FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models

作者：Karthik Raman, Miroslav Kratochvíl, Brett G. Olivier, Matthias König, Pratyay Sengupta, Dinesh Kumar Kuppa Baskaran, Tung V. N. Nguyen, Daniel Lobo, St. Elmo Wilken, Krishna Kumar Tiwari, Aswathy K. Raghu, Indumathi Palanikumar, Lavanya Raajaraam, Maziya Ibrahim, Sanjaay Balakrishnan, Shreyansh Umale, Frank Bergmann, Tanisha Malpani, Venkata Satagopam, Reinhard Schneider, Moritz E. Beber, Sarah Keating, Mihail Anton, Alina Renz, Meiyappan Lakshmanan, Dong‐Yup Lee, Lokanand Koduru, Reihaneh Mostolizadeh, Óscar Dias, Emanuel Cunha, Alexandre Oliveira, Yi Qing Lee, Karsten Zengler, Rodrigo Santibáñez-Palominos, Manish Kumar, Matteo Barberis, Bhanwar Lal Puniya, Tomáš Helikar, Hoang V. Dinh, Patrick F. Suthers, Costas D. Maranas, Isabella Casini, Seyed Babak Loghmani, Nadine Veith, Nantia Leonidou, Feiran Li, Yu Chen, Jens Nielsen, GaRyoung Lee, Sang Mi Lee, Gi Bae Kim, Pedro T. Monteiro, Miguel C. Teixeira, Hyun Uk Kim, Sang Yup Lee, Ulf W. Liebal, Lars M. Blank, Christian Lieven, Chaimaa Tarzi, Claudio Angione, Manga Enuh Blaise, Celik Pinar Aytar, Mikhail A. Kulyashov, llya Akberdin, Dohyeon Kim, Sung Ho Yoon, Zhaohui Xu, Jyotshana Gautam, William T. Scott, Peter J. Schaap, Jasper J. Koehorst, Cristal Zúñiga, Gabriela Canto-Encalada, Sara Benito-Vaquerizo, Ivette Parera Olm, María Suárez‐Diez, Qianqian Yuan, Hongwu Ma, Mohammad Mazharul Islam, Jason A. Papin, Francisco Zorrilla, Kiran Raosaheb Patil, Arianna Basile, Juan Nogales, Granado San Leon, Freddy Castillo-Alfonso, Roberto Olivares‐Hernández, Gabriela Canto-Encalada, Gabriel Vigueras-Ramírez, Henning Hermjakob, Andreas Dräger, Rahuman S. Malik‐Sheriff · 发表于：bioRxiv (Cold Spring Harbor Laboratory) · 年份：2024 · DOI：10.1101/2024.09.24.614797 · 被引用次数：11 · 研究领域：Microbial Metabolic Engineering and Bioproduction、Diet and metabolism studies

Abstract Genome-scale metabolic models (GEMs) and other constraint-based models (CBMs) play a pivotal role in understanding biological phenotypes and advancing research in areas like metabolic engineering, human disease modelling, drug discovery, and personalized medicine. Despite their growing application, a significant challenge remains in ensuring the reproducibility of GEMs, primarily due to inconsistent reporting and inadequate model documentation of model results. Addressing this gap, we introduce FROG analysis, a community-driven initiative aimed at standardizing reproducibility assessments of CBMs and GEMs. The FROG framework encompasses four key analyses—Flux variability, Reaction deletion, Objective function, and Gene deletion—to produce standardized, numerically reproducible FROG reports. These reports serve as reference datasets, enabling model evaluators, curators, and independent researchers to verify the reproducibility of GEMs systematically. BioModels, a leading repository of systems biology models, has integrated FROG analysis into its curation workflow, enhancing the reproducibility and reusability of submitted GEMs. In our study evaluating 65 GEM submissions from the community, approximately 40% reproduced without intervention, 28% requiring minor adjustments, and 32% needing input from authors. The standardization introduced by FROG analysis facilitated the detection and resolution of issues, ultimately leading to the successful reproduction of all models...