SBML (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "SBML" in English language version.

refsWebsite

Global rank English rank

21nih.gov

4^th place

15doi.org

2^nd place

8sbml.org

low place

3github.com

383^rd place

320^th place

2harvard.edu

18^th place

17^th place

1psu.edu

207^th place

136^th place

1caltech.edu

887^th place

714^th place

1groups.google.com

1,518^th place

1,072^nd place

1sun.ac.za

low place

1rfc-editor.org

6,184^th place

4,465^th place

caltech.edu

authors.library.caltech.edu

Hucka, M.; Finney, A.; Bornstein, B. J.; Keating, S. M.; Shapiro, B. E.; Matthews, J.; Kovitz, B. L.; Schilstra, M. J.; Funahashi, A.; Doyle, J. C.; Kitano, H. (2004). "Evolving a lingua franca and associated software infrastructure for computational systems biology: The Systems Biology Markup Language (SBML) project" (PDF). Systems Biology. 1 (1): 41–53. doi:10.1049/sb:20045008. PMID 17052114.

doi.org

Hucka, M.; Finney, A.; Sauro, H. M.; Bolouri, H.; Doyle, J. C.; Kitano, H.; Arkin, A. P.; Bornstein, B. J.; Bray, D; Cornish-Bowden, A.; Cuellar, A. A.; Dronov, S.; Gilles, E.D.; Ginkel, M; Gor, V.; Goryanin, I.I.; Hedley, W.J.; Hodgman, T. C.; Hofmeyr, J. -H.; Hunter, P. J.; Juty, N. S.; Kasberger, J. L.; Kremling, A.; Kummer, U.; Le Novère, N.; Loew, L. M.; Lucio, D.; Mendes, P.; Minch, E.; Mjolsness, E.D.; Nakayama, Y.; Nelson, M.R.; Nielsen, P. F.; Sakurada, T.; Schaff, J. C.; Shapiro, B.E.; Shimizu, T. S.; Spence, H. D.; Stelling, J.; Takahashi, K.; Tomita, M.; Wagner, J.; Wang, J. (2003). "The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models". Bioinformatics. 19 (4): 524–531. CiteSeerX 10.1.1.562.1085. doi:10.1093/bioinformatics/btg015. PMID 12611808.
Finney, A.; Hucka, M. (2003). "Systems biology markup language: Level 2 and beyond". Biochemical Society Transactions. 31 (6): 1472–3. doi:10.1042/BST0311472. PMID 14641091.
Hucka, M.; Finney, A.; Bornstein, B. J.; Keating, S. M.; Shapiro, B. E.; Matthews, J.; Kovitz, B. L.; Schilstra, M. J.; Funahashi, A.; Doyle, J. C.; Kitano, H. (2004). "Evolving a lingua franca and associated software infrastructure for computational systems biology: The Systems Biology Markup Language (SBML) project" (PDF). Systems Biology. 1 (1): 41–53. doi:10.1049/sb:20045008. PMID 17052114.
Kell, D. B.; Mendes, P. (2008). "The markup is the model: Reasoning about systems biology models in the Semantic Web era". Journal of Theoretical Biology. 252 (3): 538–543. Bibcode:2008JThBi.252..538K. doi:10.1016/j.jtbi.2007.10.023. PMID 18054049.
Krause, Falko; Uhlendorf, Jannis; Lubitz, Timo; Schulz, Marvin; Klipp, Edda; Liebermeister, Wolfram (2009). "Annotation and merging of SBML models with semanticSBML". Bioinformatics. 26 (3): 421–2. doi:10.1093/bioinformatics/btp642. PMID 19933161.
Alm, Rebekka; Waltemath, Dagmar; Wolfien, Markus; Wolkenhauer, Olaf; Henkel, Ron (2015). "Annotation-based feature extraction from sets of SBML models". Journal of Biomedical Semantics. 6: 20. doi:10.1186/s13326-015-0014-4. PMC 4405863. PMID 25904997.
Orth, Jeffrey D; Thiele, Ines; Palsson, Bernhard O (2010). "What is flux balance analysis?". Nature Biotechnology. 28 (3): 245–8. doi:10.1038/nbt.1614. PMC 3108565. PMID 20212490.
Oberhardt, Matthew A; Palsson, Bernhard O; Papin, Jason A (2009). "Applications of genome-scale metabolic reconstructions". Molecular Systems Biology. 5: 320. doi:10.1038/msb.2009.77. PMC 2795471. PMID 19888215.
Batt, Gregory; Ropers, Delphine; de Jong, Hidde; Geiselmann, Johannes; Mateescu, Radu; Page, Michel; Schneider, Dominique (2005). "Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli". Bioinformatics. 21: i19–28. doi:10.1093/bioinformatics/bti1048. PMID 15961457.
Helikar, Tomas; Konvalina, John; Heidel, Jack; Rogers, Jim A (2008). "Emergent decision-making in biological signal transduction networks". Proceedings of the National Academy of Sciences. 105 (6): 1913–1918. Bibcode:2008PNAS..105.1913H. doi:10.1073/pnas.0705088105. PMC 2538858. PMID 18250321.
Gauges, Ralph; Rost, Ursula; Sahle, Sven; Wegner, Katja (2006). "A model diagram layout extension for SBML". Bioinformatics. 22 (15): 1879–85. doi:10.1093/bioinformatics/btl195. PMID 16709586.
Sauro, Herbert M. (1993). "SCAMP: a general-purpose simulator and metabolic control analysis program". Bioinformatics. 9 (4): 441–450. doi:10.1093/bioinformatics/9.4.441. PMID 8402211.
Garfinkel, David (August 1968). "A machine-independent language for the simulation of complex chemical and biochemical systems". Computers and Biomedical Research. 2 (1): 31–44. doi:10.1016/0010-4809(68)90006-2. PMID 5743538.
Choi, Kiri; Medley, J. Kyle; König, Matthias; Stocking, Kaylene; Smith, Lucian; Gu, Stanley; Sauro, Herbert M. (September 2018). "Tellurium: An extensible python-based modeling environment for systems and synthetic biology". Biosystems. 171: 74–79. doi:10.1016/j.biosystems.2018.07.006. PMC 6108935. PMID 30053414.
Rodriguez, Nicolas; Pettit, Jean-Baptiste; Dalle Pezze, Piero; Li, Lu; Henry, Arnaud (2016). "The systems biology format converter". BMC Bioinformatics. 17 (1): 1–7. doi:10.1186/s12859-016-1000-2. PMC 4820913. PMID 27044654.

