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jib_references.bib
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%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/
%% Created for falks at 2015-08-13 09:51:58 +1000
%% Saved with string encoding Unicode (UTF-8)
@article{sedml2011,
Author = {Waltemath, Dagmar and Adams, Richard and Bergmann, Frank T and Hucka, Michael and Kolpakov, Fedor and Miller, Andrew K and Moraru, Ion I and Nickerson, David and Sahle, Sven and Snoep, Jacky L and others},
Date-Added = {2015-08-12 23:51:29 +0000},
Date-Modified = {2015-08-12 23:51:29 +0000},
Journal = {BMC Systems Biology},
Number = {1},
Pages = {198},
Publisher = {BioMed Central Ltd},
Title = {Reproducible computational biology experiments with {SED-ML} -- the {S}imulation {E}xperiment {D}escription {M}arkup {L}anguage},
Volume = {5},
Year = {2011}}
@article{galdzicki2014,
Author = {Galdzicki, Michal and Clancy, Kevin P. and Oberortner, Ernst and Pocock, Matthew and Quinn, Jacqueline Y. and Rodriguez, Cesar A. and Roehner, Nicholas and Wilson, Mandy L. and Adam, Laura and Anderson, J. Christopher and Bartley, Bryan A. and Beal, Jacob and Chandran, Deepak and Chen, Joanna and Densmore, Douglas and Endy, Drew and Gr\"{u}nberg, Raik and Hallinan, Jennifer and Hillson, Nathan J. and Johnson, Jeffrey D. and Kuchinsky, Allan and Lux, Matthew and Misirli, Goksel and Peccoud, Jean and Plahar, Hector A. and Sirin, Evren and Stan, Guy-Bart, B. and Villalobos, Alan and Wipat, Anil and Gennari, John H. and Myers, Chris J. and Sauro, Herbert M.},
Date-Added = {2015-08-12 23:43:49 +0000},
Date-Modified = {2015-08-12 23:47:59 +0000},
Journal = {Nature Biotechnology},
Number = {6},
Pages = {545--550},
Publisher = {Nature Publishing Group},
Title = {The {Synthetic Biology Open Language} ({SBOL}) provides a community standard for communicating designs in synthetic biology},
Volume = {32},
Year = {2014},
Bdsk-Url-1 = {http://dx.doi.org/10.1038/nbt.2891}}
@article{hucka2003,
Author = {Hucka, Michael and Finney, Andrew and Sauro, Herbert M. and Bolouri, Hamid and Doyle, John C. and Kitano, Hiroaki and Arkin, Adam P. and Bornstein, Benjamin J. and Bray, Dennis and Cornish-Bowden, Athel and Cuellar, Autumn A. and Dronov, Sergey and Gilles, Ernst-Dieter and Ginkel, Martin and Gor, Victoria and Goryanin, Igor I. and Hedley, Warren J. and Hodgman, T. Charles and Hofmeyr, Jan-Hendrik. and Hunter, Peter J. and Juty, Nick S. and Kasberger, J. L. and Kremling, Andreas and Kummer, Ursula and Nov\`{e}re, Nicolas Le and Loew, Leslie M. and Lucio, Daniel and Mendes, Pedro and Mjolsness, Eric D. and Nakayama, Y. and Nelson, Melanie R. and Nielsen, Poul F. and Sakurada, Takeshi and Schaff, James C. and Shapiro, Bruce E. and Shimizu, Thomas S. and Spence, Hugh D. and Stelling, J\"{o}rg and Takahashi, Koichi and Tomita, Masaru and Wagner, John and Wang, J.},
Date-Added = {2015-08-12 23:43:41 +0000},
Date-Modified = {2015-08-12 23:48:14 +0000},
Journal = {Bioinformatics},
Number = {4},
Pages = {524--531},
Title = {The {Systems Biology Markup Language} ({SBML}): A Medium for Representation and Exchange of Biochemical Network Models},
Volume = {19},
Year = {2003}}
@article{le2009systems,
Author = {Le Nov\`{e}re, Nicolas and Hucka, Michael and Mi, Huaiyu and Moodie, Stuart and Schreiber, Falk and Sorokin, Anatoly and Demir, Emek and Wegner, Katja and Aladjem, Mirit I and Wimalaratne, Sarala M and others},
Date-Added = {2015-08-12 23:43:39 +0000},
Date-Modified = {2015-08-12 23:43:39 +0000},
Journal = {Nature Biotechnology},
Number = {8},
Pages = {735--741},
Publisher = {Nature Publishing Group},
Title = {The {Systems Biology Graphical Notation}},
Volume = {27},
Year = {2009}}
@Article{Bergmann2014combine,
author={Bergmann, Frank T. and Adams, Richard and Moodie, Stuart and Cooper, Jonathan and Glont, Mihai and Golebiewski, Martin and Hucka, Michael and Laibe, Camille and Miller, Andrew K. and Nickerson, David P. and Olivier, Brett G. and Rodriguez, Nicolas and Sauro, Herbert M. and Scharm, Martin and Soiland-Reyes, Stian and Waltemath, Dagmar and Yvon, Florent and Le Nov{\`e}re, Nicolas},
title={{COMBINE} archive and {OMEX} format: one file to share all information to reproduce a modeling project},
journal={BMC Bioinformatics},
year={2014},
volume={15},
number={1},
pages={369},
issn={1471-2105},
doi={10.1186/s12859-014-0369-z}
}
@article{cuellar2003overview,
Author = {Cuellar, Autumn A and Lloyd, Catherine M and Nielsen, Poul F and others},
Date-Added = {2015-08-12 23:43:09 +0000},
Date-Modified = {2015-08-12 23:47:05 +0000},
Journal = {Simulation},
Number = {12},
Pages = {740--747},
Publisher = {Sage Publications},
Title = {An overview of {CellML} 1.1, a biological model description language},
Volume = {79},
Year = {2003}}
@article{hucka2015promoting,
Author = {Hucka, Michael and Nickerson, David P and Bader, Gary D and Bergmann, Frank T and Cooper, Jonathan and Demir, Emek and Garny, Alan and Golebiewski, Martin and Myers, Chris J and Schreiber, Falk and others},
Date-Added = {2015-08-07 05:10:50 +0000},
Date-Modified = {2015-08-12 23:50:50 +0000},
Journal = {Frontiers in Bioengineering and Biotechnology},
Publisher = {Frontiers Media SA},
Title = {Promoting coordinated development of community-based information standards for modeling in biology: the {COMBINE} initiative},
Volume = {3},
Pages = {19},
Year = {2015}}