{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T10:01:10Z","timestamp":1778752870973,"version":"3.51.4"},"reference-count":52,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,9,21]],"date-time":"2016-09-21T00:00:00Z","timestamp":1474416000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2016,9,21]],"date-time":"2016-09-21T00:00:00Z","timestamp":1474416000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["5U54CA143907"],"award-info":[{"award-number":["5U54CA143907"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1R01CA180149"],"award-info":[{"award-number":["1R01CA180149"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001006","name":"Breast Cancer Research Foundation","doi-asserted-by":"publisher","award":["(Not applicable)"],"award-info":[{"award-number":["(Not applicable)"]}],"id":[{"id":"10.13039\/100001006","id-type":"DOI","asserted-by":"publisher"}]},{"name":"James H. Zumberge Research and Innovation Fund"},{"name":"USC Provost's PhD fellowship"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2016,12]]},"DOI":"10.1186\/s12918-016-0337-5","type":"journal-article","created":{"date-parts":[[2016,9,21]],"date-time":"2016-09-21T13:48:54Z","timestamp":1474465734000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":22,"title":["Quantifying differences in cell line population dynamics using CellPD"],"prefix":"10.1186","volume":"10","author":[{"given":"Edwin F.","family":"Juarez","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Roy","family":"Lau","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samuel H.","family":"Friedman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ahmadreza","family":"Ghaffarizadeh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Edmond","family":"Jonckheere","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David B.","family":"Agus","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shannon M.","family":"Mumenthaler","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul","family":"Macklin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,9,21]]},"reference":[{"key":"337_CR1","doi-asserted-by":"crossref","unstructured":"Barbolosi D, Ciccolini J, Lacarelle B, Barl\u00e9si F, Andr\u00e9 N. Computational oncology - mathematical modelling of drug regimens for precision medicine. Nature Reviews Clinical Oncology. 2016;13(4):242-54.","DOI":"10.1038\/nrclinonc.2015.204"},{"key":"337_CR2","doi-asserted-by":"publisher","first-page":"e1004096","DOI":"10.1371\/journal.pcbi.1004096","volume":"11","author":"JR Karr","year":"2015","unstructured":"Karr JR, Williams AH, Zucker JD, Raue A, Steiert B, Timmer J, et al. Summary of the DREAM8 parameter estimation challenge: toward parameter identification for whole-cell models. PLoS Comput Biol. 2015;11:e1004096.","journal-title":"PLoS Comput Biol"},{"key":"337_CR3","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1016\/j.tibtech.2010.02.005","volume":"28","author":"F Zanella","year":"2010","unstructured":"Zanella F, Lorens JB, Link W. High content screening: seeing is believing. Trends Biotechnol. 2010;28:237\u201345.","journal-title":"Trends Biotechnol"},{"key":"337_CR4","doi-asserted-by":"publisher","first-page":"e1003803","DOI":"10.1371\/journal.pgen.1003803","volume":"9","author":"J Gagneur","year":"2013","unstructured":"Gagneur J, Stegle O, Zhu C, Jakob P, Tekkedil MM, Aiyar RS, et al. Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype. PLoS Genet. 2013;9:e1003803.","journal-title":"PLoS Genet"},{"key":"337_CR5","doi-asserted-by":"publisher","first-page":"29752","DOI":"10.1038\/srep29752","volume":"6","author":"CM Garvey","year":"2016","unstructured":"Garvey CM, Spiller E, Lindsay D, Chiang C-T, Choi NC, Agus DB, et al. A high-content image-based method for quantitatively studying context-dependent cell population dynamics. Sci Rep. 2016;6:29752.","journal-title":"Sci Rep"},{"key":"337_CR6","doi-asserted-by":"publisher","first-page":"206","DOI":"10.1038\/nature01254","volume":"420","author":"H Kitano","year":"2002","unstructured":"Kitano H. Computational systems biology. Nature. 2002;420:206\u201310.","journal-title":"Nature"},{"key":"337_CR7","doi-asserted-by":"publisher","first-page":"300","DOI":"10.1093\/bib\/5.3.300","volume":"5","author":"D Gilbert","year":"2004","unstructured":"Gilbert D. Bioinformatics software resources. Brief Bioinform. 