github.com

"sys-bio/antimony". UW Sauro Lab. 25 June 2023.
"MakeSBML website". UW Sauro Lab. 6 July 2023.
"MakeSBML website". UW Sauro Lab. 6 July 2023.

groups.google.com

bionet.metabolic-reg. "ANNOUNCEMENT: Portable Metabolic Binary Standard". Retrieved 13 December 2010.

harvard.edu

ui.adsabs.harvard.edu

Kell, D. B.; Mendes, P. (2008). "The markup is the model: Reasoning about systems biology models in the Semantic Web era". Journal of Theoretical Biology. 252 (3): 538–543. Bibcode:2008JThBi.252..538K. doi:10.1016/j.jtbi.2007.10.023. PMID 18054049.
Helikar, Tomas; Konvalina, John; Heidel, Jack; Rogers, Jim A (2008). "Emergent decision-making in biological signal transduction networks". Proceedings of the National Academy of Sciences. 105 (6): 1913–1918. Bibcode:2008PNAS..105.1913H. doi:10.1073/pnas.0705088105. PMC 2538858. PMID 18250321.

nih.gov

pubmed.ncbi.nlm.nih.gov

Hucka, M.; Finney, A.; Sauro, H. M.; Bolouri, H.; Doyle, J. C.; Kitano, H.; Arkin, A. P.; Bornstein, B. J.; Bray, D; Cornish-Bowden, A.; Cuellar, A. A.; Dronov, S.; Gilles, E.D.; Ginkel, M; Gor, V.; Goryanin, I.I.; Hedley, W.J.; Hodgman, T. C.; Hofmeyr, J. -H.; Hunter, P. J.; Juty, N. S.; Kasberger, J. L.; Kremling, A.; Kummer, U.; Le Novère, N.; Loew, L. M.; Lucio, D.; Mendes, P.; Minch, E.; Mjolsness, E.D.; Nakayama, Y.; Nelson, M.R.; Nielsen, P. F.; Sakurada, T.; Schaff, J. C.; Shapiro, B.E.; Shimizu, T. S.; Spence, H. D.; Stelling, J.; Takahashi, K.; Tomita, M.; Wagner, J.; Wang, J. (2003). "The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models". Bioinformatics. 19 (4): 524–531. CiteSeerX 10.1.1.562.1085. doi:10.1093/bioinformatics/btg015. PMID 12611808.
Finney, A.; Hucka, M. (2003). "Systems biology markup language: Level 2 and beyond". Biochemical Society Transactions. 31 (6): 1472–3. doi:10.1042/BST0311472. PMID 14641091.
Hucka, M.; Finney, A.; Bornstein, B. J.; Keating, S. M.; Shapiro, B. E.; Matthews, J.; Kovitz, B. L.; Schilstra, M. J.; Funahashi, A.; Doyle, J. C.; Kitano, H. (2004). "Evolving a lingua franca and associated software infrastructure for computational systems biology: The Systems Biology Markup Language (SBML) project" (PDF). Systems Biology. 1 (1): 41–53. doi:10.1049/sb:20045008. PMID 17052114.
Kell, D. B.; Mendes, P. (2008). "The markup is the model: Reasoning about systems biology models in the Semantic Web era". Journal of Theoretical Biology. 252 (3): 538–543. Bibcode:2008JThBi.252..538K. doi:10.1016/j.jtbi.2007.10.023. PMID 18054049.
