{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,22]],"date-time":"2025-11-22T17:04:16Z","timestamp":1763831056873,"version":"3.37.3"},"reference-count":23,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,10,21]],"date-time":"2019-10-21T00:00:00Z","timestamp":1571616000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2019,10,21]],"date-time":"2019-10-21T00:00:00Z","timestamp":1571616000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2019,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>At the molecular level, nonlinear networks of heterogeneous molecules control many biological processes, so that systems biology provides a valuable approach in this field, building on the integration of experimental biology with mathematical modeling. One of the biggest challenges to making this integration a reality is that many life scientists do not possess the mathematical expertise needed to build and manipulate mathematical models well enough to use them as tools for hypothesis generation. Available modeling software packages often assume some modeling expertise. There is a need for software tools that are easy to use and intuitive for experimentalists.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>This paper introduces PlantSimLab, a web-based application developed to allow plant biologists to construct dynamic mathematical models of molecular networks, interrogate them in a manner similar to what is done in the laboratory, and use them as a tool for biological hypothesis generation. It is designed to be used by experimentalists, without direct assistance from mathematical modelers.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Mathematical modeling techniques are a useful tool for analyzing complex biological systems, and there is a need for accessible, efficient analysis tools within the biological community. PlantSimLab enables users to build, validate, and use intuitive qualitative dynamic computer models, with a graphical user interface that does not require mathematical modeling expertise. It makes analysis of complex models accessible to a larger community, as it is platform-independent and does not require extensive mathematical expertise.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12859-019-3094-9","type":"journal-article","created":{"date-parts":[[2019,10,21]],"date-time":"2019-10-21T15:21:33Z","timestamp":1571671293000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["PlantSimLab - a modeling and simulation web tool for plant biologists"],"prefix":"10.1186","volume":"20","author":[{"given":"S.","family":"Ha","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"E.","family":"Dimitrova","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S.","family":"Hoops","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"D.","family":"Altarawy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M.","family":"Ansariola","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"D.","family":"Deb","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J.","family":"Glazebrook","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"R.","family":"Hillmer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"H.","family":"Shahin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"F.","family":"Katagiri","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J.","family":"McDowell","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M.","family":"Megraw","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J.","family":"Setubal","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"B. M.","family":"Tyler","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9143-9451","authenticated-orcid":false,"given":"R.","family":"Laubenbacher","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2019,10,21]]},"reference":[{"issue":"1","key":"3094_CR1","first-page":"1480150","volume":"4","author":"C Elton","year":"1935","unstructured":"Elton C. Eppur si mouve. J Animal Ecology. 1935;4(1):1480150.","journal-title":"J Animal Ecology"},{"issue":"4","key":"3094_CR2","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1111\/j.1365-3040.2010.02273.x","volume":"34","author":"M Lucas","year":"2011","unstructured":"Lucas M, Laplaze L, Bennett MJ. Plant systems biology: network matters. Plant Cell Environ. 2011;34(4):535\u201353.","journal-title":"Plant Cell Environ"},{"issue":"9","key":"3094_CR3","doi-asserted-by":"publisher","first-page":"e1005744","DOI":"10.1371\/journal.pcbi.1005744","volume":"13","author":"JL Dinh","year":"2017","unstructured":"Dinh JL, Farcot E, Hodgman C. The logic of the floral transition: reverse-engineering the switch controlling the identity of lateral organs. PLoS Comput Biol. 2017;13(9):e1005744.","journal-title":"PLoS Comput Biol"},{"issue":"4","key":"3094_CR4","doi-asserted-by":"publisher","first-page":"e1005488","DOI":"10.1371\/journal.pcbi.1005488","volume":"13","author":"ML Garcia-Gomez","year":"2017","unstructured":"Garcia-Gomez ML, Azpeitia E, Alvarez-Buylla ER. A dynamic genetic-hormonal regulatory network model explains multiple cellular behaviors of the root apical meristem of Arabidopsis thaliana. PLoS Comput Biol. 2017;13(4):e1005488.","journal-title":"PLoS Comput Biol"},{"issue":"2","key":"3094_CR5","doi-asserted-by":"publisher","first-page":"e0171927","DOI":"10.1371\/journal.pone.0171927","volume":"12","author":"V Oles","year":"2017","unstructured":"Oles V, Panchenko A, Smertenko A. Modeling hormonal control of cambium proliferation. PLoS One. 2017;12(2):e0171927.","journal-title":"PLoS One"},{"key":"3094_CR6","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1007\/978-1-4939-7125-1_19","volume":"1629","author":"JD Velderrain","year":"2017","unstructured":"Velderrain JD, Martinez-Garcia JC, Alvarez-Buylla ER. Boolean dynamic Modeling approaches to study plant gene regulatory networks: integration, validation, and prediction. Methods Mol Biol. 2017;1629:297\u2013315.","journal-title":"Methods Mol