From FAIR to CURE: Guidelines for Computational Models of Biological Systems

Authors: Sauro, Herbert M., Agmon, Eran, Blinov, Michael L., Gennari, John H., Hellerstein, Joe, Heydarabadipour, Adel, Hunter, Peter, Jardine, Bartholomew E., May, Elebeoba, Nickerson, David P., Smith, Lucian P., Bader, Gary D, Bergmann, Frank, Boyle, Patrick M., Drager, Andreas, Faeder, James R., Feng, Song, Freire, Juliana, Frohlich, Fabian, Glazier, James A., Gorochowski, Thomas E., Helikar, Tomas, Hoops, Stefan, Imoukhuede, Princess, Keating, Sarah M., Konig, Matthias, Laubenbacher, Reinhard, Loew, Leslie M., Lopez, Carlos F., Lytton, William W., McCulloch, Andrew, Mendes, Pedro, Myers, Chris J., Myers, Jerry G., Mulugeta, Lealem, Niarakis, Anna, van Niekerk, David D., Olivier, Brett G., Patrie, Alexander A., Quardokus, Ellen M., Radde, Nicole, Rohwer, Johann M., Sahle, Sven, Schaff, James C., Sego, T. J., Shin, Janis, Snoep, Jacky L., Vadigepalli, Rajanikanth, Wiley, H. Steve, Waltemath, Dagmar, Moraru, Ion

Subject Terms: Quantitative Biology - Other Quantitative Biology

Access URL: http://arxiv.org/abs/2502.15597

An Update to the SBML Human-Readable Antimony Language

Authors: Smith, Lucian, Sauro, Herbert M

Subject Terms: Quantitative Biology - Quantitative Methods, Quantitative Biology - Molecular Networks

Access URL: http://arxiv.org/abs/2405.15109

MakeSBML: A tool for converting between Antimony and SBML

Authors: Jardine, Bartholomew E., Smith, Lucian P., Sauro, Herbert M.

Subject Terms: Quantitative Biology - Molecular Networks, Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/2309.03344

Adapting Modeling and Simulation Credibility Standards to Computational Systems Biology

Authors: Tatka, Lillian T., Smith, Lucian P., Hellerstein, Joseph L., Sauro, Herbert M.

Subject Terms: Quantitative Biology - Molecular Networks

Access URL: http://arxiv.org/abs/2301.06007

MakeSBML: a tool for converting between Antimony and SBML

Authors: Jardine Bartholomew E., Smith Lucian P., Sauro Herbert M.

Source: Journal of Integrative Bioinformatics, Vol 21, Iss 1, Pp 524-31 (2024)

Subject Terms: systems biology, sbml, antimony, software, modeling, reaction networks, Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: https://doaj.org/toc/1613-4516

Access URL: https://doaj.org/article/d3755ccf88c14fee85023b9c54c5c842

BioSimulators: a central registry of simulation engines and services for recommending specific tools

Authors: Shaikh, Bilal, Smith, Lucian P., Vasilescu, Dan, Marupilla, Gnaneswara, Wilson, Michael, Agmon, Eran, Agnew, Henry, Andrews, Steven S., Anwar, Azraf, Beber, Moritz E., Bergmann, Frank T., Brooks, David, Brusch, Lutz, Calzone, Laurence, Choi, Kiri, Cooper, Joshua, Detloff, John, Drawert, Brian, Dumontier, Michel, Ermentrout, G. Bard, Faeder, James R., Freiburger, Andrew P., Fröhlich, Fabian, Funahashi, Akira, Garny, Alan, Gennari, John H., Gleeson, Padraig, Goelzer, Anne, Haiman, Zachary, Hellerstein, Joseph L., Hoops, Stefan, Ison, Jon C., Jahn, Diego, Jakubowski, Henry V., Jordan, Ryann, Kalaš, Matúš, König, Matthias, Liebermeister, Wolfram, Mandal, Synchon, McDougal, Robert, Medley, J. Kyle, Mendes, Pedro, Müller, Robert, Myers, Chris J., Naldi, Aurelien, Nguyen, Tung V. N., Nickerson, David P., Olivier, Brett G., Patoliya, Drashti, Paulevé, Loïc, Petzold, Linda R., Priya, Ankita, Rampadarath, Anand K., Rohwer, Johann M., Saglam, Ali S., Singh, Dilawar, Sinha, Ankur, Snoep, Jacky, Sorby, Hugh, Spangler, Ryan, Starruß, Jörn, Thomas, Payton J., van Niekerk, David, Weindl, Daniel, Zhang, Fengkai, Zhukova, Anna, Goldberg, Arthur P., Blinov, Michael L., Sauro, Herbert M., Moraru, Ion I., Karr, Jonathan R.

