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2020 – today
- 2024
[j56]Bartholomew E. Jardine
, Lucian P. Smith, Herbert M. Sauro:
MakeSBML: a tool for converting between Antimony and SBML. J. Integr. Bioinform. 21(1) (2024)- [j55]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) - 2023
- [j54]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) - [j53]Jin Xu, Jessie Jiang, Herbert M. Sauro:
SBMLDiagrams: a python package to process and visualize SBML layout and render. Bioinform. 39(1) (2023) - [j52]Woosub Shin, John H. Gennari, Joseph L. Hellerstein, Herbert M. Sauro:
An automated model annotation system (AMAS) for SBML models. Bioinform. 39(10) (2023) - [j51]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) - [j50]Lillian T. Tatka, Wesley Luk, Timothy C. Elston, Joseph L. Hellerstein, Herbert M. Sauro:
Cesium: A public database of evolved oscillatory reaction networks. Biosyst. 224: 104836 (2023) - [j49]Jin Xu, Gary Geng, Nhan D. Nguyen, Carmen Perena-Cortes, Claire Samuels, Herbert M. Sauro:
SBcoyote: An extensible Python-based reaction editor and viewer. Biosyst. 232: 105001 (2023) - [j48]Frank J. Bruggeman, Maaike Remeijer, Maarten Droste, Luis Salinas, Meike T. Wortel, Robert Planqué, Herbert M. Sauro, Bas Teusink, Hans V. Westerhoff:
Whole-cell metabolic control analysis. Biosyst. 234: 105067 (2023) - [j47]T. J. Sego, James P. Sluka, Herbert M. Sauro, James A. Glazier:
Tissue Forge: Interactive biological and biophysics simulation environment. PLoS Comput. Biol. 19(10) (2023) - 2022
- [j46]Michael A Kochen, H. Steven Wiley, Song Feng, Herbert M. Sauro:
SBbadger: biochemical reaction networks with definable degree distributions. Bioinform. 38(22): 5064-5072 (2022) - [j45]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 B. 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 A. 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 Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. 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): 108-114 (2022) - [i5]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 abs/2203.01175 (2022) - [i4]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 B. 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 A. 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 Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. 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 abs/2203.06732 (2022) - 2021
- [j44]Veronica Porubsky, Lucian P. Smith, Herbert M. Sauro:
Publishing reproducible dynamic kinetic models. Briefings Bioinform. 22(3) (2021) - [j43]Ciaran M. Welsh, David P. Nickerson, Anand K. Rampadarath, Maxwell Lewis Neal, Herbert M. Sauro, John H. Gennari:
libOmexMeta: enabling semantic annotation of models to support FAIR principles. Bioinform. 37(24): 4898-4900 (2021) - [j42]Hasan Baig, Pedro Fontanarossa, Vishwesh Kulkarni, James Alastair McLaughlin, Prashant Vaidyanathan, Bryan Bartley, Shyam Bhakta, Swapnil Bhatia, Mike Bissell, Kevin Clancy, Robert Sidney Cox III, Ángel Goñi-Moreno, Thomas E. Gorochowski, Raik Grünberg, Jihwan Lee, Augustin Luna, Curtis Madsen, Goksel Misirli, Tramy Nguyen, Nicolas Le Novère, Zachary Palchick, Matthew R. Pocock, Nicholas Roehner, Herbert M. Sauro, James Scott-Brown, John T. Sexton, Guy-Bart Stan, Jeffrey J. Tabor, Logan Terry, Marta Vazquez Vilar, Christopher A. Voigt, Anil Wipat, David Zong, Zach Zundel, Jacob Beal, Chris J. Myers:
