{"database":"BioModels","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000754?filename=curation_notes.txt"],"Owl":["https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000754?filename=Figueredo2013_2-biopax2.owl","https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000754?filename=Figueredo2013_2-biopax3.owl"],"Xml":["https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000754?filename=Figueredo2013_2.xml","https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000754?filename=manifest.xml"],"Other":["https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000754?filename=Figueredo2013_2.cps","https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000754?filename=Figueredo2013_2-matlab.m","https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000754?filename=Figueredo2013_2.ode","https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000754?filename=metadata.rdf","https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000754?filename=Figueredo2013_2.sedml","https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000754?filename=curation_image.png","https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000754?filename=Figueredo2013_2-octave.m"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"submitter":["Jinghao Men"],"curationStatus":["Manually curated"],"modellingApproach":["ordinary differential equation model"],"levelVersion":["L3V1"],"submitter_keywords":["Immuno-oncology"],"full_dataset_link":["https://www.ebi.ac.uk/biomodels/BIOMD0000000754"],"publication_pubmed":["23734575"],"isPrivate":["false"],"repository":["BioModels"],"omics_type":["Models"],"modelFormat":["SBML"],"tokenised_name":["Figueredo2013/2   immunointeraction model with IL2"],"publication_year":["2013"],"submissionId":["MODEL1907180002"],"first_author":["Grazziela P Figueredo"],"publication_authors":["Grazziela P Figueredo, Peer-Olaf Siebers, Uwe Aickelin"],"publication":["23734575,\n                            Many advances in research regarding immuno-interactions with cancer were developed with the help of ordinary differential equation (ODE) models. These models, however, are not effectively capable of representing problems involving individual localisation, memory and emerging properties, which are common characteristics of cells and molecules of the immune system. Agent-based modelling and simulation is an alternative paradigm to ODE models that overcomes these limitations. In this paper we investigate the potential contribution of agent-based modelling and simulation when compared to ODE modelling and simulation. We seek answers to the following questions: Is it possible to obtain an equivalent agent-based model from the ODE formulation? Do the outcomes differ? Are there any benefits of using one method compared to the other? To answer these questions, we have considered three case studies using established mathematical models of immune interactions with early-stage cancer. These case studies were re-conceptualised under an agent-based perspective and the simulation results were then compared with those from the ODE models. Our results show that it is possible to obtain equivalent agent-based models (i.e. implementing the same mechanisms); the simulation output of both types of models however might differ depending on the attributes of the system to be modelled. In some cases, additional insight from using agent-based modelling was obtained. Overall, we can confirm that agent-based modelling is a useful addition to the tool set of immunologists, as it has extra features that allow for simulations with characteristics that are closer to the biological phenomena.. null, 14 Suppl 6.\n                            Intelligent Modelling and Analysis Research Group, School of Computer Science, The University of Nottingham, UK. grazziela.figueredo@nottingham.ac.uk"],"submitter_mail":["jm2187@cam.ac.uk"],"submitter_affiliation":["University of Cambridge"],"publicationId":["BIOMD0000000754"],"pubmed_abstract":["Many advances in research regarding immuno-interactions with cancer were developed with the help of ordinary differential equation (ODE) models. These models, however, are not effectively capable of representing problems involving individual localisation, memory and emerging properties, which are common characteristics of cells and molecules of the immune system. Agent-based modelling and simulation is an alternative paradigm to ODE models that overcomes these limitations. In this paper we investigate the potential contribution of agent-based modelling and simulation when compared to ODE modelling and simulation. We seek answers to the following questions: Is it possible to obtain an equivalent agent-based model from the ODE formulation? Do the outcomes differ? Are there any benefits of using one method compared to the other? To answer these questions, we have considered three case studies using established mathematical models of immune interactions with early-stage cancer. These case studies were re-conceptualised under an agent-based perspective and the simulation results were then compared with those from the ODE models. Our results show that it is possible to obtain equivalent agent-based models (i.e. implementing the same mechanisms); the simulation output of both types of models however might differ depending on the attributes of the system to be modelled. In some cases, additional insight from using agent-based modelling was obtained. Overall, we can confirm that agent-based modelling is a useful addition to the tool set of immunologists, as it has extra features that allow for simulations with characteristics that are closer to the biological phenomena."],"pubmed_title":["Investigating mathematical models of immuno-interactions with early-stage cancer under an agent-based modelling perspective."],"pubmed_authors":["Figueredo Grazziela P GP, Siebers Peer-Olaf PO, Aickelin Uwe U"],"additional_accession":[]},"is_claimable":false,"name":"Figueredo2013/2 - immunointeraction model with IL2","description":"The paper describes a model of immune-itumor interaction with IL2.\nCreated by COPASI 4.25 (Build 207) \n\nThis model is described in the article: \nInvestigating mathematical models of immuno-interactions with early-stage cancer under an agent-based modelling perspective\nGrazziela P Figueredo, Peer-Olaf Siebers, Uwe Aickelin Kathleen \nBMC Bioinformatics 2013, 14(Suppl 6):S6\n\nAbstract: \nMany advances in research regarding immuno-interactions with cancer were developed with the help of ordinary differential equation (ODE) models. These models, however, are not effectively capable of representing problems involving individual localisation, memory and emerging properties, which are common characteristics of cells and molecules of the immune system. Agent-based modelling and simulation is an alternative paradigm to ODE models that overcomes these limitations. In this paper we investigate the potential contribution of agent-based modelling and simulation when compared to ODE modelling and simulation. We seek answers to the following questions: Is it possible to obtain an equivalent agent-based model from the ODE formulation? Do the outcomes differ? Are there any benefits of using one method compared to the other? To answer these questions, we have considered three case studies using established mathematical models of immune interactions with early-stage cancer. These case studies were re-conceptualised under an agent-based perspective and the simulation results were then compared with those from the ODE models. Our results show that it is possible to obtain equivalent agent-based models (i.e. implementing the same mechanisms); the simulation output of both types of models however might differ depending on the attributes of the system to be modelled. In some cases, additional insight from using agent-based modelling was obtained. Overall, we can confirm that agent-based modelling is a useful addition to the tool set of immunologists, as it has extra features that allow for simulations with characteristics that are closer to the biological phenomena.\n\nTo cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models . \nTo the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. \nPlease refer to CC0 Public Domain Dedication for more information.","dates":{"last_modification":"2024-08-22","publication":"2024-09-02","submission":"2019-07-18"},"accession":"BIOMD0000000754","cross_references":{"sbo":["SBO:0000610","SBO:0000179","SBO:0000393","SBO:0000281"],"pubmed":["23734575"],"ncit":["C94498","C28241","C53346","C122632","C25636","C75947"],"biomodels__db":["BIOMD0000000754","MODEL1907180002"],"go":["GO:0002418","GO:0008283","GO:0008219","GO:0002419","GO:0001816"],"cl":["CL:0001064"],"taxonomy":["9606"],"uniprot":["P60568"]}}