Subject Terms: Quantitative Biology - Quantitative Methods, Computer Science - Computational Engineering, Finance, and Science, Quantitative Biology - Molecular Networks

Access URL: http://arxiv.org/abs/2203.06732

libRoadRunner 2.0: A High-Performance SBML Simulation and Analysis Library

Authors: Welsh, Ciaran, Xu, Jin, Smith, Lucian, König, Matthias, Choi, Kiri, Sauro, Herbert M.

Subject Terms: Quantitative Biology - Quantitative Methods, Computer Science - Computational Engineering, Finance, and Science, Quantitative Biology - Molecular Networks, Quantitative Biology - Subcellular Processes

Access URL: http://arxiv.org/abs/2203.01175

SED-ML Validator: tool for debugging simulation experiments

Authors: Shaikh, Bilal, Freiburger, Andrew Philip, König, Matthias, Bergmann, Frank T., Nickerson, David P., Sauro, Herbert M., Blinov, Michael L., Smith, Lucian P., Moraru, Ion I., Karr, Jonathan R.

Subject Terms: Quantitative Biology - Quantitative Methods, Quantitative Biology - Cell Behavior, Quantitative Biology - Molecular Networks

Access URL: http://arxiv.org/abs/2106.00844

The simulation experiment description markup language (SED-ML): language specification for level 1 version 5

Authors: Smith Lucian P., Bergmann Frank T., Garny Alan, Helikar Tomáš, Karr Jonathan, Nickerson David, Sauro Herbert, Waltemath Dagmar, König Matthias

Source: Journal of Integrative Bioinformatics, Vol 21, Iss 1 (2024)

Subject Terms: Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: https://doaj.org/toc/1613-4516

Access URL: https://doaj.org/article/ecf0894e52704818b8ab11825f64a6c9

A Profile of Today's SBML-Compatible Software

Authors: Hucka, Michael, Bergmann, Frank T., Keating, Sarah M., Smith, Lucian P.

Source: 2011 IEEE Seventh International Conference on e-Science Workshops e-Science Workshops (eScienceW), 2011 IEEE Seventh International Conference on. :143-150 Dec, 2011

Relation: 2011 IEEE Seventh International Conference on e-Science Workshops (eScienceW)

SBML level 3 package: spatial processes, version 1, release 1

Authors: Schaff James C., Lakshminarayana Anuradha, Murphy Robert F., Bergmann Frank T., Funahashi Akira, Sullivan Devin P., Smith Lucian P.

Source: Journal of Integrative Bioinformatics, Vol 20, Iss 1 (2023)

Subject Terms: Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: https://doaj.org/toc/1613-4516

Access URL: https://doaj.org/article/f53a158868fc4ed9861524443532f67a

Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs

Authors: Hadi, Kevin, Yao, Xiaotong, Behr, Julie M., Deshpande, Aditya, Xanthopoulakis, Charalampos, Tian, Huasong, Kudman, Sarah, Rosiene, Joel, Darmofal, Madison, DeRose, Joseph, Mortensen, Rick, Adney, Emily M., Shaiber, Alon, Gajic, Zoran, Sigouros, Michael, Eng, Kenneth, Wala, Jeremiah A., Wrzeszczyński, Kazimierz O., Arora, Kanika, Shah, Minita, Emde, Anne-Katrin, Felice, Vanessa, Frank, Mayu O., Darnell, Robert B., Ghandi, Mahmoud, Huang, Franklin, Dewhurst, Sally, Maciejowski, John, de Lange, Titia, Setton, Jeremy, Riaz, Nadeem, Reis-Filho, Jorge S., Powell, Simon, Knowles, David A., Reznik, Ed, Mishra, Bud, Beroukhim, Rameen, Zody, Michael C., Robine, Nicolas, Oman, Kenji M., Sanchez, Carissa A., Kuhner, Mary K., Smith, Lucian P., Galipeau, Patricia C., Paulson, Thomas G., Reid, Brian J., Li, Xiaohong, Wilkes, David, Sboner, Andrea, Mosquera, Juan Miguel, Elemento, Olivier, Imielinski, Marcin

