DEMETER: Efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations

1 code implementation • 11 Jun 2021 • Almut Heinken, Stefanía Magnúsdóttir, Ronan M. T. Fleming, Ines Thiele

Motivation: Manual curation of genome-scale reconstructions is laborious, yet existing automated curation tools typically do not take species-specific experimental data and manually refined genome annotations into account.

ARTENOLIS: Automated Reproducibility and Testing Environment for Licensed Software

2 code implementations • 1 Dec 2017 • Laurent Heirendt, Sylvain Arreckx, Christophe Trefois, Yohan Yarosz, Maharshi Vyas, Venkata P. Satagopam, Reinhard Schneider, Ines Thiele, Ronan M. T. Fleming

The COnstraint-Based Reconstruction and Analysis (COBRA) Toolbox is a suite of open-source code for computational modelling with dependencies on licensed software.

Software Engineering

Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0

2 code implementations • 11 Oct 2017 • Laurent Heirendt, Sylvain Arreckx, Thomas Pfau, Sebastián N. Mendoza, Anne Richelle, Almut Heinken, Hulda S. Haraldsdóttir, Jacek Wachowiak, Sarah M. Keating, Vanja Vlasov, Stefania Magnusdóttir, Chiam Yu Ng, German Preciat, Alise Žagare, Siu H. J. Chan, Maike K. Aurich, Catherine M. Clancy, Jennifer Modamio, John T. Sauls, Alberto Noronha, Aarash Bordbar, Benjamin Cousins, Diana C. El Assal, Luis V. Valcarcel, Iñigo Apaolaza, Susan Ghaderi, Masoud Ahookhosh, Marouen Ben Guebila, Andrejs Kostromins, Nicolas Sompairac, Hoai M. Le, Ding Ma, Yuekai Sun, Lin Wang, James T. Yurkovich, Miguel A. P. Oliveira, Phan T. Vuong, Lemmer P. El Assal, Inna Kuperstein, Andrei Zinovyev, H. Scott Hinton, William A. Bryant, Francisco J. Aragón Artacho, Francisco J. Planes, Egils Stalidzans, Alejandro Maass, Santosh Vempala, Michael Hucka, Michael A. Saunders, Costas D. Maranas, Nathan E. Lewis, Thomas Sauter, Bernhard Ø. Palsson, Ines Thiele, Ronan M. T. Fleming

This protocol can be adapted for the generation and analysis of a constraint-based model in a wide variety of molecular systems biology scenarios.

Experimental Design