merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models

Abstract

Genome-scale metabolic models have been recognised as useful tools for better understanding living organisms’ metabolism. merlin (https://www.merlin-sysbio.org/) is an open-source and user-friendly resource that hastens the models’ reconstruction process, conjugating manual and automatic procedures, while leveraging the user's expertise with a curation-oriented graphical interface. An updated and redesigned version of merlin is herein presented. Since 2015, several features have been implemented in merlin, along with deep changes in the software architecture, operational flow, and graphical interface. The current version (4.0) includes the implementation of novel algorithms and third-party tools for genome functional annotation, draft assembly, model refinement, and curation. Such updates increased the user base, resulting in multiple published works, including genome metabolic (re-)annotations and model reconstructions of multiple (lower and higher) eukaryotes and prokaryotes. merlin version 4.0 is the only tool able to perform template based and de novo draft reconstructions, while achieving competitive performance compared to state-of-the art tools both for well and less-studied organisms.

Dynamic genome-based metabolic modeling of the predominant cellulolytic rumen bacteriumFibrobacter succinogenesS85

“…Many independent methods have been developed to generate genome scale models, including some toolboxes and workspaces, such as Pathway Tools (36), RAVEN (73), merlin (74), KBase (75), The SEED (76), AuReMe (35), AutoKEGGRec (63), CarVeMe (77), and gapseq (78). They rely on one or several metabolic databases such as MetaCyc (45), KEGG (79), ModelSEED (80) or BiGG (64).…”

An updated genome-scale model forXylella fastidiosasubsp.paucaDe Donno

“…The reconstruction process was supported by the metabolic models’ reconstruction using genome-scale information ( merlin ) [16] framework. This software provides a friendly interface for genome annotation and manual curation, offering multiple features and plugins that accelerate the process.…”

“…A genome-scale information framework ( merlin ) [17] was used to reconstruct the metabolic model. With this software, genome annotation and manual curation can be performed in an easy and intuitive manner, with a variety of features and plugins available to speed up the process.…”

Towards applications of genome‐scale metabolic model‐based approaches in designing synthetic microbial communities

“…Thousands of GEMs have been built for many kinds of cells, such as bacteria [37,38], archaea [39], yeasts [40], plants [41] and even human cells [42]. As the manual process for GEM construction is complex and laborious [26], many computational tools have been developed to make the procedures automatic or semi-automatic, such as the online tools, ModelSEED [31] and Kbase [43], the canonical modeling toolboxes like the COBRA toolbox [44], and other approaches such as Pathway Tools [45], CarveMe [30], AGORA [46], AGREDA [47], RAVEN [48] or Merlin [49]. These tools greatly accelerate the GEM construction process, leading to generation of an increasing number of GEMs [29].…”