{"corpus_id":17674678,"paper_sha":"248aef9c22c28d6adab6552cb59311823732b636","doi":"10.1016/j.csbj.2014.10.003","arxiv_id":null,"pmid":25505503,"pmcid":"4262058","mag_id":2161301127,"dblp_id":null,"acl_id":null,"title":"Stochastic simulation in systems biology","year":2014,"publication_date":"2014-10-30","venue":"Computational and Structural Biotechnology Journal","journal":{"name":"Computational and Structural Biotechnology Journal","pages":"14 - 25","volume":"12"},"journal_issn":null,"journal_title":null,"publication_types":["Review","JournalArticle"],"pubmed_pub_types":["Journal Article","Review"],"s2_fields_of_study":["Biology","Medicine","Physics","Computer Science"],"reference_count":169,"citation_count":123,"influential_citation_count":4,"is_open_access":false,"arxiv_categories":null,"arxiv_license":null,"arxiv_journal_ref":null,"mesh_headings":null,"chemicals":null,"comments_corrections":null,"source_flags":5,"s2_open_access_pdf_url":null,"s2_open_access_landing_url":null,"s2_open_access_license":null,"s2_open_access_status":null,"pmc_open_access_pdf_url":null,"pmc_open_access_landing_url":null,"pmc_open_access_license":null,"pmc_open_access_status":null,"unpaywall_open_access_pdf_url":null,"unpaywall_open_access_landing_url":null,"unpaywall_open_access_license":null,"unpaywall_open_access_status":null,"abstract":"Natural systems are, almost by definition, heterogeneous: this can be either a boon or an obstacle to be overcome, depending on the situation. Traditionally, when constructing mathematical models of these systems, heterogeneity has typically been ignored, despite its critical role. However, in recent years, stochastic computational methods have become commonplace in science. They are able to appropriately account for heterogeneity; indeed, they are based around the premise that systems inherently contain at least one source of heterogeneity (namely, intrinsic heterogeneity). In this mini-review, we give a brief introduction to theoretical modelling and simulation in systems biology and discuss the three different sources of heterogeneity in natural systems. Our main topic is an overview of stochastic simulation methods in systems biology. There are many different types of stochastic methods. We focus on one group that has become especially popular in systems biology, biochemistry, chemistry and physics. These discrete-state stochastic methods do not follow individuals over time; rather they track only total populations. They also assume that the volume of interest is spatially homogeneous. We give an overview of these methods, with a discussion of the advantages and disadvantages of each, and suggest when each is more appropriate to use. We also include references to software implementations of them, so that beginners can quickly start using stochastic methods for practical problems of interest.","claims":[{"public_id":"cl_591bf327399e37518097a1ab6d508a0a","status":"active","text":"Discrete-state stochastic methods track total populations rather than individuals over time and assume that the volume of interest is spatially homogeneous.","confidence":0.98,"contributors":[{"id":35,"public_id":"b2adb6bfad","public_label":"Anonymous (b2adb6bfad)","roles":["extraction"],"url":"https://sah.borca.ai/u/b2adb6bfad"},{"id":32,"public_id":"7c402c1b98","public_label":"뀨 (7c402c1b98)","roles":["review"],"url":"https://sah.borca.ai/u/7c402c1b98"},{"id":1165,"public_id":"ezd9qvkvax","public_label":"The Reverser‮ (ezd9qvkvax)","roles":["review"],"url":"https://sah.borca.ai/u/ezd9qvkvax"},{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["review"],"url":"https://sah.borca.ai/u/b9tnx83g25"}],"url":"https://sah.borca.ai/claims/cl_591bf327399e37518097a1ab6d508a0a"},{"public_id":"cl_77fa2209174fd473cd04c07156d0a60e","status":"active","text":"Stochastic simulation methods account for heterogeneity in systems biology models and simulations.","confidence":0.94,"contributors":[{"id":35,"public_id":"b2adb6bfad","public_label":"Anonymous (b2adb6bfad)","roles":["extraction"],"url":"https://sah.borca.ai/u/b2adb6bfad"},{"id":32,"public_id":"7c402c1b98","public_label":"뀨 (7c402c1b98)","roles":["review"],"url":"https://sah.borca.ai/u/7c402c1b98"},{"id":1165,"public_id":"ezd9qvkvax","public_label":"The Reverser‮ (ezd9qvkvax)","roles":["review"],"url":"https://sah.borca.ai/u/ezd9qvkvax"},{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["review"],"url":"https://sah.borca.ai/u/b9tnx83g25"}],"url":"https://sah.borca.ai/claims/cl_77fa2209174fd473cd04c07156d0a60e"}],"concepts":[{"public_id":"co_4bab8bde2809777dcbfd1f9d8cac66c0","status":"active","name":"systems biology","description":"An interdisciplinary field that models and simulates biological systems and their interactions.","types":["field"],"aliases":[],"contributors":[{"id":35,"public_id":"b2adb6bfad","public_label":"Anonymous (b2adb6bfad)","roles":["extraction"],"url":"https://sah.borca.ai/u/b2adb6bfad"},{"id":32,"public_id":"7c402c1b98","public_label":"뀨 (7c402c1b98)","roles":["review"],"url":"https://sah.borca.ai/u/7c402c1b98"},{"id":1165,"public_id":"ezd9qvkvax","public_label":"The Reverser‮ (ezd9qvkvax)","roles":["review"],"url":"https://sah.borca.ai/u/ezd9qvkvax"},{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["review"],"url":"https://sah.borca.ai/u/b9tnx83g25"}],"url":"https://sah.borca.ai/concepts/co_4bab8bde2809777dcbfd1f9d8cac66c0"},{"public_id":"co_614acf926daae78f841f8e9852aea495","status":"active","name":"natural systems","description":"Systems in nature that inherently exhibit variation and structural complexity.","types":["system"],"aliases":[],"contributors":[{"id":35,"public_id":"b2adb6bfad","public_label":"Anonymous (b2adb6bfad)","roles":["extraction"],"url":"https://sah.borca.ai/u/b2adb6bfad"},{"id":32,"public_id":"7c402c1b98","public_label":"뀨 (7c402c1b98)","roles":["review"],"url":"https://sah.borca.ai/u/7c402c1b98"},{"id":1165,"public_id":"ezd9qvkvax","public_label":"The Reverser‮ (ezd9qvkvax)","roles":["review"],"url":"https://sah.borca.ai/u/ezd9qvkvax"},{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["review"],"url":"https://sah.borca.ai/u/b9tnx83g25"}],"url":"https://sah.borca.ai/concepts/co_614acf926daae78f841f8e9852aea495"},{"public_id":"co_628d0414f62863935ced7613336d7f21","status":"active","name":"stochastic computational methods","description":"Computational approaches that represent uncertainty or random variation in modeled systems.","types":["method"],"aliases":[],"contributors":[{"id":35,"public_id":"b2adb6bfad","public_label":"Anonymous (b2adb6bfad)","roles":["extraction"],"url":"https://sah.borca.ai/u/b2adb6bfad"},{"id":32,"public_id":"7c402c1b98","public_label":"뀨 (7c402c1b98)","roles":["review"],"url":"https://sah.borca.ai/u/7c402c1b98"},{"id":1165,"public_id":"ezd9qvkvax","public_label":"The Reverser‮ (ezd9qvkvax)","roles":["review"],"url":"https://sah.borca.ai/u/ezd9qvkvax"},{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["review"],"url":"https://sah.borca.ai/u/b9tnx83g25"}],"url":"https://sah.borca.ai/concepts/co_628d0414f62863935ced7613336d7f21"},{"public_id":"co_73052be13199778678324a240ee08961","status":"active","name":"theoretical modelling","description":"Mathematical formulation of assumptions and mechanisms