Adrien Rougny

State variables are not loaded properly from SBGN-ML when the element inside the state variable element is prefixed (e.g., ). The state variable is represented but it has no text...

Start point and end point export problem

1

Sometimes, the start point and end points of arcs (positions) are not well exported in SBGN-ML. Attached is an example SBGN-ML file created using newt (start_end_point.txt). Rendering it using exact...

AF delay operator has no ports

1

The delay operator in AF maps is rendered with no ports and does not have the same behavior as other logical operators.

explicitly unknown stoichiometry ("?") could be stored as NaN

1

From Amdreas: As far as storing in SBGN-ML goes, one could represent the ? with the actual numerical value NaN, so that the data type is always a number but...

Cannot "add complex for selected" a receptor in SBML maps

1

In SBML, When trying to add a complex around a generic protein and a receptor using the "add complex for selected" feature, the complex is only added around the generic...

Currently one cannot start to add SBML glyphs (for example) to a map without setting the type of the map to SBML first. I could be nice to set the...

SBML maps: copying and moving glyphs around sometimes produces strange behavior

3

In the attached map, copying and moving the copy of the phosphorylated STAT glyph in the cell compartment produces strange behavior (the size of the glyph changes while moving it,...

The map produced when using the "Post-translational modification" brick of the SBGN Bricks feature is bugged: it has units of information (shown graphically with stadium shapes) instead of state variables.

Currently it seems there is no support for reading and displaying terminals inside submaps. An example of a map with such terminals can be found here: [https://github.com/sbgn/libsbgn/blob/master/test-files/PD/submap_expanded.sbgn](https://github.com/sbgn/libsbgn/blob/master/test-files/PD/submap_expanded.sbgn)