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Table 5 The optimal SR level, the perception of a saturation and the willingness to double Description SR investor Non-SR investor Total χ 2 Goodman Kruskal γ N % N % N % Opt.
Current computation frameworks for enumerating EFMs are variants of the Double Description method [ 1],[ 8]–[ 10].
The order in which reactions are processed greatly affects the performance of the Double Description method.
Unlike the Double Description method, the algorithm enables accelerated enumeration of all EFMs satisfying a set of constraints.
We enumerate the extreme rays { r, r,..., r k} of W using the double description method [ 50].
Similarly as in Step 2, the double description method is employed to enumerate the extreme rays of P X (C ).
The classical Double Description method generates a massive number of intermediate modes before arriving at the final set of EFMs.
SympyCore can be extended by implementing the double description method [ 40] which is an integral part of Elementary Flux Mode Analysis (EFMA).
For solving vertex and facet enumeration problems we use a Python package pycddlib [ 44], a wrapper of the cddlib (version 094g) that implements the double description method [ 40].
The speed of the algorithm was comparable to efmtool, a mainstream Double Description method, when enumerating all EFMs; the attrition power gained from performing flux feasibility tests offsets the increased computational demand of running an LP solver.
Even for moderately-sized models (<400 reactions), existing approaches based on the <span class="lh">Double Description method must iterate through a large number of combinatorial candidates, thus imposing an immense processor and memory demand.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com