Team:Imperial College/Education
Education
Synthetic Biology isn't a simple field, and not one that's taught in general studies either. As a newly budding research area, many are yet to become aware of the immense impact it could have, but also the dangers and ethical implications
too.
With our education, we sought to provide a means to enable people within the synthetic biology community to learn about the field, and empower them to contribute to it. This includes our mentoring of five teams with their
modelling, as seen here, as well as our Introduction to Mathematical Modelling in Synthetic Biology package.
While some may not be interested in the finer details, the progression of science
affects all. We therefore also sought to engage the public in the conversation. We did this by participating in the Science Slam hosted by Heidelberg and hosting two of our own Webinars, all open to the public.
Click on the
images below to find out more!
Science Slam
The ethics of automation
When we presented a talk on the ethics of automation at the Heidelberg Science Slam, we gave the general public an accessible flavour of the topic. The ethics of automation is central to our project - we are aiming to bring
automation to more scientists. We need to know how we will affect our users, and whether we are delivering what they desire.
Specifically, we wanted to ask:
What changes is automation bringing in the lab?
Which consequences are inevitable?
For such complex questions, we needed experts:
Dr. Brandon Sepulvado, data scientist at NORC at the University of Chicago (http://www.brandonsepulvado.com/)
Dr. Marco Brandizi, software engineer and bioinformatics specialist at Rothamsted Research (https://www.rothamsted.ac.uk/our-people/marco-brandizi)
→ turn into pic + description
We hosted a publicly available and advertised webinar on the ethics of automation, with our experts, so not only could we learn from these experts, but others could too! Automation
is a very complex and polarising topic, and we know we aren't the only ones with these questions. In the webinar, the topics covered included:
The evolution of ethics in synthetic biology
The role automation
has (or hasn't) played in synthetic biology ethical discourse
Open data and its consequences
In answer to one of our questions, Dr. Brandon Sepulvado responded that ethical discourse should be integrated in research, not independent of it.
This was very positive for us to hear, as our core values encompass this ideology. Therefore, by integrating human practices into our project and establishing our guiding values early on, we are ensuring that we are tailoring
our product to the ethical discourse around it.
introduction to modelling
Our inspiration
Gabe, one of our mathematical modelers, participated in the IGEM 2017 competition with his high school, Judd_UK. At the time, he had very limited knowledge of mathematical modeling, and there weren’t any resources accessible
to high school students to learn from either. Thanks to his mentorship from Oxford University however, he was able to formulate a thorough model which had a significant impact on his team’s project, winning them the award
for Best Model.
Modelling in synthetic biology is a 3rd year university course, so all educational resources are aimed at late undergraduates and beyond. It’s no wonder high school teams like Gabe’s find modelling
so challenging – there simply aren’t any resources accessible to them! To tackle this, we aimed to create a thorough, accessible introduction to modelling, only assuming knowledge up to high school level. The package will
act as a foundation upon which further, more specific research can be conducted. The goal is for more advanced literature to be accessible once someone has understood the content in our package.
Our content
structure
We ultimately concluded that the most useful package would be a combination of both a document to read, video tutorials alongside this to provide a visual and auditory explanation of the concepts, and "coding challenges"
to provide hands-on experience with the concepts.
The content covered in the final version is as follows:
Deterministic Modelling: Perhaps the most accessible modelling framework, deterministic modelling is a very powerful framework from which many
models in synthetic biology are built. It was therefore an obvious starting point to introduce modelling.
Stochastic Modelling: Many models can be developed further using stochastic techniques. These
enable randomness and discrete events to be integrated into a model. This follows nicely from deterministic modelling as a means to eliminate the continuity assumption necessary for deterministic models.
Additional modelling frameworks: There are many frameworks to model a system, as well as specific examples, which can each be explored thoroughly. We explore some of these, but this is where we invite future teams with modelling experience to add to this
package.