Krause, Falko; Uhlendorf, Jannis; Lubitz, Timo; Schulz, Marvin; Klipp, Edda; Liebermeister, Wolfram (2009). "Annotation and merging of SBML models with semanticSBML". Bioinformatics. 26 (3): 421–2. doi:10.1093/bioinformatics/btp642. PMID 19933161.
Alm, Rebekka; Waltemath, Dagmar; Wolfien, Markus; Wolkenhauer, Olaf; Henkel, Ron (2015). "Annotation-based feature extraction from sets of SBML models". Journal of Biomedical Semantics. 6: 20. doi:10.1186/s13326-015-0014-4. PMC 4405863. PMID 25904997.
Orth, Jeffrey D; Thiele, Ines; Palsson, Bernhard O (2010). "What is flux balance analysis?". Nature Biotechnology. 28 (3): 245–8. doi:10.1038/nbt.1614. PMC 3108565. PMID 20212490.
Oberhardt, Matthew A; Palsson, Bernhard O; Papin, Jason A (2009). "Applications of genome-scale metabolic reconstructions". Molecular Systems Biology. 5: 320. doi:10.1038/msb.2009.77. PMC 2795471. PMID 19888215.
Batt, Gregory; Ropers, Delphine; de Jong, Hidde; Geiselmann, Johannes; Mateescu, Radu; Page, Michel; Schneider, Dominique (2005). "Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli". Bioinformatics. 21: i19–28. doi:10.1093/bioinformatics/bti1048. PMID 15961457.
Helikar, Tomas; Konvalina, John; Heidel, Jack; Rogers, Jim A (2008). "Emergent decision-making in biological signal transduction networks". Proceedings of the National Academy of Sciences. 105 (6): 1913–1918. Bibcode:2008PNAS..105.1913H. doi:10.1073/pnas.0705088105. PMC 2538858. PMID 18250321.
Gauges, Ralph; Rost, Ursula; Sahle, Sven; Wegner, Katja (2006). "A model diagram layout extension for SBML". Bioinformatics. 22 (15): 1879–85. doi:10.1093/bioinformatics/btl195. PMID 16709586.
Sauro, Herbert M. (1993). "SCAMP: a general-purpose simulator and metabolic control analysis program". Bioinformatics. 9 (4): 441–450. doi:10.1093/bioinformatics/9.4.441. PMID 8402211.
Garfinkel, David (August 1968). "A machine-independent language for the simulation of complex chemical and biochemical systems". Computers and Biomedical Research. 2 (1): 31–44. doi:10.1016/0010-4809(68)90006-2. PMID 5743538.
Choi, Kiri; Medley, J. Kyle; König, Matthias; Stocking, Kaylene; Smith, Lucian; Gu, Stanley; Sauro, Herbert M. (September 2018). "Tellurium: An extensible python-based modeling environment for systems and synthetic biology". Biosystems. 171: 74–79. doi:10.1016/j.biosystems.2018.07.006. PMC 6108935. PMID 30053414.
Rodriguez, Nicolas; Pettit, Jean-Baptiste; Dalle Pezze, Piero; Li, Lu; Henry, Arnaud (2016). "The systems biology format converter". BMC Bioinformatics. 17 (1): 1–7. doi:10.1186/s12859-016-1000-2. PMC 4820913. PMID 27044654.

