Transactions on Computational Systems Biology IX
This issue of the journal reports regular papers. The ?rst contribution is by ParasChopra and Andreas Bender and discusses quantitative modelling aspects of the bgl operon for E. coli. The second contribution is by Rodrick Wallace and Deborah Wallace and deals with ecosystem transitions a?ecting phenotype - pressions and selection mechanisms. The techniques used are statistical models. The thirdcontributionis byRoberto Barbuti,Andrea Maggiolo-Schettini,Paolo Milazzo, Paolo Tiberi and Angelo Troina and presents the Stochastic Calculus of Looping Sequences (SCLS) suitable for the description of microbiologicals- tems, such as cellular pathways, and their evolution. The last contribution is by Federica Ciocchetta and describes the use of biological transactions to make atomic sequences of interactions in the BlenX language. May 2008 Corrado Priami LNCS Transactions on Computational Systems Biology – Editorial Board Corrado Priami, Editor-in-chief University of Trento, Italy Charles Au?ray Genexpress, CNRS and Pierre & Marie Curie University, France Matthew Bellgard Murdoch University, Australia Soren Brunak Technical University of Denmark, Denmark Luca Cardelli Microsoft Research Cambridge, UK Zhu Chen Shanghai Institute of Hematology, China Vincent Danos CNRS, University of Paris VII, France Eytan Domany Center for Systems Biology, Weizmann Institute, Israel Walter Fontana Santa Fe Institute, USA Takashi Gojobori National Institute of Genetics, Japan Martijn A.
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A Quantitative bgl Operon Model for E coli Requires BglF Conformational Change for Sugar Transport
How Sudden Ecosystem Transitions Can Entrain Both Phenotype Expression and Darwinian Selection
Stochastic Calculus of Looping Sequences for the Modelling and Simulation of Cellular Pathways
The BlenX Language with Biological Transactions
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abstract action active allows application approach associated assume becomes BglF BglG biological BlenX boxes Calculated cell cognitive communication complex Comput concentration concrete consider constant critical deﬁned deﬁnition denote describe diﬀerent distortion distribution dynamics ecosystem elements environment enzymes equation example expression extended ﬁrst formal function gene gene expression genetic given gives glucose increases inducer information sources interaction involved kind lac Repressor lactose language limit manifolds mathematical means mechanisms membrane molecules Note occurrences operator operon parameters particular paths pattern phase transition physical possible present probability production properties protein reactants reaction regulation relation renormalization represent respectively rewrite rules rules sense sequence simulation species split stochastic structure symbol Table Theorem theory tion topological transactions transcription uncertainty University values variables