By Antti Häkkinen, Fred G. Biddle (auth.), Corrado Priami, Ralph-Johan Back, Ion Petre, Erik de Vink (eds.)
The LNCS magazine Transactions on Computational structures Biology is dedicated to inter- and multidisciplinary study within the fields of computing device technological know-how and lifestyles sciences and helps a paradigmatic shift within the suggestions from machine and knowledge technological know-how to deal with the recent demanding situations bobbing up from the structures orientated standpoint of organic phenomena.
This, the 13thTransactions on Computational platforms Biology quantity, visitor edited through Ralph-Johan again, Ion Petre, and Erik de Vink, makes a speciality of Computational types for mobile Processes and lines a few rigorously chosen and more desirable contributions at the beginning provided on the CompMod workshop, which came about in Eindhoven, The Netherlands, in November 2009. From various issues of view and following a variety of methods, the papers disguise a variety of themes in platforms biology, addressing the dynamics and the computational ideas of this rising field.
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Extra info for Transactions on Computational Systems Biology XIII
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1 A Model of the Cholesterol Synthesis Pathway Here we illustrate our translation workflow by using the cholesterol synthesis pathway as an example. We first draw an SBGN-PD map of this pathway (Figure 4) in the Edinburgh Pathway Editor (EPE) [46] based on the biochemical reactions listed in KEGG [27]. Then we add the necessary quantitative extensions as attributes to the corresponding glyphs in EPE (for screenshot see Figure 2), before we export the model from EPE to SBGNtext. SBGNtext is automatically translated to Bio-PEPA with the help of SBGNtext2BioPEPA [34].
Parameters such as kinetic constants and initial amounts of species must be scaled from the start in the Edinburgh Pathway Editor to represent discrete molecule counts. process ID and no further information about a process is required here, there is no need to loop over all processes as well. By combining the information stored in the TreeMaps of entities and arcs, it is possible to compile the relevant information for BioPEPA species components. The fact that multiple arcs can connect the same entity to multiple reactions and the same reaction to multiple entities facilitates the preservation of SBGNs capacity to model reactions with many entities during the translation process.
Here we describe several pre-existing dynamic simulation methods, some intended for rigid bodies and others designed for deformable structures. 1 Dynamic Simulation of Rigid Bodies This section reviews methods for the dynamic simulation of rigid bodies. In these methods, object deformation may be represented by a loss of kinetic energy, for example, or an overlapping of objects. If an object’s changing shape is modeled, however, then we classify it as a deformable structure instead of a rigid body.