2026-10-07T13:29:26Z https://api.figshare.com/v2/oai

oai:figshare.com:article/34036813 2026-09-30T20:20:06Z category_13 category_14 category_21 category_24 category_734 category_931 category_64 category_69 portal_5 item_type_1 month_year_09_2026

<p>The Blasi et al. (2016) [13] model selection problem in PEtab Select.</p> Dilan Pathirana (6292544) Frank T. Bergmann (10036117) Domagoj Doresic (25146007) Polina Lakrisenko (10036138) Sebastian Persson (9241307) Niklas Neubrand (25146010) Jens Timmer (25170) Clemens Kreutz (315828) Harald Binder (39439) Marija Cvijovic (4070044) Daniel Weindl (1844341) Jan Hasenauer (328495) Genetics Molecular Biology Biotechnology Evolutionary Biology Biological Sciences not elsewhere classified Information Systems not elsewhere classified Cancer Inorganic Chemistry yield different models parameter estimation problems often competing hypotheses including basic brute g ., akaike existing computational pipelines bayesian information criteria associated calibration problems fair research software model selection tasks model selection problems flexible selection methods petab select introduces petab select builds petab select addresses model selection petab select backward selection sampling methods model alternatives supporting software software package petab standard xlink "> systems biology swift evaluation standard facilitates promoting interoperability one example mathematical modeling first standardization essential contribution ensure flexibility easily extended critical gap compact representation central question broad spectrum biological systems art modelling also advanced <p><b>(a)</b> The reaction network for the published best model, represented as a graph similarly to <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1014774#pcbi.1014774.g002" target="_blank">Figs 2b</a>-<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1014774#pcbi.1014774.g002" target="_blank">2c</a>’. The histone chemical species can undergo acetylation reactions at four different positions (5, 8, 12, and 16). Nodes are acetylation states (motifs) of the histone, and arrows are acetylation reactions. The model selection problem involves two different possibilities for the rate constant of each reaction; it is either: the shared basal rate constant (the value is fixed to 1), or an estimated motif-specific rate constant (the value is estimated). The model selection problem is to identify the reactions with motif-specific rate constants, and the published best model contains seven (solid arrows). <b>(b)</b> There are 32 reactions, and therefore 32 independent hypotheses for motif-specific rate constants. Only two parameterized hypotheses (a_0ac_k05 and a_0ac_k08) are shown here for brevity, with the remaining 30 parameters represented by the ellipses. This two-row, 34-column table encodes the full model space of billion models.</p> 2026-09-30T18:02:09Z Image Figure 10.1371/journal.pcbi.1014774.g003 https://figshare.com/articles/figure/_p_The_Blasi_et_al_2016_13_model_selection_problem_in_PEtab_Select_p_/34036813 CC BY 4.0