Modelling in practice: The theory of modelling is fascinating in and of itself, but what purpose does a model serve in the context of an IGEM project? Here, we justify and contextualize the
benefits, as well as explore the limitations of modelling.
Integrated feedback
The content was determined organically based on our meetings with our collaborators. They then validated our package by reading through our resources and watching our tutorials, verifying whether they understood the content
as well as giving feedback. Their input was invaluable in the development of the package. For example, the Korea HS team indicated the language we used in version 1 of the document was aimed at high school seniors, which
some of them weren’t yet, so it wasn’t quite accessible to them. The Lausanne team suggested we include stochastic modelling techniques, a crucial but complicated topic in mathematical modelling. We took this feedback and
adapted the document. In this way, the teams we collaborated and partnered with acted to validate our package.
From our meetings with our mentees, we also determined that programming was an essential skill for
simulating models, but one which many had limited experience with. For each team, we provided bespoke guidance on their code, but we also wanted to provide some learning resource in our introductory package. We therefore
added programming as an element of the tutorials and introduced “coding challenges” to test a reader's understanding of both the theory of the model and the script writing.
Conclusion
We feel we have been thorough in our development of the package. By including the input and feedback of a range of potential end-users, we validated its usefulness. However, we recognise that there is certainly room for expansion.
We have therefore included the source LaTeX file for future teams to expand upon as part of their own Human Practices. We hope this package will continue to develop, until it becomes a truly comprehensive introductory guide
to modelling in synthetic biology.
DOWNLOAD handbook
DOWNLOAD LaTeX files
Click HERE for the Tutorial playlist
Click HERE to view the Coding Challenge answers
Science slam
We were invited to present at a science slam organised by the Heidelberg iGEM team, as a way to present science to the general public in an easy-to-understand and entertaining way. We realised that to convey our project to
the general public, we needed to explain the context behind it and why it was important.
Consequently, we came up with the topic of 'Ethics of Automation', with a specific focus on synthetic biology,
and a short introduction of our project at the end. By choosing this format, we were able to educate the public about synthetic biology and laboratory automation, two topics that are often inaccessible to the general population.
Topics we covered included:
-> The barriers to automation in synthetic biology and science in general
->The definition of total laboratory automation, or TLA
->A brief history laboratory
automation
->The benefits and disadvantages of laboratory automation
->Our solution - a presentation of our project as a way to overcome the barriers to automation that currently exist
We hope
that our presentation was interesting and useful to our audience!
developing for biology
One of the key goals of our project is to connect wet-lab scientists with software developers. We therefore asked: how are wet-lab scientists and software developers collaborating right now? What can we learn from them?
We hosted a webinar, with the aim to promote interoperability and communication between bench scientists and developers, and to learn for ourselves how the communication we want to promote is happening in the real
world.
We also recognised the important distinction between collaboration in academia and collaboration in tech companies, two entirely different ecosystems with very different ways of working. We recruited experts
from both of these areas, so that not only can we and others learn how collaboration is taking place, but academics and company employees can learn from each other! Maybe there is a such thing as the best of both worlds.
Our experts were:
Michael Crone, Research Assistant in the Freemont group at Imperial College (https://www.imperial.ac.uk/people/m.crone15)
Mike Fero, CEO @ TeselaGen Biotechnology (https://www.linkedin.com/in/mikefero/)
Keltoum Boukra, Software Engineer @ LabGenius (https://labgeni.us/team/keltoum-boukra)
Our Highlights
The benefits our experts have observed from automation in biotechnology include higher workflow reproducibility, reliability, and throughput.
This supports the results of our research about the benefits of automation, giving us an even stronger case of why automation is important!
The common aim of both bench scientists and developers is to turn science into production.
Bench scientists are seeking means to scale up their research to improve efficiency and reduce timeframes, something which automation enables. The software developers provide the means to access the benefits of automation
for their specific needs, thanks to the solid line of communication between wet lab scientists and developers. → could be a nice diagram
We hope other attendees were able to learn about new ways to promote collaboration
and why it is so important!