Synthetic biology open language visual (SBOL Visual) version 2.3. J. Integr. Bioinform. 18(3) (2021) - [j41]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) - 2020
- [j40]J. Kyle Medley, Joseph L. Hellerstein, Herbert M. Sauro:
libsbmljs - Enabling web-based SBML tools. Biosyst. 195: 104150 (2020) - [j39]Hasan Baig, Pedro Fontanarrosa, Vishwesh Kulkarni, James Alastair McLaughlin, Prashant Vaidyanathan, Bryan Bartley, Swapnil Bhatia, Shyam Bhakta, Michael Bissell, Kevin Clancy, Robert Sidney Cox III, Ángel Goñi-Moreno, Thomas E. Gorochowski, Raik Grünberg, Augustin Luna, Curtis Madsen, Goksel Misirli, Tramy Nguyen, Nicolas Le Novère, Zachary Palchick, Matthew R. Pocock, Nicholas Roehner, Herbert M. Sauro, James Scott-Brown, John T. Sexton, Guy-Bart Stan, Jeffrey J. Tabor, Marta Vazquez Vilar, Christopher A. Voigt, Anil Wipat, David Zong, Zach Zundel, Jacob Beal, Chris J. Myers:
Synthetic biology open language visual (SBOL visual) version 2.2. J. Integr. Bioinform. 17(2-3) (2020) - [j38]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) - [j37]Jason A. Papin, Feilim Mac Gabhann, Herbert M. Sauro, David P. Nickerson, Anand K. Rampadarath:
Improving reproducibility in computational biology research. PLoS Comput. Biol. 16(5) (2020) - [j36]J. Kyle Medley, Jonathan J. Y. Teo, Sung Sik Woo, Joseph L. Hellerstein, Rahul Sarpeshkar, Herbert M. Sauro:
A compiler for biological networks on silicon chips. PLoS Comput. Biol. 16(9) (2020)
2010 – 2019
- 2019
- [j35]Maxwell Lewis Neal, Matthias König, David P. Nickerson, Goksel Misirli, Reza Kalbasi, Andreas Dräger, Koray Atalag, Vijayalakshmi Chelliah, Michael T. Cooling, Daniel L. Cook, Sharon M. Crook, Miguel de Alba, Samuel H. Friedman, Alan Garny, John H. Gennari, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nick S. Juty, Chris J. Myers, Brett G. Olivier, Herbert M. Sauro, Martin Scharm, Jacky L. Snoep, Vasundra Touré, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath:
Harmonizing semantic annotations for computational models in biology. Briefings Bioinform. 20(2): 540-550 (2019) - [j34]Curtis Madsen, Ángel Goñi-Moreno, Umesh P, Zachary Palchick, Nicholas Roehner, Christian Atallah, Bryan Bartley, Kiri Choi, Robert Sidney Cox III, Thomas E. Gorochowski, Raik Grünberg, Chris Macklin, James Alastair McLaughlin, Xianwei Meng, Tramy Nguyen, Matthew R. Pocock, Meher Samineni, James Scott-Brown, Ysis Tarter, Michael Zhang, Zhen Zhang, Zach Zundel, Jacob Beal, Michael Bissell, Kevin Clancy, John H. Gennari, Goksel Misirli, Chris J. Myers, Ernst Oberortner, Herbert M. Sauro, Anil Wipat:
Synthetic Biology Open Language (SBOL) Version 2.3. J. Integr. Bioinform. 16(2) (2019) - [j33]Curtis Madsen, Ángel Goñi-Moreno, Zachary Palchick, Umesh P, Nicholas Roehner, Bryan Bartley, Swapnil Bhatia, Shyam Bhakta, Mike Bissell, Kevin Clancy, Robert Sidney Cox III, Thomas E. Gorochowski, Raik Grünberg, Augustin Luna, James Alastair McLaughlin, Tramy Nguyen, Nicolas Le Novère, Matthew R. Pocock, Herbert M. Sauro, James Scott-Brown, John T. Sexton, Guy-Bart Stan, Jeffrey J. Tabor, Christopher A. Voigt, Zach Zundel, Chris J. Myers, Jacob Beal, Anil Wipat:
Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1. J. Integr. Bioinform. 16(2) (2019) - [i3]Parker S. Ruth, Herbert M. Sauro:
