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Paper on rule-based multi-level modeling in BMC Systems Biology [Update]
The paper "Rule-based multi-level modeling of cell biological systems" has been accepted by BMC Systems Biology.
You will find the paper here and a comment "Toward a comprehensive language for biological systems" by James R. Faeder in BMC Biology about our paper here.
Update (20 Mar 2012): the paper became a featured article on the journal's homepage (editor's picks) and with more than 3800 views it is among the top 3 of the most viewed articles of the last year.
New JAMES II (0.9.1) release