Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Autor: Santosh Vempala, Jennifer Modamio, Alejandro Maass, Costas D. Maranas, Sylvain Arreckx, Masoud Ahookhosh, Miguel A.P. Oliveira, Stefania Magnusdottir, Nathan E. Lewis, Chiam Yu Ng, Aarash Bordbar, Bernhard O. Palsson, Inna Kuperstein, Lemmer P. El Assal, Lin Wang, Benjamin Cousins, German Preciat, Sarah M. Keating, Egils Stalidzans, Iñigo Apaolaza, Nicolas Sompairac, William A. Bryant, Vanja Vlasov, Phan Tu Vuong, Siu Hung Joshua Chan, Andrejs Kostromins, Laurent Heirendt, Yuekai Sun, Sebastián N. Mendoza, Ronan M. T. Fleming, Francisco J. Aragón Artacho, Michael Hucka, Hulda S. Haraldsdóttir, Jacek Wachowiak, Susan Ghaderi, Marouen Ben Guebila, Almut Heinken, Ines Thiele, Hoai M. Le, Thomas Sauter, James T. Yurkovich, Alise Žagare, Diana C. El Assal, Maike K. Aurich, H. Scott Hinton, Alberto Noronha, Catherine M. Clancy, Thomas Pfau, Andrei Zinovyev, Michael A. Saunders, Luis Vitores Valcárcel, John T. Sauls, Anne Richelle, Ding Ma, Francisco J. Planes

Publikováno v: Nature Protocols
Nature Protocols, Nature Publishing Group, 2019, 14 (3), pp.639-702. ⟨10.1038/s41596-018-0098-2⟩
Nature Protocols, 14(3), 639-702. Nature Publishing Group
RUA. Repositorio Institucional de la Universidad de Alicante
Universidad de Alicante (UA)
Nature protocols, vol 14, iss 3
Heirendt, L, Arreckx, S, Pfau, T, Mendoza, S N, Richelle, A, Heinken, A, Haraldsdóttir, H S, Wachowiak, J, Keating, S M, Vlasov, V, Magnusdóttir, S, Ng, C Y, Preciat, G, Žagare, A, Chan, S H J, Aurich, M K, Clancy, C M, Modamio, J, Sauls, J T, Noronha, A, Bordbar, A, Cousins, B, El Assal, D C, Valcarcel, L V, Apaolaza, I, Ghaderi, S, Ahookhosh, M, Ben Guebila, M, Kostromins, A, Sompairac, N, Le, H M, Ma, D, Sun, Y, Wang, L, Yurkovich, J T, Oliveira, M A P, Vuong, P T, El Assal, L P, Kuperstein, I, Zinovyev, A, Hinton, H S, Bryant, W A, Aragón Artacho, F J, Planes, F J, Stalidzans, E, Maass, A, Vempala, S, Hucka, M, Saunders, M A, Maranas, C D, Lewis, N E, Sauter, T, Palsson, B, Thiele, I & Fleming, R M T 2019, ' Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0 ', Nature Protocols, vol. 14, no. 3, pp. 639-702 . https://doi.org/10.1038/s41596-018-0098-2
Heirendt, L, Arreckx, S, Pfau, T, Mendoza, S N, Richelle, A, Heinken, A, Haraldsdottir, H S, Wachowiak, J, Keating, S M, Vlasov, V, Magnusdottir, S, Ng, C Y, Preciat, G, Zagare, A, Chan, S H J, Aurich, M K, Clancy, C M, Modamio, J, Sauls, J T, Noronha, A, Bordbar, A, Cousins, B, El Assal, D C, Valcarcel, L V, Apaolaza, I, Ghaderi, S, Ahookhosh, M, Ben Guebila, M, Kostromins, A, Sompairac, N, Le, H M, Ma, D, Sun, Y, Wang, L, Yurkovich, J T, Oliveira, M A P, Vuong, P T, El Assal, L P, Kuperstein, I, Zinovyev, A, Hinton, H S, Bryant, W A, Aragon Artacho, F J, Planes, F J, Stalidzans, E, Maass, A, Vempala, S, Hucka, M, Saunders, M A, Maranas, C D, Lewis, N E, Sauter, T, Palsson, B O, Thiele, I & Fleming, R M T 2019, ' Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0 ', Nature Protocols, vol. 14, no. 3, pp. 639-702 . https://doi.org/10.1038/s41596-018-0098-2

Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental molecular systems biology data and quantitative prediction of physicochemically and biochemically feasible phenot

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b74785501fe1d16bceba71588b87c863
https://hal.archives-ouvertes.fr/hal-03211136

Two stage optimization of biochemical pathways using parallel runs of global stochastic optimization methods

Autor: Egils Stalidzans, Andrejs Kostromins, Jurijs Sulins

Publikováno v: 2012 IEEE 13th International Symposium on Computational Intelligence and Informatics (CINTI).

A disadvantage of global stochastic optimization methods is the stochastic convergence of the best value of the objective function to the global optimum. In spite those methods are widely used optimizing kinetic models of biochemical pathways. Moreov

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::a7c203e21674ed9ccb703393c929e457
https://doi.org/10.1109/cinti.2012.6496792

ConvAn: a convergence analyzing tool for optimization of biochemical networks

Autor: Andrejs Kostromins, Egils Stalidzans, Ivars Mozga

Publikováno v: Bio Systems. 108(1-3)

Dynamic models of biochemical networks usually are described as a system of nonlinear differential equations. In case of optimization of models for purpose of parameter estimation or design of new properties mainly numerical methods are used. That ca

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f915a672f50fac6b7ee969472c619cdb
https://pubmed.ncbi.nlm.nih.gov/22212352