SmithMal2025

documentation/amici_refs.bib

@@ -1441,6 +1441,21 @@ @Article{LakrisenkoPat2024
   url              = {https://doi.org/10.1371/journal.pone.0312148},
 }
 
+@Article{SmithMal2025,
+  author           = {Smith, Lucian and Malik-Sheriff, Rahuman S. and Nguyen, Tung V. N. and Hermjakob, Henning and Karr, Jonathan and Shaikh, Bilal and Drescher, Logan and Moraru, Ion I. and Schaff, James C. and Agmon, Eran and Patrie, Alexander A. and Blinov, Michael L. and Hellerstein, Joseph L. and May, Elebeoba E. and Nickerson, David P. and Gennari, John H. and Sauro, Herbert M.},
+  journal          = {bioRxiv},
+  title            = {Using {SED-ML} for reproducible curation: Verifying {BioModels} across multiple simulation engines},
+  year             = {2025},
+  abstract         = {The BioModels Repository contains over 1000 manually curated mechanistic models drawn from published literature, most of which are encoded in the Systems Biology Markup Language (SBML). This community-based standard formally specifies each model, but does not describe the computational experimental conditions to run a simulation. Therefore, it can be challenging to reproduce any given figure or result from a publication with an SBML model alone. The Simulation Experiment Description Markup Language (SED-ML) provides a solution: a standard way to specify exactly how to run a specific experiment that corresponds to a specific figure or result. BioModels was established years before SED-ML, and both systems evolved over time, both in content and acceptance. Hence, only about half of the entries in BioModels contained SED-ML files, and these files reflected the version of SED-ML that was available at the time. Additionally, almost all of these SED-ML files had at least one minor mistake that made them invalid. To make these models and their results more reproducible, we report here on our work updating, correcting and providing new SED-ML files for 1055 curated mechanistic models in BioModels. In addition, because SED-ML is implementation-independent, it can be used for verification, demonstrating that results hold across multiple simulation engines. Here, we use a wrapper architecture for interpreting SED-ML, and report verification results across five different ODE-based biosimulation engines. Our work with SED-ML and the BioModels collection aims to improve the utility of these models by making them more reproducible and credible.Author summary Reproducing computationally-derived scientific results seems like it should be straightforward, but is often elusive. Code is lost, file formats change, and knowledge of what was done is only partially recorded and/or forgotten. Model repositories such as BioModels address this failing in the Systems Biology domain by encoding models in a standard format that can reproduce a figure from the paper from which it was drawn. Here, we delved into the BioModels repository to ensure that every curated model additionally contained instructions on what to do with that model, and then tested those instructions on a variety of simulation platforms. Not only did this improve the BioModels repository itself, but also improved the infrastructure necessary to run these validation comparisons in the future.Author contributions LS: Writing, Conceptualization, Data Curation, Investigation, Methodology, Project Administration, Software, Validation. RMS: Reading, Writing, Data Curation, Methodology TN: Reading, Data Curation, Methodology HH: Reading JK: Conceptualization, Data Curation, Investigation, Methodology, Software. BS: Software LD: Software IIM: Reading, Conceptualization, Funding JCS: Software, Methodology EA: Reading, Writing AAP: Software MLB: Reading, Writing JH: Writing, Methodology EM: Reading, Writing DPN: Reading, Writing, Methodology JG: Reading, Writing, Methodology HMS: Reading, Writing, FundingCompeting Interest StatementThe authors have declared no competing interest.},
+  creationdate     = {2025-01-27T09:08:10},
+  doi              = {10.1101/2025.01.16.633337},
+  elocation-id     = {2025.01.16.633337},
+  eprint           = {https://www.biorxiv.org/content/early/2025/01/20/2025.01.16.633337.full.pdf},
+  modificationdate = {2025-01-27T09:08:41},
+  publisher        = {Cold Spring Harbor Laboratory},
+  url              = {https://www.biorxiv.org/content/early/2025/01/20/2025.01.16.633337},
+}
+
 @Comment{jabref-meta: databaseType:bibtex;}
 
 @Comment{jabref-meta: grouping:

documentation/references.md

@@ -1,6 +1,6 @@
 # References
 
-List of publications using AMICI. Total number is 94.
+List of publications using AMICI. Total number is 95.
 
 If you applied AMICI in your work and your publication is missing, please let us know via a new
 [GitHub issue](https://github.com/AMICI-dev/AMICI/issues/new?labels=documentation&title=Add+publication&body=AMICI+was+used+in+this+manuscript:+DOI).
@@ -12,6 +12,18 @@ If you applied AMICI in your work and your publication is missing, please let us
 }
 </style>
 
+<h1 class="unnumbered" id="section">2025</h1>
+<div id="refs" class="references csl-bib-body hanging-indent"
+role="list">
+<div id="ref-SmithMal2025" class="csl-entry" role="listitem">
+Smith, Lucian, Rahuman S. Malik-Sheriff, Tung V. N. Nguyen, Henning
+Hermjakob, Jonathan Karr, Bilal Shaikh, Logan Drescher, et al. 2025.
+<span>“Using <span>SED-ML</span> for Reproducible Curation: Verifying
+<span>BioModels</span> Across Multiple Simulation Engines.”</span>
+<em>bioRxiv</em>. <a
+href="https://doi.org/10.1101/2025.01.16.633337">https://doi.org/10.1101/2025.01.16.633337</a>.
+</div>
+</div>
 <h1 class="unnumbered" id="section">2024</h1>
 <div id="refs" class="references csl-bib-body hanging-indent"
 role="list">