Getting Starting With BioFabric: Importing a .sif File

[wlong...@systemsbiology.org]

As a general rule, you will need to get started with BioFabric by importing a tab-delimited .sif file of your network using File->Import->Import SIF File....  As a reminder, a .sif file is of the format: node1<tab>interaction<tab>node2, one per line.  Note the requirement that it be tab-delimited; using a file that just uses spaces and quote marks to delineate the three fields will not work!   Another thing to keep in mind is that the interaction tag should be from a limited set of tags, since BioFabric pops up a dialog after the .sif file loads asking you to specify whether each tag denotes a directed or undirected relationship.  If your interaction tags are, e.g. floating point values, the table of tags in this dialog will be very large.  You can actually answer the directed/undirected question by specifying a file with that information, but I still recommend using a limited set; v 1.0.0 is not smart enough to skip trying to create a table of all interaction tags for the dialog if the set is large.  One last note: singleton nodes are supported in the .sif input, by just having a line with a single node name in it.  Singleton nodes are placed by the default layout algorithm in a single column in the far lower right of the network presentation.

Bill