2004;5:300\u20134.","journal-title":"Brief Bioinform"},{"key":"337_CR8","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1093\/molbev\/mst187","volume":"31","author":"BG Hall","year":"2014","unstructured":"Hall BG, Acar H, Nandipati A, Barlow M. Growth rates made easy. Mol Biol Evol. 2014;31:232\u20138.","journal-title":"Mol Biol Evol"},{"key":"337_CR9","unstructured":"D. James, N. Wilkins-Diehr, V. Stodden, D. Colbry, C. Rosales, M. Fahey, et al. Standing together for reproducibility in large-scale computing: Report on reproducibility@ XSEDE. arXiv preprint arXiv:1412.5557. 2014."},{"key":"337_CR10","doi-asserted-by":"publisher","first-page":"e1003285","DOI":"10.1371\/journal.pcbi.1003285","volume":"9","author":"GK Sandve","year":"2013","unstructured":"Sandve GK, Nekrutenko A, Taylor J, Hovig E. Ten simple rules for reproducible computational research. PLoS Comput Biol. 2013;9:e1003285.","journal-title":"PLoS Comput Biol"},{"key":"337_CR11","doi-asserted-by":"crossref","first-page":"303","DOI":"10.12688\/f1000research.5930.1","volume":"3","author":"DA Soergel","year":"2014","unstructured":"Soergel DA. Rampant software errors may undermine scientific results. F1000Research. 2014;3:303.","journal-title":"F1000Research"},{"issue":"4","key":"337_CR12","doi-asserted-by":"publisher","first-page":"1309","DOI":"10.1214\/09-AOAS291","volume":"3","author":"KA Baggerly","year":"2009","unstructured":"Baggerly KA, Coombes KR. Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology. The Annals of Applied Statistics. 2009;3(4):1309\u201334.","journal-title":"The Annals of Applied Statistics"},{"key":"337_CR13","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1093\/cje\/bet075","volume":"38","author":"T Herndon","year":"2014","unstructured":"Herndon T, Ash M, Pollin R. Does high public debt consistently stifle economic growth? A critique of Reinhart and Rogoff. Camb J Econ. 2014;38:257\u201379.","journal-title":"Camb J Econ"},{"key":"337_CR14","unstructured":"Macklin P, Friedman SH. MultiCellDS MultiCellular Data Standard Project. Available: \n                    http:\/\/MultiCellDS.org\n                    \n                  . (Accessed 15 Sept 2015)"},{"key":"337_CR15","doi-asserted-by":"crossref","unstructured":"Facilitating reproducibility. Nat Chem Biol. 2013; 9: 345.","DOI":"10.1038\/nchembio.1269"},{"key":"337_CR16","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1038\/483531a","volume":"483","author":"CG Begley","year":"2012","unstructured":"Begley CG, Ellis LM. Drug development: Raise standards for preclinical cancer research. Nature. 2012;483:531\u20133.","journal-title":"Nature"},{"key":"337_CR17","doi-asserted-by":"publisher","first-page":"e63221","DOI":"10.1371\/journal.pone.0063221","volume":"8","author":"A Mobley","year":"2013","unstructured":"Mobley A, Linder SK, Braeuer R, Ellis LM, Zwelling L. A survey on data reproducibility in cancer research provides insights into our limited ability to translate findings from the laboratory to the clinic. PLoS One. 2013;8:e63221.","journal-title":"PLoS One"},{"key":"337_CR18","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1007\/BF01807363","volume":"9","author":"CK Osborne","year":"1987","unstructured":"Osborne CK, Hobbs K, Trent JM. Biological differences among MCF-7 human breast cancer cell lines from different laboratories. Breast Cancer Res Treat. 1987;9:111\u201321.","journal-title":"Breast Cancer Res Treat"},{"key":"337_CR19","unstructured":"Gagneur J, Neudecker A. cellGrowth: Fitting cell population growth models. R package version. 2012. Available Online from:\n                    https:\/\/www.bioconductor.org\/packages\/release\/bioc\/manuals\/cellGrowth\/man\/cellGrowth.pdf\n                    \n                  . (Accessed 27 Sept 2015)."},{"key":"337_CR20","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v033.i07","volume":"33","author":"M Kahm","year":"2010","unstructured":"Kahm M, Hasenbrink G, Lichtenberg F. grofit: fitting biological growth curves with R. J Stat Softw. 2010;33:1\u201321.","journal-title":"J Stat Softw"},{"key":"337_CR21","unstructured":"Elzhov TV, Mullen KM, Bolker B. minpack. lm: R Interface to the Levenberg-Marquardt Nonlinear Least-Squares Algorithm Found in MINPACK. R package version. 2009"},{"key":"337_CR22","unstructured":"Elzhov TV, Mullen KM, Bolker B. minpack. lm: R Interface to the Levenberg-Marquardt Nonlinear Least-Squares Algorithm Found in MINPACK. R package version. 2009. Available Online from: \n                    https:\/\/cran.rproject.org\/web\/packages\/minpack.lm\/minpack.lm.pdf\n                    \n                  . (Accessed 30 Dec 2015)."