A Commentary on the Linearity and Time-Invariance of ODE-Based Systems. CoRR abs/1912.07830 (2019) - 2018
- [j32]Yosef Bedaso, Frank T. Bergmann, Kiri Choi, Kyle Medley, Herbert M. Sauro:
A portable structural analysis library for reaction networks. Biosyst. 169-170: 20-25 (2018) - [j31]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: 74-79 (2018) - [j30]Robert Sidney Cox III, Curtis Madsen, James Alastair McLaughlin, Tramy Nguyen, Nicholas Roehner, Bryan Bartley, Jacob Beal, Michael Bissell, Kiri Choi, Kevin Clancy, Raik Grünberg, Chris Macklin, Goksel Misirli, Ernst Oberortner, Matthew R. Pocock, Meher Samineni, Michael Zhang, Zhen Zhang, Zach Zundel, John H. Gennari, Chris J. Myers, Herbert M. Sauro, Anil Wipat:
Synthetic Biology Open Language (SBOL) Version 2.2.0. J. Integr. Bioinform. 15(1) (2018) - [j29]Robert Sidney Cox III, Curtis Madsen, James Alastair McLaughlin, Tramy Nguyen, Nicholas Roehner, Bryan Bartley, Swapnil Bhatia, Mike Bissell, Kevin Clancy, Thomas E. Gorochowski, Raik Grünberg, Augustin Luna, Nicolas Le Novère, Matthew R. Pocock, Herbert M. Sauro, John T. Sexton, Guy-Bart Stan, Jeffrey J. Tabor, Christopher A. Voigt, Zach Zundel, Chris J. Myers, Jacob Beal, Anil Wipat:
Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0. J. Integr. Bioinform. 15(1) (2018) - [j28]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) - 2016
- [j27]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): 1650035:1-1650035:11 (2016) - [j26]Jacob Beal, Robert Sidney Cox III, Raik Grünberg, James Alastair McLaughlin, Tramy Nguyen, Bryan Bartley, Michael Bissell, Kiri Choi, Kevin Clancy, Chris Macklin, Curtis Madsen, Goksel Misirli, Ernst Oberortner, Matthew R. Pocock, Nicholas Roehner, Meher Samineni, Michael Zhang, Zhen Zhang, Zach Zundel, John H. Gennari, Chris J. Myers, Herbert M. Sauro, Anil Wipat:
Synthetic Biology Open Language (SBOL) Version 2.1.0. J. Integr. Bioinform. 13(3) (2016) - 2015
- [j25]Endre T. Somogyi, Jean-Marie Bouteiller, James A. Glazier, Matthias König, J. Kyle Medley, Maciej H. Swat, Herbert M. Sauro:
libRoadRunner: a high performance SBML simulation and analysis library. Bioinform. 31(20): 3315-3321 (2015) - [j24]Bryan Bartley, Jacob Beal, Kevin Clancy, Goksel Misirli, Nicholas Roehner, Ernst Oberortner, Matthew R. Pocock, Michael Bissell, Curtis Madsen, Tramy Nguyen, Zhen Zhang, John H. Gennari, Chris J. Myers, Anil Wipat, Herbert M. Sauro:
Synthetic Biology Open Language (SBOL) Version 2.0.0. J. Integr. Bioinform. 12(2) (2015) - [j23]Kyung Hyuk Kim, Kiri Choi, Bryan Bartley, Herbert M. Sauro:
Controlling E. coli Gene Expression Noise. IEEE Trans. Biomed. Circuits Syst. 9(4): 497-504 (2015) - [i2]Endre T. Somogyi, Jean-Marie Bouteiller, James A. Glazier, Matthias König, J. Kyle Medley, Maciej H. Swat, Herbert M. Sauro:
libRoadRunner: A High Performance SBML Simulation and Analysis Library. CoRR abs/1503.01095 (2015) - 2014
- [j22]Maxwell Lewis Neal, Michal Galdzicki, J. T. Gallimore, Herbert M. Sauro:
A C library for retrieving specific reactions from the BioModels database. Bioinform. 30(1): 129-130 (2014) - [j21]Lucian P. Smith, Erik Butterworth, James B. Bassingthwaighte, Herbert M. Sauro:
