Registration for Bio-Design Week is now open! Please note that registration includes entry to the Monday workshops and IWBDA sessions. Register using this link!

Call for Papers

Join us for the 15th annual IWBDA meeting, in Boston, September 11-14, 2023. This year, IWBDA will take place during Bio Design Week and will include presentation and poster talks selected from submitted abstracts, Birds of a Feather discussions, and breakout sessions on selected topics. We aim to bring together academic researchers and industry partners to push the field of bio-design automation for synthetic biology forward.

The field of biology is still lagging behind the industry when it comes to implementation and adoption of computational and digital solutions. This is primarily because it is extremely difficult to offer a one-size-fits-all solution to engineer biology. Some BDA solutions serve as templates for a larger problem, but, to make it usable in a practical setting, the solutions often have to be redesigned for bespoke biological workflows. Without understanding the requirements of the broader synthetic biology community, it is hard to design a solution that can have a wider impact.

Increasing the efficiency of biological processes and workflows with biodesign automation is a continuous journey that requires fresh exchange of ideas. It is crucial for the BDA community to have a forum where they can collaborate, gather new perspectives, and understand the requirements of the broader synthetic biology community. IWBDA provides this forum for cross-disciplinary discussion, with the aim of seeding and fostering collaboration between the researchers from the synthetic biology, systems biology, and design automation communities.

Topics of Interest

Design methodologies for synthetic biology
Standardization of biological components
Biosecurity in lab automation processes
Biopreparedness through bio-design automation
Artificial intelligence and machine learning in synthetic biology
Computer aided design tools and automation for engineering biology
Biofoundries and their impact on synthetic biology
Formalized protocol capture
Design Build Test Case studies
Synthetic Biology education and outreach
Impact of Large Language Models in Bio Design

Registration

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Conference Logistics

Location Details

Bio-Design Week will be held at two main venues:

Boston University’s Center for Computing & Data Sciences, 665 Commonwealth Ave, Boston, MA 02215
Asimov, 201 Brookline Avenue, Boston, MA 02215

Hotels

Hotels close to Boston University and Asimov during Bio-Design Week may be more expensive than usual due to a Red Sox-Yankees series happening during the same week. We recommend looking at hotels along the MBTA’s Green Line (B) or within a reasonable walking distance to Boston University. There are options over in the Longwood Medical area (~25 minute walk or ~15 min by public transportation). Hotels in Cambridge may also be less expensive, but would require a longer commute.

Parking

If you require on-site parking, please let us know so we can explore some options to accommodate you. Please email Traci with the specific dates that you would need parking.

Agenda

Bio-Design Week - September 11-14, 2023

Monday, September 11 - 665 Commonwealth Avenue, 17th Floor

08:00-09:00 Registration and breakfast
09:00-09:10 Welcome and kick-off of Bio-Design Week
09:10-10:30 Workshop: SBOL Data Model
10:30-11:00 Coffee break
11:00-12:30 Workshop: SBOL Visual
12:30-13:30 Lunch
13:30-15:00 Workshop: Programmatic genetic design automation using LOICA
15:00-15:30 Coffee break
15:30-17:00 Nona Works Team Building and Mixer

