Thursday, July 21, 2011

More visual cues for showing contents of equations

When hovering over components with a function, TinkerCell used to show a function tool-tip indicating how the function is defined for that component. Now, TinkerCell also highlights all the other components that are involved in that function. For example, if the activity of a gene is describes as plasmid.copy * operator1 * operator2, then TinkerCell will circle the plasmid and both operators when the mouse hovers over the gene component. See screenshots below.

Thursday, July 7, 2011

Sequence annotation widget

It was always possible to add any type of annotation to any component, including sequence annotations, in TinkerCell, but this had to be done programmatically, i.e a couple of lines of python or octave code. For sequence annotation, now the sequence-viewer plug-in also provides a simple widget for adding position and description to the selected part. The table will be saved as "sequence annotation", i.e it can be accessed via a python or octave program using:
p = tc_find("cod2");   #get the part
sa = tc_getTextDataTable(x, "sequence annotation"); #get sequence annotation
tc_getTableValue( sa, 0, 0)