Addressing <i>barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology</i>

Niarakis, Anna; Waltemath, Dagmar; Glazier, James A.; Schreiber, Falk; Keating, Sarah M.; Nickerson, David; Chaouiya, Claudine; Siegel, Anne; Noël, Vincent; Hermjakob, Henning; Helikar, Tomáš; Soliman, Sylvain; Calzone, Laurence

doi:10.1093/bib/bbac212

Cited by 14 publications

(12 citation statements)

References 79 publications

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“…Besides building and analysing large-scale biological models, one of the main challenges in systems modelling is the use of standards and proper annotation of such models to enhance a model’s reusability (Niarakis et al , 2022, 2021). The models obtained in our pipeline are in a standard format (SBML-Qual) and thoroughly annotated using the MIRIAM scheme (Le Novère et al , 2005), including PubMed IDs and pathway identifiers to annotate components and reactions.…”

Section: Methodsmentioning

confidence: 99%

A large-scale Boolean model of the Rheumatoid Arthritis Fibroblast-Like Synoviocytes predicts drug synergies in the arthritic joint

Singh

Naldi

Soliman

et al. 2023

Preprint

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Rheumatoid arthritis (RA) is a complex autoimmune disease with an unknown aetiology. However, rheumatoid arthritis fibroblast-like synoviocytes (RA-FLS) play a significant role in initiating and perpetuating destructive joint inflammation by expressing immuno-modulating cytokines, adhesion molecules, and matrix remodelling enzymes. In addition, RA-FLS are primary drivers of inflammation, displaying high proliferative rates and an apoptosis-resistant phenotype. Thus, RA-FLS-directed therapies could become a complementary approach to immune-directed therapies by predicting the optimal conditions that would favour RA-FLS apoptosis, limit inflammation, slow the proliferation rate and minimise bone erosion and cartilage destruction. In this paper, we present a large-scale Boolean model for RA-FLS that consists of five submodels focusing on apoptosis, cell proliferation, matrix degradation, bone erosion and inflammation. The five phenotype-specific submodels can be simulated independently or as a global model. In-silico simulations and perturbations reproduced the expected biological behaviour of the system under defined initial conditions and input values. The model was then used to mimic the effect of mono or combined therapeutic treatments and predict novel targets and drug candidates through drug repurposing analysis.

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Section: Methodsmentioning

confidence: 99%

A large-scale Boolean model of the Rheumatoid Arthritis Fibroblast-Like Synoviocytes predicts drug synergies in the arthritic joint

Singh

Naldi

Soliman

et al. 2023

Preprint

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“…Modular design of a disease map means developing diagrams that are manageable and reusable [38] for faster curation, reuse in other projects and downstream use in computational modelling [39][40][41]. A module is a diagram part that is self-contained and can be developed and maintained independently while being included in a larger network.…”

Section: Modularisationmentioning

confidence: 99%

“…Disease Maps approaches evolve together with other systems biology communities such as COMBINE [74], CoLoMoTo [74], SysMod [75], SBGN [19], SBML [76] and FAIR [69] to enhance the accessibility and reusability of the resources [39].…”

Section: Fair Principles For Disease Maps Available In Minervamentioning

confidence: 99%

High-quality Reconstruction of Disease Mechanisms: Planning, Development and Maintenance

Mazein¹,

Acencio²,

Balaur³

et al. 2022

Preprint

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As a conceptual model of disease mechanisms, a disease map integrates available knowledge and is applied for data interpretation, predictions and hypothesis generation. It is possible to model disease mechanisms on different levels of granularity and adjust the approach to the goals of a particular project. This rich environment together with requirements for high-quality network reconstruction makes it challenging for new curators and groups to be quickly introduced to the development methods. In this review, we offer a step-by-step guide for developing a disease map within its mainstream pipeline that involves using the CellDesigner tool for creating and editing diagrams and the MINERVA Platform for online visualisation and exploration. We also describe how the Neo4j graph database environment can be used for managing and querying efficiently such a resource. For assessing the interoperability and reproducibility we apply FAIR principles.

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“…The developed maps and models are available on GitLab (https://git-r3lab.uni.lu/covid/models/) and FAIRDOMHub (58). We have worked on tool interoperability and promoting community standards; therefore, most input formats are GML, SIF or SBML, and SBML Qual files in an effort to enhance model reusability (59). All maps and models are available under a CC-BY license.…”

Section: Fairness and Availability For Proper Data Managementmentioning

confidence: 99%

A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms

Niarakis

Ostaszewski

Mazein

et al. 2022

Preprint

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The COVID-19 Disease Map project is a large-scale community effort uniting 277 scientists from 130 Institutions around the globe. We use high-quality, mechanistic content describing SARS-CoV-2-host interactions and develop interoperable bioinformatic pipelines for novel target identification and drug repurposing. Community-driven and highly interdisciplinary, the project is collaborative and supports community standards, open access, and the FAIR data principles. The coordination of community work allowed for an impressive step forward in building interfaces between Systems Biology tools and platforms. Our framework links key molecules highlighted from broad omics data analysis and computational modeling to dysregulated pathways in a cell-, tissue- or patient-specific manner. We also employ text mining and AI-assisted analysis to identify potential drugs and drug targets and use topological analysis to reveal interesting structural features of the map. The proposed framework is versatile and expandable, offering a significant upgrade in the arsenal used to understand virus-host interactions and other complex pathologies.

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Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology

Cited by 14 publications

References 79 publications

A large-scale Boolean model of the Rheumatoid Arthritis Fibroblast-Like Synoviocytes predicts drug synergies in the arthritic joint

A large-scale Boolean model of the Rheumatoid Arthritis Fibroblast-Like Synoviocytes predicts drug synergies in the arthritic joint

High-quality Reconstruction of Disease Mechanisms: Planning, Development and Maintenance

A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms

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