| 1. |
- Kühn, Clemens, 1981, et al.
(författare)
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Formal Representation of the High Osmolarity Glycerol Pathway in Yeast
- 2009
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Ingår i: Genome informatics. International Conference on Genome Informatics. - 0919-9454. ; 22, s. 69-83
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Tidskriftsartikel (refereegranskat)abstract
- The high osmolarity glycerol (HOG) signalling system in yeast belongs to the class of Mitogen Activated Protein Kinase (MAPK) pathways that are found in all eukaryotic organisms. It includes at least three scaffold proteins that form complexes, and involves reactions that are strictly dependent on the set of species bound to a certain complex. The scaffold proteins lead to a combinatorial increase in the number of possible states. To date, representations of the HOG pathway have used simplifying assumptions to avoid this combinatorial problem. Such assumptions are hard to make and may obscure or remove essential properties of the system.This paper presents a detailed generic formal representation of the HOG system without such assumptions, showing the molecular interactions known from the literature. The model takes complexes into account, and summarises existing knowledge in an unambiguous and detailed representation. It can thus be used to anchor discussions about the HOG system. In the commonly used Systems Biology Markup Language (SBML), such a model would need to explicitly enumerate all state variables. The \emph{Kappa} modelling language which we use supports representation of complexes without such enumeration.To conclude, we compare \emph{Kappa} with a few other modelling languages and software tools that could also be used to represent and model the HOG system.
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| 2. |
- Prasad, K V S, 1952
(författare)
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A Prospectus for Mobile Broadcasting Systems
- 2006
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Ingår i: Electronic Notes in Theoretical Computer Science. - 1571-0661. ; 162, s. 295-300
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Tidskriftsartikel (refereegranskat)abstract
- Computer messages are often broadcast over ethernets, and sent point-to-point between them: globally asynchronous, locally synchronous (GALS). This paradigm is captured here by a primitive calculus, MBS (mobile broadcasting systems). MBS processes talk in rooms by local broadcast, and walk between rooms at unspecified speeds. Names are like object names in the π-calculus, but its “get/put b on channel a” becomes in MBS “go to a and hear/say b”. Speakers wait for departing processes, who are grouped by destination, and walkers can enter only silent rooms. These rules, and a primitive to make a room wait for a walker from a given room, seem adequate for programming.
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| 3. |
- Prasad, K V S, 1952
(författare)
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Biology as Rules of Interaction
- 2009
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Ingår i: Biobytes. - 0971-3271. ; 5
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Interaction is characteristic of life, whether between an organism and its environment, or between different subsystems of an organism, and so on all the way down to molecular interactions. One computational abstraction of a biological system is a set of rules saying how each kind of molecule (or other agent) interacts with others; the states the system can reach via interactions can then be worked out. The number of states will be enormous in general, but because not all interactions are possible in every state, some rule sets give a limited state space and interesting behavior. States-and-interactions can model all of computation and concurrency. We note some ideas from computer science that enable our computational view of biology, and some areas to be studied.
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