molpigs, The Molecular Programming Interest Group, is an international group of researchers interested in topics such as molecular programming, DNA computing, and other aspects of biomolecular nanotechnology. We host regular seminars, poster sessions, journal clubs, send out newsletters, and host a forum for discussion and fostering collaboration.
Hello and welcome back to the molpigs newsletter! Feel free to hang out at the molpigs Forum! We are also on twitter!
All the past podcasts and tutorial can be found here. You can also now find our podcasts on Apple Podcasts, Spotify, Google, Stitcher, TuneIn, and more (as well as manually in your favorite podcast client with our RSS feed)! Enjoy!
- Podcast—Panel session #1—Meet the Committee!
- New event coming—Chat with William Poole!
- Job Advertisements!
- Interested in helping out, sharing something interesting, or have an idea for something we could do?
1. Podcast—Panel session #1—Meet the Committee!
The Molpigs committee are experimenting with a new podcast format–Panel discussion!
The idea of the Panel session is to initiate some discussion from students’ perspective about graduate school/research related questions. The conversation represents attendants’ personal thoughts at the current stage of life.
Different from the other podcast style where we chat with our guests, currently the panel session is a discussion among the molpigs committee (Hannah Earley, Anastasia Ershova, Georgeos Hardo and Boya Wang).
As the four of us have together pushed molpigs forward (excitingly we have released more than 10 podcast episodes!), the first episode of the panel discussion is a brief introduction and discussion about ourselves! Interestingly, half of us are located in the UK and half are in the US (distance didn’t separate us apart!), so we start with some background about the education system between the two. We chatted about why we joined the molpigs committee. We had a friendly conversation about the term “molecular programming”. We slightly touched on the topic of graduate school mental health. And we disclosed what we want to achieve the most at the current stage.
We hope that this episode serves as a start for more difficult topics in the future! ;-) As we move on to future episodes, we would like to hear about your feedback/support! If you like it, please let us know! If you would like to hear about certain topics or have any suggestions, please send them here. Molpigs Forum is also open for discussion!
Enjoy this episode!
2. New events coming—Chat with William Poole!
We will talk with William Poole in a few days!
William Poole received his B.Sc. from Brown University in Biological Physics and is scheduled to complete his PhD in Computation and Neural Systems from Caltech in summer 2021 (co-advised by Erik Winfree and Richard Murray). Broadly, his research interests involve developing mathematical and computational tools to understand “how cells think” and “how to program cells”. He views systems biology and synthetic biology as two sides of the same coin; to truly understand and control biological systems we will need fundamentally new ways of thinking about biochemical computation. For inspiration, he has looked to statistical physics, machine learning, and computer science. He also believes that doing theory in a vacuum, without close contact to experimentalists, is counterproductive towards developing the tools that will drive science and technology forward. Towards this end, he also dabbles in the wet lab side of synthetic biology with an eye towards applications in green technology and sustainability.
- Theory: He has worked to enable the design and analysis of biochemical networks through techniques inspired by machine learning. Recent work implements specific machine learning algorithms with biochemical models and uses ideas from statistical physics and information theory to interpret broad classes of biochemical networks as machine learning algorithms.
- Computation: He has been inspired by the machine learning libraries like pytorch and tensorflow which provide abstract frameworks for specifying and efficiently training diverse machine learning architectures. In order to successfully engineer and understand the complexity inherent in any biological system, we will need powerful computer aided design tools. This means the ability to easily compile diverse models of biochemical circuits (BioCRNpyler), fast simulation techniques custom-tailored to utilize and learn from biological data (bioscrape), and the ability to connect, combine, and simulate diverse models across many scales (Vivarium).
- Experiment: He has worked on understanding and modeling the metabolism of E. coli cell extract. It amazes him that in this “not even living” biological system we still have only barely begun to understand how to model, engineer, and optimize metabolic activity. Ultimately, he sees metabolic engineering as a cornerstone of a green-economy which produces all kinds of chemicals and materials from living matter instead of fossil fuels.
If you have any questions, please send them here!
3. Job Advertisements!
The Ti Lab is looking for an ambitious postdoc with interests in developing a new nanotechnology. For applicants, background with material chemistry/self-assembly experience is a plus, but is not required. Greg Tikhomirov is happy to help with fellowship applications.
The Shih Lab at Harvard is looking for graduate students, postdoctoral fellows and research technicians, with specific openings for:
- Postdoctoral Fellow for DNA Nanoswitch Calipers
- Research Technician for programmable self-assembly of DNA nanostructures
- Research Technician for DNA nanostructure-based cancer immunotherapies
- General inquiries are also welcome
4. Interested in helping out, sharing something interesting, or have an idea for something we could do?
If so, please get in touch with us! Shoot us an email at
contributions AT <this domain>, there are loads of ways you can get involved, and many we haven’t even thought of, but here’s a few ideas of what you could do:
- Be a guest on our podcast series: you can talk about anything vaguely related to the field, whether it’s comments on life as a student/researcher, some thoughts you’ve had about the field, some interesting work you want to share, or if you want to speak out about something like mental health, this is the perfect place to do it!
- Present a poster-podcast! This is something we’re very excited to try out, and we hope you feel the same: the idea is to try to explain something (it doesn’t have to be your own work) within a 20-30 minute podcast, with the challenge that all reference material needs to fit into a poster format.
- Want to advertise something on our newsletter? Perhaps you’ve just passed your thesis defense, or are looking for a team for a hackathon, or have a job posting to share, or have just written a blog post you think might be of interest; whatever the case we’d love to help you share the good news!
- We’re also open to more conventional seminar-esque things like talks or journal clubs.
We’re looking forward to getting to hear from you, and getting to know you better!