Reproducibility and FAIR principles: the case of a segment polarity network model

Mendes, Pedro

doi:10.3389/fcell.2023.1201673

Cited by 3 publications

(2 citation statements)

References 80 publications

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“…As a scripting module BASICO lends itself for constructing large networks, as is for example done in the reproducibility study in Mendes (2023).…”

Section: Statement Of Needmentioning

confidence: 99%

BASICO: A simplified Python interface to COPASI

Bergmann

2023

JOSS

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Biological systems are highly complex and dynamic, whose behavior in response to changed conditions or perturbations cannot be predicted easily. Thus computational modeling can serve as a valuable analysis tool which allows an understanding of these systems that cannot be achieved with wet lab experiments alone. It can be used to gain a deeper understanding of the system or to answer more applied questions such as predicting drug targets. COPASI is a powerful environment for creating, editing, simulating and analyzing computational models. It provides a user-friendly GUI that is easy to use even by people who are not experts in the field. At the same time, its broad range of tasks makes it attractive for more advanced computational biologists. By using a scripting language in conjunction with COPASI, scientists can automate tasks such as parameter estimation, sensitivity analysis, optimization, and model fitting. They can also create custom scripts to perform complex operations or analyses that are not available in COPASI's GUI, such as model identification. Scripting languages can also facilitate the communication. documentation and reproducibility of computational models, by allowing scientists to share their code and results with others.Here we introduce BASICO, a simplified Python interface to COPASI. It provides a set of functions that allow to create, edit, simulate and analyze models in a more automated way. BASICO can be easily installed using: pip install copasi-basico.

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“…As a scripting module BASICO lends itself for constructing large networks, as is for example done in the reproducibility study in Mendes (2023).…”

Section: Statement Of Needmentioning

confidence: 99%

BASICO: A simplified Python interface to COPASI

Bergmann

2023

JOSS

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“…During the last couple of decades, many classic models have been added to model repositories. Public standards and repositories can facilitate the reuse and regeneration of computational biology models that will outlive the original used specific software [4].…”

Section: Introductionmentioning

confidence: 99%

Curating models from BioModels: Developing a workflow for creating OMEX files

Xu,

Smith

2024

Preprint

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The reproducibility of computational biology models can be greatly facilitated by widely adopted standards and public repositories. We examined 50 models from the BioModels Database and attempted to validate the original curation and correct some of them if necessary. For each model, we reproduced these published results using Tellurium. Once reproduced we manually created a new set of files, with the model information stored by the Systems Biology Markup Language (SBML), and simulation instructions stored by the Simulation Experiment Description Markup Language (SED-ML), and everything included in an Open Modeling EXchange (OMEX) file, which could be used with a variety of simulators to reproduce the same results. On the one hand, the validation procedure of 50 models developed a manual workflow that we would use to build an automatic platform to help users more easily curate and verify models in the future. On the other hand, these exercises allowed us to find the limitations and possible enhancement of the current curation and tooling to verify and curate models.

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Curating models from BioModels: Developing a workflow for creating OMEX files

Xu,

Smith

2024

PLoS ONE

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The reproducibility of computational biology models can be greatly facilitated by widely adopted standards and public repositories. We examined 50 models from the BioModels Database and attempted to validate the original curation and correct some of them if necessary. For each model, we reproduced these published results using Tellurium. Once reproduced we manually created a new set of files, with the model information stored by the Systems Biology Markup Language (SBML), and simulation instructions stored by the Simulation Experiment Description Markup Language (SED-ML), and everything included in an Open Modeling EXchange (OMEX) file, which could be used with a variety of simulators to reproduce the same results. On the one hand, the reproducibility procedure of 50 models developed a manual workflow that we would use to build an automatic platform to help users more easily curate and verify models in the future. On the other hand, these exercises allowed us to find the limitations and possible enhancement of the current curation and tooling to verify and curate models.

show abstract

Reproducibility and FAIR principles: the case of a segment polarity network model

Cited by 3 publications

References 80 publications

BASICO: A simplified Python interface to COPASI

BASICO: A simplified Python interface to COPASI

Curating models from BioModels: Developing a workflow for creating OMEX files

Curating models from BioModels: Developing a workflow for creating OMEX files

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