| KEATING, Sarah M, Dagmar WALTEMATH, Matthias KÖNIG, Fengkai ZHANG, Andreas DRÄGER, Claudine CHAOUIYA, Frank T BERGMANN, Andrew FINNEY, Colin S GILLESPIE, Tomáš HELIKAR, Stefan HOOPS, Rahuman S Malik SHERIFF, Stuart L MOODIE, Ion I MORARU, Chris J MYERS, Aurélien NALDI, Brett G OLIVIER, Sven SAHLE, James C SCHAFF, Lucian P SMITH, Maciej J SWAT, Denis THIEFFRY, Leandro WATANABE, Darren J WILKINSON, Michael L BLINOV, Kimberly BEGLEY, James R FAEDER, Harold F GÓMEZ, Thomas M HAMM, Yuichiro INAGAKI, Wolfram LIEBERMEISTER, Allyson L LISTER, Daniel LUCIO, Eric MJOLSNESS, Carole J PROCTOR, Karthik RAMAN, Nicolas RODRIGUEZ, CLIFFORD, SHAFFER, Bruce E SHAPIRO, Joerg STELLING, Neil SWAINSTON, Naoki TANIMURA, John WAGNER, Martin Meier SCHELLERSHEIM, Herbert M SAURO, Bernhard PALSSON, Hamid BOLOURI, Hiroaki KITANO, Akira FUNAHASHI, Henning HERMJAKOB, John C DOYLE, Michael HUCKA, SBML Level Community MEMBERS, Richard R ADAMS, NICHOLAS, ALLEN, Bastian R ANGERMANN, Marco ANTONIOTTI, Gary D BADER, Jan ČERVENÝ, Mélanie COURTOT, Chris D COX, Piero Dalle PEZZE, Emek DEMIR, William S DENNEY, Harish DHARURI, Julien DORIER, Dirk DRASDO, Ali EBRAHIM, Johannes EICHNER, Johan ELF, Lukas ENDLER, Chris T EVELO, Christoph FLAMM, Ronan MT FLEMING, Martina FRÖHLICH, Mihai GLONT, Emanuel GONÇALVES, Martin GOLEBIEWSKI, Hovakim GRABSKI, Alex GUTTERIDGE, Damon HACHMEISTER, LEONARD, HARRIS, Benjamin D HEAVNER, Ron HENKEL, William S HLAVACEK, Bin HU, Daniel R HYDUKE, Hidde de JONG, Nick JUTY, Peter D KARP, Jonathan R KARR, Douglas B KELL, Roland KELLER, Ilya KISELEV, Steffen KLAMT, Edda KLIPP, Christian KNÜPFER, Fedor KOLPAKOV, Falko KRAUSE, Martina KUTMON, Camille LAIBE, Conor LAWLESS, Lu LI, Leslie M LOEW, Rainer MACHNE, Yukiko MATSUOKA, Pedro MENDES, Huaiyu MI, Florian MITTAG, Pedro T MONTEIRO, Kedar Nath NATARAJAN, Poul MF NIELSEN, Tramy NGUYEN, Alida PALMISANO, Jean Baptiste PETTIT, Thomas PFAU, Robert D PHAIR, Tomas RADIVOYEVITCH, Johann M ROHWER, OLIVER, RUEBENACKER, Julio Saez RODRIGUEZ, Martin SCHARM, Henning SCHMIDT, Falk SCHREIBER, Michael SCHUBERT, Roman SCHULTE, Stuart C SEALFON, Kieran SMALLBONE, Sylvain SOLIMAN, Melanie I STEFAN, Devin P SULLIVAN, Koichi TAKAHASHI, Bas TEUSINK, David TOLNAY, Ibrahim VAZIRABAD, Axel von KAMP, Ulrike WITTIG, Clemens WRZODEK, Finja WRZODEK, Ioannis XENARIOS, Anna ZHUKOVA and Jeremy ZUCKER. SBML Level 3: an extensible format for the exchange and reuse of biological modelsAutoři. Online. Molecular systems biology. EMBOpress, 2020, vol. 16, No 8, p. e9110. Available from: https://dx.doi.org/10.15252/msb.20199110. |
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@article{1678123,
