Bauerstätter P (2022) Compartment Modeling of Overweight in Toddler Age: Modeling and Simulating a Diets Effect with COPASI. SNE Simulation Notes Europe 32:221–224
Physiology
Computational Method
Link
Bergman D, Marazzi L, Chowkwale M, Maheshvare M D, Bidanta S, Mapder T, Li J (2022) PhysiPKPD: A pharmacokinetics and pharmacodynamics module for PhysiCell. Gigabyte 2022:1–11
Computational Method
Pharmacology
Link
Daas JCJ, Förster J, Pahle J (2022) Dynamic publication media with the COPASI R Connector (CoRC). Mathematical Biosciences 348:108822
Computational Method
Link
Erdem C, Mutsuddy A, Bensman EM, Dodd WB, Saint-Antoine MM, Bouhaddou M, Blake RC, Gross SM, Heiser LM, Feltus FA, Birtwistle MR (2022) A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling. Nature Communications 13:3555
Computational Method
Signaling
Link
Esposito M, Picchiami L (2022) A Comparative Study of AI Search Methods for Personalised Cancer Therapy Synthesis in COPASI. In: Bandini S, Gasparini F, Mascardi V, Palmonari M and Vizzari G (eds) AIxIA 2021 – Advances in Artificial Intelligence. Lecture Notes in Computer Science 13196:638–654
Pharmacology
Physiology
Computational Method
Link
Garay-Ruiz D, Bo C (2022) Chemical reaction network knowledge graphs: the OntoRXN ontology. Journal of Cheminformatics 14:29
Software
Computational Method
Link
Greenyer H (2022) Evaluation of network inference algorithms and their effects on network analysis for the study of small metabolomic data sets. MS Thesis, University of Victoria, Canada.
Computational Method
Metabolism
Link
Kumar S (2022) Compact, Causal and Multivariate Functional Statistics in Model-Free Discrete Pattern Discovery. Ph.D. Thesis, New Mexico State University, USA.
Computational Method
Link
Lee JY, Styczynski MP (2022) Diverse classes of constraints enable broader applicability of a linear programming-based dynamic metabolic modeling framework. Scientific Reports 12:762
Computational Method
Metabolism
Link
Lo-Thong-Viramoutou O, Charton P, Cadet XF, Grondin-Perez B, Saavedra E, Damour C, Cadet F (2022) Non-linearity of Metabolic Pathways Critically Influences the Choice of Machine Learning Model. Frontiers in Artificial Intelligence 5:744755
Computational Method
Link
Maestri S, Merelli E, Pettini M (2022) Agent-based models for detecting the driving forces of biomolecular interactions. Scientific Reports 12:1878
Computational Method
Metabolism
Link
Marazzi L, Shah M, Balakrishnan S, Patil A, Vera-Licona P (2022) NETISCE: a network-based tool for cell fate reprogramming. npj Systems Biology and Applications 8:21
Computational Method
Link
Ramachandran K, König M, Scharm M, Nguyen TVN, Hermjakob H, Waltemath D, Sheriff RSM (2022) FAIR Sharing of Reproducible Models of Epidemic and Pandemic Forecast. Preprints 2022060137
Computational Method
Epidemiology
Link
Range J, Halupczok C, Lohmann J, Swainston N, Kettner C, Bergmann FT, Weidemann A, Wittig U, Schnell S, Pleiss J (2022) EnzymeML-a data exchange format for biocatalysis and enzymology. FEBS Journal 289:5864–5874
Enzymology
Computational Method
Link
Santos JPG, Pajo K, Trpevski D, Stepaniuk A, Eriksson O, Nair AG, Keller D, Hellgren Kotaleski J, Kramer A (2022) A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience. Neuroinformatics 20:241–259
Computational Method
Link
Shaikh B, Smith LP, Vasilescu D, Marupilla G, Wilson M, Agmon E, Agnew H, Andrews SS, Anwar A, Beber ME, Bergmann FT, Brooks D, Brusch L, Calzone L, Choi K, Cooper J, Detloff J, Drawert B, Dumontier M, Ermentrout GB, Faeder JR, Freiburger AP, Fröhlich F, Funahashi A, Garny A, Gennari JH, Gleeson P, Goelzer A, Haiman Z, Hasenauer J, Hellerstein JL, Hermjakob H, Hoops S, Ison JC, Jahn D, Jakubowski HV, Jordan R, Kalaš M, König M, Liebermeister W, Malik-Sheriff RS, Mandal S, McDougal R, Medley JK, Mendes P, Müller R, Myers CJ, Naldi A, Nguyen TVN, Nickerson DP, Olivier BG, Patoliya D, Paulevé L, Petzold LR, Priya A, Rampadarath AK, Rohwer JM, Saglam AS, Singh D, Sinha A, Snoep JL, Sorby H, Spangler R, Starruß J, Thomas PJ, van Niekerk DD, Weindl D, Zhang F, Zhukova A, Goldberg AP, Schaff JC, Blinov ML, Sauro HM, Moraru II, Karr JR (2022) BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Research 50: W108–W114
Computational Method
Link
Wysocka EM, Page M, Snowden J, Simpson TI (2022) Comparison of rule- and ordinary differential equation-based dynamic model of DARPP-32 signalling network. PeerJ 10:e14516
Computational Method
Link
Yuan L, Wu C, Guo X, Yang C (2022) ParaCopasi: A package for parallel biochemical simulation and analysis. Journal of Computational Chemistry 43:144–154
Computational Method
Software
Link