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We present DiSH-Sim, a simulator for large discrete models of biological signal transduction pathways, capable of simulating networks with multi-valued elements in both deterministic and stochastic manner. We focus on order of update and thus incorporate information about timing, taking into account that biological processes are not synchronized and certain biochemical changes occur slower than others. Another feature of our simulator is the use of grouped rules to model multi-valued elements and delays. The DiSH-Sim is publicly available and is being used to validate discrete cancer microenvironment and infectious disease models. It is also incorporated within a large architecture that includes natural language processing tools that read biological literature to assemble logical models. This paper demonstrates the functionalities and ease of use of DiSH-Sim, making it a very useful tool for discrete modeling.

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Highlights d YAP1 is expressed in hepatoblasts during liver development d Yap1 loss from hepatoblasts led to absent intrahepatic bile duct (IHBD) formation d YAP1 is required for formation of the second layer of patent IHBD in development d Yap1 KO mice without IHBD survive by altering bile acid transport and metabolism

We present a study of carrier dynamics in GaAs during and just after creation by ultrashort laser pulses. We observe a quasi-instantaneous spread of the carrier population in momentum-energy space. Attempts to fit the scattering rates in the relaxation time approximation result in parameters outside the range of validity of the theory. We interpret this as a failure of the Boltzmann kinetic approach in the quantum kinetic regime. [S0031-9007(96)01340-3]