Hi everyone! My name is Owen, and I am a Technical Intern here at JMP. I have a background in biology, notably synthetic biology and biotechnology. In this second post of the series, I share case studies I have created using examples in the context of synthetic biology and ways to engage with the synthetic biology community. Part 1 introduced synthetic biology and opportunities for JMP.
Design of experiments for biological research
My work has focused solely on design of experiments. In the past few weeks, I've had the privilege to interview several key academics and industry professionals working in the field of synthetic biology in the UK. We had a fruitful discussion on DOE applications for biological research and teaching courses about DOE. All the experts we interviewed agreed on the importance of teaching DOE to students. However, the penetration of DOE in biology is still poor. While there are courses available in selected universities (such as UCL), it has not gained widespread adoption and there is a great NEED to spread awareness of this methodology. Thankfully, there is also a great INTEREST for biologists to learn about DOE. As an example, Synthace recently released a three-part webinar series about DOE for biologists with over 700 registrants in attendance.
In my own work, I have begun to compile synthetic biology resources that may be beneficial for JMP. I created three journals based on research papers that use DOE for their research. The reports have been uploaded into JMP Public and the journals are attached in this article:
- Understanding the metabolic interactions for ethanol biosynthesis using DoE | JMP Public
- Improving metabolic pathway efficiency using DoE | JMP Public
- Understanding reaction components affect the kinetics and performance of cell-free protein synthesis | JMP Public
I hope that these journal files can be used for demonstrating DOE to biological researchers. Some further information on all three journals to suit different levels of users:
- Violacein pathway (Beginner): Plackett-Burman screening design followed by Box-Behnken optimization design; modelling using Least Squares
- Ethanol biosynthesis (Advanced): Split-plot design; modelling using Partial Least Squares (SIMPLS, K(10) cross validation)
- Cell free systems (Advanced): 2x DSD designs followed by RSM design; modelling using Least Squares
I have also created a database of other synthetic biology research papers using DOE, which I will continue to update (see attached JMP journal: "Bio Papers using DoE").
Engaging with the synthetic biology community
The term 'synthetic biology' might still be foreign for most people, including those who are studying biology-related disciplines. From my own personal experience, I first heard the term early in my undergraduate studies from a lecturer who was recruiting students to form a team to compete in the prestigious iGEM competition, which is an annual, global competition focused on synthetic biology.
The iGEM Foundation is an independent, non-profit global organization dedicated to the advancement of synthetic biology, education and competition, and the development of an open, collaborative and cooperative community. They host the premier international synthetic biology competition with 350 multidisciplinary teams participating annually from all over the world. The iGEM competition is often a student’s first exposure to synthetic biology. Alumni from the competition have continued to cultivate innovation and create start-ups within the field. So far, over 150 startups have been built by iGEM participants.
Every year nearly 7,000 people dedicate their summer to iGEM and then come together in the fall to present their work and compete at the conference. Most of the attendees are undergraduate students in universities from all over the world. There is also a smaller pool of graduate students and high school students. The judging panel comprises ~120 academics ranging from PhD students, Post-Docs, Principal Investigators (PI) and Professors. A list of teams that have registered for the 2022 competition can be found here. As of this writing, over 370 teams have registered.
The iGEM competition is made possible through sponsorships. MathWorks, a competitor to JMP, has sponsored iGEM for many years.
JMP has an opportunity to engage with the iGEM community, either through direct sponsorships or through hosting exhibitor booths and demonstrations during the conference. By engaging with students early, we are investing in future researchers, entrepreneurs and global leaders in the field. More information can be found in the two attached documents on iGEM.
While iGEM is the premier student and academic conference, there is also an annual industry-focused conference hosted by Built With Biology. Built With Biology is the leading innovation network for biological engineers, innovators, entrepreneurs and investors who share a passion for using biology to build a better, more sustainable planet. They provide their community members with personal and professional development, as well as valuable opportunities for networking, partnership, collaboration and education.
Every year they host The Global Synthetic Biology Summit which showcases the cutting-edge developments in biology that are transforming how we fuel, heal and feed the world. In addition, they stage a variety of other conferences, thought leader retreats and local meetups throughout the year, in both the United States and around the world. Furthermore, they sometimes host webinars and courses within their community. This could be a potential area of collaboration for JMP in the future Experience (builtwithbiology.com).
I hope this post has provided some information, resources and ways to engage with this field. I believe JMP has a lot to offer in helping researchers and scientists in this field to push these innovative products into the market faster. I will update this article as I create future resources for JMP. I look forward to hearing your thoughts in the comments and will be happy to answer any questions!
