Today Eran returned to Build-A-Cell after a couple years hiatus to lead the in-silico cell working group. The goal of this working group is to develop a comprehensive model of a minimal synthetic cell. We worked with Akshay Maheshwari of b.next to integrate Vivarium with their Nucleus platform for building real synthetic cells.

Eran’s essay outlining a vision for compositional systems biology is up on arXiv.

Colin is a HRP student from the UConn Storrs Biomedical Engineering Dept. For his summer internship, Colin developed a PDE model of Peristalsis, and a reusable Vivarium process for simulating the affect of peristalsis on the spatial distributions of bacterial and nutrient in the gut. Great job, Colin! Looking forward to continuing this work with you.

We are pleased to announce the renewal of the NIH Center for Reproducible Biomedical Modeling, With Eran Agmon as a Co-Lead Investigator focused on model and simulation composition. Nearly $6 million will be provided by the National Institute of Biomedical Imaging and Bioengineering to continue the work of the Center. This is a unique collaborative, multi-institutional project, with leading investigators at the University of Connecticut (Ion Moraru, Eran Agmon), University of Wisconsin-Madison (Elebeoba May), the University of Auckland (David Nickerson) and the UW Department of Biomedical Informatics and Medical Education (John Gennari), as well as the UW eScience Institute (Joseph Hellerstein). The goal of the center is to improve multi-scale and integrative modeling of biomedical systems that can support precision medicine and credible predictive models for biomedicine. The center aims to CURE these models by making them credible, understandable, reproducible, and extensible.

Edwin and Amin, a grad student and postdoc in the Agmon lab, share a birthday. What are the chances of that?

Eran And Edwin attended the 8th Annual Distinguished Microbiologist Lecture and Microbiology Symposium And Edwin presented a poster outline the gut microbiome model:

Eran presented at the DARPA workshop on Discovering Unknown Function (DUF), which took place in Boston on December 12, 2023. The agenda is posted here.

The first photo of the Agmon lab all together!

The International Conference for Systems Biology (ICSB) took place in Hartford, CT, and was hosted by UConn Health. Dr. Agmon presented recent progress on Process Bigraphs as a framework for multiscale modeling in Biology.

Jayde Schlesener, welcome to C-CoMP and welcome to the Agmon lab! Jayde is a new bridge-to-PhD fellow at the Center for Chemical Currencies of a Microbial Planet (C-CoMP), joining us for two years to do research on the marine carbon cycle as she prepares to apply for graduate school next year.

Edwin Appiah, welcome to UConn Health! Edwin will be working on new innovative methods for modeling the gut microbiome. We’re excited for all the great things he will achieve as a PhD student in Biomedical Sciences.

Isha is a bright young student at UConn Storrs Biomedical Engineering. For her summer internship, she developed two original spatial models of E. coli’s migration through the human gut mucosal barrier. Fantastic job, Isha!

I recently returned from the IMAG symposium conference, held June 28-29 at the NIH headquarters in Bethesda, MD. IMAG, the Interagency Modeling and Analysis Group, is a collective of program officials from various U.S. federal agencies that supports research funding for modeling and analyzing biomedical, biological, and behavioral systems. Connecting with this community is immensely importance as it provides a platform for interacting with a large group of multiscale modelers in biology, fostering collaboration, knowledge exchange, and potential funding opportunities and partnerships. Notably, the prevalent use of hybrid simulation techniques at the conference underscored the relevance of Vivarium as a general framework for model integration. I presented this poster on Process Bigraphs.

The first paper on vivarium-ecoli is out! Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses has been published in PLoS Computational Biology. This project used Vivarium to reconstruct an existing E. coli whole-cell model, expand it with several new submodels, and nest it within a spatial environment shared by many independent whole-cell E. coli models running in parallel. This effectively connects molecular-level events with colony-level phenonema. Perhaps the most multiscale model ever?

I am back from the HARMONY conference, which took place in Seattle April 24-26. Here it is described by the Center for Reproducible Biomedical Modeling: https://reproduciblebiomodels.org/harmony-2023/

Building the next generation of virtual cells to understand cellular biology is out in Biophysical Society Journal. In this paper, we propose the development of dynamic 3D models that integrate various sources of data, to comprehensively understand cellular behaviors, bridge the gap between theory and experimental data, and foster interdisciplinary research collaborations. Very excited to work with this team to bring about the next generation of virtual cell models!

Amin Boroomand, PhD in Quantitative and Systems Biology from UC Merced, has arrived. Welcome, Amin!

I am honored to join the C-CoMP team as an inaugural faculty fellow! The Center for Chemical Currencies of a Microbial Planet (C-CoMP) is an interdisciplinary collaboration to leverage advances in analytical and data sciences, incorporate ocean sampling technologies and an open-science framework, and engage educators and policy-makers to promote a deeper understanding and appreciation of the chemicals and microbial processes that underpin ocean ecosystems and other microbiomes.

Vivarium-ecoli is the Covert lab’s new version of the E. coli whole-cell model, built entirely with the Vivarium framework. This combines over a dozen independent sub-models, which have been fitted with the Vivarium interface to make them into reusable modules – these can now be recombined in alternate models, and will be a valuable resource for the modeling community and for future research. In addition to modularizing the whole-cell model, we combined agent-based modeling to support running multiple heterogeneous E. coli models in parallel within a shared environment. The result was a multiscale model that facilitates the study of emergent population-level behaviors with single-cell molecular resolution. Paper coming soon.