Tuesday, September 12 - 665 Commonwealth Avenue, 17th Floor

08:00-09:00 Registration and breakfast
09:00-09:10 Welcome to IWBDA
09:10-10:15 IWBDA Talks: Sequence Manipulation and Gene Expression
- 09:10-09:30 Energy Aware Technology Mapping. Erik Kubaczka, Tobias Schwarz, Jérémie Marlhens, Maximilian Ge, Nicolai Engelmann, Christian Hochberger and Heinz Koeppl.
- 09:30-09:50 Local RNA Feedback: More Logic, Less Leakage. Nicolai Engelmann, Maik Molderings and Heinz Koeppl.
- 09:50-10:10 Using learned representations of genetic circuits to evaluate sequence-level mutations. Olivia Gallup and Harrison Steel.
- 10:10-10:15 Lightning Talk
  - Multi-Site Mutagenic Protein Library Design with Controlled Annealing Temperature. Yehuda Binik, Ayesha Chaudry, Akira Takada, Georgios Papamichail and Dimitris Papamichail.
10:15-10:45 Coffee break
10:45-11:45 Keynote: Dr. Nicole Wheeler
- Dr. Nicole Wheeler is a Turing Fellow at the University of Birmingham and also serves as a technical consultant for the Nuclear Threat Initiative. Dr Wheeler’s work focuses on the development of computational screening tools for identifying DNA from emerging biological threats, establishing genomic pathogen surveillance in resource-limited settings, One Health surveillance of antimicrobial resistance, and the ethical development of artificial intelligence (AI) for health applications. She has a background in biochemistry and microbial genomics, complemented by experience in developing machine learning methods for predicting the effects of genetic variation on the virulence of pathogens. She has provided expertise on machine learning for genomic pathogen surveillance for several international programs, including a world-first AI-driven One Health AMR surveillance system. She is also actively involved in public outreach and the development of governance frameworks to ensure the safe and responsible development of technologies for health improvement.
11:45-13:30 Lunch
13:30-14:30 IWBDA Talks: Biosecurity
- 13:30-13:50 Biological Malware Detector. Muntaha Samad, Dan Wyschogrod and Jacob Beal.
- 13:50-14:10 DNA Editing Game (DEGA) Theory. Nicholas Roehner.
- 14:10-14:30 Splicing-based Biocontainment Devices. Allison Taggart, Miles Rogers and Jacob Beal.
14:30-15:00 Coffee break
15:00-16:30 Biosecurity Panel and Discussion Session
- We are pleased to announce that IWBDA will host a biosecurity panel with panelists Dr. Nicole Wheeler and Dr. Peter Carr, moderated by Dr. Jacob Beal. This panel will explore the relationship between design tools and biosecurity.
- Dr. Peter Carr is a Senior Scientist at the Massachusetts Institute of Technology’s Lincoln Laboratory, where he leads the Synthetic Biology research program. His research interests include genome engineering, rapid prototyping of both hardware and wetware, DNA synthesis and error correction, and biosecurity. He is the Director of Judging for the International Genetically Engineered Machine (iGEM) competition and a founding member of the Synthetic Biology Center at MIT. He received his bachelor’s degree in Biochemistry from Harvard, and his PhD in Biochemistry and Molecular Biophysics from Columbia University.
- Dr. Jacob Beal is an Engineering Fellow at Raytheon BBN and is the lead developer for FAST-NA Scanner, a signature-based biosecurity screening tool used by multiple DNA synthesis companies. He also co-led the IGSC’s Regulated Pathogen Database update, and is co-organizing international standards for testing biosecurity sequence screening systems.
16:30-17:00 Break and travel time to dinner
17:00-20:00 Dinner at Sunset Cantina

Wednesday, September 13 - 201 Brookline Avenue, 4th Floor

08:30-09:00 Breakfast
09:00-10:05 IWBDA Talks: Modeling
- 09:00-09:20 A Collection of Biological Models for the Development of Infinite-State Stochastic Model Checking Tools. Lukas Buecherl, Payton J. Thomas, Mohammad Ahmadi, Josh Jeppson, Andrew Gerber, Eric Reiss, Chris Winstead, Hao Zheng, Zhen Zhang and Chris J. Myers.
- 09:20-09:40 A neural-mechanistic hybrid approach improving the predictive power of genome-scale metabolic models. Bastien Mollet, Jean-Loup Faulon, Léon Faure and Wolfram Liebermeister.
- 09:40-10:00 Knowledge-Based Pathway Extraction and Verification. Gaoxiang Zhou and Natasa Miskov-Zivanov.
- 10:00-10:05 Lightning Talk:
  - Model Checking of Interval Discrete-Time Markov Chain for Biochemical Pathways. Krishnendu Ghosh.
10:05-10:35 Coffee break
10:35-11:40 IWBDA Talks: Genetic Design
- 10:35-10:55 Guided Design of Genetic Circuits Exploiting Stochastic Model Verification. Lukas Buecherl, Mohammad Ahmadi, Hao Zheng and Chris J. Myers.
- 10:55-11:15 Design-Build-Test-Learn of Sponge RNAs for Synthetic Gene Circuits. Scott Stacey, Harrison Steel and Antonis Papachristodoulou.
- 11:15-11:35 Rule-based generation of synthetic genetic circuits. Masayuki Yamamura, Ryoji Sekine, Kazuteru Miyazaki, Sota Okuda, Naoki Kodama and Daisuke Kiga.
- 11:35-11:40 Lightning Talk:
  - Analysis of ASR inducible promoter in different conditions in Escherichia coli. Maria Jose Mesa-Rodriguez, Domenica Cuneo-Campodonico, Martin Gutierrez and Alberto J. Donayre-Torres.
11:40-13:00 Lunch
13:00-13:40 Invited Talks
- 13:00-13:20 Kernel: Evolving Genetic Design. Kevin LeShane
- 13:20-13:40 A Genetic Construct Simulator for Faster Design Alina Ferdman
13:40-14:45 Discussion session: Growing our Community
14:45-15:15 Coffee break
15:15-15:45 Discussion summary
15:45-16:45 IWBDA Talks: Automating Evolution
- 15:45-16:05 Long-term evolution of bacteria for maximal growth rate. Antoine Vigouroux and Johan Paulsson.
- 16:05-16:25 Engineering Continuous Directed Evolution with Single Cell Optogenetic Selection and Microfluidics. Jess James, Sebastian Towers, Idris Kempf, Jingyu Wang, Jakob Foerster and Harrison Steel.
- 16:25-16:45 An Automated Platform for Accelerating Adaptive Laboratory Evolution. Marco Corrao and Harrison Steel.
16:45-16:50 Late breaking lightning talk
- Biology that starts at a computer. Dave Vance
16:50-17:00 Break and travel to the reception
17:00-19:30 Networking Reception sponsored by Asimov

