Difference between revisions of "Summer 2012 SynBio Project (Davidson and MWSU)"
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* Are they naturally occurring or synthetic? | * Are they naturally occurring or synthetic? | ||
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* Do they involve screening or selection? | * Do they involve screening or selection? | ||
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* Are they anabolic or catabolic? | * Are they anabolic or catabolic? | ||
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* How many steps are in each pathway? | * How many steps are in each pathway? | ||
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* How can they relate to cell fitness? | * How can they relate to cell fitness? | ||
Revision as of 20:05, 25 May 2012
Contents
Student Proposals from Ind. Studies
- Erich Baker Proposal: Media:Erich_Baker_proposal.docx This proposal deals with Phytochromes and Light Sensitive Channel Proteins
-I think the use of Phytochromes might be a good way to have either a continual stimulus that would repress/express certain genes that could be turned off and on depending on what we want them to do. There are other aspects of the research in this proposal that if not used outright, could be adapted to our continuing projects as either controls or feedback mechanisms. As for the proposed Salis RBS sites, I would like to see more information in the efficacy of the predicted RBS sequence. Possibly if we could use some of the C-Dog information based on a few known sequences to determine if the computer can predict those RBS's we know to be effective then we might be able to count on the calculator as a tool for our experimental design. -Caleb Carr
- Ben Clarkson Proposal: Media:Ben_Clarkson_proposal.docx
- Duke DeLoache Proposal: Media:Duke_DeLoache_Proposal.docx
- Becca Evans Proposal: Media:Becca_Evans_proposal.docx
- Ellen Johnson Proposal: Media:Ellen_Johnson_proposal.docx
PPT Presentations
- This PPT file contains all the slides from student presentations addressing the idea proposed by MWSU.
Media:Reports_on_Circuits.pptx
- This PPT contains slides summarizing some of the best and most complicated papers from Week 11.
Papers
Methods Papers
- DNA assembly for synthetic biology: from parts to pathways and beyond
Tom Ellis, Tom Adieac and Geoff S. Baldwin
Integr. Biol., 2011, 3, 109–118
- Everyone should watch this 5 minute video on optogenetics. Combine that video with the 2010 champoinship iGEM invention of E. glowi.
Older Lab Papers
- Engineering bacteria to solve the Burnt Pancake Problem.
Haynes, Karmella, et al.
Journal of Biological Engineering. Vol. 2(8): 1 – 12.
- Solving a Hamiltonian Path Problem with a Bacterial Computer.
Baumgardner, Jordan et al.
Journal of Biological Engineering. Vol. 3:11
- Bacterial Hash Function Using DNA-Based XOR Logic Reveals Unexpected Behavior of the LuxR Promoter.
Brianna Pearson*, Kin H. Lau* et al.
Interdisciplinary Bio Central. Vol. 3, article no. 10.
Time Delayed Growth Movie
Network Papers
Jonathan M. Raser and Erin K. O’Shea
Science. Vol. 309, page 2010
Please post pdf.
Nagarajan Nandagopal and Michael B. Elowitz
Science. Vol. 333, page 1244.
Please post pdf.
R. Milo, S. Shen-Orr, et al
Science. Vol. 298, page 824.
Please post pdf.
Yang-Yu Liu, Jean-Jacques Slotine, & Albert-La ́szlo ́ Baraba ́si
Nature. 2011. Vol. 473, page 167.
Please post pdf.
Ethics Papers
Colin Mcilswain
Nature. Vol 465, page 867.
- Word selection affects perceptions of synthetic biology. Brianna Pearson, Sam Snell, Kyri Bye-Nagel, Scott Tonidandel, Laurie J Heyer, and A Malcolm Campbell.
- Read "Moral" ethics paper on synthetic biology. Media:Moral.pdf
- Read "Future" ethics paper on synthetic biology. Media:Future.pdf
Questions to Consider About Network Pathways
- Are they naturally occurring or synthetic?
- Do they involve screening or selection?
- Are they anabolic or catabolic?
- How many steps are in each pathway?
- How can they relate to cell fitness?
- What specific challenges would need to be addressed if we worked with the pathway?
Cellular Automata
- [1] General CA introduction
- [2], [3] Elementary Cellular Automata
- [4] Good explanation of how elementary CAs work
- [5] Rule 110
- iGEM Team Groningen
- iGEM Team IPN-UNAM Mexico
- MIT 2011 iGEM Tissue Design
- In Vivo Cellular Automata
- Edge Detection PDF
- Patterning of E. coli
- Tunable Bacterial Band-Pass Filter
- E. coli Predator-Prey Ecosystem
- Multicellular System for Programmed Pattern Formation
Other Ideas
- Networks (Modeling Focused)
- Field might be kind of saturated; it seems like a lot of work has been done.
- But not with netLogo. How could that work?
- RePast: another ABM suite that might be mroe suited to networks [6]
- General
- Network motifs in the transcriptional regulation network of Escherichia coli
- [7] Gene Regulatory Network wikipedia page
- [8] long dissertation on modeling GRNs
- Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles
- Process Calculus
- [9] Process Calculus wikipedia page
- [BioAmbients: An abstraction for biological compartments Process Calculi for bio modelling; might be at the level of cells as opposed to genes etc.
- Boolean Networks
- [10] Boolean Network wiki page; elementary CA are special cases of Boolean networks
- Boolean modeling of GRNs
- 'The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response
- Or-Not Logic Gate with E.Coli
- Dynamical Systems
- Discrete dynamical system modelling for gene regulatory networks of 5-hydroxymethylfurfural tolerance for ethanologenic yeast
- A Linear Discrete Dynamic System Model for Temporal Gene Interaction and Regulatory Network Influence in Response to Bioethanol Conversion Inhibitor HMF for Ethanologenic Yeast
- Neural Networks
- Field might be kind of saturated; it seems like a lot of work has been done.
- General
