TY - STD TI - Barbolosi D, Ciccolini J, Lacarelle B, Barlési F, André N. Computational oncology - mathematical modelling of drug regimens for precision medicine. Nature Reviews Clinical Oncology. 2016;13(4):242-54. ID - ref1 ER - TY - JOUR AU - Karr, J. R. AU - Williams, A. H. AU - Zucker, J. D. AU - Raue, A. AU - Steiert, B. AU - Timmer, J. PY - 2015 DA - 2015// TI - Summary of the DREAM8 parameter estimation challenge: toward parameter identification for whole-cell models JO - PLoS Comput Biol VL - 11 UR - https://doi.org/10.1371/journal.pcbi.1004096 DO - 10.1371/journal.pcbi.1004096 ID - Karr2015 ER - TY - JOUR AU - Zanella, F. AU - Lorens, J. B. AU - Link, W. PY - 2010 DA - 2010// TI - High content screening: seeing is believing JO - Trends Biotechnol VL - 28 UR - https://doi.org/10.1016/j.tibtech.2010.02.005 DO - 10.1016/j.tibtech.2010.02.005 ID - Zanella2010 ER - TY - JOUR AU - Gagneur, J. AU - Stegle, O. AU - Zhu, C. AU - Jakob, P. AU - Tekkedil, M. M. AU - Aiyar, R. S. PY - 2013 DA - 2013// TI - Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype JO - PLoS Genet VL - 9 UR - https://doi.org/10.1371/journal.pgen.1003803 DO - 10.1371/journal.pgen.1003803 ID - Gagneur2013 ER - TY - JOUR AU - Garvey, C. M. AU - Spiller, E. AU - Lindsay, D. AU - Chiang, C. -. T. AU - Choi, N. C. AU - Agus, D. B. PY - 2016 DA - 2016// TI - A high-content image-based method for quantitatively studying context-dependent cell population dynamics JO - Sci Rep VL - 6 UR - https://doi.org/10.1038/srep29752 DO - 10.1038/srep29752 ID - Garvey2016 ER - TY - JOUR AU - Kitano, H. PY - 2002 DA - 2002// TI - Computational systems biology JO - Nature VL - 420 UR - https://doi.org/10.1038/nature01254 DO - 10.1038/nature01254 ID - Kitano2002 ER - TY - JOUR AU - Gilbert, D. PY - 2004 DA - 2004// TI - Bioinformatics software resources JO - Brief Bioinform VL - 5 UR - https://doi.org/10.1093/bib/5.3.300 DO - 10.1093/bib/5.3.300 ID - Gilbert2004 ER - TY - JOUR AU - Hall, B. G. AU - Acar, H. AU - Nandipati, A. AU - Barlow, M. PY - 2014 DA - 2014// TI - Growth rates made easy JO - Mol Biol Evol VL - 31 UR - https://doi.org/10.1093/molbev/mst187 DO - 10.1093/molbev/mst187 ID - Hall2014 ER - TY - STD TI - 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. ID - ref9 ER - TY - JOUR AU - Sandve, G. K. AU - Nekrutenko, A. AU - Taylor, J. AU - Hovig, E. PY - 2013 DA - 2013// TI - Ten simple rules for reproducible computational research JO - PLoS Comput Biol VL - 9 UR - https://doi.org/10.1371/journal.pcbi.1003285 DO - 10.1371/journal.pcbi.1003285 ID - Sandve2013 ER - TY - JOUR AU - Soergel, D. A. PY - 2014 DA - 2014// TI - Rampant software errors may undermine scientific results JO - F1000Research VL - 3 ID - Soergel2014 ER - TY - JOUR AU - Baggerly, K. A. AU - Coombes, K. R. PY - 2009 DA - 2009// TI - Deriving chemosensitivity from cell lines: Forensic bioinformatics and reproducible research in high-throughput biology JO - The Annals of Applied Statistics VL - 3 UR - https://doi.org/10.1214/09-AOAS291 DO - 10.1214/09-AOAS291 ID - Baggerly2009 ER - TY - JOUR AU - Herndon, T. AU - Ash, M. AU - Pollin, R. PY - 2014 DA - 2014// TI - Does high public debt consistently stifle economic growth? A critique of Reinhart and Rogoff JO - Camb J Econ VL - 38 UR - https://doi.org/10.1093/cje/bet075 DO - 10.1093/cje/bet075 ID - Herndon2014 ER - TY - STD TI - Macklin P, Friedman SH. MultiCellDS MultiCellular Data Standard Project. Available: http://MultiCellDS.org. (Accessed 15 Sept 2015) UR - http://MultiCellDS.org ID - ref14 ER - TY - STD TI - Facilitating reproducibility. Nat Chem Biol. 2013; 9: 345. ID - ref15 ER - TY - JOUR AU - Begley, C. G. AU - Ellis, L. M. PY - 2012 DA - 2012// TI - Drug development: Raise standards for preclinical cancer research JO - Nature VL - 483 UR - https://doi.org/10.1038/483531a DO - 10.1038/483531a ID - Begley2012 ER - TY - JOUR AU - Mobley, A. AU - Linder, S. K. AU - Braeuer, R. AU - Ellis, L. M. AU - Zwelling, L. PY - 2013 DA - 2013// TI - A survey on data reproducibility in cancer research provides insights into our limited ability to translate findings from the laboratory to the clinic JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0063221 DO - 10.1371/journal.pone.0063221 ID - Mobley2013 ER - TY - JOUR AU - Osborne, C. K. AU - Hobbs, K. AU - Trent, J. M. PY - 1987 DA - 1987// TI - Biological differences among MCF-7 human breast cancer cell lines from different laboratories JO - Breast Cancer Res Treat VL - 9 UR - https://doi.org/10.1007/BF01807363 DO - 10.1007/BF01807363 ID - Osborne1987 ER - TY - STD TI - Gagneur J, Neudecker A. cellGrowth: Fitting cell population growth models. R package version. 2012. Available Online from:https://www.bioconductor.org/packages/release/bioc/manuals/cellGrowth/man/cellGrowth.pdf. (Accessed 27 Sept 2015). UR - https://www.bioconductor.org/packages/release/bioc/manuals/cellGrowth/man/cellGrowth.pdf ID - ref19 ER - TY - JOUR AU - Kahm, M. AU - Hasenbrink, G. AU - Lichtenberg, F. PY - 2010 DA - 2010// TI - grofit: fitting biological growth curves with R JO - J Stat Softw VL - 33 UR - https://doi.org/10.18637/jss.v033.i07 DO - 10.18637/jss.v033.i07 ID - Kahm2010 ER - TY - STD TI - 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 ID - ref21 ER - TY - STD TI - 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: https://cran.rproject.org/web/packages/minpack.lm/minpack.lm.pdf. (Accessed 30 Dec 2015). UR - https://cran.rproject.org/web/packages/minpack.lm/minpack.lm.pdf ID - ref22 ER - TY - JOUR AU - Jaccard, N. AU - Griffin, L. D. AU - Keser, A. AU - Macown, R. J. AU - Super, A. AU - Veraitch, F. S. PY - 2014 DA - 2014// TI - Automated method for the rapid and precise estimation of adherent cell culture characteristics from phase contrast microscopy images JO - Biotechnol Bioeng VL - 111 UR - https://doi.org/10.1002/bit.25115 DO - 10.1002/bit.25115 ID - Jaccard2014 ER - TY - JOUR AU - Schmidt, H. AU - Jirstrand, M. PY - 2007 DA - 2007// TI - SBaddon: high performance simulation for the Systems Biology Toolbox for MATLAB JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btl668 DO - 