SBML and CellML translation in Antimony and JSim. Bioinform. 30(7): 903-907 (2014) - [j20]Frank T. Bergmann, Richard R. Adams, Stuart L. Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K. Miller, David P. Nickerson, Brett G. Olivier, Nicolas Rodriguez, Herbert M. Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère:
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Bioinform. 15: 369 (2014) - [j19]Pablo Meyer, Thomas Cokelaer, Deepak Chandran, Kyung Hyuk Kim, Po-Ru Loh, George Tucker, Mark Lipson, Bonnie Berger, Clemens Kreutz, Andreas Raue, Bernhard Steiert, Jens Timmer, Erhan Bilal, Herbert M. Sauro, Gustavo Stolovitzky, Julio Saez-Rodriguez:
Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. BMC Syst. Biol. 8: 13 (2014) - [j18]Chris J. Myers, Herbert M. Sauro, Anil Wipat:
Introduction to the Special Issue on Computational Synthetic Biology. ACM J. Emerg. Technol. Comput. Syst. 11(3): 20:1-20:5 (2014) - [j17]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) - [i1]Frank T. Bergmann, Richard Adams, Stuart L. Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K. Miller, David P. Nickerson, Brett G. Olivier, Nicolas Rodriguez, Herbert M. Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath, Florent Yvon, Nicolas Le Novère:
COMBINE archive: One File To Share Them All. CoRR abs/1407.4992 (2014) - 2012
- [j16]Kyung Hyuk Kim, Herbert M. Sauro:
Adjusting Phenotypes by Noise Control. PLoS Comput. Biol. 8(1) (2012) - [c9]Sean C. Sleight, Herbert M. Sauro:
Design and construction of a prototype CMY (Cyan-Magenta-Yellow) genetic circuit as a mutational readout device to measure evolutionary stability dynamics and determine design principles for robust synthetic systems. ALIFE 2012 - [c8]Kyung Hyuk Kim, Herbert M. Sauro:
Measuring the degree of modularity in gene regulatory networks from the relaxation of finite perturbations. CDC 2012: 5330-5335 - [c7]Natasa Miskov-Zivanov, James R. Faeder, Chris J. Myers, Herbert M. Sauro:
Modeling and design automation of biological circuits and systems. ICCAD 2012: 291-293 - 2011
- [j15]Dagmar Waltemath, Richard R. Adams, Daniel A. Beard, Frank T. Bergmann, Upinder S. Bhalla, Randall Britten, Vijayalakshmi Chelliah, Mike T. Cooling, Jonathan Cooper, Edmund J. Crampin, Alan Garny, Stefan Hoops, Michael Hucka, Peter J. Hunter, Edda Klipp, Camille Laibe, Andrew K. Miller, Ion I. Moraru, David P. Nickerson, Poul M. F. Nielsen, Macha Nikolski, Sven Sahle, Herbert M. Sauro, Henning Schmidt, Jacky L. Snoep, Dominic P. Tolle, Olaf Wolkenhauer, Nicolas Le Novère:
Minimum Information About a Simulation Experiment (MIASE). PLoS Comput. Biol. 7(4) (2011) - 2010
- [j14]Si Yuan Shen, Frank T. Bergmann, Herbert M. Sauro:
SBML2TikZ: supporting the SBML render extension in LaTeX. Bioinform. 26(21): 2794-2795 (2010)
2000 – 2009
- 2009
- [j13]Lucian P. Smith, Frank T. Bergmann, Deepak Chandran, Herbert M. Sauro:
Antimony: a modular model definition language. Bioinform. 25(18): 2452-2454 (2009) - [r1]Herbert M. Sauro:
Biological Models of Molecular Network Dynamics. Encyclopedia of Complexity and Systems Science 2009: 554-570 - 2008
- [j12]Frank T. Bergmann, Herbert M. Sauro:
Comparing simulation results of SBML capable simulators. Bioinform. 24(17): 1963-1965 (2008) - 2007
- [j11]Ravishankar Rao Vallabhajosyula, Herbert M. Sauro:
Stochastic simulation GUI for biochemical networks. Bioinform. 23(14): 1859-1861 (2007) - [j10]Vijay Chickarmane, Animesh Ray, Herbert M. Sauro, Ali Nadim:
