John T Sauls1, Joerg M Buescher. 1. BRAIN Aktiengesellschaft, Microbial Production Technologies, Platform for Quantitative Biology and Sequencing, D-64673 Zwingenberg, Germany.
Abstract
MOTIVATION: Genome-scale reconstructions and models, as collections of genomic and metabolic information, provide a useful means to compare organisms. Comparison requires that models are similarly notated to pair shared components. RESULT: Matching and comparison of genome-scale reconstructions and models are facilitated by modelBorgifier. It reconciles models in light of different annotation schemes, allowing diverse models to become useful for synchronous investigation. AVAILABILITY AND IMPLEMENTATION: The modelBorgifier toolbox is freely available at http://www.brain-biotech.de/downloads/modelBorgifier.zip.
MOTIVATION: Genome-scale reconstructions and models, as collections of genomic and metabolic information, provide a useful means to compare organisms. Comparison requires that models are similarly notated to pair shared components. RESULT: Matching and comparison of genome-scale reconstructions and models are facilitated by modelBorgifier. It reconciles models in light of different annotation schemes, allowing diverse models to become useful for synchronous investigation. AVAILABILITY AND IMPLEMENTATION: The modelBorgifier toolbox is freely available at http://www.brain-biotech.de/downloads/modelBorgifier.zip.
Authors: 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 Journal: Nat Protoc Date: 2019-03 Impact factor: 13.491
Authors: Jennifer Levering; Jared Broddrick; Christopher L Dupont; Graham Peers; Karen Beeri; Joshua Mayers; Alessandra A Gallina; Andrew E Allen; Bernhard O Palsson; Karsten Zengler Journal: PLoS One Date: 2016-05-06 Impact factor: 3.240