2026-10-08T20:54:54Z
https://api.figshare.com/v2/oai
oai:figshare.com:article/34036810
2026-09-30T20:20:04Z
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>Example model space.</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 model space table encodes model subspaces as rows. Each model subspace has an ID and an associated superset PEtab problem, which includes the mathematical model. This superset problem is customized into single models according to the remaining columns, which contain semicolon-delimited lists of values that parameters (column headers) can take in the subspace. The next subfigures represent models as graphs. Nodes (colored circles) are variables (e.g., biochemical species), and arrows are processes, e.g., conversion (• •), import (, or export () of the variables. The arrows are annotated with their associated parameters, e.g., k_4 is the rate constant associated with export of variables <i>A</i> and <i>B</i> due to an interaction between <i>A</i> and <b><i>B</i>. (b,c)</b> Each subspace is associated with a superset model, where all possible parameters are estimated. Based on the superset models, candidate models are encoded by turning (estimation of unknown) parameters on or off. The total number of models in this example is 16 in subspace supersetA_models, plus (c’) 8 in subspace supersetB_models.</p>
2026-09-30T18:02:09Z
Image
Figure
10.1371/journal.pcbi.1014774.g002
https://figshare.com/articles/figure/_p_Example_model_space_p_/34036810
CC BY 4.0