SBML Level 3: an extensible format for the exchange and reuse of biological models

Autor: Sarah M Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, Claudine Chaouiya, Frank T Bergmann, Andrew Finney, Colin S Gillespie, Tomáš Helikar, Stefan Hoops, Rahuman S Malik‐Sheriff, Stuart L Moodie, Ion I Moraru, Chris J Myers, Aurélien Naldi, Brett G Olivier, Sven Sahle, James C Schaff, Lucian P Smith, Maciej J Swat, Denis Thieffry, Leandro Watanabe, Darren J Wilkinson, Michael L Blinov, Kimberly Begley, James R Faeder, Harold F Gómez, Thomas M Hamm, Yuichiro Inagaki, Wolfram Liebermeister, Allyson L Lister, Daniel Lucio, Eric Mjolsness, Carole J Proctor, Karthik Raman, Nicolas Rodriguez, Clifford A Shaffer, Bruce E Shapiro, Joerg Stelling, Neil Swainston, Naoki Tanimura, John Wagner, Martin Meier‐Schellersheim, Herbert M Sauro, Bernhard Palsson, Hamid Bolouri, Hiroaki Kitano, Akira Funahashi, Henning Hermjakob, John C Doyle, Michael Hucka, SBML Level 3 Community members, Richard R Adams, Nicholas A Allen, Bastian R Angermann, Marco Antoniotti, Gary D Bader, Jan Červený, Mélanie Courtot, Chris D Cox, Piero Dalle Pezze, Emek Demir, William S Denney, Harish Dharuri, Julien Dorier, Dirk Drasdo, Ali Ebrahim, Johannes Eichner, Johan Elf, Lukas Endler, Chris T Evelo, Christoph Flamm, Ronan MT Fleming, Martina Fröhlich, Mihai Glont, Emanuel Gonçalves, Martin Golebiewski, Hovakim Grabski, Alex Gutteridge, Damon Hachmeister, Leonard A Harris, Benjamin D Heavner, Ron Henkel, William S Hlavacek, Bin Hu, Daniel R Hyduke, Hidde de Jong, Nick Juty, Peter D Karp, Jonathan R Karr, Douglas B Kell, Roland Keller, Ilya Kiselev, Steffen Klamt, Edda Klipp, Christian Knüpfer, Fedor Kolpakov, Falko Krause, Martina Kutmon, Camille Laibe, Conor Lawless, Lu Li, Leslie M Loew, Rainer Machne, Yukiko Matsuoka, Pedro Mendes, Huaiyu Mi, Florian Mittag, Pedro T Monteiro, Kedar Nath Natarajan, Poul MF Nielsen, Tramy Nguyen, Alida Palmisano, Jean‐Baptiste Pettit, Thomas Pfau, Robert D Phair, Tomas Radivoyevitch, Johann M Rohwer, Oliver A Ruebenacker, Julio Saez‐Rodriguez, Martin Scharm, Henning Schmidt, Falk Schreiber, Michael Schubert, Roman Schulte, Stuart C Sealfon, Kieran Smallbone, Sylvain Soliman, Melanie I Stefan, Devin P Sullivan, Koichi Takahashi, Bas Teusink, David Tolnay, Ibrahim Vazirabad, Axel von Kamp, Ulrike Wittig, Clemens Wrzodek, Finja Wrzodek, Ioannis Xenarios, Anna Zhukova, Jeremy Zucker

Publikováno v: Molecular Systems Biology, Vol 16, Iss 8, Pp 1-21 (2020)

Abstract Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edi

Externí odkaz: https://doaj.org/article/86e517962df24b21af078b7f951f7487

PEtab-Interoperable specification of parameter estimation problems in systems biology.

Autor: Leonard Schmiester, Yannik Schälte, Frank T Bergmann, Tacio Camba, Erika Dudkin, Janine Egert, Fabian Fröhlich, Lara Fuhrmann, Adrian L Hauber, Svenja Kemmer, Polina Lakrisenko, Carolin Loos, Simon Merkt, Wolfgang Müller, Dilan Pathirana, Elba Raimúndez, Lukas Refisch, Marcus Rosenblatt, Paul L Stapor, Philipp Städter, Dantong Wang, Franz-Georg Wieland, Julio R Banga, Jens Timmer, Alejandro F Villaverde, Sven Sahle, Clemens Kreutz, Jan Hasenauer, Daniel Weindl

Publikováno v: PLoS Computational Biology, Vol 17, Iss 1, p e1008646 (2021)

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 PEtab, a

Externí odkaz: https://doaj.org/article/c3dd6d0bbd004deaba2fc5b1d5df8992

Inspecting the Solution Space of Genome-Scale Metabolic Models

Autor: Seyed Babak Loghmani, Nadine Veith, Sven Sahle, Frank T. Bergmann, Brett G. Olivier, Ursula Kummer

Publikováno v: Metabolites, Vol 12, Iss 1, p 43 (2022)

Genome-scale metabolic models are frequently used in computational biology. They offer an integrative view on the metabolic network of an organism without the need to know kinetic information in detail. However, the huge solution space which comes wi

Externí odkaz: https://doaj.org/article/76ab4049043d4d4e9231f435a2a8afa8

Calibration of high voltages at the ppm level by the difference of $$^{83{\mathrm{m}}}$$ 83m Kr conversion electron lines at the KATRIN experiment