},{"key":"337_CR23","doi-asserted-by":"publisher","first-page":"504","DOI":"10.1002\/bit.25115","volume":"111","author":"N Jaccard","year":"2014","unstructured":"Jaccard N, Griffin LD, Keser A, Macown RJ, Super A, Veraitch FS, et al. Automated method for the rapid and precise estimation of adherent cell culture characteristics from phase contrast microscopy images. Biotechnol Bioeng. 2014;111:504\u201317.","journal-title":"Biotechnol Bioeng"},{"key":"337_CR24","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1093\/bioinformatics\/btl668","volume":"23","author":"H Schmidt","year":"2007","unstructured":"Schmidt H, Jirstrand M. SBaddon: high performance simulation for the Systems Biology Toolbox for MATLAB. Bioinformatics. 2007;23:646\u20137.","journal-title":"Bioinformatics"},{"key":"337_CR25","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-14-283","volume":"14","author":"A Ver\u00edssimo","year":"2013","unstructured":"Ver\u00edssimo A, Paix\u00e3o L, Neves AR, Vinga S. BGFit: management and automated fitting of biological growth curves. BMC bioinformatics. 2013;14:1.","journal-title":"BMC bioinformatics"},{"key":"337_CR26","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1038\/nprot.2014.025","volume":"9","author":"J Liepe","year":"2014","unstructured":"Liepe J, Kirk P, Filippi S, Toni T, Barnes CP, Stumpf MPH. A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation. Nat Protoc. 2014;9:439\u201356.","journal-title":"Nat Protoc"},{"key":"337_CR27","doi-asserted-by":"publisher","first-page":"e0119807","DOI":"10.1371\/journal.pone.0119807","volume":"10","author":"PP Jung","year":"2015","unstructured":"Jung PP, Christian N, Kay DP, Skupin A, Linster CL. Protocols and programs for high-throughput growth and aging phenotyping in yeast. PLoS One. 2015;10:e0119807.","journal-title":"PLoS One"},{"key":"337_CR28","first-page":"42","volume-title":"Big data: a review","author":"S Sagiroglu","year":"2013","unstructured":"Sagiroglu S, Sinanc D. Big data: a review. 2013. p. 42\u20137."},{"key":"337_CR29","unstructured":"Macklin P, Juarez EF. CellPD: Cell Phenotype Digitizer. Available: \n                    http:\/\/CellPD.sf.net\n                    \n                  . (Accessed 8 Feb 2016)"},{"key":"337_CR30","unstructured":"Macklin P, Juarez EF. MultiCellDS\/CellPD: Cell Phenotype Digitizer. Available: \n                    http:\/\/MultiCellDS.org\/CellPD\/\n                    \n                  . (Accessed 8 Feb 2016)."},{"issue":"6","key":"337_CR31","doi-asserted-by":"publisher","first-page":"497","DOI":"10.1038\/nmeth.3852","volume":"13","author":"LA Harris","year":"2016","unstructured":"Harris LA, Frick PL, Garbett SP, Hardeman KN, Paudel BB, Lopez CF, et al. An unbiased metric of antiproliferative drug effect in vitro. Nat Methods. 2016;13(6):497\u2013500.","journal-title":"Nat Methods"},{"key":"337_CR32","doi-asserted-by":"publisher","first-page":"423","DOI":"10.1038\/nmeth.1333","volume":"6","author":"AW Bell","year":"2009","unstructured":"Bell AW, Deutsch EW, Au CE, Kearney RE, Beavis R, Sechi S, et al. A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nat Methods. 2009;6:423\u201330.","journal-title":"Nat Methods"},{"key":"337_CR33","doi-asserted-by":"publisher","first-page":"2276","DOI":"10.1038\/nprot.2007.319","volume":"2","author":"JR Masters","year":"2007","unstructured":"Masters JR, Stacey GN. Changing medium and passaging cell lines. Nat Protoc. 2007;2:2276\u201384.","journal-title":"Nat Protoc"},{"key":"337_CR34","unstructured":"ORCID. ORCID Connecting Research and Researchers. Available: \n                    http:\/\/orcid.org\/\n                    \n                  . (Accessed 1 Oct 2015)."},{"key":"337_CR35","unstructured":"LibreOffice.org. LibreOffice The Document Foundation. Available: \n                    https:\/\/www.libreoffice.org\/\n                    \n                  . (Accessed 2 Nov 2015)"},{"key":"337_CR36","unstructured":"Newville M. LMFIT Non-Linear Least-Square Minimization and Curve-Fitting for Python. Available: \n                    http:\/\/cars9.uchicago.edu\/software\/python\/lmfit\/\n                    \n                  . (Accessed 15 Sept 2015)"},{"key":"337_CR37","unstructured":"Newville M. LMFIT License. Available: \n                    http:\/\/cars9.uchicago.edu\/software\/python\/lmfit\/installation.html#license\n                    \n                  . (Accessed 15 Sept 2015)."