Year: 2024
Type: article
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. By establishing a standardized and comprehensive approach to evaluating GEM reproducibility, FROG analysis significantly contributes to making CBMs and GEMs more transparent, reusable, and reliable for the broader scientific community.
DOI: 10.13016/m2lscx-vucj
Authors: Raman, Karthik, Kratochvíl, Miroslav, Olivier, Brett G., König, Matthias, Sengupta, Pratyay, Baskaran, Dinesh Kumar Kuppa, Nguyen, Tung V. N., Lobo, Daniel, Wilken, St Elmo, Tiwari, Krishna Kumar, Raghu, Aswathy K., Palanikumar, Indumathi, Raajaraam, Lavanya, Ibrahim, Maziya, Balakrishnan, Sanjaay, Umale, Shreyansh, Bergmann, Frank, Malpani, Tanisha, Satagopam, Venkata P., Schneider, Reinhard, Beber, Moritz E., Keating, Sarah, Anton, Mihail, Renz, Alina, Lakshmanan, Meiyappan, Lee, Dong-Yup, Koduru, Lokanand, Mostolizadeh, Reihaneh, Dias, Oscar, Cunha, Emanuel, Oliveira, Alexandre, Lee, Yi Qing, Zengler, Karsten, Santibáñez-Palominos, Rodrigo, Kumar, Manish, Barberis, Matteo, Puniya, Bhanwar Lal, Helikar, Tomáš, Dinh, Hoang V., Suthers, Patrick F., Maranas, Costas D., Casini, Isabella, Loghmani, Seyed Babak, Veith, Nadine, Leonidou, Nantia, Li, Feiran, Chen, Yu, Nielsen, Jens, Lee, GaRyoung, Lee, Sang Mi, Kim, Gi Bae, Monteiro, Pedro T., Teixeira, Miguel C., Kim, Hyun Uk, Lee, Sang Yup, Liebal, Ulf W., Blank, Lars M., Lieven, Christian, Tarzi, Chaimaa, Angione, Claudio, Blaise, Manga Enuh, Aytar, Çelik P?Nar, Kulyashov, Mikhail, Akberdin, Llya, Kim, Dohyeon, Yoon, Sung Ho, Xu, Zhaohui, Gautam, Jyotshana, Scott, William T., Schaap, Peter J., Koehorst, Jasper J., Zuñiga, Cristal, Canto-Encalada, Gabriela, Benito-Vaquerizo, Sara, Olm, Ivette Parera, Suarez-Diez, Maria, Yuan, Qianqian, Ma, Hongwu, Islam, Mohammad Mazharul, Papin, Jason A., Zorrilla, Francisco, Patil, Kiran Raosaheb, Basile, Arianna, Nogales, Juan, León, Granado San, Castillo-Alfonso, Freddy, Olivares-Hernández, Roberto, Canto-Encalada, Gabriela, Vigueras-Ramírez, Gabriel, Hermjakob, Henning, Dräger, Andreas, Malik-Sheriff, Rahuman S.
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
Funders: Université du Luxembourg, National Research Foundation, Deutsche Forschungsgemeinschaft, Bundesministerium für Bildung und Forschung, University of Surrey, National Research Foundation of Korea, Ministry of Education, India, Ministry of Science and ICT, South Korea, German Network for Bioinformatics Infrastructure, Fundação para a Ciência e a Tecnologia
Awards: G1147967356, G1159569226, G1254183670, de.NBI - Etablierungsphase - Heidelberg Center for Human Bioinformatics - HD-HuB, G2082019117, de.NBI - Etablierungsphase - Leistungszentrum - BiGi - Bioinformatisches Resourcenzentrum für mikrobielle Genomforschung in Biotechnologie und Medizin, G2514841155, G2634730870, Instituto de Bioengenharia e Biociências, G2813928278, de.NBI - Etablierungsphase - Leistungszentrum CiBi - Zentrum für integrative Bioinformatik, Instituto de Bioengenharia e Biociências, G4804467517, G5121333388, G5139259834, G5576285491, G5658107541, de.NBI - Etablierungsphase - Leistungszentrum: RBC - RNA Bioinformatic, Simulationsgestützte Bewertung von Spenderorganen vor Lebertransplantation (SimLivA) kontinuumsbiomechanische Modellierung für die Beurteilung von IschämieReperfusionsschäden, de.NBI - Etablierungsphase - Leistungszentrum - BioInfra.Prot - Bioinformatik der Proteomik, CompLS - Runde 5 - Verbundprojekt: ATLAS - Al and Simulation for Tumor Liver Assessment - Entwicklung eines Systems zur klinischen Entscheidungsunterstützung in der Diagnose und Behandlung von Lebertumoren auf Basis von künstlicher Intelligenz und Simulationen - Teilprojekt B, de.NBI - Etablierungsphase - Koordinierungs- und Administrationseinheit - CAU - Geschäftsstelle, FOR 5151: Quantifizierung des Zusammenhanges zwischen Leberperfusion und funktion bei erweiterter Leberresektion Ein systemmedizinischer Ansatz (QuaLiPerF), de.NBI - Etablierungsphase - Leistungszentrum - BiGi - Bioinformatisches Resourcenzentrum für mikrobielle Genomforschung in Biotechnologie und Medizin, de.NBI - Etablierungsphase-European Molecular Biology Laboratory-HD-HUB
OpenAlex ID: W6940799528
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