Eran has been in voted as the next SED-ML editor. SED-ML, or Simulation Experiment Description Markup Language, is an standardized XML-based format developed to encode the settings and parameters of simulation experiments, facilitating their exchangeability and reproducibility. I intend to enhance SED-ML by improving its composability, enabling more complex and integrative simulation pipelines to be reliably configured and reproduced across different software platforms and environments.

C-CoMP’s first All-Center Meeting took place October 17-20 2022 at the Woods Hole Oceanographic Institution. It was a pleasure to attend for all of these days, during which I learned about all the different projects taking place within the center. It was great to meet many collaborators in-person for the first time, and to brainstorm the next phase of the center’s research.

Eran has joined the Center for Reproducible Biomedical Modeling (CRBM) as an investigator in Technology Research and Development for Online Simulation. The long-term goal of CRBM is to achieve comprehensive predictive models of biological systems, such as whole-cell models, which can guide precision medicine and synthetic biology. Toward this long-term goal, the center is making models understandable, reproducible, reusable, and composable by (1) developing model building, annotation, and simulation tools and (2) combining these and other existing tools into a user-friendly reproducible modeling workflow.

Eran is giving a talk at Find Your Inner Modeler V (FYIM) with Matt Akamatsu on their recent collaborations with the Allen Institute for Cell Science. FYIM is a collaborative project incubator for quantitative cell biologists and computational modelers. This year, the theme of their annual conference was “Toward Whole Cell Models” – a topic near and dear to Eran’s heart.

The DARPA Automating Scientific Knowledge Extraction and Modeling (ASKEM) program is kicking off this week. ASKEM’s overall goal is to develop tools for agile creation and maintenance of complex models and simulators, to support decision making in diverse mission and scientific domains.

As of today, the Agmon Lab (also known as the Vivarium lab) is open in the Center for Cell Analysis and Modeling. Our research is twofold: 1) we are developing computational methods for combining multi-omics datasets and diverse models into multi-scale simulations, and 2) we are applying these approaches to build mechanistic simulations of whole cells and microbiomes, which span molecular to multi-cellular scales.

I have returned from a fascinating week in Prague, where I attended the Templeton Foundation funded IdeasLab “Bringing Chemistry, Physics and Computing to Life”. See announcement. This was a wonderful opportunity to connect with other early-career researchers, and brainstorm novel approaches to researching the origins of life. The IdeasLab format is fascinating, forcing us to come up with many new ideas, riff off of others’ ideas, and integrate them together into emergent multidisciplinary research plans that break disciplinary barriers.

I am very pleased to announce that I will be rising to the ranks of Assistant Professor this July, as a faculty member at UConn Health’s Center for Cell Analysis and Modeling, and the Molecular Biology and Biophysics Department. See news release: Eran Agmon joins CCAM

The paper on the Vivarium framework, “Vivarium: an interface and engine for integrative multi-scale modeling in computational biology,” has been accepted for publication at Bioinformatics. Check it out here.

As an undergrad at UCSD’s Dept of Cognitive Science, I was deeply influenced by Gilles Fauconnier and am saddened to learn of his passing earlier this year. In revisting his landmark book, The Way We Think, I am excited to see just how much his notion of conceptual blending still resonates with my research. The figure below illustrates “double-scope integration”, in which two input conceptual frames are brought together into a blended frame that can lead to novel insights. This is what I aim to systematize with integrative modeling software – the capacity to blend models of different biological properties, and through their integration to reveal novel biology.

Combine simulations @Vivarium! We’re in the BioSimulators pipeline: https://biosimulators.org. BioSimulators is a free registry of biosimulation tools, with a standardized interface. The simulators support a broad range of frameworks (e.g., logical, kinetic), simulation algorithms (e.g., FBA, SSA), and formats (e.g., BNGL, CellML, NeuroML/LEMS, SBML, Smoldyn). And with Vivarium, they can now be combined to create novel multi-scale simulations.

This dives into the code – how to make a simulation process, a simulation composite, and how to run co-simulations across hierarchies and at different scales. https://vivarium-core.readthedocs.io/en/latest/tutorials.html

Vivarium-ecoli documentation I have been working with a talented team of students to migrate the Covert Lab’s E. coli Whole Cell Model to the Vivarium framework. This took the models of cellular subprocesses (such as metabolism, transcription, and chromosome replication) modularized them, refactored their parameter handling, and rewired them together into a composite model. These can now be recombined in alternate models, and built upon by wiring in different models of mechanisms. We are excited to see how it will be used by the computational systems biology community.

I’m excited to join NASA’s Center for the Emergence of Life as a research affiliate – see here. I’ve been working on a project with Gabrielle Cohn, Andrew Pohorille, Milena Popovic, and Mark Ditzler to use machine learning to characterize RNA function from sequence and structure. The results promise to reveal the fitness landscape and evolution of early life in the RNA world.

The Vivarium Collective website is up. This is a central forum for posting vivarium projects, providing a friendly front-end to the internet.

The Vivarium preprint is out! Available here