Using PSAMM for the Curation and Analysis of Genome-Scale Metabolic Models

Dufault‐Thompson, Keith; Steffensen, Jon Lund; Zhang, Ying

doi:10.1007/978-1-4939-7528-0_6

Cited by 8 publications

(7 citation statements)

References 24 publications

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“…Our algorithm called “ExtraFastCC” is based on the “FastCC” algorithm of Ponce-de-Leon et al [10], but has a significantly improved ability to check the consistency of dead reversible reactions. The FastCC algorithm is used in consistency checking tools, such as PSAMM [25]. Tools, such as MC3 [26], have based their consistency checking on flux variability analysis (FVA) [16] of every reaction, which is a much slower approach.…”

Section: Resultsmentioning

confidence: 99%

ModelExplorer - software for visual inspection and inconsistency correction of genome-scale metabolic reconstructions

Martyushenko

Almaas

2019

BMC Bioinformatics

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BackgroundGenome-scale metabolic network reconstructions are low level chemical representations of biological organisms. These models allow the system-level investigation of metabolic phenotypes using a variety of computational approaches. The link between a metabolic network model and an organisms’ higher-level behaviour is usually found using a constraint-based analysis approach, such as FBA (Flux Balance Analysis). However, the process of model reconstruction rarely proceeds without error. Often, considerable parts of a model cannot carry flux under any condition. This is termed model inconsistency and is caused by faulty topology and/or stoichiometry of the underlying reconstructed network. While there exist several automated gap-filling tools that may solve some of the inconsistencies, much of the work still needs to be carried out manually. The common “linear list” format of writing biochemical reactions makes it difficult to intuit what is at the root of the inconsistent behaviour. Unfortunately, we have frequently observed that model builders do not correct their models past the abilities of automated tools, leaving many widely used models significantly inconsistent.ResultsWe have developed the software ModelExplorer, which main purpose is to fill this gap by providing an intuitive and visual framework that allows the user to explore and correct inconsistencies in genome-scale metabolic models. The software will automatically visualize metabolic networks as graphs with distinct separation and delineation of cellular compartments. ModelExplorer highlights reactions and species that are unable to carry flux (blocked), with several different consistency checking modes available. Our software also allows the automatic identification of neighbours and production pathways of any species or reaction. Additionally, the user may focus on any chosen inconsistent part of the model on its own. This facilitates a rapid and visual identification of reactions and species responsible for model inconsistencies. Finally, ModelExplorer lets the user freely edit, add or delete model elements, allowing straight-forward correction of discovered issues.ConclusionOverall, ModelExplorer is currently the fastest real-time metabolic network visualization program available. It implements several consistency checking algorithms, which in combination with its set of tracking tools, gives an efficient and systematic model-correction process.Electronic supplementary materialThe online version of this article (10.1186/s12859-019-2615-x) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

ModelExplorer - software for visual inspection and inconsistency correction of genome-scale metabolic reconstructions

Martyushenko

Almaas

2019

BMC Bioinformatics

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“…COBRApy supports many other file formats, including the latest Systems Biology Markup Language (SBML) with the Flux Balance Constraints (FBC) extension [ 18 ]. The JSON specification for COBRA models is also being adopted by other tools [ 11 ].…”

Section: Methodsmentioning

confidence: 99%

“…COBRA Toolbox [ 9 ] and COBRApy [ 10 ] require knowledge of the MATLAB and Python programming languages, respectively. PSAMM is yet another Python-based toolbox [ 11 ]. The only popular application for FBA that does not require computer programming is OptFlux [ 12 ].…”

Section: Introductionmentioning

confidence: 99%

Escher-FBA: a web application for interactive flux balance analysis

2018

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BackgroundFlux balance analysis (FBA) is a widely-used method for analyzing metabolic networks. However, most existing tools that implement FBA require downloading software and writing code. Furthermore, FBA generates predictions for metabolic networks with thousands of components, so meaningful changes in FBA solutions can be difficult to identify. These challenges make it difficult for beginners to learn how FBA works.ResultsTo meet this need, we present Escher-FBA, a web application for interactive FBA simulations within a pathway visualization. Escher-FBA allows users to set flux bounds, knock out reactions, change objective functions, upload metabolic models, and generate high-quality figures without downloading software or writing code. We provide detailed instructions on how to use Escher-FBA to replicate several FBA simulations that generate real scientific hypotheses.ConclusionsWe designed Escher-FBA to be as intuitive as possible so that users can quickly and easily understand the core concepts of FBA. The web application can be accessed at https://sbrg.github.io/escher-fba.Electronic supplementary materialThe online version of this article (10.1186/s12918-018-0607-5) contains supplementary material, which is available to authorized users.

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“…COBRApy supports many other file formats, including the latest Systems Biology Markup Language (SBML) with the Flux Balance Constraints (FBC) extension [17] . The JSON specification for COBRA models is also being adopted by other tools [11] .…”

Section: Methodsmentioning

confidence: 99%

“…COBRA Toolbox [9] and COBRApy [10] require knowledge of the MATLAB and Python programming languages, respectively. PSAMM is a another Python-based toolbox [11] . The only popular application for FBA that does not require computer programming is OptFlux [12] .…”

Section: Introductionmentioning

confidence: 99%

Escher-FBA: A web application for interactive flux balance analysis

Rowe

Kim

King

2018

Preprint

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BackgroundFlux balance analysis (FBA) is a widely-used method for analyzing metabolic networks.However, most existing tools that implement FBA require downloading software and writing code. Furthermore, FBA generates predictions for metabolic networks with thousands of components, so meaningful changes in FBA solutions can be difficult to identify. These challenges make it difficult for beginners to learn how FBA works. ResultsTo meet this need, we present Escher-FBA, a web application for interactive FBA simulations within a pathway visualization. Escher-FBA allows users to set flux bounds, knock out reactions, change objective functions, upload metabolic models, and generate high-quality figures without downloading software or writing code. We provide detailed instructions on how to use Escher-FBA to replicate several FBA simulations that generate real scientific hypotheses. ConclusionsWe designed Escher-FBA to be as intuitive as possible so that users can quickly and easily understand the core concepts of FBA. The web application can be accessed at https://sbrg.github.io/escher-fba .

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Using PSAMM for the Curation and Analysis of Genome-Scale Metabolic Models

Cited by 8 publications

References 24 publications

ModelExplorer - software for visual inspection and inconsistency correction of genome-scale metabolic reconstructions

ModelExplorer - software for visual inspection and inconsistency correction of genome-scale metabolic reconstructions

Escher-FBA: a web application for interactive flux balance analysis

Escher-FBA: A web application for interactive flux balance analysis

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