Dear friends,

Sybil Update:

- Added: Sybil can edit compartment hierarchy, with successful import to VCell
- Fixed: Sometimes species references were mentioned multiple time
in reactions, now fixed.
- Added: Compartment table now has explicit "none" option for
external (useful to correct a wrongly entered choice)

Known issues:

- Generation of SBML IDs has weaknesses: Names are inconveniently
long, and cause occasionally problems with VCell if longer than 64
characters. Also, Sybil's id generation depends on Jena's way of
splitting of URIs into namespace and local name, which is not based on
any standard and might not always be well behaved. Also, if two
different URIs end up with the same local name, this causes problems
(though this should be extremely rare). There should be generation of
short labels and a stronger scheme for generating IDs, probably with
explicit uniqueness check per model.

- Sybil has not really been tested against files other than from Reactome.

Take care
Oliver

--
Oliver Ruebenacker, Post-Doc Researcher
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org