Thursday, September 14 - 665 Commonwealth Ave, 17th Floor

08:30-09:00 Breakfast
09:00-09:45 Workshop: How to Write a Technical Note for ACS Synthetic Biology
09:45-10:45 Nona Works: Presentations
10:45-11:15 Coffee break
11:15-12:20 IWBDA Talks: Machine Learning
- 11:15-11:35 SeqImprove: Machine Learning Assisted Curation of Genetic Circuit Sequence Information. Zach Sents, Duncan Britt, William Mo and Chris J. Myers.
- 11:35-11:55 Automated model curation using LLMs: Integration of ChatGPT with the DySE framework. Emilee Holtzapple, Tanvi Verma and Natasa Miskov-Zivanov.
- 11:55-12:15 Encoding Process Markers with Neural Networks to Simplify the Complexity of Engineering CAR T Cells. Haomiao Luo, Anya Zivanov and Natasa Miskov-Zivanov.
- 12:15-12:30 Lightning Talks:
  - How to build and train your ANN (In-Vivo) From zero to hero. Tomás Fuentes Araya and Martín Gutiérrez.
  - AI algorithms for classification and generation of spatial/temporal patterns in cell colonies. Valeria Navarrete, Freddy Aguilar and Martín Gutiérrez.
  - Using Machine Learning to Infer RNA Velocity Fields. Taos Transue and Payton Thomas.
12:30-13:30 Lunch and Nona Works Voting
13:30-14:25 IWBDA Talks: Improving Workflows through Software
- 13:30-13:50 A Report on SynBio Data Management Practices. Carolus Vitalis, Sai Samineni, Chris Myers and Pedro Fontanarrosa.
- 13:50-14:10 Software for Synthetic Biology Workflows: How to Improve Your Productivity and Impact. Chris J. Myers, Lukas Buecherl, Daniel Fang, Pedro Fontanarrosa, William Mo, Sai P. Samineni, Gonzalo Vidal, Carolus Vitalis, Guillermo Yanez-Feliu and Timothy J. Rudge.
- 14:10-14:25 Lightning Talks:
  - DBTL Engineering cycle automation: Improving basic parts characterization in the Learn stage by Automation of the Test stage. Yadira Boada, Anna Pushkareva, Harold Díaz-Iza, Andrés Arboleda-García, Jesús Picó and Alejandro Vignoni.
  - PUDU: Simple Liquid Handling Robot Control for Synthetic Biology Workflows. Gonzalo Andrés Vidal Peña, Carolus Vitalis, Matt Burridge, Lukas Buecherl, David Markham, Chris Myers and Timothy Rudge.
  - A fully in-silico workflow for treating colon cancer with engineered cells: a study case. Cristobal Hofmann, Francisco Salcedo and Martin Gutierrez.
14:25-14:45 Awards and Closing Remarks

Virtual Special Issue

ACS Synthetic Biology would like to invite all IWBDA attendees to submit their original work to the journal to appear in the “IWBDA 2023” Virtual Special Issue. Any article type is welcome. The submission deadline is April 30, 2024.

If you wish to be part of this special collection, please see the ACS Synthetic Biology Invitation for further information and instructions.

Submission Guidelines

Abstracts and workshop proposals must be submitted via EasyChair. Submissions cannot exceed two pages (excluding figures and tables). If you do not have an EasyChair account, please create one by following the instructions specified here.

All abstracts must use the IWBDA template and must not exceed two pages excluding the figures and tables. The following versions of the template are available for use:

All abstracts will undergo a single-blind peer review process on EasyChair. The accepted abstracts will be invited to present their work as a poster or a talk at the conference.

We encourage abstracts for posters and/or talks at IWBDA 2023 on ongoing research that may be submitted as a full journal paper later. We are currently in talks with ACS Synthetic Biology to set up a special issue on bio-design automation for such extended journal submissions.

Call for Workshop Proposals

Do you have an idea for a workshop for Bio Design Week? Submit a proposal for your workshop by uploading a PDF with the following information: workshop title, short description (100 words or less), overall goal(s), format, and expected length in hours for the workshop.

Upload your proposals using this link.

Workshop proposal deadline: July 30th 2023

Bio Design Week

Introducing Bio Design Week, a new annual event to bring people together to meet and discuss topics focused on the intersection of synthetic biology, systems biology, computer aided design, and lab automation. Bio Design Week will include the annual International Workshop on Bio-Design Automation (IWBDA), additional meetings and workshops on relevant topics, social events, and a Nona Works hackathon. Bio Design Week offers a forum for cross-disciplinary discussion, with the aim of seeding and fostering collaboration between the biological and the design automation research communities.

Bio Design Week and IWBDA are organized by the non-profit Bio-Design Automation Consortium (BDAC). The Nona Works Hackathon is organized by the Nona Research Foundation. BDAC and the Nona Research Foundation are both officially recognized 501(c)(3) tax exempt organizations.