10.1093/bioinformatics/btl668 ID - Schmidt2007 ER - TY - JOUR AU - Veríssimo, A. AU - Paixão, L. AU - Neves, A. R. AU - Vinga, S. PY - 2013 DA - 2013// TI - BGFit: management and automated fitting of biological growth curves JO - BMC bioinformatics VL - 14 UR - https://doi.org/10.1186/1471-2105-14-283 DO - 10.1186/1471-2105-14-283 ID - Veríssimo2013 ER - TY - JOUR AU - Liepe, J. AU - Kirk, P. AU - Filippi, S. AU - Toni, T. AU - Barnes, C. P. AU - Stumpf, M. P. H. PY - 2014 DA - 2014// TI - A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation JO - Nat Protoc VL - 9 UR - https://doi.org/10.1038/nprot.2014.025 DO - 10.1038/nprot.2014.025 ID - Liepe2014 ER - TY - JOUR AU - Jung, P. P. AU - Christian, N. AU - Kay, D. P. AU - Skupin, A. AU - Linster, C. L. PY - 2015 DA - 2015// TI - Protocols and programs for high-throughput growth and aging phenotyping in yeast JO - PLoS One VL - 10 UR - https://doi.org/10.1371/journal.pone.0119807 DO - 10.1371/journal.pone.0119807 ID - Jung2015 ER - TY - BOOK AU - Sagiroglu, S. AU - Sinanc, D. PY - 2013 DA - 2013// TI - Big data: a review ID - Sagiroglu2013 ER - TY - STD TI - Macklin P, Juarez EF. CellPD: Cell Phenotype Digitizer. Available: http://CellPD.sf.net. (Accessed 8 Feb 2016) UR - http://cellpd.sf.net ID - ref29 ER - TY - STD TI - Macklin P, Juarez EF. MultiCellDS/CellPD: Cell Phenotype Digitizer. Available: http://MultiCellDS.org/CellPD/. (Accessed 8 Feb 2016). UR - http://multicellds.org/CellPD/ ID - ref30 ER - TY - JOUR AU - Harris, L. A. AU - Frick, P. L. AU - Garbett, S. P. AU - Hardeman, K. N. AU - Paudel, B. B. AU - Lopez, C. F. PY - 2016 DA - 2016// TI - An unbiased metric of antiproliferative drug effect in vitro JO - Nat Methods VL - 13 UR - https://doi.org/10.1038/nmeth.3852 DO - 10.1038/nmeth.3852 ID - Harris2016 ER - TY - JOUR AU - Bell, A. W. AU - Deutsch, E. W. AU - Au, C. E. AU - Kearney, R. E. AU - Beavis, R. AU - Sechi, S. PY - 2009 DA - 2009// TI - A HUPO test sample study reveals common problems in mass spectrometry-based proteomics JO - Nat Methods VL - 6 UR - https://doi.org/10.1038/nmeth.1333 DO - 10.1038/nmeth.1333 ID - Bell2009 ER - TY - JOUR AU - Masters, J. R. AU - Stacey, G. N. PY - 2007 DA - 2007// TI - Changing medium and passaging cell lines JO - Nat Protoc VL - 2 UR - https://doi.org/10.1038/nprot.2007.319 DO - 10.1038/nprot.2007.319 ID - Masters2007 ER - TY - STD TI - ORCID. ORCID Connecting Research and Researchers. Available: http://orcid.org/. (Accessed 1 Oct 2015). UR - http://orcid.org/ ID - ref34 ER - TY - STD TI - LibreOffice.org. LibreOffice The Document Foundation. Available: https://www.libreoffice.org/. (Accessed 2 Nov 2015) UR - https://www.libreoffice.org/ ID - ref35 ER - TY - STD TI - Newville M. LMFIT Non-Linear Least-Square Minimization and Curve-Fitting for Python. Available: http://cars9.uchicago.edu/software/python/lmfit/. (Accessed 15 Sept 2015) UR - http://cars9.uchicago.edu/software/python/lmfit/ ID - ref36 ER - TY - STD TI - Newville M. LMFIT License. Available: http://cars9.uchicago.edu/software/python/lmfit/installation.html#license. (Accessed 