A Model for p53 Dynamics Triggered by DNA Damage. SIAM J. Appl. Dyn. Syst. 6(1): 61-78 (2007) - 2006
- [j9]Ravishankar Rao Vallabhajosyula, Vijay Chickarmane, Herbert M. Sauro:
Conservation analysis of large biochemical networks. Bioinform. 22(3): 346-353 (2006) - [j8]Anastasia Deckard, Frank T. Bergmann, Herbert M. Sauro:
Supporting the SBML layout extension. Bioinform. 22(23): 2966-2967 (2006) - [j7]Nicolas Le Novère, Benjamin J. Bornstein, Alexander Broicher, Mélanie Courtot, Marco Donizelli, Harish Dharuri, Lu Li, Herbert M. Sauro, Maria J. Schilstra, Bruce E. Shapiro, Jacky L. Snoep, Michael Hucka:
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res. 34(Database-Issue): 689-691 (2006) - [j6]Vijay Chickarmane, Carl Troein, Ulrike A. Nuber, Herbert M. Sauro, Carsten Peterson:
Transcriptional Dynamics of the Embryonic Stem Cell Switch. PLoS Comput. Biol. 2(9) (2006) - [c6]Herbert M. Sauro:
Simulation of biochemical networks - Cellular networks as dynamic control systems. EMBC 2006: 44-50 - [c5]Herbert M. Sauro:
Innovation in software for systems biology: is there any? WSC 2006: 1586 - [c4]Frank T. Bergmann, Herbert M. Sauro:
SBW - a modular framework for systems biology. WSC 2006: 1637-1645 - [c3]Ravishankar Rao Vallabhajosyula, Herbert M. Sauro:
Complexity reduction of biochemical networks. WSC 2006: 1690-1697 - [c2]Herbert M. Sauro, David Harel, Marta Z. Kwiatkowska, Clifford A. Shaffer, Adelinde M. Uhrmacher, Michael Hucka, Pedro Mendes, Lena Strömbäck, John J. Tyson:
Challenges for modeling and simulation methods in systems biology. WSC 2006: 1720-1730 - 2005
- [j5]Cameron Wellock, Vijay Chickarmane, Herbert M. Sauro:
The SBW-CMATLAB interface. Bioinform. 21(6): 823-824 (2005) - [j4]Vijay Chickarmane, Sri R. Paladugu, Frank T. Bergmann, Herbert M. Sauro:
Bifurcation discovery tool. Bioinform. 21(18): 3688-3690 (2005) - 2003
- [j3]Michael Hucka, Andrew Finney, Herbert M. Sauro, H. Bolouri, John C. Doyle, Hiroaki Kitano, Adam P. Arkin, Benjamin J. Bornstein, Dennis Bray, Athel Cornish-Bowden, Autumn A. Cuellar, Serge Dronov, Ernst Dieter Gilles, Martin Ginkel, Victoria Gor, Igor Goryanin, W. J. Hedley, T. Charles Hodgman, Jan-Hendrik S. Hofmeyr, Peter J. Hunter, Nick S. Juty, J. L. Kasberger, Andreas Kremling, Ursula Kummer, Nicolas Le Novère, Leslie M. Loew, D. Lucio, Pedro Mendes, E. Minch, Eric Mjolsness, Yoichi Nakayama, M. R. Nelson, Poul M. F. Nielsen, T. Sakurada, James C. Schaff, Bruce E. Shapiro, Thomas Simon Shimizu, Hugh D. Spence, Jörg Stelling, Koichi Takahashi, Masaru Tomita, J. Wagner, J. Wang:
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinform. 19(4): 524-531 (2003) - 2002
- [c1]Michael Hucka, Andrew Finney, Herbert M. Sauro, H. Bolouri, John C. Doyle, Hiroaki Kitano:
The ERATO Systems Biology Workbench: Enabling Interaction and Exchange Between Software Tools for Computational Biology. Pacific Symposium on Biocomputing 2002: 450-461
1990 – 1999
- 1997
- [j2]J. H. Woods, Herbert M. Sauro:
Elasticities in Metabolic Control Analysis: algebraic derivation of simplified expressions. Comput. Appl. Biosci. 13(2): 123-130 (1997) - 1993
- [j1]Herbert M. Sauro:
SCAMP: a general-purpose simulator and metabolic control analysis program. Comput. Appl. Biosci. 9(4): 441-450 (1993)
Coauthor Index
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