You may use MATLAB/Octave, Gro, or Python for the analysis of your system. It might be harder to find help with other frameworks or languages, so we strongly suggest sticking to these options!
DELIVERABLESThe term project will be graded on four submissions:
- A 1-2 page Project Description
- A 2-3 page Model Description
- A 3-5 page Final Write-up
- A 3-10 minute Video Presentation
The major outcome of the term project is a presentation in the form of a video recording. The videos should not exceed 10 minutes in length and should cover the extent of your project, including problem statement, the synthetic system created, model formulation, and analysis of the simulations.
In addition to your presentation, you will be required to provide a short, 2-5 page document that includes a general description of your project, the specifics of your model (equations, parameters, and assumptions), simulation code, accompanying figures, and any supplemental information you wish to include. This document can be assembled from portions of the Project and Model Descriptions turned in with PS4 and PS5 (see above) and should contain an overview of your analysis results as well as the insights you found.
SYSTEM REQUIREMENTSProjects should be contained to no more than 12 system pieces (regulatory elements like repressor-operator pairs, miRNA-target pairs, reporter proteins etc.) to guarantee feasibility of the design and analysis by the end of the course.
- February 28 (due with PS4) – Project Description
- March 20 (due with PS5) – Model Description
- April 3 – Video Presentation and Final Write-up
- 2.5% Project Description
- 2.5% Model Description
- 4% Final write-up
- 6% Final presentation
- clarity of presentation
- motivation for the project
- originality of the proposed circuit or method of analysis
- careful definition of the project scope
- feasibility of the project
- description of the approach to analysis
- e.g. stability analysis, comprehensive study of the parameter space, temporal vs. spatio-temporal analyses
- relevance to project
- level of detail, thoroughness
- clarity of statements of any assumptions and the appropriateness of the justifications made for the assumptions
- clarity of presentation
- approach to analysis
- how much of the proposal was achieved
- insight into the properties and limitations of the circuit design
POTENTIAL PROJECT IDEASIn the 2010 iteration of this course, students from Berkeley and MIT compiled their results into a mock journal, feel free to read it but note that the prompt for the term project was different then and focused heavily on the write-up, whereas in this course more emphasis is put on a recorded presentation of your results.
Below is a list of potential projects. Some of these ideas require very sophisticated implementation or analysis that might be outside of the scope of this course; feel free to focus on more manageable aspects of such ideas.You are encouraged to come up with your own project ideas! If you come up with multiple exciting ideas, feel free to share them with others!
- Design a biological system that can self-organize into a two-layer onion structure.
- Design a bacterial cell that is capable of both self-renewal and differentiation during cell division: one daughter cell remains in a self-renewable, differentiable state while the other daughter cell terminally differentiates.
- Create the simplest biological circuit that can take three environmental inputs and turn on eight different response systems. Create the system from parts that have already been used in synbio circuits or parts known to function similarly. Compare their operational properties such as speed, signal rectification, susceptibility to intrinsic noise and fluctuations on the input.
- Design a biological system in which different cell types search for partner cells and upon encountering the right cell type irreversibly adhere to them. Make this system "addressable" in that one can "program" a large number of different cell types derived from the same common chassis. Can we do cellular "origami" with this system (i.e. design and build complex multicellular structures)?
- Design a biological system with a form of simple associative learning.
- Design a bacterium that can circulate safely in blood, recognize arterial plaque, and degrade it. Ensure that it can survive long enough to have an effect yet can be cleared from the circulatory system on demand.
- Analysis of various oscillator designs (single cell and/or population synchronized).
- Spatiotemporal modeling of bacterial quorum sensing, including hysteresis.
- Analysis of noise propagation for various network topologies and transcription factor interactions with DNA and RNA polymerase.
- Design of a noise generator and its use in analyzing the robustness of circuits like the toggle, pulse generator, oscillators.
- Simulation of a phosphorylation-only toggle switch, ring oscillator or a relaxation oscillator design.
- Design and spatiotemporal simulation of a predator-prey ecosystem or a rock-paper-scissors type oscillating ecosystem.
- Design and simulation of a cell division counter.
- Design a synthetic system that is robust to mutations (as long as they are below a certain threshold). If the number of mutations exceeds the threshold, then the mutations result in cell death.
- Design a genetic "bandpass filter" – assuming an oscillating input signal, only propagate certain frequencies to the output of the genetic circuit.
- Design a system to recapitulate the Sierpinski triangle pattern commonly seen on clam shells or some other fractal shapes and analyze it spatiotemporally (example 1, example 2, example 3)
The final presentation videos can be assembled using any of the methods below:
- the Office Mix plug-in for PowerPoint 2013 (PC only)
- PowerPoint 2010 (instructions)
- Keynote (instructions and more instructions)
- Google Air (note Google Air automatically posts recordings as public video to your YouTube and Google+ account) using these instructions:
- Create a Google and YouTube account if you do not already have these.
- Click the ''Upload'' button in the upper part of the screen, select the "Broadcast" button under Google+ Hangouts Air.
- You may be prompted to link Hangouts with YouTube. If so, click "Connect Account" button, verify your account, and repeat above step
- Name the Hangout the title of your project
- The program will take a few minutes to fully load before you can "broadcast", or record yourself.
- Click the green "start broadcast" button at the bottom of the screen to begin recording.
- You can switch to screenshare mode (let others view your screen and presentation) using the button on the left dashboard (shown to the right). Please select the "Fullscreen" option to share your presentation.
- When you are done, the video is automatically uploaded to YouTube after you hit the red "Stop Recording" button. To find the video, go to YouTube and "My channel" on the left hand side of the screen, then click the "Videos" tab. The video may take a few minutes to upload.
- Camtasia (free trial available)
Instructions on how to submit the videos will be given later in the term.