaction F by
twofold while reducing flux through reaction G by
threefold. Remove product inhibition in pathway Q
…”
Magic
Compiler
Box
gRNAs
Primers
Protocols
Genes
Promotors
Libraries
…
(b) Workflow
Workcell
Freezers and
incubation
PCR
Robotics
arm
Liquid
handling
Plate
reader
Plate/test-tube
magazine
AUTOPROTOCOL
Data Protocol
API
Materials
Shipping
29. Acknowledgements
The project has received funding from the
European Union’s Horizon 2020 research and
innovation programme under grant
agreement No 686070
Get in touch with us via:
http://dd-decaf.eu/
@dddecaf (Twitter)
Zachary King (UCSD)
30. Presented in the Synthetic Biology & Gene
Editing strand of the 4Bio Summit.
To find out more, visit:
www.global-engage.com