Zobrazeno 1 - 10
of 207
pro vyhledávání: '"Karr Jonathan"'
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:
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
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:
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:
Chew, Yin Hoon, Karr, Jonathan R.
Despite substantial potential to transform bioscience, medicine, and bioengineering, whole-cell models remain elusive. One of the biggest challenges to whole-cell models is assembling the large and diverse array of data needed to model an entire cell
Externí odkaz:
http://arxiv.org/abs/2105.10627
Autor:
Blinov, Michael L., Gennari, John H., Karr, Jonathan R., Moraru, Ion I., Nickerson, David P., Sauro, Herbert M.
Although reproducibility is a core tenet of the scientific method, it remains challenging to reproduce many results. Surprisingly, this also holds true for computational results in domains such as systems biology where there have been extensive stand
Externí odkaz:
http://arxiv.org/abs/2104.04604
Autor:
Ferrie, John J., Karr, Jonathan P., Graham, Thomas G.W., Dailey, Gina M., Zhang, Gloria, Tjian, Robert, Darzacq, Xavier
Publikováno v:
In Molecular Cell 18 January 2024 84(2):234-243
Autor:
Marucci, Lucia, Barberis, Matteo, Karr, Jonathan, Ray, Oliver, Race, Paul R., Andrade, Miguel de Souza, Grierson, Claire, Hoffmann, Stefan Andreas, Landon, Sophie, Rech, Elibio, Rees-Garbutt, Joshua, Seabrook, Richard, Shaw, William, Woods, Christopher
Computer-aided design for synthetic biology promises to accelerate the rational and robust engineering of biological systems; it requires both detailed and quantitative mathematical and experimental models of the processes to (re)design, and software
Externí odkaz:
http://arxiv.org/abs/2006.02720
Comprehensive simulations of the entire biochemistry of cells have great potential to help physicians treat disease and help engineers design biological machines. But such simulations must model networks of millions of molecular species and reactions
Externí odkaz:
http://arxiv.org/abs/2005.05295
Autor:
Karr, Jonathan R., Liebermeister, Wolfram, Goldberg, Arthur P., Sekar, John A. P., Shaikh, Bilal
A central challenge in science is to understand how systems behaviors emerge from complex networks. This often requires aggregating, reusing, and integrating heterogeneous information. Supplementary spreadsheets to articles are a key data source. Spr
Externí odkaz:
http://arxiv.org/abs/2005.05227