Source: In Cell 1 October 2020 183(1):197-210

The simulation experiment description markup language (SED-ML): language specification for level 1 version 4

Authors: Smith Lucian P., Bergmann Frank T., Garny Alan, Helikar Tomáš, Karr Jonathan, Nickerson David, Sauro Herbert, Waltemath Dagmar, König Matthias

Source: Journal of Integrative Bioinformatics, Vol 18, Iss 3 (2021)

Subject Terms: computational modeling, reproducibility, simulation experiment, Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: https://doaj.org/toc/1613-4516

Access URL: https://doaj.org/article/3e082884483b497e96fb673bde173426

Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1

Authors: Smith Lucian P., Moodie Stuart L., Bergmann Frank T., Gillespie Colin, Keating Sarah M., König Matthias, Myers Chris J., Swat Maciek J., Wilkinson Darren J., Hucka Michael

Source: Journal of Integrative Bioinformatics, Vol 17, Iss 2-3 (2020)

Subject Terms: distributions, modeling, sbml, systems biology, uncertainty, Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: https://doaj.org/toc/1613-4516

Access URL: https://doaj.org/article/f0c50c7308ce49e5a3746301c7215aed

Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2

Authors: Zhang Fengkai, Smith Lucian P., Blinov Michael L., Faeder James, Hlavacek William S., Juan Tapia Jose, Keating Sarah M., Rodriguez Nicolas, Dräger Andreas, Harris Leonard A., Finney Andrew, Hu Bin, Hucka Michael, Meier-Schellersheim Martin

Source: Journal of Integrative Bioinformatics, Vol 17, Iss 2-3 (2020)

Subject Terms: rule-based modeling, specification, standard, systems biology, Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: https://doaj.org/toc/1613-4516

Access URL: https://doaj.org/article/d421821be04f470bbb1e01bec3b7f69d

Comparing Likelihood and Bayesian Coalescent Estimation of Population Parameters.

Alternate Title: With Appendix

Authors: Kuhner, Mary K., Smith, Lucian P.

Source: Genetics; January 2007, Vol. 175 Issue 1, p155-165, 11p

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2

Authors: Hucka Michael, Bergmann Frank T., Chaouiya Claudine, Dräger Andreas, Hoops Stefan, Keating Sarah M., König Matthias, Novère Nicolas Le, Myers Chris J., Olivier Brett G., Sahle Sven, Schaff James C., Sheriff Rahuman, Smith Lucian P., Waltemath Dagmar, Wilkinson Darren J., Zhang Fengkai

Source: Journal of Integrative Bioinformatics, Vol 16, Iss 2 (2019)

Subject Terms: systems biology markup language, standards, visualization, representation, Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: https://doaj.org/toc/1613-4516

Access URL: https://doaj.org/article/e263ddd1c38f4b3d9fe553b1d0efe52a

Apoglobin Stability Is the Major Factor Governing both Cell-free and in Vivo Expression of Holomyoglobin

Authors: Samuel, Premila P., Smith, Lucian P., Phillips, George N., Jr., Olson, John S.

Source: In Journal of Biological Chemistry 25 September 2015 290(39):23479-23495

SBML Level 3 package: Groups, Version 1 Release 1

Authors: Hucka Michael, Smith Lucian P.

Source: Journal of Integrative Bioinformatics, Vol 13, Iss 3, Pp 8-29 (2016)

Subject Terms: Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: https://doaj.org/toc/1613-4516

Access URL: https://doaj.org/article/91d92dc29e3f465a8be08535b449c427

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

Authors: Hucka Michael, Bergmann Frank T., Dräger Andreas, Hoops Stefan, Keating Sarah M., Le Novère Nicolas, Myers Chris J., Olivier Brett G., Sahle Sven, Schaff James C., Smith Lucian P., Waltemath Dagmar, Wilkinson Darren J.

Source: Journal of Integrative Bioinformatics, Vol 12, Iss 2, Pp 731-901 (2015)

Subject Terms: Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: https://doaj.org/toc/1613-4516

Access URL: https://doaj.org/article/5462cdfe0e9849799b23477c1d01c93c