Towards an engineering theory of evolution

SD Castle, CS Grierson, TE Gorochowski - Nature Communications, 2021 - nature.com
Biological technologies are fundamentally unlike any other because biology evolves.
Bioengineering therefore requires novel design methodologies with evolution at their core …

A new era of synthetic biology—microbial community design

A Matuszyńska, O Ebenhöh, MD Zurbriggen… - Synthetic …, 2024 - academic.oup.com
Synthetic biology conceptualizes biological complexity as a network of biological parts,
devices, and systems with predetermined functionalities and has had a revolutionary impact …

Biological standards for the Knowledge-Based BioEconomy: What is at stake

V de Lorenzo, M Schmidt - New Biotechnology, 2018 - Elsevier
The contribution of life sciences to the Knowledge-Based Bioeconomy (KBBE) asks for the
transition of contemporary, gene-based biotechnology from being a trial-and-error …

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)

D Waltemath, M Golebiewski, ML Blinov… - Journal of integrative …, 2020 - degruyter.com
This paper presents a report on outcomes of the 10th Computational Modeling in Biology
Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The …

Adapting modeling and simulation credibility standards to computational systems biology

LT Tatka, LP Smith, JL Hellerstein… - Journal of translational …, 2023 - Springer
Computational models are increasingly used in high-impact decision making in science,
engineering, and medicine. The National Aeronautics and Space Administration (NASA) …

Automatic reuse, adaption, and execution of simulation experiments via provenance patterns

P Wilsdorf, A Wolpers, J Hilton, F Haack… - ACM Transactions on …, 2023 - dl.acm.org
Simulation experiments are typically conducted repeatedly during the model development
process, for example, to revalidate if a behavioral property still holds after several model …

Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024

M Golebiewski, G Bader, P Gleeson… - Journal of Integrative …, 2024 - degruyter.com
The “COmputational Modeling in BIology NEtwork”(COMBINE) initiative aims to harmonise
the development of diverse community standards for computational models in biology [1, 2] …

standard-GEM: standardization of open-source genome-scale metabolic models

M Anton, E Almaas, R Benfeitas, S Benito-Vaquerizo… - bioRxiv, 2023 - biorxiv.org
The field of metabolic modelling at the genomescale continues to grow with more models
being created and curated. This comes with an increasing demand for adopting common …

Advancing reproducibility can ease the 'hard truths' of synthetic biology

MW Lux, EA Strychalski, GJ Vora - Synthetic Biology, 2023 - academic.oup.com
Reproducibility has been identified as an outstanding challenge in science, and the field of
synthetic biology is no exception. Meeting this challenge is critical to allow the transformative …

Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022

M König, P Gleeson, M Golebiewski… - Journal of Integrative …, 2023 - degruyter.com
This special issue of the Journal of Integrative Bioinformatics contains updated
specifications of COMBINE standards in systems and synthetic biology. The 2022 special …