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bioRxiv · 10.1101/2021.06.03.446189

NLoed: A Python package for nonlinear optimal experimental design in systems biology

Braniff, N.·Pearce, T.·Lu, Z.·Astwood, M.·Forrest, W. S.·Receno, C.·Ingalls, B. P.
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Abstract

MotivationModelling in systems and synthetic biology relies on accurate parameter estimates and predictions. Accurate model calibration relies, in turn, on data, and on how well-suited the available data is to a particular modelling task. Optimal experimental design (OED) techniques can be used to identify experiments and data collection procedures that will most efficiently contribute to a given modelling objective. However, implementation of OED is limited by currently available software tools that are not well-suited for the diversity of nonlinear models and non-normal data commonly encountered in biological research. Moreover, existing OED tools do not make use of the state-of-the-art numerical tools, resulting in inefficient computation. ResultsHere we present the NLoed software package. NLoed is an open-source Python library providing convenient access to OED methods, with particular emphasis on experimental design for systems biology research. NLoed supports a wide variety of nonlinear, multi-input/output, and dynamic models, and facilitates modelling and design of experiments over a wide variety of data types. To support OED investigations, the NLoed package implements maximum likelihood fitting and diagnostic tools, providing a comprehensive modelling workflow. NLoed offers an accessible, modular, and flexible OED tool-set suited to the wide variety of experimental scenarios encountered in systems biology research. We demonstrate NLOEDs capabilities by applying it to experimental design for characterization of a bacterial optogenetic system. AvailabilityNLoed is available via pip from the PyPi repository; https://pypi.org/project/nloed/. Source code, documentation and examples can be found on Github at https://github.com/ingallslab/NLoed. Contactbingalls@uwaterloo.ca Supplementary informationSupplementary materials are available online.

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Braniff, N., Pearce, T., Lu, Z., Astwood, M., Forrest, W. S., Receno, C., Ingalls, B. P.. 2021-06-03. NLoed: A Python package for nonlinear optimal experimental design in systems biology. https://doi.org/10.1101/2021.06.03.446189

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