author = {Keating, Sarah M and Waltemath, Dagmar and König, Matthias and Zhang, Fengkai and Dräger, Andreas and Chaouiya, Claudine and Bergmann, Frank T and Finney, Andrew and Gillespie, Colin S and Helikar, Tomáš and Hoops, Stefan and Sheriff, Rahuman S Malik and Moodie, Stuart L and Moraru, Ion I and Myers, Chris J and Naldi, Aurélien and Olivier, Brett G and Sahle, Sven and Schaff, James C and Smith, Lucian P and Swat, Maciej J and Thieffry, Denis and Watanabe, Leandro and Wilkinson, Darren J and Blinov, Michael L and Begley, Kimberly and Faeder, James R and Gómez, Harold F and Hamm, Thomas M and Inagaki, Yuichiro and Liebermeister, Wolfram and Lister, Allyson L and Lucio, Daniel and Mjolsness, Eric and Proctor, Carole J and Raman, Karthik and Rodriguez, Nicolas and Clifford, and Shaffer, and Shapiro, Bruce E and Stelling, Joerg and Swainston, Neil and Tanimura, Naoki and Wagner, John and Schellersheim, Martin Meier and Sauro, Herbert M and Palsson, Bernhard and Bolouri, Hamid and Kitano, Hiroaki and Funahashi, Akira and Hermjakob, Henning and Doyle, John C and Hucka, Michael and members, SBML Level Community and Adams, Richard R and Nicholas, and Allen, and Angermann, Bastian R and Antoniotti, Marco and Bader, Gary D and Červený, Jan and Courtot, Mélanie and Cox, Chris D and Pezze, Piero Dalle and Demir, Emek and Denney, William S and Dharuri, Harish and Dorier, Julien and Drasdo, Dirk and Ebrahim, Ali and Eichner, Johannes and Elf, Johan and Endler, Lukas and Evelo, Chris T and Flamm, Christoph and Fleming, Ronan MT and Fröhlich, Martina and Glont, Mihai and Gonçalves, Emanuel and Golebiewski, Martin and Grabski, Hovakim and Gutteridge, Alex and Hachmeister, Damon and Leonard, and Harris, and Heavner, Benjamin D and Henkel, Ron and Hlavacek, William S and Hu, Bin and Hyduke, Daniel R and Jong, Hidde de and Juty, Nick and Karp, Peter D and Karr, Jonathan R and Kell, Douglas B and Keller, Roland and Kiselev, Ilya and Klamt, Steffen and Klipp, Edda and Knüpfer, Christian and Kolpakov, Fedor and Krause, Falko and Kutmon, Martina and Laibe, Camille and Lawless, Conor and Li, Lu and Loew, Leslie M and Machne, Rainer and Matsuoka, Yukiko and Mendes, Pedro and Mi, Huaiyu and Mittag, Florian and Monteiro, Pedro T and Natarajan, Kedar Nath and Nielsen, Poul MF and Nguyen, Tramy and Palmisano, Alida and Pettit, Jean Baptiste and Pfau, Thomas and Phair, Robert D and Radivoyevitch, Tomas and Rohwer, Johann M and Oliver, and Ruebenacker, and Rodriguez, Julio Saez and Scharm, Martin and Schmidt, Henning and Schreiber, Falk and Schubert, Michael and Schulte, Roman and Sealfon, Stuart C and Smallbone, Kieran and Soliman, Sylvain and Stefan, Melanie I and Sullivan, Devin P and Takahashi, Koichi and Teusink, Bas and Tolnay, David and Vazirabad, Ibrahim and Kamp, Axel von and Wittig, Ulrike and Wrzodek, Clemens and Wrzodek, Finja and Xenarios, Ioannis and Zhukova, Anna and Zucker, Jeremy},
article_number = {8},
doi = {http://dx.doi.org/10.15252/msb.20199110},
keywords = {computational modeling, file format, interoperability, reproducibility, systems biology},
journal = {Molecular systems biology},
title = {SBML Level 3: an extensible format for the exchange and reuse of biological modelsAutoři},
volume = {16},
year = {2020}
}
TY - JOUR
ID - 1678123
