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6 results on '"Karr, Jonathan R."'

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

Author

Shaikh, Bilal, 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, Hasenauer, Jan, Hellerstein, Joseph L, Hermjakob, Henning, Hoops, Stefan, Ison, Jon C, Jahn, Diego, Jakubowski, Henry V, Jordan, Ryann, Kalaš, Matúš, König, Matthias, Liebermeister, Wolfram, Sheriff, Rahuman S Malik, Mandal, Synchon, McDougal, Robert, Medley, J Kyle, Mendes, Pedro, Müller, Robert, Myers, Chris J, Naldi, Aurelien, Nguyen, Tung VN, 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, Schaff, James C, Blinov, Michael L, Sauro, Herbert M, Moraru, Ion I, Karr, Jonathan R, Shaikh, Bilal, 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, Hasenauer, Jan, Hellerstein, Joseph L, Hermjakob, Henning, Hoops, Stefan, Ison, Jon C, Jahn, Diego, Jakubowski, Henry V, Jordan, Ryann, Kalaš, Matúš, König, Matthias, Liebermeister, Wolfram, Sheriff, Rahuman S Malik, Mandal, Synchon, McDougal, Robert, Medley, J Kyle, Mendes, Pedro, Müller, Robert, Myers, Chris J, Naldi, Aurelien, Nguyen, Tung VN, 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, Schaff, James C, Blinov, Michael L, Sauro, Herbert M, Moraru, Ion I, and Karr, Jonathan R

Abstract

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 and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators.org), a central registry of the capabilities of simulation tools and consistent Python, command-line and containerized interfaces to each version of each tool. The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML and the COMBINE archive format, and validation tools for simulation projects and simulation tools that ensure these standards are used consistently. To help modelers find tools for particular projects, we have also used the registry to develop recommendation services. We anticipate that BioSimulators will help modelers exchange, reproduce, and combine simulations.

Published
2022

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

Author

Shaikh, Bilal, 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, Hasenauer, Jan, Hellerstein, Joseph L, Hermjakob, Henning, Hoops, Stefan, Ison, Jon C, Jahn, Diego, Jakubowski, Henry V, Jordan, Ryann, Kalaš, Matúš, König, Matthias, Liebermeister, Wolfram, Sheriff, Rahuman S Malik, Mandal, Synchon, McDougal, Robert, Medley, J Kyle, Mendes, Pedro, Müller, Robert, Myers, Chris J, Naldi, Aurelien, Nguyen, Tung VN, 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, Schaff, James C, Blinov, Michael L, Sauro, Herbert M, Moraru, Ion I, Karr, Jonathan R, Shaikh, Bilal, 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, Hasenauer, Jan, Hellerstein, Joseph L, Hermjakob, Henning, Hoops, Stefan, Ison, Jon C, Jahn, Diego, Jakubowski, Henry V, Jordan, Ryann, Kalaš, Matúš, König, Matthias, Liebermeister, Wolfram, Sheriff, Rahuman S Malik, Mandal, Synchon, McDougal, Robert, Medley, J Kyle, Mendes, Pedro, Müller, Robert, Myers, Chris J, Naldi, Aurelien, Nguyen, Tung VN, 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, Schaff, James C, Blinov, Michael L, Sauro, Herbert M, Moraru, Ion I, and Karr, Jonathan R

Abstract

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 and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators.org), a central registry of the capabilities of simulation tools and consistent Python, command-line and containerized interfaces to each version of each tool. The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML and the COMBINE archive format, and validation tools for simulation projects and simulation tools that ensure these standards are used consistently. To help modelers find tools for particular projects, we have also used the registry to develop recommendation services. We anticipate that BioSimulators will help modelers exchange, reproduce, and combine simulations.

Published
2022

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

Author

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., 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., and Karr, Jonathan R.

