Zobrazeno 1 - 10
of 164
pro vyhledávání: '"Bergmann, Frank T."'
BioSimulators: a central registry of simulation engines and services for recommending specific tools
Autor:
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.
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various subsystems
Externí odkaz:
http://arxiv.org/abs/2203.06732
Autor:
Smith Lucian P., Bergmann Frank T., Garny Alan, Helikar Tomáš, Karr Jonathan, Nickerson David, Sauro Herbert, Waltemath Dagmar, König Matthias
Publikováno v:
Journal of Integrative Bioinformatics, Vol 21, Iss 1 (2024)
Modern biological research is increasingly informed by computational simulation experiments, which necessitate the development of methods for annotating, archiving, sharing, and reproducing the conducted experiments. These simulations increasingly re
Externí odkaz:
https://doaj.org/article/ecf0894e52704818b8ab11825f64a6c9
Autor:
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.
Summary: More sophisticated models are needed to address problems in bioscience, synthetic biology, and precision medicine. To help facilitate the collaboration needed for such models, the community developed the Simulation Experiment Description Mar
Externí odkaz:
http://arxiv.org/abs/2106.00844
Autor:
Schmiester, Leonard, Schälte, Yannik, Bergmann, Frank T., Camba, Tacio, Dudkin, Erika, Egert, Janine, Fröhlich, Fabian, Fuhrmann, Lara, Hauber, Adrian L., Kemmer, Svenja, Lakrisenko, Polina, Loos, Carolin, Merkt, Simon, Müller, Wolfgang, Pathirana, Dilan, Raimúndez, Elba, Refisch, Lukas, Rosenblatt, Marcus, Stapor, Paul L., Städter, Philipp, Wang, Dantong, Wieland, Franz-Georg, Banga, Julio R., Timmer, Jens, Villaverde, Alejandro F., Sahle, Sven, Kreutz, Clemens, Hasenauer, Jan, Weindl, Daniel
Reproducibility and reusability of the results of data-based modeling studies are essential. Yet, there has been -- so far -- no broadly supported format for the specification of parameter estimation problems in systems biology. Here, we introduce PE
Externí odkaz:
http://arxiv.org/abs/2004.01154
Autor:
Bendig, Tamara, Ulmer, Andreas, Luzia, Laura, Müller, Susanne, Sahle, Sven, Bergmann, Frank T., Lösch, Maren, Erdemann, Florian, Zeidan, Ahmad A., Mendoza, Sebastian N., Teusink, Bas, Takors, Ralf, Kummer, Ursula, Figueiredo, Ana Sofia
Publikováno v:
In Journal of Biotechnology 10 September 2023 374:90-100
Autor:
Schaff James C., Lakshminarayana Anuradha, Murphy Robert F., Bergmann Frank T., Funahashi Akira, Sullivan Devin P., Smith Lucian P.
Publikováno v:
Journal of Integrative Bioinformatics, Vol 20, Iss 1 (2023)
While many biological processes can be modeled by abstracting away the space in which those processes occur, some modeling (particularly at the cellular level) requires space itself to be modeled, with processes happening not in well-mixed compartmen
Externí odkaz:
https://doaj.org/article/f53a158868fc4ed9861524443532f67a
Ordinary differential equations (ODE) are widely used for modeling in Systems Biology. As most commonly only some of the kinetic parameters are measurable or precisely known, parameter estimation techniques are applied to parametrize the model to exp
Externí odkaz:
http://arxiv.org/abs/1601.04458
Autor:
Bergmann, Frank T., Adams, Richard, Moodie, Stuart, Cooper, Jonathan, Glont, Mihai, Golebiewski, Martin, Hucka, Michael, Laibe, Camille, Miller, Andrew K., Nickerson, David P., Olivier, Brett G., Rodriguez, Nicolas, Sauro, Herbert M., Scharm, Martin, Soiland-Reyes, Stian, Waltemath, Dagmar, Yvon, Florent, Novère, Nicolas Le
Publikováno v:
BMC Bioinformatics 15 (2014) 369
Background: With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been p
Externí odkaz:
http://arxiv.org/abs/1407.4992
Autor:
Smith Lucian P., Bergmann Frank T., Garny Alan, Helikar Tomáš, Karr Jonathan, Nickerson David, Sauro Herbert, Waltemath Dagmar, König Matthias
Publikováno v:
Journal of Integrative Bioinformatics, Vol 18, Iss 3 (2021)
Computational simulation experiments increasingly inform modern biological research, and bring with them the need to provide ways to annotate, archive, share and reproduce the experiments performed. These simulations increasingly require extensive co
Externí odkaz:
https://doaj.org/article/3e082884483b497e96fb673bde173426
Autor:
Aguilera, Luis, Bergmann, Frank T., Dalmasso, Giovanni, Elmas, Sinan, Elsässer, Tobias, Großeholz, Ruth, Holzheu, Pascal, Kalra, Priyata, Kummer, Ursula, Sahle, Sven, Veith, Nadine
Publikováno v:
In Biophysical Chemistry February 2019 245:17-24