Zobrazeno 1 - 10
of 112
pro vyhledávání: '"Weindl, Daniel"'
Estimating parameters of dynamic models from experimental data is a challenging, and often computationally-demanding task. It requires a large number of model simulations and objective function gradient computations, if gradient-based optimization is
Externí odkaz:
http://arxiv.org/abs/2405.16524
Autor:
Schälte, Yannik, Fröhlich, Fabian, Jost, Paul J., Vanhoefer, Jakob, Pathirana, Dilan, Stapor, Paul, Lakrisenko, Polina, Wang, Dantong, Raimúndez, Elba, Merkt, Simon, Schmiester, Leonard, Städter, Philipp, Grein, Stephan, Dudkin, Erika, Doresic, Domagoj, Weindl, Daniel, Hasenauer, Jan
Mechanistic models are important tools to describe and understand biological processes. However, they typically rely on unknown parameters, the estimation of which can be challenging for large and complex systems. We present pyPESTO, a modular framew
Externí odkaz:
http://arxiv.org/abs/2305.01821
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:
Lakrisenko, Polina, Weindl, Daniel
As metabolomics datasets are becoming larger and more complex, there is an increasing need for model-based data integration and analysis to optimally leverage these data. Dynamical models of metabolism allow for the integration of heterogeneous data
Externí odkaz:
http://arxiv.org/abs/2105.10365
Autor:
Fröhlich, Fabian, Weindl, Daniel, Schälte, Yannik, Pathirana, Dilan, Paszkowski, Łukasz, Lines, Glenn Terje, Stapor, Paul, Hasenauer, Jan
Ordinary differential equation models facilitate the understanding of cellular signal transduction and other biological processes. However, for large and comprehensive models, the computational cost of simulating or calibrating can be limiting. AMICI
Externí odkaz:
http://arxiv.org/abs/2012.09122
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
Publikováno v:
PLoS ONE; 10/23/2024, Vol. 19 Issue 10, p1-19, 19p
Akademický článek
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Autor:
Terje Lines, Glenn, Paszkowski, Łukasz, Schmiester, Leonard, Weindl, Daniel, Stapor, Paul, Hasenauer, Jan
Publikováno v:
In IFAC PapersOnLine 2019 52(26):32-37
Akademický článek
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