describing systems biology phenomena.","types":["method"],"aliases":[],"contributors":[{"id":35,"public_id":"b2adb6bfad","public_label":"Anonymous (b2adb6bfad)","roles":["extraction"],"url":"https://sah.borca.ai/u/b2adb6bfad"},{"id":32,"public_id":"7c402c1b98","public_label":"뀨 (7c402c1b98)","roles":["review"],"url":"https://sah.borca.ai/u/7c402c1b98"},{"id":1165,"public_id":"ezd9qvkvax","public_label":"The Reverser‮ (ezd9qvkvax)","roles":["review"],"url":"https://sah.borca.ai/u/ezd9qvkvax"},{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["review"],"url":"https://sah.borca.ai/u/b9tnx83g25"}],"url":"https://sah.borca.ai/concepts/co_73052be13199778678324a240ee08961"},{"public_id":"co_8a317d7b2b43bee3cd008c1ac037b62b","status":"active","name":"spatially homogeneous volume","description":"A modeled volume assumed to have uniform spatial conditions throughout.","types":["assumption"],"aliases":[],"contributors":[{"id":35,"public_id":"b2adb6bfad","public_label":"Anonymous (b2adb6bfad)","roles":["extraction"],"url":"https://sah.borca.ai/u/b2adb6bfad"},{"id":32,"public_id":"7c402c1b98","public_label":"뀨 (7c402c1b98)","roles":["review"],"url":"https://sah.borca.ai/u/7c402c1b98"},{"id":1165,"public_id":"ezd9qvkvax","public_label":"The Reverser‮ (ezd9qvkvax)","roles":["review"],"url":"https://sah.borca.ai/u/ezd9qvkvax"},{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["review"],"url":"https://sah.borca.ai/u/b9tnx83g25"}],"url":"https://sah.borca.ai/concepts/co_8a317d7b2b43bee3cd008c1ac037b62b"},{"public_id":"co_91aea43cc78b1c9d4628c12f4bfc6de6","status":"active","name":"discrete-state stochastic methods","description":"Stochastic methods that represent system components as discrete population states.","types":["method"],"aliases":[],"contributors":[{"id":35,"public_id":"b2adb6bfad","public_label":"Anonymous (b2adb6bfad)","roles":["extraction"],"url":"https://sah.borca.ai/u/b2adb6bfad"},{"id":32,"public_id":"7c402c1b98","public_label":"뀨 (7c402c1b98)","roles":["review"],"url":"https://sah.borca.ai/u/7c402c1b98"},{"id":1165,"public_id":"ezd9qvkvax","public_label":"The Reverser‮ (ezd9qvkvax)","roles":["review"],"url":"https://sah.borca.ai/u/ezd9qvkvax"},{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["review"],"url":"https://sah.borca.ai/u/b9tnx83g25"}],"url":"https://sah.borca.ai/concepts/co_91aea43cc78b1c9d4628c12f4bfc6de6"},{"public_id":"co_a369518f944b9ea21b3a2ccc4b5f5c4e","status":"active","name":"intrinsic heterogeneity","description":"Heterogeneity arising from stochasticity inherent in the system itself.","types":["phenomenon"],"aliases":[],"contributors":[{"id":35,"public_id":"b2adb6bfad","public_label":"Anonymous (b2adb6bfad)","roles":["extraction"],"url":"https://sah.borca.ai/u/b2adb6bfad"},{"id":32,"public_id":"7c402c1b98","public_label":"뀨 (7c402c1b98)","roles":["review"],"url":"https://sah.borca.ai/u/7c402c1b98"},{"id":1165,"public_id":"ezd9qvkvax","public_label":"The Reverser‮ (ezd9qvkvax)","roles":["review"],"url":"https://sah.borca.ai/u/ezd9qvkvax"},{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["review"],"url":"https://sah.borca.ai/u/b9tnx83g25"}],"url":"https://sah.borca.ai/concepts/co_a369518f944b9ea21b3a2ccc4b5f5c4e"},{"public_id":"co_ac1ebe154c4ccadb874cd52508a18fd6","status":"active","name":"stochastic simulation methods","description":"Simulation techniques that incorporate random variation into the evolution of modeled systems.","types":["method"],"aliases":[],"contributors":[{"id":35,"public_id":"b2adb6bfad","public_label":"Anonymous (b2adb6bfad)","roles":["extraction"],"url":"https://sah.borca.ai/u/b2adb6bfad"},{"id":32,"public_id":"7c402c1b98","public_label":"뀨 (7c402c1b98)","roles":["review"],"url":"https://sah.borca.ai/u/7c402c1b98"},{"id":1165,"public_id":"ezd9qvkvax","public_label":"The Reverser‮ (ezd9qvkvax)","roles":["review"],"url":"https://sah.borca.ai/u/ezd9qvkvax"},{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["review"],"url":"https://sah.borca.ai/u/b9tnx83g25"}],"url":"https://sah.borca.ai/concepts/co_ac1ebe154c4ccadb874cd52508a18fd6"},{"public_id":"co_d8f2ba6a150dd9900b504a913a001f05","status":"active","name":"heterogeneity","description":"Variation among components or conditions within a natural system.","types":["phenomenon"],"aliases":[],"contributors":[{"id":35,"public_id":"b2adb6bfad","public_label":"Anonymous (b2adb6bfad)","roles":["extraction"],"url":"https://sah.borca.ai/u/b2adb6bfad"},{"id":32,"public_id":"7c402c1b98","public_label":"뀨 (7c402c1b98)","roles":["review"],"url":"https://sah.borca.ai/u/7c402c1b98"},{"id":1165,"public_id":"ezd9qvkvax","public_label":"The Reverser‮ (ezd9qvkvax)","roles":["review"],"url":"https://sah.borca.ai/u/ezd9qvkvax"},{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["review"],"url":"https://sah.borca.ai/u/b9tnx83g25"}],"url":"https://sah.borca.ai/concepts/co_d8f2ba6a150dd9900b504a913a001f05"},{"public_id":"co_dd4900f2f4d32d8ea7fd85dd0c3db7b0","status":"active","name":"total populations","description":"Aggregate counts of system entities tracked by discrete-state stochastic methods.","types":["measurement"],"aliases":[],"contributors":[{"id":35,"public_id":"b2adb6bfad","public_label":"Anonymous (b2adb6bfad)","roles":["extraction"],"url":"https://sah.borca.ai/u/b2adb6bfad"},{"id":32,"public_id":"7c402c1b98","public_label":"뀨 (7c402c1b98)","roles":["review"],"url":"https://sah.borca.ai/u/7c402c1b98"},{"id":1165,"public_id":"ezd9qvkvax","public_label":"The Reverser‮ (ezd9qvkvax)","roles":["review"],"url":"https://sah.borca.ai/u/ezd9qvkvax"},{"id":171,"public_id":"b9tnx83g25","public_label":"eunsjani (b9tnx83g25)","roles":["review"],"url":"https://sah.borca.ai/u/b9tnx83g25"}],"url":"https://sah.borca.ai/concepts/co_dd4900f2f4d32d8ea7fd85dd0c3db7b0"}],"external_ids":{"DOI":"10.1016/j.csbj.2014.10.003","ArXiv":null,"PubMed":25505503,"PubMedCentral":"4262058","MAG":2161301127,"DBLP":null,"ACL":null},"open_access":{"is_open_access":false,"pdf_url":null,"landing_url":"https://sah.borca.ai/papers/17674678","source":null,"pdf_url_source":null,"license":null,"reason":"pdf_url_not_indexed"},"reference_availability":{"status":"available","references_indexed":true,"full_text_available":false,"full_text_source":null,"count_basis":"semantic_scholar_metadata","extraction_status":"not_applicable","reason":null},"source":{"provider":"episteme2","base_corpus":"semantic_scholar_dump","freshness_mode":"unknown","basis":["semantic_scholar_metadata","postgres_metadata"],"limits":["paper metadata is based on indexed upstream scholarly datasets","claims and concepts are available only for extracted papers","absence of claims or concepts means no extracted graph data is available in this response"],"status":"available","degraded":false,"degraded_reasons":[],"diagnostics":{"status":"available","degraded":false,"degraded_reasons":[],"metadata_status":"available","graph_status":"available","abstract_status":"available"},"source_flags":5},"paper_id":638585,"paper_uid":"a701f5a9-4ade-4a8e-8da1-1979c44a01aa","canonical_identity":{"paper_id":638585,"paper_uid":"a701f5a9-4ade-4a8e-8da1-1979c44a01aa","identity_status":"available","lookup_basis":"semantic_scholar_external_id","compatibility_path":"corpus_id"},"url":"https://sah.borca.ai/papers/17674678"}