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[cellml-discussion] CellML API 1.0rc1 (release candidate forCellMLAPI 1.0) out


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  • From: david.nickerson at nus.edu.sg (David Nickerson)
  • Subject: [cellml-discussion] CellML API 1.0rc1 (release candidate forCellMLAPI 1.0) out
  • Date: Mon, 06 Nov 2006 12:23:21 +0800
> You haven't renamed the variable or the component, I assume? It stores
> variables by the index of the import (i.e. the order it started loading,
> 0 for the main model), the component name, and the variable name. One
> possibility is that the import number could be different (perhaps it
> started loading later, because the order the importing models finished
> loading was different). There is no generic way to tie imports together
> between two loads, since they don't need to have any unique name (and
> the same model can be imported more than once), so I'm not sure how we
> could resolve that issue.

no - I haven't changed anything. Once the simulation has run and I
select the appropriate variable (V) again I can flick between different
runs of the same model and have the graph remain valid and update itself
with the appropriate values. Its just the initial clone and then
simulation run that seems to result in the invalid Y variable. The X
variable remains valid.

>> I really dislike the idea of using points/graph to discretise my graphs.
>> I want to be able to say give me a point every 1 ms or every 10 ms.
>>
> As a result of discussions on cellml-discussion (of which you were a
> part of, and seemed to have agreed with the outcome), it was decided
> that the CIS would no longer produce points interpolated onto a regular
> grid, but would instead utilise the step size of the integrator to
> ensure that more data is provided in regions of the graph where lots of
> detail is needed, and less data is shown in relatively linear parts of
> the graph. The problem is, if you do this, you get far too many points
> if you are doing large runs with small error tolerances. The points /
> graph control does not define a regular grid on which points are
> gathered, but rather, is used to define a minimum distance between steps
> required for the point to be reported.

I thought that discussion failed to arrive at any consensus apart from
the fact that there are valid reasons for a whole bunch of different
ways to determine what values in a given simulation should be
reported/stored/graphed. I'm just suggesting that personally I would
like to see an alternative method offered by pcenv - particularly one
that is probably about the most common amongst similar tools.

>> I am not convinced that I need to clone my model just to change the
>> integration parameters and re-integrate. This is especially painful
>> given how slow it is to clone and then select the cloned model. This
>> seems like a feature forced upon the user to support the idea of another
>> client accessing the same model through the cellml_corba_server.
> The freezing of models is not for the benefit of cellml_corba_server,
> but rather, to enforce the one-to-one relationship between models and
> sets of results. If we didn't enforce this, we could have one model in
> the model selector, with more than one associated run, and there would
> be no way to know what parameters the data you have came from (unless
> you are proposing throwing away the old data).

that is what I'm proposing. maybe when the dialog pops up the user has
the option of cloning a model or throwing away any results or cancelling
the modification.

> I can look at ways to improve this, but I think it would require too big
> a change to land on the 0.1 branch.

possibly - but as I said, at least to me this is a prohibitive cost in
performance that puts me off using the tool.

>> Standard user interface behaviour suggests that when I right click on
>> something but choose nothing from the menu that pops up then either
>> nothing is done or the menu remains visible when I release the mouse
>> button. This is true for most right-clicks I have tried, but right
>> clicking on a model in the model tree will always result in the model
>> rename dialog box unless I specifically choose some option or navigate
>> the mouse away from the menu. If I hold the button down, it is clear
>> that the rename option is not selected, yet as soon as I release the
>> mouse button up pops the dialog box.
>>
> I have been unable to reproduce this. A few questions:
> Where was the cursor when you released the right mouse button?

I don't move the cursor, I'm hovering over a model's name when I click
down and release the mouse button.

> Had you chosen rename earlier but not got the dialog box yet?

nope.

> Can you reproduce this every time, or is it only an occasional issue?

every time.

> What platform?

Linux, Fedora Core 5.

> Do you ever see the same issue in Mozilla on your platform?

nope - its only the model view. Even the other right clicks in pcenv do
not display this behaviour...


--
David Nickerson, PhD
Research Fellow
Division of Bioengineering
Faculty of Engineering
National University of Singapore
Email: david.nickerson at nus.edu.sg


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