Example Features

Levels Of Detail

In many situations, certain details in metabolic networks are not of interest depending on the field of application. For instance, energetic cofactors and network regulation mechanisms are often not considered in metabolic flux analysis. Hence, Omix supports a context-dependent view of network diagrams without the necessity to edit the diagram.

A network diagram can be displayed in various levels of detail because the user can hide certain types of components of the network. Entire classes of diagram components can be hidden in the diagram. For instance, pathways are hidden as well as cofactors and effector edges. Reaction nodes can be faded out leading to a hypergraph representation. Likewise, metabolite nodes can be hidden. In this case the metabolites are represented as dots. This dot representation as well as the label of a hidden reaction and metabolite only appears if the corresponding node is still connected with at least one visible edge. When all types of network components are hidden except pathways the network can be examined from a higher abstraction level.

Beyond the option to globally hide entire classes of network components, all single reactions and metabolites as well as pathways and compartments can be hidden individually. The possibility of representing a diagram in various levels of details as well as the option to hide single components allows to use one network diagram for multiple purposes with different and, if the case may be, contradictory requirements.