Processes 2018, 6,39
arrows (Figure 4b)). Another important parameter is the word REV. It indicates reversibility of reactions.
It is part of the ID and if a reaction has a positive flux, it will be removed; if a reaction has a negative
flux, it will be replaced by a “-”. An example of reversibility (ID format: REACTION_REVCOUNTER)
is given in Figure 4 on the left side and its use on Figure 5. A COUNTER is not required but if a counter
is used, it must be used for every reaction ID, even if the reaction consists only of one arrow.
Figure 4. (a) A simple example of IDs of reaction arrows with reversibility (ID format:
REACTION_REVCOUNTER) and (b) with several arrows for one reaction (ID format:
REACTION_COUNTER).
5555
5555
555
5555
555
555
555
/LVWRIWKH()0V IURP &HOO1HW$QDO\]HU
Figure 5. A simple example of the generation of Elementary Mode of Flux (EFMs) representation.
The customer’s SVG (Scalable Vector Graphics) file is given in the top left of the figure (labelled
‘place_here’). The list of EFMs from CellNetAnalyzer in this form is in middle top images. With the
option ‘cna (CellNetAnalyzer) export list’ (Figure 2) this list is entered as CNA file (Figure 3a) and
generates the successive EFMs, EFM_1 until EFM_7.
149
arrows (Figure 4b)). Another important parameter is the word REV. It indicates reversibility of reactions.
It is part of the ID and if a reaction has a positive flux, it will be removed; if a reaction has a negative
flux, it will be replaced by a “-”. An example of reversibility (ID format: REACTION_REVCOUNTER)
is given in Figure 4 on the left side and its use on Figure 5. A COUNTER is not required but if a counter
is used, it must be used for every reaction ID, even if the reaction consists only of one arrow.
Figure 4. (a) A simple example of IDs of reaction arrows with reversibility (ID format:
REACTION_REVCOUNTER) and (b) with several arrows for one reaction (ID format:
REACTION_COUNTER).
5555
5555
555
5555
555
555
555
/LVWRIWKH()0V IURP &HOO1HW$QDO\]HU
Figure 5. A simple example of the generation of Elementary Mode of Flux (EFMs) representation.
The customer’s SVG (Scalable Vector Graphics) file is given in the top left of the figure (labelled
‘place_here’). The list of EFMs from CellNetAnalyzer in this form is in middle top images. With the
option ‘cna (CellNetAnalyzer) export list’ (Figure 2) this list is entered as CNA file (Figure 3a) and
generates the successive EFMs, EFM_1 until EFM_7.
149