AU - Keating, Sarah M - Waltemath, Dagmar - König, Matthias - Zhang, Fengkai - Dräger, Andreas - Chaouiya, Claudine - Bergmann, Frank T - Finney, Andrew - Gillespie, Colin S - Helikar, Tomáš - Hoops, Stefan - Sheriff, Rahuman S Malik - Moodie, Stuart L - Moraru, Ion I - Myers, Chris J - Naldi, Aurélien - Olivier, Brett G - Sahle, Sven - Schaff, James C - Smith, Lucian P - Swat, Maciej J - Thieffry, Denis - Watanabe, Leandro - Wilkinson, Darren J - Blinov, Michael L - Begley, Kimberly - Faeder, James R - Gómez, Harold F - Hamm, Thomas M - Inagaki, Yuichiro - Liebermeister, Wolfram - Lister, Allyson L - Lucio, Daniel - Mjolsness, Eric - Proctor, Carole J - Raman, Karthik - Rodriguez, Nicolas - Clifford,
AU - Shaffer,
AU - Shapiro, Bruce E - Stelling, Joerg - Swainston, Neil - Tanimura, Naoki - Wagner, John - Schellersheim, Martin Meier - Sauro, Herbert M - Palsson, Bernhard - Bolouri, Hamid - Kitano, Hiroaki - Funahashi, Akira - Hermjakob, Henning - Doyle, John C - Hucka, Michael - members, SBML Level Community - Adams, Richard R - Nicholas,
AU - Allen,
AU - Angermann, Bastian R - Antoniotti, Marco - Bader, Gary D - Červený, Jan - Courtot, Mélanie - Cox, Chris D - Pezze, Piero Dalle - Demir, Emek - Denney, William S - Dharuri, Harish - Dorier, Julien - Drasdo, Dirk - Ebrahim, Ali - Eichner, Johannes - Elf, Johan - Endler, Lukas - Evelo, Chris T - Flamm, Christoph - Fleming, Ronan MT - Fröhlich, Martina - Glont, Mihai - Gonçalves, Emanuel - Golebiewski, Martin - Grabski, Hovakim - Gutteridge, Alex - Hachmeister, Damon - Leonard,
AU - Harris,
AU - Heavner, Benjamin D - Henkel, Ron - Hlavacek, William S - Hu, Bin - Hyduke, Daniel R - Jong, Hidde de - Juty, Nick - Karp, Peter D - Karr, Jonathan R - Kell, Douglas B - Keller, Roland - Kiselev, Ilya - Klamt, Steffen - Klipp, Edda - Knüpfer, Christian - Kolpakov, Fedor - Krause, Falko - Kutmon, Martina - Laibe, Camille - Lawless, Conor - Li, Lu - Loew, Leslie M - Machne, Rainer - Matsuoka, Yukiko - Mendes, Pedro - Mi, Huaiyu - Mittag, Florian - Monteiro, Pedro T - Natarajan, Kedar Nath - Nielsen, Poul MF - Nguyen, Tramy - Palmisano, Alida - Pettit, Jean Baptiste - Pfau, Thomas - Phair, Robert D - Radivoyevitch, Tomas - Rohwer, Johann M - Oliver,
AU - Ruebenacker,
AU - Rodriguez, Julio Saez - Scharm, Martin - Schmidt, Henning - Schreiber, Falk - Schubert, Michael - Schulte, Roman - Sealfon, Stuart C - Smallbone, Kieran - Soliman, Sylvain - Stefan, Melanie I - Sullivan, Devin P - Takahashi, Koichi - Teusink, Bas - Tolnay, David - Vazirabad, Ibrahim - Kamp, Axel von - Wittig, Ulrike - Wrzodek, Clemens - Wrzodek, Finja - Xenarios, Ioannis - Zhukova, Anna - Zucker, Jeremy
PY - 2020
TI - SBML Level 3: an extensible format for the exchange and reuse of biological modelsAutoři
JF - Molecular systems biology
VL - 16
IS - 8
SP - e9110
EP - e9110
PB - EMBOpress
KW - computational modeling, file format, interoperability, reproducibility, systems biology
N2 - Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction‐based models and packages that extend the core with features suited to other model types including constraint‐based models, reaction‐diffusion models, logical network models, and rule‐based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single‐cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution.
