Engineering/Design
Design
On this page you will find information on: Introduction, Selecting the Right Fluorescent Protein(s), and. Quantitative vs. Qualitative Measurements.
Introduction
The starting point for any iGEM project, dry lab or wet lab, begins with the design stage of the engineering cycle.
In this stage of the cycle, you should create a specification which defines what is required to meet the aims of your project and use this to guide your design. You should also think through the entire engineering cycle and decide what you will be doing at each stage. This is very important as without it you may end up with something which works perfectly but isn’t fit for purpose. Thinking back to the example of designing an aircraft on the introduction page, without a proper specification you may end up with a passenger aeroplane which flies perfectly but has no space for luggage.
In the design stage you can also make good use of models and simulations to predict how your design will function. This can help identify any issues before lots of time and money is spent building and testing a design which is incorrect.
It is also important at this stage to consider how you will test your design to determine whether it meets your specification. This will help avoid the problem of, for example, building a genetic circuit with no reporters which can be measured. You can also use models to help identify how best to test your design.
You will pass the Design or Redesign stage several times while going through iterations of the DBTL cycle. As such, stay open minded and keep your design modular, such that you can easily change and adjust it later on. Modularity is an important criterion for the design but will also help make the implementation of an engineered biological system easier.
Questions to Consider for wet lab projects
When starting your design, these are important questions to ask:
- What is the purpose of your design?
- What will be the function of your engineered biological system?
- In which chassis will you implement your design? Bacteria, yeast, maybe a cell-free system?
- How will you build your design? Will it be synthesised; will you assemble it from existing DNA parts; what plasmids will you use?
- Which biological parts will be required to implement your function?
- How well are these functions characterized or described in literature?
- Can you model the performance of these functions and how they work together?
- How will you test the function of your design?
- What will your experimental data look like if the design is working as intended?
Once you have created your design(s) using the questions above as a guide, you can move on to the Build stage.
Tips to Get Started
A good place to start with the Design stage is to define the problem you are trying to solve, and what your solution is. Use these to determine what essential functions your system needs to ensure that you are solving the problem, and then begin working out how you will test whether your system is meeting these requirements. These guidelines can then form the basis of your design specification.
When designing the genetics for your system, it can be helpful to start with a very abstract view. Split your system up into large functions. Maybe you need to express a protein in the presence of two inducers. In this case, you would need two biosensors for each of the inducers, an AND gate which uses the two sensors as inputs, and a protein expression unit as the AND gate output. Then you can start thinking about how these functions can be built using biological parts. For example, a protein expression unit in bacteria would need a promoter, an RBS, a CDS coding for your protein of interest, and a terminator. Maybe there are already designs for these available that can be reused in your own system! Once you have this abstract view of your system, you can then start to consider which specific parts you will actually use. For example, will you use a strong or weak RBS? Do you need to codon optimise your CDS? Maybe your model can help guide these decisions if appropriate! This method of design is sometimes referred to as top-down design and is seen as a hallmark of Synthetic Biology.
It is also important to ensure that your solution is fit for purpose and can/will be used by your intended users. Check out the Human Practices hub for more information on this aspect of the Design stage.
In silico Design Stage
As discussed above, models can help inform your designs. There are also plenty of projects which are fully in silico. The DBTL cycle can be useful in developing models, and also for other fully in silico projects.
The questions to consider listed above can be adapted for in silico projects or for the development of a model:
- What is the purpose of your model?
- What will be the output of your model?
- What type of model do you need? Deterministic? Stochastic? Agent-based?
- In which language will you implement your model? Java, Python, SBML?
- How will you run your model? Can it be run on a command line; will you use a tool such as COPASI?
- Which parameters and/or libraries will be required to implement your model?
- How well are these parameters characterized or described in literature? How well documented are the tools/libraries you are using?
- Have similar models been developed and described before?
- How will you test the function of your model?
- What will your simulation data look like if the model is working as intended?
Once you have created your model or other in silico design(s) using the questions above as a guide, you can move on to the Build stage.
Tips to Get Started
One of the most difficult aspects of building a model is working out what the model should be. A good place to start is to decide what question you want your model to answer. Is there an aspect of your system that can’t be measured experimentally? Are you trying to determine the optimal promoter strengths in your genetic constructs? Are you building hardware which needs modelling to inform its design before building it? You can then use this information to help answer the rest of the questions to consider above.
If you are struggling with what needs to be modelled, start by drawing out your entire system on paper and label any interactions which are happening. Then, start to draw boxes around processes which are important, but don’t need to be simulated individually and can be grouped together. For example, in some models you may need to split protein expression up into transcription and translation (for example, if you are trying to determine how strong your RBS needs to be), but for others these can be grouped into one process DNA produces protein). You can also start to remove any processes which aren’t needed. For example, do you need to model how ribosomes are produced, or can you just assume that they are present in the system? From this modified diagram, you can then start to pull out the processes which are occurring and use this as a basis for your model design.
Design Stage Resources
Our 2020 and 2021 iGEM webinar series on the following topics may be useful resources for the design stage:
- How to get started
- Modeling: ODEs and Hill Functions
- DNA parts and Basic Molecular Biology
- Modeling circuits with ODEs and experimental data
There are also several tools which can help you with designing your system:
- iGEM registry (http://parts.igem.org): A registry of all past DNA parts and constructs created by previous iGEM teams. This can be used to identify any existing parts to use in your project.
- Benchling (benchling.com): An online tool to help you create, edit, store, and share DNA and protein designs. It also includes tools to simulate molecular biology procedures such as restriction digest, PCR, and DNA assembly.
- SynBioHub (https://synbiohub.org/): Similar to the iGEM registry but also contains constructs from other sources.
- Elixr RDM Kit (https://rdmkit.elixir-europe.org/microbial_biotechnology): An online guide for storing and sharing your design according to FAIR (findable, accessible, interoperable, and re-usable) principles.
- SBOL (https://sbolstandard.org/applications/): A standard language for storing information about biological systems. There are SBOL-compatible tools available to help you design your system at various levels of abstraction and help with top-down design.
- BioModels (https://www.ebi.ac.uk/biomodels): A repository of mathematical models for various biological systems.
- AutoCad (autodesk.co.uk/products/autocad): A CAD tool for designing hardware or other aspects of your project. Available for free to students.
- ANSYS Suite (https://www.ansys.com/en-gb/academic/students): A suite of tools for modelling hardware such as pumps, microfluidic chips, and other similar aspects of your project. Academic package available for free to students.
- Tinkercad (https://www.tinkercad.com/): A tool for making 3D designs, electronics, and coding.
Please email the Engineering Committee at engineering [AT] igem [DOT] org and provide links to material with a short description. We’ll check it out and if we believe it will be helpful, we’ll add it to this page!
iGEM Foundation
The International Genetically Engineered Machine (iGEM) Foundation is an independent, non-profit organization dedicated to the advancement of synthetic biology, education and competition, and the development of an open community and collaboration. Visit us at igem.org
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