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SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks

Andreas Dräger, Daniel C Zielinski, Roland Keller, Matthias Rall, Johannes Eichner, Bernhard O Palsson, Andreas Zell
2015 BMC Systems Biology  
This algorithm is implemented in the software package SBMLsqueezer 2.  ...  However, the construction of large biochemical network models is a laborious and error-prone task.  ...  Acknowledgements The authors are grateful for contributions of (in alphabetical order) to Meike  ... 
doi:10.1186/s12918-015-0212-9 pmid:26452770 pmcid:PMC4600286 fatcat:ohvmzqevvndk7jz7wzjqzvyq4y

From word models to executable models of signaling networks using automated assembly [article]

Benjamin M Gyori, John A Bachman, Kartik Subramanian, Jeremy L Muhlich, Lucian Galescu, Peter K Sorger
2017 bioRxiv   pre-print
Word models (natural language descriptions of molecular mechanisms) are a common currency in spoken and written communication in biomedicine but are of limited use in predicting the behavior of complex  ...  biological networks.  ...  Oncogene 26: 3279-3290 Dräger A, Zielinski DC, Keller R, Rall M, Eichner J, Palsson BO & Zell A (2015) SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks.  ... 
doi:10.1101/119834 fatcat:2ex6vmzyxvbzdlcu7eqrebw32e