Autor: M. Arenz, W.-J. Baek, M. Beck, A. Beglarian, J. Behrens, T. Bergmann, A. Berlev, U. Besserer, K. Blaum, T. Bode, B. Bornschein, L. Bornschein, T. Brunst, N. Buzinsky, S. Chilingaryan, W. Q. Choi, M. Deffert, P. J. Doe, O. Dragoun, G. Drexlin, S. Dyba, F. Edzards, K. Eitel, E. Ellinger, R. Engel, S. Enomoto, M. Erhard, D. Eversheim, M. Fedkevych, S. Fischer, J. A. Formaggio, F. M. Fränkle, G. B. Franklin, F. Friedel, A. Fulst, W. Gil, F. Glück, A. Gonzalez Ureña, S. Grohmann, R. Grössle, R. Gumbsheimer, M. Hackenjos, V. Hannen, F. Harms, N. Haußmann, F. Heizmann, K. Helbing, W. Herz, S. Hickford, D. Hilk, D. Hillesheimer, M. A. Howe, A. Huber, A. Jansen, J. Kellerer, N. Kernert, L. Kippenbrock, M. Kleesiek, M. Klein, A. Kopmann, M. Korzeczek, A. Kovalík, B. Krasch, M. Kraus, L. Kuckert, T. Lasserre, O. Lebeda, J. Letnev, A. Lokhov, M. Machatschek, A. Marsteller, E. L. Martin, S. Mertens, S. Mirz, B. Monreal, H. Neumann, S. Niemes, A. Off, A. Osipowicz, E. Otten, D. S. Parno, A. Pollithy, A. W. P. Poon, F. Priester, P. C.-O. Ranitzsch, O. Rest, R. G. H. Robertson, F. Roccati, C. Rodenbeck, M. Röllig, C. Röttele, M. Ryšavý, R. Sack, A. Saenz, L. Schimpf, K. Schlösser, M. Schlösser, K. Schönung, M. Schrank, H. Seitz-Moskaliuk, J. Sentkerestiová, V. Sibille, M. Slezák, M. Steidl, N. Steinbrink, M. Sturm, M. Suchopar, M. Suesser, H. H. Telle, L. A. Thorne, T. Thümmler, N. Titov, I. Tkachev, N. Trost, K. Valerius, D. Vénos, R. Vianden, A. P. Vizcaya Hernández, M. Weber, C. Weinheimer, C. Weiss, S. Welte, J. Wendel, J. F. Wilkerson, J. Wolf, S. Wüstling, S. Zadoroghny

Publikováno v: European Physical Journal C: Particles and Fields, Vol 78, Iss 5, Pp 1-7 (2018)

Abstract The neutrino mass experiment KATRIN requires a stability of 3 ppm for the retarding potential at − 18.6 kV of the main spectrometer. To monitor the stability, two custom-made ultra-precise high-voltage dividers were developed and built in

Externí odkaz: https://doaj.org/article/5b371021576b461bba6cb491a362d07d

Development of $$^{100}\hbox {Mo}$$ 100 Mo -containing scintillating bolometers for a high-sensitivity neutrinoless double-beta decay search

Autor: E. Armengaud, C. Augier, A. S. Barabash, J. W. Beeman, T. B. Bekker, F. Bellini, A. Benoît, L. Bergé, T. Bergmann, J. Billard, R. S. Boiko, A. Broniatowski, V. Brudanin, P. Camus, S. Capelli, L. Cardani, N. Casali, A. Cazes, M. Chapellier, F. Charlieux, D. M. Chernyak, M. de Combarieu, N. Coron, F. A. Danevich, I. Dafinei, M. De Jesus, L. Devoyon, S. Di Domizio, L. Dumoulin, K. Eitel, C. Enss, F. Ferroni, A. Fleischmann, N. Foerster, J. Gascon, L. Gastaldo, L. Gironi, A. Giuliani, V. D. Grigorieva, M. Gros, L. Hehn, S. Hervé, V. Humbert, N. V. Ivannikova, I. M. Ivanov, Y. Jin, A. Juillard, M. Kleifges, V. V. Kobychev, S. I. Konovalov, F. Koskas, V. Kozlov, H. Kraus, V. A. Kudryavtsev, M. Laubenstein, H. Le Sueur, M. Loidl, P. Magnier, E. P. Makarov, M. Mancuso, P. de Marcillac, S. Marnieros, C. Marrache-Kikuchi, S. Nagorny, X-F. Navick, M. O. Nikolaichuk, C. Nones, V. Novati, E. Olivieri, L. Pagnanini, P. Pari, L. Pattavina, M. Pavan, B. Paul, Y. Penichot, G. Pessina, G. Piperno, S. Pirro, O. Plantevin, D. V. Poda, E. Queguiner, T. Redon, M. Rodrigues, S. Rozov, C. Rusconi, V. Sanglard, K. Schäffner, S. Scorza, V. N. Shlegel, B. Siebenborn, O. Strazzer, D. Tcherniakhovski, C. Tomei, V. I. Tretyak, V. I. Umatov, L. Vagneron, Ya. V. Vasiliev, M. Velázquez, M. Vignati, M. Weber, E. Yakushev, A. S. Zolotarova

Publikováno v: European Physical Journal C: Particles and Fields, Vol 77, Iss 11, Pp 1-25 (2017)

Abstract This paper reports on the development of a technology involving $$^{100}\hbox {Mo}$$ 100 Mo -enriched scintillating bolometers, compatible with the goals of CUPID, a proposed next-generation bolometric experiment to search for neutrinoless d

Externí odkaz: https://doaj.org/article/b6830c9db853457fa0a0b71874a1da6e