Re: [cellml-discussion] Proposal: BCP for including external codeinCellML models
> ECMAScript is not practical for use in modelling, because it is an > interpreted, non-typed language, which necessarily means that it cannot > be compiled and will be slower than compiled code. But CellML is an language for the description and exchange of mathematical models. It is not meant to be a one-off wonder describing the most efficient and best performing method for executing numerical computations. To turn a CellML model description into something useful for computation that description has to be interpreted and compiled into some other format suitable for the environment using it... Surely in the same manner, a standard description of procedural code could then be interpreted by any number of applications in whatever manner they feel best suits their environment? > External code needs to be extensible, and hence outside the scope of the > CellML specifications, for several reasons: > 1) Performance. Code may need to be written in a way which is specific > to a particular platform in order to be able to perform well. some response as above. > 2) Access to existing libraries. There are often extensive libraries and > other software packages into which a model needs to be integrated. This > could be in practically any language, and so it would be necessary to > access to data structures of these libraries to have the model work. I > believe that this is the case for much of the CMISS-CellML work (I don't > really think that a proposal to re-write CMISS in ECMAScript would be > very popular!). In every case of people using CMISS that I know of, the use of CellML is to define model specific mathematical equations for integration into a larger model. I'm not suggesting re-writing CMISS in ECMAScript - rather you seem to be suggesting including CMISS in a CellML model?!? This would hold for most such cases of using existing libraries that I can think of, with the exception of someone wanting to solve a particular equation or set of equations in a model using a very specific numerical method that their CellML simulation tool does not support. Even if you take a step back and look at the larger picture of using things like FieldML, CellML, MathModelML (or something), etc... to describe something like an electrical propagation model in the heart, the tool (eg, CMISS) pulls it all together and plugs fields and variables together based on the model annotations. Otherwise you'll end up with cell models that say things like "give me the current load at this point in space by solving the bidomain model over this geometric domain" - making the cell model description useless for any other application. What you rather want is a simply a variable in the model which is the current load that has an interface of in. Your cell model integrator doesn't care where this value comes from, it just knows that when the tool calls for the cell model to be integrated that it will provide some appropriate value. > 3) Access to specialised hardware. A model could potentially even > require that a function is evaluated by some sort of online experimental > procedure (perhaps automated probing of a hardware model) for a given > set of inputs. Again, this seems more like a case where you define a mathematical model which given some input(s) produces some output(s). The controlling software would take the mathematical model definition in CellML and connect the appropriate inputs and outputs. I would really need a concrete example of why you would want to describe a mathematical model in CellML which requires input from specialised hardware. Surely you just define a variable that has an interface of in and annotate it such that the controlling software can find it and plug in the appropriate value(s)? > 4) Multiple standards, with different communities who favour them. It > would not be practical to get everyone involved with CellML to agree on > a certain procedural programming language (even deciding on Fortran vs > C++ etc... has been a challenge at this institute, and will probably be > impossible for the wider CellML community). As above, you are not performing computations using CellML directly - you always turn the model description into something suitable for the computational environment in which the model is being used. Thats the beauty of CellML - you can turn it into Fortran or C++, depending on your personal preference! CellML is all about being able to exchange a standard description of a mathematical model between potentially very different software environments. The whole idea is specifically not specifying the best way to compute outputs from the model - which seems to be what you are driving atand the best way to compute outputs from a model is always going to be dependent on the target computational environment. > As an example, consider my PhD project, where I plan to put machine > learning components into CellML models: > 1) Performan
Re: [cellml-discussion] Proposal: BCP for including external code inCellML models
David Nickerson wrote: >> 3) Do you agree with the basic premise of the proposal, that is that >> it is better to have a model which is partly expressed in CellML, than >> to have a model which is entirely expressed in a more general >> programming language? >> > > yes. > > >> 4) Do the best practice guidelines for CellML authors adequately >> protect the utility of CellML as a model interchange format? >> > > I think so. > > >> 5) Does the proposed approach fit well with the design of CellML? >> > > not really. The design philosophy of CellML is to utilise existing > standards where possible. I seem to recall the original intention for > the inclusion of required procedural code in a model was through the > csymbol mechanism you describe, but the code referenced is defined in a > standard format - with ECMAScript the preferred choice at that time. And > I see now there is a ECMAScript for XML extension, E4X, which might be > useful? > ECMAScript is not practical for use in modelling, because it is an interpreted, non-typed language, which necessarily means that it cannot be compiled and will be slower than compiled code. > By using a standard format for the external code (particularly if > available support for that format is good), you could reasonably expect > multiple applications to support your model. Although, similarly, if the > support you describe is built into the CellML API (CCGS?) then you could > also expect multiple applications to support a given model with external > code. > > Maybe some examples of where the use of external code is required would > be useful? > External code needs to be extensible, and hence outside the scope of the CellML specifications, for several reasons: 1) Performance. Code may need to be written in a way which is specific to a particular platform in order to be able to perform well. 2) Access to existing libraries. There are often extensive libraries and other software packages into which a model needs to be integrated. This could be in practically any language, and so it would be necessary to access to data structures of these libraries to have the model work. I believe that this is the case for much of the CMISS-CellML work (I don't really think that a proposal to re-write CMISS in ECMAScript would be very popular!). 3) Access to specialised hardware. A model could potentially even require that a function is evaluated by some sort of online experimental procedure (perhaps automated probing of a hardware model) for a given set of inputs. 4) Multiple standards, with different communities who favour them. It would not be practical to get everyone involved with CellML to agree on a certain procedural programming language (even deciding on Fortran vs C++ etc... has been a challenge at this institute, and will probably be impossible for the wider CellML community). As an example, consider my PhD project, where I plan to put machine learning components into CellML models: 1) Performance is likely to be important. If it is too slow, it might not be feasible to do at all. 2) I plan to use existing libraries, in a range of different languages. 3) I also have another (perhaps not as common) gain from specifying the external functions without describing their details: I need to run different code in 'training' and 'simulation' modes, and if I just wrote generic ECMAscript for the simulation case, there would be no simple way to deduce the training case. Because of this, it is probably good to keep the non-algebraic parts of the model completely separate, and leave it up to whoever implements the specific CellML processor. That said, I think we could have multiple levels of degeneracy away from standardised code, where you only go down to the next item if the current one is impossible: 1) Pure CellML. 2) CellML with standardised Turing-complete code support. 3) CellML with external (non-standardised) code. Best regards, Andrew Miller ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] Proposal: BCP for including external code inCellML models
> 3) Do you agree with the basic premise of the proposal, that is that > it is better to have a model which is partly expressed in CellML, than > to have a model which is entirely expressed in a more general > programming language? yes. > 4) Do the best practice guidelines for CellML authors adequately > protect the utility of CellML as a model interchange format? I think so. > 5) Does the proposed approach fit well with the design of CellML? not really. The design philosophy of CellML is to utilise existing standards where possible. I seem to recall the original intention for the inclusion of required procedural code in a model was through the csymbol mechanism you describe, but the code referenced is defined in a standard format - with ECMAScript the preferred choice at that time. And I see now there is a ECMAScript for XML extension, E4X, which might be useful? By using a standard format for the external code (particularly if available support for that format is good), you could reasonably expect multiple applications to support your model. Although, similarly, if the support you describe is built into the CellML API (CCGS?) then you could also expect multiple applications to support a given model with external code. Maybe some examples of where the use of external code is required would be useful? David. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
