From: Matthias K. <kon...@go...> - 2014-10-07 11:30:55
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Hi Stefan, I see your point. Perhaps I misunderstood the direction of the package and it should be clearly stated what the package should do. I understood the main goal of the package is to provide the additional structures to implement multi-cell simulations like agent-based simulations. The implementation based on CBO terms implied this somehow. My arguments are based on this understanding. If the package is only concerned with the dynamic creation and destruction of objects things are different. The problem is in my opinion that nowhere clearly is written what the package should encode. There is some vague introduction in the draft. Intrinsic dynamic cellular behaviors characteristic of multicellular > systems (e.g., proliferation, differentiation, > endocytosis, exocytosis, and cell death) may be modeled using a variety of > mathematical and spatial frameworks. > However, fully representing systems that undergo discrete structural > changes during simulation cannot currently be > accomplished using either SBML Level 3 Version 1 Core’s structural > constructs or available language extensions. > But this could be interpreted either in the 'only handle dynamic construction/destruction' or 'provide things for mulicellular systems' way. I think it would be a good idea to clearly state: This package will handle ... Matthias On Tue, Oct 7, 2014 at 2:18 AM, Stefan Hoops <sh...@vb...> wrote: > Hello All, > > On Mon, 6 Oct 2014 13:35:16 -0600 > "Chris J. Myers" <my...@ec...> wrote: > > > While I always felt movement was part of this package, I agree with > > Lucian that perhaps a new package name is in order. The "Cell > > Behavior Package" or "Multi-cellular Modeling Package' may be good. > > > > I do not like either of the names. I can write multi-cellular models > in the core and behavior reminds me of to much of social interaction. > > I would prefer the current name as this package was anticipated to > address issues related to modification of existing sbml elements > especially creation and destruction (other are not excluded). Cell > division or death are just examples and might be actually to high level > to allow general application of this package. This discussion > especially Mathias remarks are pointing into this direction. > > With respect to movement I do not think that movement should be part of > this package as movement can be specified with the spatial package. How > the movement is implemented is a tool problem. Whether it is continuous > or lattice based does not play a role in the specification similar to > the fact that we never distinguish between stochastic or deterministic > models in the core. > > Thanks, > Stefan > > > > > What has happened is CBO is now out there and supposedly be used > > without a modeling language. We would like to see SBML become its > > modeling language as this would get SBML used by multi-cellular > > modeling community. > > > > Chris > > > > > > -- > Stefan Hoops, Ph.D. > Senior Project Associate > Virginia Bioinformatics Institute > Virginia Tech > 1015 Life Science Circle (0477) > Blacksburg, Va 24061, USA > > Phone: (540) 231-1799 > Fax: (540) 231-2606 > Email: sh...@vb... > > > ------------------------------------------------------------------------------ > Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer > Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports > Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper > Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer > > http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk > _______________________________________________ > sbml-dynamic mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-dynamic > -- --------------------------------------------------- Matthias König Computational Systems Biochemistry Institute of Biochemistry Charité - Universitätsmedizin Berlin http://www.charite.de/sysbio/people/koenig/ Tel: + 49 30 450 528 197 Tel: + 49 176 81168480 --------------------------------------------------- |