15 Sept 2015). UR - http://cars9.uchicago.edu/software/python/lmfit/installation.html#license ID - ref37 ER - TY - STD TI - N. developers. NumPy. Available: http://www.numpy.org/. (Accessed 15 Sept 2015) UR - http://www.numpy.org/ ID - ref38 ER - TY - STD TI - N. developers. Numpy license. Available: http://www.numpy.org/license.html. (Accessed 15 Sept 2015) UR - http://www.numpy.org/license.html ID - ref39 ER - TY - STD TI - S. developers. SciPy library. Available: http://www.scipy.org/scipylib/index.html. (Accessed 15 Sept 2015) UR - http://www.scipy.org/scipylib/index.html ID - ref40 ER - TY - STD TI - S. developers. SciPy license. Available: http://www.scipy.org/scipylib/license.html. (Accessed 15 Sept 2015) UR - http://www.scipy.org/scipylib/license.html ID - ref41 ER - TY - STD TI - Hunter J, Dale D, Firing E, Droettboom M, Matplotlib-development-team. matplotlib. Available: http://matplotlib.org/. (Accessed 15 Sept 2015). UR - http://matplotlib.org/ ID - ref42 ER - TY - STD TI - Hunter J, Dale D, Firing E, Droettboom M and Matplotlib-development-team. matplotlib license. Available: http://matplotlib.org/users/license.html. (Accessed 15 Sept 2015) UR - http://matplotlib.org/users/license.html ID - ref43 ER - TY - STD TI - Regebro L. tzlocal 1.2.2. Available: https://pypi.python.org/pypi/tzlocal. (Accessed 2 Dec 2015) UR - https://pypi.python.org/pypi/tzlocal ID - ref44 ER - TY - STD TI - Astanin S. tabulate 0.7.5. Available: https://pypi.python.org/pypi/tabulate. (Accessed 26 Nov 2015) UR - https://pypi.python.org/pypi/tabulate ID - ref45 ER - TY - STD TI - Gazoni E, Clark C. openpyxl - A Python library to read/write Excel 2010 xlsx/xlsm files. Available: https://openpyxl.readthedocs.org/en/2.3.3/. (Accessed 29 Sept 2015) UR - https://openpyxl.readthedocs.org/en/2.3.3/ ID - ref46 ER - TY - STD TI - Zibricky M, Goebel H, Cortesi D, Vierra D. PyInstaller. Available: http://www.pyinstaller.org/. (Accessed 30 Sept 2015) UR - http://www.pyinstaller.org/ ID - ref47 ER - TY - STD TI - Amenta J. Joe Amenta’s Blog. Available: http://www.startcodon.com/wordpress/category/3to2/. (Accessed 16 Jan 2016) UR - http://www.startcodon.com/wordpress/category/3to2/ ID - ref48 ER - TY - STD TI - Amenta J. 3to2 1.1.1. Available: https://pypi.python.org/pypi/3to2/1.1.1. (Accessed 16 Jan 2016) UR - https://pypi.python.org/pypi/3to2/1.1.1 ID - ref49 ER - TY - BOOK AU - Newville, M. AU - Stensitzki, T. AU - Allen, D. B. AU - Ingargiola, A. PY - 2014 DA - 2014// TI - LMFIT: Non-linear least-square minimization and curve-fitting for python ID - Newville2014 ER - TY - BOOK AU - Press, W. H. PY - 2007 DA - 2007// TI - Numerical recipes 3rd edition: The art of scientific computing PB - University press CY - Cambridge ID - Press2007 ER - TY - STD TI - Gavin H. The Levenberg-Marquardt method for nonlinear least squares curve-fitting problems. 2011.Availble Online from: http://people.duke.edu/~hpgavin/ce281/lm.pdf.. (Accessed 15 Sept 2015). UR - http://people.duke.edu/~hpgavin/ce281/lm.pdf. ID - ref52 ER -