ncbi.nlm.nih.gov

Alm, Rebekka; Waltemath, Dagmar; Wolfien, Markus; Wolkenhauer, Olaf; Henkel, Ron (2015). "Annotation-based feature extraction from sets of SBML models". Journal of Biomedical Semantics. 6: 20. doi:10.1186/s13326-015-0014-4. PMC 4405863. PMID 25904997.
Orth, Jeffrey D; Thiele, Ines; Palsson, Bernhard O (2010). "What is flux balance analysis?". Nature Biotechnology. 28 (3): 245–8. doi:10.1038/nbt.1614. PMC 3108565. PMID 20212490.
Oberhardt, Matthew A; Palsson, Bernhard O; Papin, Jason A (2009). "Applications of genome-scale metabolic reconstructions". Molecular Systems Biology. 5: 320. doi:10.1038/msb.2009.77. PMC 2795471. PMID 19888215.
Helikar, Tomas; Konvalina, John; Heidel, Jack; Rogers, Jim A (2008). "Emergent decision-making in biological signal transduction networks". Proceedings of the National Academy of Sciences. 105 (6): 1913–1918. Bibcode:2008PNAS..105.1913H. doi:10.1073/pnas.0705088105. PMC 2538858. PMID 18250321.
Choi, Kiri; Medley, J. Kyle; König, Matthias; Stocking, Kaylene; Smith, Lucian; Gu, Stanley; Sauro, Herbert M. (September 2018). "Tellurium: An extensible python-based modeling environment for systems and synthetic biology". Biosystems. 171: 74–79. doi:10.1016/j.biosystems.2018.07.006. PMC 6108935. PMID 30053414.
Rodriguez, Nicolas; Pettit, Jean-Baptiste; Dalle Pezze, Piero; Li, Lu; Henry, Arnaud (2016). "The systems biology format converter". BMC Bioinformatics. 17 (1): 1–7. doi:10.1186/s12859-016-1000-2. PMC 4820913. PMID 27044654.

psu.edu

citeseerx.ist.psu.edu

Hucka, M.; Finney, A.; Sauro, H. M.; Bolouri, H.; Doyle, J. C.; Kitano, H.; Arkin, A. P.; Bornstein, B. J.; Bray, D; Cornish-Bowden, A.; Cuellar, A. A.; Dronov, S.; Gilles, E.D.; Ginkel, M; Gor, V.; Goryanin, I.I.; Hedley, W.J.; Hodgman, T. C.; Hofmeyr, J. -H.; Hunter, P. J.; Juty, N. S.; Kasberger, J. L.; Kremling, A.; Kummer, U.; Le Novère, N.; Loew, L. M.; Lucio, D.; Mendes, P.; Minch, E.; Mjolsness, E.D.; Nakayama, Y.; Nelson, M.R.; Nielsen, P. F.; Sakurada, T.; Schaff, J. C.; Shapiro, B.E.; Shimizu, T. S.; Spence, H. D.; Stelling, J.; Takahashi, K.; Tomita, M.; Wagner, J.; Wang, J. (2003). "The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models". Bioinformatics. 19 (4): 524–531. CiteSeerX 10.1.1.562.1085. doi:10.1093/bioinformatics/btg015. PMID 12611808.

rfc-editor.org

Kovitz, Benjamin (June 2004). "MIME Media Type for the Systems Biology Markup Language (SBML)". IETF Request for Comments 3823. Retrieved 3 January 2010.

sbml.org

Hucka, Michael. "History of SBML". Retrieved 3 January 2010.
SBML Team. "The 1st Workshop on Software Platforms for Systems Biology". Retrieved 3 December 2010.
SBML Team. "The 2nd Workshop on Software Platforms for Systems Biology". Retrieved 13 December 2010.
SBML Team. "The 5th Workshop on Software Platforms for Systems Biology". Retrieved 3 January 2010.
SBML Team. "The 13th SBML Forum". Retrieved 3 January 2010.
Brett G. Olivier & Frank T. Bergmann. "SBML Level 3 Package: Flux Balance Constraints ('fbc')". Retrieved 24 November 2015.
SBML Team. "The 8th SBML Forum". Retrieved 3 January 2010.
Ralph Gauges; Sven Sahle; Katjia Wengler; Frank T. Bergmann & Sarah M. Keating. "SBML Level 3 Package: Rendering ('render')". Retrieved 24 November 2015.

sun.ac.za

academic.sun.ac.za

Sauro, Herbert (2001). "JARNAC: a system for interactive metabolic analysis" (PDF). Animating the Cellular Map. Proceedings of the 9th International Meeting on BioThermoKinetics: 221–228.