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Reproducibility and FAIR Principles: The Case of a Segment Polarity Network Model

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Paper breakdownThe authors' claims, conditions and measurements, as JSON Signed receiptProof this review has not been altered
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Pedro Mendes

Molecular Networks · Submitted 18 Apr 2023

abstract compiled · 2026-09-23 · no language-model review

The authors' main claim This demonstrates how the FAIR principles can be successfully enabled by using open source software, widely adopted standards, and public repositories, facilitating reproducibility and reuse of computational cell biology models that will outlive the specific software used.

how it is stated · asserted 1.00 read the record →

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arXiv ID2304.08688 (version 1)
Pith IDCDQRQOOB, Pith's permanent record of this paper and its review
CitationPedro Mendes. "Reproducibility and FAIR Principles: The Case of a Segment Polarity Network Model." arXiv:2304.08688 (2023). https://pith.science/paper/CDQRQOOB
Claim paper

The compiled record

The paper's own sentences, arranged. Each label is drawn from a closed vocabulary; the number beside it is the probability the classifier gave that label. Numbers in the tables are the authors', checked by code. No sentence in this record was written by a model.

Open the compiled record

Compiled by classifier-1.13.0 via TypeSafe API, question bank abstract-p1-20260923, 2026-09-23: 1 request, 5,563 input tokens.

What the abstract itself states, as probabilities: claims first 0.03 · states limitation 0.18 · human participants 0.02 · controlled comparison 0.02 · randomized assignment 0.01 · states quantitative result 0.79 · compares with prior results 0.16 · mentions code or data availability 0.62.

The abstract, sentence by sentence

arXiv listing abstract v1. Results and the main claim are underlined; .

The issue of reproducibility of computational models and the related FAIR principles (findable, accessible, interoperable, and reusable) are examined in a specific test case. I analyze a computational model of the segment polarity network in Drosophila embryos published in 2000. Despite the high number of citations to this publication, 23 years later the model is barely accessible, and consequently not interoperable. Following the text of the original publication allowed successfully encoding the model for the open source software COPASI. Subsequently saving the model in the SBML format allowed it to be reused in other open source software packages. Submission of this SBML encoding of the model to the BioModels database enables its findability and accessibility. This demonstrates how the FAIR principles can be successfully enabled by using open source software, widely adopted standards, and public repositories, facilitating reproducibility and reuse of computational cell biology models that will outlive the specific software used.

background contribution method result interpretation main claim

What the classifier reports for each sentence. The number is the probability it gave the label.
#sentencerolethe authors' own workstates the main conclusionstrength
s0 The issue of reproducibility of computational models and the related FAIR principles (findable, accessible, interoperable, and reusable) are examined in a specific test case. background 0.84 0.32 0.05 asserted 0.63
s1 I analyze a computational model of the segment polarity network in Drosophila embryos published in 2000. contribution 0.50 0.82 0.02 asserted 0.97
s2 Despite the high number of citations to this publication, 23 years later the model is barely accessible, and consequently not interoperable. gap 0.50 0.61 0.07 asserted 1.00
s3 Following the text of the original publication allowed successfully encoding the model for the open source software COPASI. method 0.75 0.92 0.06 asserted 1.00
s4 Subsequently saving the model in the SBML format allowed it to be reused in other open source software packages. method 0.53 0.89 0.06 asserted 0.99
s5 Submission of this SBML encoding of the model to the BioModels database enables its findability and accessibility. result 0.43 0.88 0.10 asserted 0.98
s6 This demonstrates how the FAIR principles can be successfully enabled by using open source software, widely adopted standards, and public repositories, facilitating reproducibility and reuse of computational cell biology models that will outlive the specific software used. interpretation 1.00 0.60 0.92 asserted 1.00

What kind of paper the classifier reports this is: position or commentary 0.47 · evidence from analysis of existing data 0.47.

What was examined, and what was not

sources read
  • arXiv listing abstract v1
not examined
  • full text
  • figures and tables
  • references and citing sentences
  • relations to other papers
levels run
  • P abstract
not run
  • S sections
  • T body sentences
  • C citations
  • R cross-paper relations

Every quoted sentence on this record is the authors'. Every label is from Pith's closed vocabulary, with the probability shown beside it. Every number in the measurements table is the authors', checked by code. Record as JSON

The paper
Original abstract

The issue of reproducibility of computational models and the related FAIR principles (findable, accessible, interoperable, and reusable) are examined in a specific test case. I analyze a computational model of the segment polarity network in Drosophila embryos published in 2000. Despite the high number of citations to this publication, 23 years later the model is barely accessible, and consequently not interoperable. Following the text of the original publication allowed successfully encoding the model for the open source software COPASI. Subsequently saving the model in the SBML format allowed it to be reused in other open source software packages. Submission of this SBML encoding of the model to the BioModels database enables its findability and accessibility. This demonstrates how the FAIR principles can be successfully enabled by using open source software, widely adopted standards, and public repositories, facilitating reproducibility and reuse of computational cell biology models that will outlive the specific software used.

Human review

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References
How the literature uses it

What this paper does with the arXiv papers it cites

Each citing sentence is taken from the citing paper's LaTeX source and typed by Pith's classifier. A label appears at probability 0.8 or more (0.95 for support), a contest at 0.7 or more; the quoted words are the citing authors'. How each label was checked · JSON

What it cites

Cites as background 1 paper

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