A Regularized Factorization-Free Method for Equality-Constrained Optimization

Autor: Dominique Orban, Sylvain Arreckx

Publikováno v: SIAM Journal on Optimization. 28:1613-1639

We propose a method for equality-constrained optimization based on a problem in which all constraints are systematically regularized. The regularization is equivalent to applying an augmented Lagra...

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::6ee8ef8a5974ee244aaba68353da0834
https://doi.org/10.1137/16m1088570

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

COBREXA.jl: constraint-based reconstruction and exascale analysis

Autor: Christophe Trefois, Taneli Pusa, Venkata P. Satagopam, Wei Gu, Oliver Ebenhöh, St. Elmo Wilken, Reinhard Schneider, Alberto Noronha, Laurent Heirendt, Miroslav Kratochvíl, Marvin van Aalst, Sylvain Arreckx

Publikováno v: Bioinformatics

Summary COBREXA.jl is a Julia package for scalable, high-performance constraint-based reconstruction and analysis of very large-scale biological models. Its primary purpose is to facilitate the integration of modern high performance computing environ

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::04def7eb8ff773cfe95e2dfa74a719cc