Agile Data Curation for Modeling and Design

Investigating complex biological systems requires integrating many different types of information in an iterative process of design and experimentation. In synthetic biology, this has often been enunciated as a “Design-Build-Test-Learn” (DBTL) loop, but the current reality typically falls far from its promise. One key reason for this is the field’s lack of effective established practices for curation, quality control, and integration across designs, experiment plans, metadata, and data. Software engineering has historically had analogous challenges relating to testing, documentation, and integration. Over the past two decades, however, the agile software community has radically transformed professional software development by developing processes that bring management of correctness, completeness, and compatibility into the core activities of software development and supporting them with complementary automation tools. We observe that, with appropriate choices of representation and process controls, the same processes and tools can be directly applied to synthetic biology designs, data, metadata, and models. Early application of this approach have given promising results, we illustrate with three examples: collective development of genetic designs for the iGEM 2022 distribution, model-driven analysis of tunable CRISPR safety switch architectures, and automation-assisted analysis of flow cytometry experiments. Dr. Jacob Beal is an Engineering Fellow at Raytheon BBN Technologies. His work in synthetic biology includes development of standards for representation and communication of biological designs and experiments, signature-based detection of controlled pathogens, methods for calibrated flow cytometry, precision analysis and design of genetic regulatory networks, and engineering of biological information processing devices. For more information see: https://www.researchgate.net/profile/Jacob-Beal-2 *Contents* 00:00 - Introduction 04:19 - Agile Data Curation for Modeling and Design 44:08 - Questions and Discussions Moderator: James A. Glazier, PhD, Indiana University, Bloomington If you found this video useful, please check out our other videos on computational modeling, infection and immunology: https://youtube.com/playlist?list=PLiEtieOeWbMKh9VcQoinSwODcSZKMTGat Please consider joining our IMAG/MSM WG on Multiscale Modeling and Viral Pandemics: https://www.imagwiki.nibib.nih.gov/content/msm-viral-pandemics-meetings Please also consider joining the Global Alliance for Immune Prediction and Intervention: http://glimprint.org/