Lucian P. Smith

Publication Activity (10 Years)

Years Active: 2009-2024
Publications (10 Years): 23

Top Topics

High Throughput

Systems Biology

Markup Language

Top Venues

J. Integr. Bioinform.

PLoS Comput. Biol.

Publications

Bartholomew E. Jardine, Lucian P. Smith, Herbert M. Sauro
MakeSBML: a tool for converting between Antimony and SBML. J. Integr. Bioinform. 21 (1) (2024)
Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomás Helikar, Jonathan R. Karr, David P. Nickerson, Herbert M. Sauro, Dagmar Waltemath, Matthias König
The simulation experiment description markup language (SED-ML): language specification for level 1 version 5. J. Integr. Bioinform. 21 (1) (2024)
James C. Schaff, Anuradha Lakshminarayana, Robert F. Murphy, Frank T. Bergmann, Akira Funahashi, Devin P. Sullivan, Lucian P. Smith
SBML level 3 package: spatial processes, version 1, release 1. J. Integr. Bioinform. 20 (1) (2023)
Ciaran M. Welsh, Jin Xu, Lucian P. Smith, Matthias König, Kiri Choi, Herbert M. Sauro
libRoadRunner 2.0: a high performance SBML simulation and analysis library. Bioinform. 39 (1) (2023)
Steve Ma, Longxuan Fan, Sai Anish Konanki, Eva Liu, John H. Gennari, Lucian P. Smith, Joseph L. Hellerstein, Herbert M. Sauro
VSCode-Antimony: a source editor for building, analyzing, and translating antimony models. Bioinform. 39 (12) (2023)
Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali S. Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr
BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. 50 (W1) (2022)
Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary Haiman, Joseph L. Hellerstein, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Synchon Mandal, Robert McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali S. Saglam, Dilawar Singh, Ankur Sinha, Jacky Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr
BioSimulators: a central registry of simulation engines and services for recommending specific tools. CoRR (2022)
Ciaran M. Welsh, Jin Xu, Lucian P. Smith, Matthias König, Kiri Choi, Herbert M. Sauro
libRoadRunner 2.0: A High-Performance SBML Simulation and Analysis Library. CoRR (2022)
Lucian P. Smith, Frank T. Bergmann, Alan Garny, Tomás Helikar, Jonathan R. Karr, David P. Nickerson, Herbert M. Sauro, Dagmar Waltemath, Matthias König
The simulation experiment description markup language (SED-ML): language specification for level 1 version 4. J. Integr. Bioinform. 18 (3) (2021)
Veronica Porubsky, Lucian P. Smith, Herbert M. Sauro
Publishing reproducible dynamic kinetic models. Briefings Bioinform. 22 (3) (2021)
Dagmar Waltemath, Martin Golebiewski, Michael L. Blinov, Padraig Gleeson, Henning Hermjakob, Michael Hucka, Esther Thea Inau, Sarah M. Keating, Matthias König, Olga Krebs, Rahuman S. Malik-Sheriff, David P. Nickerson, Ernst Oberortner, Herbert M. Sauro, Falk Schreiber, Lucian P. Smith, Melanie I. Stefan, Ulrike Wittig, Chris J. Myers
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). J. Integr. Bioinform. 17 (2-3) (2020)
Lucian P. Smith, Stuart L. Moodie, Frank T. Bergmann, Colin S. Gillespie, Sarah M. Keating, Matthias König, Chris J. Myers, Maciek J. Swat, Darren J. Wilkinson, Michael Hucka
Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1. J. Integr. Bioinform. 17 (2-3) (2020)
Fengkai Zhang, Lucian P. Smith, Michael L. Blinov, James R. Faeder, William S. Hlavacek, José Juan Tapia, Sarah M. Keating, Nicolas Rodriguez, Andreas Dräger, Leonard A. Harris, Andrew Finney, Bin Hu, Michael Hucka, Martin Meier-Schellersheim
Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2. J. Integr. Bioinform. 17 (2-3) (2020)
Michael Hucka, Frank T. Bergmann, Claudine Chaouiya, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Matthias König, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Rahuman S. Malik-Sheriff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson, Fengkai Zhang
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. J. Integr. Bioinform. 16 (2) (2019)
Lucian P. Smith, Jon A Yamato, Mary K. Kuhner
CNValidator: validating somatic copy-number inference. Bioinform. 35 (15) (2019)
Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. J. Integr. Bioinform. 15 (1) (2018)
Kiri Choi, J. Kyle Medley, Matthias König, Kaylene Stocking, Lucian P. Smith, Stanley Gu, Herbert M. Sauro
Tellurium: An extensible python-based modeling environment for systems and synthetic biology. Biosyst. 171 (2018)
Frank T. Bergmann, Jonathan Cooper, Matthias König, Ion I. Moraru, David P. Nickerson, Nicolas Le Novère, Brett G. Olivier, Sven Sahle, Lucian P. Smith, Dagmar Waltemath
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3). J. Integr. Bioinform. 15 (1) (2018)
Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. J. Integr. Bioinform. 15 (1) (2018)
J. Kyle Medley, Kiri Choi, Matthias König, Lucian P. Smith, Stanley Gu, Joseph L. Hellerstein, Stuart C. Sealfon, Herbert M. Sauro
Tellurium notebooks - An environment for reproducible dynamical modeling in systems biology. PLoS Comput. Biol. 14 (6) (2018)
Michael Hucka, Lucian P. Smith
SBML Level 3 package: Groups, Version 1 Release 1. J. Integr. Bioinform. 13 (3) (2016)
Kiri Choi, Lucian P. Smith, J. Kyle Medley, Herbert M. Sauro
phraSED-ML: A paraphrased, human-readable adaptation of SED-ML. J. Bioinform. Comput. Biol. 14 (6) (2016)
Lucian P. Smith, Maciej J. Swat, Jacob Barhak
Sharing formats for disease models. SummerSim (2016)
Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson
Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. J. Integr. Bioinform. 12 (2) (2015)
Michael Hucka, Frank T. Bergmann, Stefan Hoops, Sarah M. Keating, Sven Sahle, James C. Schaff, Lucian P. Smith, Darren J. Wilkinson
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. J. Integr. Bioinform. 12 (2) (2015)
Maxwell Lewis Neal, Michael T. Cooling, Lucian P. Smith, Christopher T. Thompson, Herbert M. Sauro, Brian E. Carlson, Daniel L. Cook, John H. Gennari
A Reappraisal of How to Build Modular, Reusable Models of Biological Systems. PLoS Comput. Biol. 10 (10) (2014)
Lucian P. Smith, Erik Butterworth, James B. Bassingthwaighte, Herbert M. Sauro
SBML and CellML translation in Antimony and JSim. Bioinform. 30 (7) (2014)
Michael Hucka, Frank T. Bergmann, Sarah M. Keating, Lucian P. Smith
A Profile of Today's SBML-Compatible Software. e-Science Workshops (2011)
Lucian P. Smith, Frank T. Bergmann, Deepak Chandran, Herbert M. Sauro
Antimony: a modular model definition language. Bioinform. 25 (18) (2009)