Meeting Minutes 21 March 2007
Meeting Minutes 21 March 2007
Present: Tommy Yu, James Lawson, Andrew Miller
James has been working on getting the CellML models from the Oxford group (that Penny Noble has made) working in PCEnv. He noted that he had got 2 models working, and had 1 model in progress (which is almost complete). The problems with the models were mainly expressions involving derivatives other than on the left-hand side (which PCEnv doesn't currently support), as well as models which were overconstrained and underconstrained. He has also begun the process of familiarising himself with the CellML specification.
James noted that CellML 1.1 models can't be uploaded into the repository. Tommy hopes that Tingting's work will address this.
James noted that he was not very familiar with cardiac modelling, as most of his experience was with signal transduction and non-cardiac electrophysiology, and not higher-level physiological models. He is therefore unsure whether his fixed model is reliably reproducing the paper or not. He will look into this further. Andrew thinks that James might be able to seek help from some of the experts at the institute, e.g. Peter Hunter.
James was also keen to access some more training on the mathematics behind the modelling. Andrew suggested that he ask Poul if he can get a copy of some of the lecture notes for relevant papers. James was also keen to attend some of the papers on this.
Tommy has now finished the RDF metadata library. He currently plans to commit it and update the live site to start using this on Friday (if all goes to plan). Andrew suggested that the CCGS be updated on the live site at around the same time, as it is currently using a very old version with problems which have been fixed months ago. However, tests need to be done to ensure that it still works with the repository. Tommy will look into this. Tommy is also looking to fix an issue where the repository doesn't support the case where one model refers to more than one paper.
James noted that the undo function on the CellML repository doesn't work. Tommy noted that this was a broken Plone feature, and since we are using an older version of Plone, there is not much chance of getting this fixed. Tommy will help James to restore an unintentional change manually.
James noted that Matt had asked him to identify improvements to PCEnv, as he might be able to see issues that 'insiders' can't see. He has suggested that tooltips (i.e. boxes which pop-up when the mouse moves over a UI element, with explanatory text), as well as a more up to date manual, would be a useful thing to have. Andrew noted that the manual has not been updated since the stable release (and James is working with a snapshot), but agrees that the manual needs to be updated to describe more recent functionality. James also suggested a box zoom feature. Andrew noted that it was already there, but you need to use the left-mouse plus shift to access it.
James has been working on getting the CellML models from the Oxford group (that Penny Noble has made) working in PCEnv. He noted that he had got 2 models working, and had 1 model in progress (which is almost complete). The problems with the models were mainly expressions involving derivatives other than on the left-hand side (which PCEnv doesn't currently support), as well as models which were overconstrained and underconstrained. He has also begun the process of familiarising himself with the CellML specification.
James noted that CellML 1.1 models can't be uploaded into the repository. Tommy hopes that Tingting's work will address this.
James noted that he was not very familiar with cardiac modelling, as most of his experience was with signal transduction and non-cardiac electrophysiology, and not higher-level physiological models. He is therefore unsure whether his fixed model is reliably reproducing the paper or not. He will look into this further. Andrew thinks that James might be able to seek help from some of the experts at the institute, e.g. Peter Hunter.
James was also keen to access some more training on the mathematics behind the modelling. Andrew suggested that he ask Poul if he can get a copy of some of the lecture notes for relevant papers. James was also keen to attend some of the papers on this.
Tommy has now finished the RDF metadata library. He currently plans to commit it and update the live site to start using this on Friday (if all goes to plan). Andrew suggested that the CCGS be updated on the live site at around the same time, as it is currently using a very old version with problems which have been fixed months ago. However, tests need to be done to ensure that it still works with the repository. Tommy will look into this. Tommy is also looking to fix an issue where the repository doesn't support the case where one model refers to more than one paper.
James noted that the undo function on the CellML repository doesn't work. Tommy noted that this was a broken Plone feature, and since we are using an older version of Plone, there is not much chance of getting this fixed. Tommy will help James to restore an unintentional change manually.
James noted that Matt had asked him to identify improvements to PCEnv, as he might be able to see issues that 'insiders' can't see. He has suggested that tooltips (i.e. boxes which pop-up when the mouse moves over a UI element, with explanatory text), as well as a more up to date manual, would be a useful thing to have. Andrew noted that the manual has not been updated since the stable release (and James is working with a snapshot), but agrees that the manual needs to be updated to describe more recent functionality. James also suggested a box zoom feature. Andrew noted that it was already there, but you need to use the left-mouse plus shift to access it.