ER -
KEATING, Sarah M, Dagmar WALTEMATH, Matthias KÖNIG, Fengkai ZHANG, Andreas DRÄGER, Claudine CHAOUIYA, Frank T BERGMANN, Andrew FINNEY, Colin S GILLESPIE, Tomáš HELIKAR, Stefan HOOPS, Rahuman S Malik SHERIFF, Stuart L MOODIE, Ion I MORARU, Chris J MYERS, Aurélien NALDI, Brett G OLIVIER, Sven SAHLE, James C SCHAFF, Lucian P SMITH, Maciej J SWAT, Denis THIEFFRY, Leandro WATANABE, Darren J WILKINSON, Michael L BLINOV, Kimberly BEGLEY, James R FAEDER, Harold F GÓMEZ, Thomas M HAMM, Yuichiro INAGAKI, Wolfram LIEBERMEISTER, Allyson L LISTER, Daniel LUCIO, Eric MJOLSNESS, Carole J PROCTOR, Karthik RAMAN, Nicolas RODRIGUEZ, CLIFFORD, SHAFFER, Bruce E SHAPIRO, Joerg STELLING, Neil SWAINSTON, Naoki TANIMURA, John WAGNER, Martin Meier SCHELLERSHEIM, Herbert M SAURO, Bernhard PALSSON, Hamid BOLOURI, Hiroaki KITANO, Akira FUNAHASHI, Henning HERMJAKOB, John C DOYLE, Michael HUCKA, SBML Level Community MEMBERS, Richard R ADAMS, NICHOLAS, ALLEN, Bastian R ANGERMANN, Marco ANTONIOTTI, Gary D BADER, Jan ČERVENÝ, Mélanie COURTOT, Chris D COX, Piero Dalle PEZZE, Emek DEMIR, William S DENNEY, Harish DHARURI, Julien DORIER, Dirk DRASDO, Ali EBRAHIM, Johannes EICHNER, Johan ELF, Lukas ENDLER, Chris T EVELO, Christoph FLAMM, Ronan MT FLEMING, Martina FRÖHLICH, Mihai GLONT, Emanuel GON$\backslash$C CALVES, Martin GOLEBIEWSKI, Hovakim GRABSKI, Alex GUTTERIDGE, Damon HACHMEISTER, LEONARD, HARRIS, Benjamin D HEAVNER, Ron HENKEL, William S HLAVACEK, Bin HU, Daniel R HYDUKE, Hidde de JONG, Nick JUTY, Peter D KARP, Jonathan R KARR, Douglas B KELL, Roland KELLER, Ilya KISELEV, Steffen KLAMT, Edda KLIPP, Christian KNÜPFER, Fedor KOLPAKOV, Falko KRAUSE, Martina KUTMON, Camille LAIBE, Conor LAWLESS, Lu LI, Leslie M LOEW, Rainer MACHNE, Yukiko MATSUOKA, Pedro MENDES, Huaiyu MI, Florian MITTAG, Pedro T MONTEIRO, Kedar Nath NATARAJAN, Poul MF NIELSEN, Tramy NGUYEN, Alida PALMISANO, Jean Baptiste PETTIT, Thomas PFAU, Robert D PHAIR, Tomas RADIVOYEVITCH, Johann M ROHWER, OLIVER, RUEBENACKER, Julio Saez RODRIGUEZ, Martin SCHARM, Henning SCHMIDT, Falk SCHREIBER, Michael SCHUBERT, Roman SCHULTE, Stuart C SEALFON, Kieran SMALLBONE, Sylvain SOLIMAN, Melanie I STEFAN, Devin P SULLIVAN, Koichi TAKAHASHI, Bas TEUSINK, David TOLNAY, Ibrahim VAZIRABAD, Axel von KAMP, Ulrike WITTIG, Clemens WRZODEK, Finja WRZODEK, Ioannis XENARIOS, Anna ZHUKOVA and Jeremy ZUCKER. SBML Level 3: an extensible format for the exchange and reuse of biological modelsAutoři. Online. \textit{Molecular systems biology}. EMBOpress, 2020, vol.~16, No~8, p.~e9110. Available from: https://dx.doi.org/10.15252/msb.20199110.
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