Biol"},{"key":"3094_CR7","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1186\/1752-0509-6-96","volume":"6","author":"T Helikar","year":"2012","unstructured":"Helikar T, et al. The cell collective: toward an open and collaborative approach to systems biology. BMC Syst Biol. 2012;6:96.","journal-title":"BMC Syst Biol"},{"key":"3094_CR8","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1007\/978-1-61779-361-5_23","volume":"804","author":"C Chaouiya","year":"2012","unstructured":"Chaouiya C, Naldi A, Thieffry D. Logical modelling of gene regulatory networks with GINsim. Methods Mol Biol. 2012;804:463\u201379.","journal-title":"Methods Mol Biol"},{"issue":"10","key":"3094_CR9","doi-asserted-by":"publisher","first-page":"1378","DOI":"10.1093\/bioinformatics\/btq124","volume":"26","author":"C Mussel","year":"2010","unstructured":"Mussel C, Hopfensitz M, Kestler HA. BoolNet--an R package for generation, reconstruction and analysis of Boolean networks. Bioinformatics. 2010;26(10):1378\u201380.","journal-title":"Bioinformatics"},{"key":"3094_CR10","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.biosystems.2017.08.006","volume":"162","author":"JS Dussaut","year":"2017","unstructured":"Dussaut JS, et al. GeRNet: a gene regulatory network tool. Biosystems. 2017;162:1\u201311.","journal-title":"Biosystems"},{"issue":"1","key":"3094_CR11","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1109\/TVCG.2017.2745280","volume":"24","author":"AG Forbes","year":"2018","unstructured":"Forbes AG, et al. Dynamic influence networks for rule-based models. IEEE Trans Vis Comput Graph. 2018;24(1):184\u201394.","journal-title":"IEEE Trans Vis Comput Graph"},{"issue":"4","key":"3094_CR12","doi-asserted-by":"publisher","first-page":"705","DOI":"10.1038\/nprot.2017.144","volume":"13","author":"A Livigni","year":"2018","unstructured":"Livigni A, et al. A graphical and computational modeling platform for biological pathways. Nat Protoc. 2018;13(4):705\u201322.","journal-title":"Nat Protoc"},{"key":"3094_CR13","doi-asserted-by":"publisher","first-page":"16032","DOI":"10.1038\/npjsba.2016.32","volume":"2","author":"H Wu","year":"2016","unstructured":"Wu H, et al. MUFINS: multi-formalism interaction network simulator. NPJ Syst Biol Appl. 2016;2:16032.","journal-title":"NPJ Syst Biol Appl"},{"key":"3094_CR14","unstructured":"PlantSimLab. PlantSimlab Tutorial #1: Model building. 2017; available from: https:\/\/www.youtube.com\/watch?v=97qa7rWYelU ."},{"key":"3094_CR15","unstructured":"PlantSimLab, PlantSimLab Tutorial #2: Experimental Setup. 2017; available from https:\/\/www.youtube.com\/watch?v=3sFwsxmJ-Qg ."},{"key":"3094_CR16","unstructured":"PlantSimLab, PlantSimLab Tutorial #3: Network analysis results viewer. 2017; available from https:\/\/www.youtube.com\/watch?v=aI96BQF1eC8 ."},{"key":"3094_CR17","unstructured":"Shneiderman B, Plaisant C. Designing the user interface; Strategies for effective human-computer interaction. 2010. Boston: Addison-Wesley."},{"key":"3094_CR18","doi-asserted-by":"publisher","first-page":"2923","DOI":"10.1105\/tpc.104.021725","volume":"16","author":"C Espinosa-Soto","year":"2004","unstructured":"Espinosa-Soto C, Padilla-Longaria P, Alvarez-Buylla ER. A gene regulatory network model for cell-fate determination during Arabidopsis thaliana flower development that is robust and recovers experimental gene expression profiles. Plant Cell. 2004;16:2923\u201339.","journal-title":"Plant Cell"},{"issue":"6","key":"3094_CR19","doi-asserted-by":"publisher","first-page":"783","DOI":"10.1089\/cmb.2011.0031","volume":"18","author":"A Veliz-Cuba","year":"2011","unstructured":"Veliz-Cuba A, Stigler B. Boolean models can explain bistability in the lac operon. J Comput Biol. 2011;18(6):783\u201394.","journal-title":"J Comput Biol"},{"issue":"1","key":"3094_CR20","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1186\/s12918-018-0580-z","volume":"12","author":"E Dimitrova","year":"2018","unstructured":"Dimitrova E, et al. The innate immune response to ischemic injury: a multiscale modeling perspective. BMC Syst Biol. 2018;12(1):50.","journal-title":"BMC Syst Biol"},{"issue":"5","key":"3094_CR21","doi-asserted-by":"crossref","first-page":"770","DOI":"10.1093\/bioinformatics\/btw682","volume":"33","author":"H Klarner","year":"2017","unstructured":"Klarner H, Streck A, Siebert H. PyBoolNet: a python package for the generation, analysis and visualization of boolean networks. Bioinformatics. 2017;33(5):770\u20132.","journal-title":"Bioinformatics"},{"key":"3094_CR22","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1007\/978-1-4419-7046-6_12","volume":"696","author":"QN Tran","year":"2011","unstructured":"Tran QN. Algebraic model checking for Boolean gene regulatory networks. Adv Exp Med Biol. 2011;696:113\u201322.","journal-title":"Adv Exp Med Biol"},{"issue":"17","key":"3094_CR23","doi-asserted-by":"publisher","first-page":"i772","DOI":"10.1093\/bioinformatics\/btw457","volume":"32","author":"P Traynard","year":"2016","unstructured":"Traynard P, et al. Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation. Bioinformatics. 2016;32(17):i772\u201380.","journal-title":"Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-3094-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-019-3094-9\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-3094-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,21]],"date-time":"2023-09-21T22:30:46Z","timestamp":1695335446000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-019-3094-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,10,21]]},"references-count":23,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2019,12]]}},"alternative-id":["3094"],"URL":"https:\/\/doi.org\/10.1186\/s12859-019-3094-9","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2019,10,21]]},"assertion":[{"value":"3 December 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 September 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 October 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"508"}}