Hello and welcome back to the molpigs newsletter! All the past podcasts and tutorial can be found here. Enjoy! Feel free to hang out at the molpigs Forum!

  1. Events and podcasts announcement!
  2. Interested in Chemical Reaction Network (CRN) Modeling for synthetic or systems biology? Check out the new Build-a-cell tutorial series!
  3. Another reminder about the grassroots textbook initiative: The Art of Molecular Programming!
  4. Interested in helping out, sharing something interesting, or have an idea for something we could do?

1. Events and podcasts announcement

We will soon be recording three podcasts with Dr. Tom Ouldridge, Dr. Josie Kishi and Dr. Yuan-Jyue Chen! Please send us your questions by this Friday, next Wednesday and the 25th respectively so we can get their thoughts!

Tom Ouldridge is a Royal Society University Research Fellow in the Bioengineering Department, where he leads the “Principles of Biomolecular Systems” group. His group probes the fundamental principles underlying complex biochemical systems through theoretical modelling, simulation and experiment. In particular, they focus on the interplay between the detailed biochemistry and the overall output of a process such as sensing, replication or self-assembly. They are inspired by natural systems, and aim to explore the possibilities of engineering artificial analogs.

Josie Kishi‘s interest in molecular programming was sparked when she took an elective course in biomolecular computing during college. She went on to work with Peng Yin and others at the Wyss Institute, where her primary focus was to develop the Primer Exchange Reaction (PER) synthesis method. She showed how PER cascades can be used to perform logical operations and record temporal molecular events (Nature Chemistry 2017) and for generating long single-stranded concatemers for amplifying multiplexed fluorescence imaging signal (Nature Methods 2019). Josie holds a B.S. in Computer Science from Caltech and a Ph.D. in Systems Biology from Harvard.

Yuan-Jyue Chen is a senior researcher at Microsoft Research. He is also an affiliate professor in the Paul G. Allen School of Computer Science & Engineering at the University of Washington. His research focuses on DNA Storage and DNA computing. He collaborate closely with Molecular Information System Lab (MISL) from University of Washington to make DNA storage a reality. Prior to Microsoft, he received his PhD in Electrical Engineering from University of Washington in 2015, advised by Georg Seelig. His PhD project was a collaboration between the biological computation research group at MSR Cambridge and Caltech. He came to Microsoft Research as a postdoc in 2015 and became a researcher in the DNA storage group in 2017.


2. Interested in Chemical Reaction Network (CRN) Modeling for synthetic or systems biology? Check out the new Build-a-cell tutorial series!

Make sure to check out the build-a-cell tutorial series :)

Build-a-cell workshop series is an introduction to chemical reaction network (CRN) modeling for synthetic and systems biology using a suite of python software tools that make model building, exploration, and simulation easy and accessible.

The software tools introduced in this series allow for sophisticated models to be easily built (BioCRNpyler), simulated & parameterized (Bioscrape), and combined together into systems level models (SubSBML and Vivarium). These tools require only the most rudimentary scripting experience in python and no modeling or mathematical background will be assumed. The series also includes coding tutorials with publicly available python notebooks to help you get started.

The full playlist can be found here!


3. Another reminder about the grassroots textbook initiative: The Art of Molecular Programming

Remember to fill out the application form for The Art of Molecular Programming—you can contribute as little or as much as you like, so do make sure to be a part of this exciting project!

To hear Dominic talk about the idea behind this initiative, check out his announcement and our discussion at the end of the last podcast!

We are launching a grassroots initiative to create a textbook called “The Art of Molecular Programming.” We need YOUR help!

The principles of molecular programming are currently scattered across thousands of papers, which presents a barrier for new researchers entering the field. The Art of Molecular Programming will collect these principles in one location, provide tutorial lessons to guide students’ learning, and present a collective vision on where the field is heading. We are seeking participation from anyone who considers themselves a molecular programmer (i.e. You), regardless of your career stage. The final textbook will be published open access and attributed to all the authors and editors. Please fill out this survey to join the effort!

If you have any questions, comments, or concerns, feel free to contact us:


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:

We’re looking forward to getting to hear from you, and getting to know you better!