},{"key":"337_CR38","unstructured":"N. developers. NumPy. Available: \n                    http:\/\/www.numpy.org\/\n                    \n                  . (Accessed 15 Sept 2015)"},{"key":"337_CR39","unstructured":"N. developers. Numpy license. Available: \n                    http:\/\/www.numpy.org\/license.html\n                    \n                  . (Accessed 15 Sept 2015)"},{"key":"337_CR40","unstructured":"S. developers. SciPy library. Available: \n                    http:\/\/www.scipy.org\/scipylib\/index.html\n                    \n                  . (Accessed 15 Sept 2015)"},{"key":"337_CR41","unstructured":"S. developers. SciPy license. Available: \n                    http:\/\/www.scipy.org\/scipylib\/license.html\n                    \n                  . (Accessed 15 Sept 2015)"},{"key":"337_CR42","unstructured":"Hunter J, Dale D, Firing E, Droettboom M, Matplotlib-development-team. matplotlib. Available: \n                    http:\/\/matplotlib.org\/\n                    \n                  . (Accessed 15 Sept 2015)."},{"key":"337_CR43","unstructured":"Hunter J, Dale D, Firing E, Droettboom M and Matplotlib-development-team. matplotlib license. Available: \n                    http:\/\/matplotlib.org\/users\/license.html\n                    \n                  . (Accessed 15 Sept 2015)"},{"key":"337_CR44","unstructured":"Regebro L. tzlocal 1.2.2. Available: \n                    https:\/\/pypi.python.org\/pypi\/tzlocal\n                    \n                  . (Accessed 2 Dec 2015)"},{"key":"337_CR45","unstructured":"Astanin S. tabulate 0.7.5. Available: \n                    https:\/\/pypi.python.org\/pypi\/tabulate\n                    \n                  . (Accessed 26 Nov 2015)"},{"key":"337_CR46","unstructured":"Gazoni E, Clark C. openpyxl - A Python library to read\/write Excel 2010 xlsx\/xlsm files. Available: \n                    https:\/\/openpyxl.readthedocs.org\/en\/2.3.3\/\n                    \n                  . (Accessed 29 Sept 2015)"},{"key":"337_CR47","unstructured":"Zibricky M, Goebel H, Cortesi D, Vierra D. PyInstaller. Available: \n                    http:\/\/www.pyinstaller.org\/\n                    \n                  . (Accessed 30 Sept 2015)"},{"key":"337_CR48","unstructured":"Amenta J. Joe Amenta\u2019s Blog. Available: \n                    http:\/\/www.startcodon.com\/wordpress\/category\/3to2\/\n                    \n                  . (Accessed 16 Jan 2016)"},{"key":"337_CR49","unstructured":"Amenta J. 3to2 1.1.1. Available: \n                    https:\/\/pypi.python.org\/pypi\/3to2\/1.1.1\n                    \n                  . (Accessed 16 Jan 2016)"},{"key":"337_CR50","volume-title":"LMFIT: Non-linear least-square minimization and curve-fitting for python","author":"M Newville","year":"2014","unstructured":"Newville M, Stensitzki T, Allen DB, Ingargiola A. LMFIT: Non-linear least-square minimization and curve-fitting for python. 2014."},{"key":"337_CR51","volume-title":"Numerical recipes 3rd edition: The art of scientific computing","author":"WH Press","year":"2007","unstructured":"Press WH. Numerical recipes 3rd edition: The art of scientific computing. Cambridge: University press; 2007."},{"key":"337_CR52","unstructured":"Gavin H. The Levenberg-Marquardt method for nonlinear least squares curve-fitting problems. 2011.Availble Online from: \n                    http:\/\/people.duke.edu\/~hpgavin\/ce281\/lm.pdf.\n                    \n                  . (Accessed 15 Sept 2015)."}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12918-016-0337-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12918-016-0337-5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12918-016-0337-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,15]],"date-time":"2020-05-15T11:33:15Z","timestamp":1589542395000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/s12918-016-0337-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,9,21]]},"references-count":52,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2016,12]]}},"alternative-id":["337"],"URL":"https:\/\/doi.org\/10.1186\/s12918-016-0337-5","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,9,21]]},"assertion":[{"value":"27 May 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 September 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 September 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"92"}}