Abstract

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 and scales remain siloed by different software tools. For example, each tool must be executed through a distinct interface. To help investigators find and use simulation tools, we developed BioSimulators (https://biosimulators.org), a central registry of the capabilities of simulation tools and consistent Python, command-line, and containerized interfaces to each version of each tool. The foundation of BioSimulators is standards, such as CellML, SBML, SED-ML, and the COMBINE archive format, and validation tools for simulation projects and simulation tools that ensure these standards are used consistently. To help modelers find tools for particular projects, we have also used the registry to develop recommendation services. We anticipate that BioSimulators will help modelers exchange, reproduce, and combine simulations., Comment: 6 pages, 2 figures

Published
2022

4. ObjTables: structured spreadsheets that promote data quality, reuse, and integration

Author

Karr, Jonathan R., Liebermeister, Wolfram, Goldberg, Arthur P., Sekar, John A. P., Shaikh, Bilal, Karr, Jonathan R., Liebermeister, Wolfram, Goldberg, Arthur P., Sekar, John A. P., and Shaikh, Bilal

Abstract

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. Spreadsheets are popular because they are easy to read and write. However, spreadsheets are often difficult to reanalyze because they capture data ad hoc without schemas that define the objects, relationships, and attributes that they represent. To help researchers reuse and compose spreadsheets, we developed ObjTables, a toolkit that makes spreadsheets human- and machine-readable by combining spreadsheets with schemas and an object-relational mapping system. ObjTables includes a format for schemas; markup for indicating the class and attribute represented by each spreadsheet and column; numerous data types for scientific information; and high-level software for using schemas to read, write, validate, compare, merge, revision, and analyze spreadsheets. By making spreadsheets easier to reuse, ObjTables could enable unprecedented secondary meta-analyses. By making it easy to build new formats and associated software for new types of data, ObjTables can also accelerate emerging scientific fields., Comment: 5 pages, 1 figures, 18 pages of supplementary information, 3 supplementary datasets

Published
2020

5. Exact Parallelization of the Stochastic Simulation Algorithm for Scalable Simulation of Large Biochemical Networks

Author

Goldberg, Arthur P., Jefferson, David R., Sekar, John A. P., Karr, Jonathan R., Goldberg, Arthur P., Jefferson, David R., Sekar, John A. P., and Karr, Jonathan R.

Abstract

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. The Stochastic Simulation Algorithm (SSA) is widely used for simulating biochemistry, especially systems with species populations small enough that discreteness and stochasticity play important roles. However, existing serial SSA methods are prohibitively slow for comprehensive networks, and existing parallel SSA methods, which use periodic synchronization, sacrifice accuracy. To enable fast, accurate, and scalable simulations of biochemistry, we present an exact parallel algorithm for SSA that partitions a biochemical network into many SSA processes that simulate in parallel. Our parallel SSA algorithm exactly coordinates the interactions among these SSA processes and the species state they share by structuring the algorithm as a parallel discrete event simulation (DES) application and using an optimistic parallel DES simulator to synchronize the interactions. We anticipate that our method will enable unprecedented biochemical simulations., Comment: 21 pages, 4 figures; 2020-05-20 submission: updated authors, affiliations, emails, acknowledgments and layout

Published
2020

6. Towards a whole-cell modeling approach for synthetic biology

Author

Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology. Research Laboratory of Electronics, Purcell, Oliver, Jain, Bonny, Lu, Timothy K., Karr, Jonathan R., Covert, Markus W., Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology. Research Laboratory of Electronics, Purcell, Oliver, Jain, Bonny, Lu, Timothy K., Karr, Jonathan R., and Covert, Markus W.

Abstract

Despite rapid advances over the last decade, synthetic biology lacks the predictive tools needed to enable rational design. Unlike established engineering disciplines, the engineering of synthetic gene circuits still relies heavily on experimental trial-and-error, a time-consuming and inefficient process that slows down the biological design cycle. This reliance on experimental tuning is because current modeling approaches are unable to make reliable predictions about the in vivo behavior of synthetic circuits. A major reason for this lack of predictability is that current models view circuits in isolation, ignoring the vast number of complex cellular processes that impinge on the dynamics of the synthetic circuit and vice versa. To address this problem, we present a modeling approach for the design of synthetic circuits in the context of cellular networks. Using the recently published whole-cell model of Mycoplasma genitalium, we examined the effect of adding genes into the host genome. We also investigated how codon usage correlates with gene expression and find agreement with existing experimental results. Finally, we successfully implemented a synthetic Goodwin oscillator in the whole-cell model. We provide an updated software framework for the whole-cell model that lays the foundation for the integration of whole-cell models with synthetic gene circuit models. This software framework is made freely available to the community to enable future extensions. We envision that this approach will be critical to transforming the field of synthetic biology into a rational and predictive engineering discipline., Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science (Advanced Undergraduate Research Program), United States. Defense Advanced Research Projects Agency, National Institutes of Health (U.S.) (New Innovator Award 1DP2OD008435), National Science Foundation (U.S.) (1124247)

Published
2016

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