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At this point in the existential analytic, worldhood is usefully identified as the abstract network mode of organizational configuration that is shared by all concrete totalities of involvements.
A step is here interpreted as one round in the abstract network, e.g. from one hormone to the subsequent one.
Qualitative simulations can then be used during the design step to anticipate the global behavior of the abstract network.
User defined networks, which are created on the EndoNet webpage follow the semantics of the abstract network described above.
BioNetCAD assists the network design by iteratively matching the basic components of the abstract network with CompuBioTicDB components.
To efficiently implement the abstract network of interest we propose a retro-implementation method using BioNetCAD in combination with CompuBioTicDB.
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At this level, the user can already check the qualitative behavior of this abstract network by launching qualitative simulations (Fig. 2B).
When designing an abstract network, the user has to identify existing molecules that can perform the desired functionalities.
First, the user designs an abstract network according to specific requirements and draws it using CellDesigner (Fig. 2A).
We propose to start this step by the construction of an abstract network, i.e. a biochemical network made of theoretical molecules, which will be implemented with well-characterized components.
Except that in that approach the abstract (simpler) network and the concrete (more complex) network should have, as much as possible, the same behavior for any parameter range.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com