[cellml-discussion] CellML Tracker being tested at http://bowmore.elyt.com/bugzilla/
Hi all, Following discussions with the IT group yesterday, we have arranged to set up the Bugzilla based CellML tracker for testing on an externally hosted site. The URL is http://bowmore.elyt.com/bugzilla/ This will not be the final tracker URL (and may not be the final tracker technology), as there is currently a process underway to evaluate the best tracker. However, part of this process will require actually using a tracker to see what the final result is. Users are encouraged to try out the tracker to submit and view real questions and bugs (at this point in time, this tracker is the best place at least to report PCEnv and CellML API bugs, because at the very least the correct person should get an e-mail about your submission). You feedback on using the tracker will also be valuable, as it will help inform future decisions on what tracker technology to use and/or improvements to the tracker resources. If you are able to do so, putting it on the tracker would be a good way to handle such comments, otherwise they could also be e-mailed directly to the list. Note that all new tracker items are sent to this list (unless you choose one of the private question / security issue options), and you also have the option when commenting on an issue to send your comment to the list. Best regards, Andrew Miller ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] CellML Tracker being tested athttp://bowmore.elyt.com/bugzilla/
Hi Andrew, Just to point out that you might want to update the front page to indicate that this tracker is not in fact maintained at the University of Auckland. David. Andrew Miller wrote: Hi all, Following discussions with the IT group yesterday, we have arranged to set up the Bugzilla based CellML tracker for testing on an externally hosted site. The URL is http://bowmore.elyt.com/bugzilla/ This will not be the final tracker URL (and may not be the final tracker technology), as there is currently a process underway to evaluate the best tracker. However, part of this process will require actually using a tracker to see what the final result is. Users are encouraged to try out the tracker to submit and view real questions and bugs (at this point in time, this tracker is the best place at least to report PCEnv and CellML API bugs, because at the very least the correct person should get an e-mail about your submission). You feedback on using the tracker will also be valuable, as it will help inform future decisions on what tracker technology to use and/or improvements to the tracker resources. If you are able to do so, putting it on the tracker would be a good way to handle such comments, otherwise they could also be e-mailed directly to the list. Note that all new tracker items are sent to this list (unless you choose one of the private question / security issue options), and you also have the option when commenting on an issue to send your comment to the list. Best regards, Andrew Miller ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion -- David Nickerson, PhD Research Fellow Division of Bioengineering Faculty of Engineering National University of Singapore Email: [EMAIL PROTECTED] ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] embedded stimulus currents in CellML models
Still, I have managed to recompile it. Oops, this got sent too early and I have yet to get CellML2Dot to compile... In fact, I have given up and I think it does illustrate the point I made in a previous message of mine: documentation, documentation, documentation... :) I was a bit surprised that you had managed it :-) The first step is to get the CellML API built, from there it should be easy ;-) ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] [Tracker Item 43] New: typo in simplified (?)interface
just to follow up, submitting this tracker item resulted in An internal server error occurred. Please try again later. even though it would appear that the tracker item was successfully entered into the tracker database. [EMAIL PROTECTED] wrote: http://bowmore.elyt.com/bugzilla/show_bug.cgi?id=43 Summary: typo in simplified (?) interface Product: cellml.org site Version: unspecified Platform: All OS/Version: All Status: NEW Severity: major Priority: Very high priority Component: CellML Tracker AssignedTo: [EMAIL PROTECTED] ReportedBy: [EMAIL PROTECTED] on the page http://bowmore.elyt.com/bugzilla/enter_bug.cgi?product=Using%20CellMLformat=generalhelp there is a missing space in the second sentence of the Keep Private help text. -- David Nickerson, PhD Research Fellow Division of Bioengineering Faculty of Engineering National University of Singapore Email: [EMAIL PROTECTED] ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] [Tracker Item 44] New: Severity field help
http://bowmore.elyt.com/bugzilla/show_bug.cgi?id=44 Summary: Severity field help Product: cellml.org site Version: unspecified Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: Moderate priority Component: CellML Tracker AssignedTo: [EMAIL PROTECTED] ReportedBy: [EMAIL PROTECTED] it would be good if the descriptions for the severity field matched those available in this tracker. Some relevant guidance in the use with respect to CellML would also be good. -- Configure bugmail: http://bowmore.elyt.com/bugzilla/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the tracker item. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] [Tracker Item 45] New: Big empty box in step 1 of Ask a general question about CellML
http://bowmore.elyt.com/bugzilla/show_bug.cgi?id=45 Summary: Big empty box in step 1 of Ask a general question about CellML Product: cellml.org site Version: unspecified Platform: PC OS/Version: Linux Status: NEW Severity: major Priority: Moderate priority Component: CellML Tracker AssignedTo: [EMAIL PROTECTED] ReportedBy: [EMAIL PROTECTED] Clicking the Ask a general question about CellML brings up a page with Step 1 of 3 - has your question already been answered? and then a big empty box. Scrolling down, I can then find the actual form to enter my question. -- Configure bugmail: http://bowmore.elyt.com/bugzilla/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the tracker item. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] [Tracker Item 46] New: Components for CellML Core Specifications
http://bowmore.elyt.com/bugzilla/show_bug.cgi?id=46 Summary: Components for CellML Core Specifications Product: cellml.org site Version: unspecified Platform: All OS/Version: All Status: NEW Severity: normal Priority: Moderately high priority Component: CellML Tracker AssignedTo: [EMAIL PROTECTED] ReportedBy: [EMAIL PROTECTED] Have both a miscellaneous and an other component for the CellML Core Specifications product seems a bit of an overkill. I'd suggest removing miscellaneous. It may also be useful to add a future improvement or new feature component for use in submitting proposals for new features for consideration in future versions of CellML. -- Configure bugmail: http://bowmore.elyt.com/bugzilla/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the tracker item. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] [Tracker Item 48] New: Deprecation of the reaction element
http://bowmore.elyt.com/bugzilla/show_bug.cgi?id=48 Summary: Deprecation of the reaction element Product: CellML Core Specifications Version: Future versions Platform: PC OS/Version: Linux Status: NEW Severity: feature Priority: Moderate priority Component: Reactions AssignedTo: [EMAIL PROTECTED] ReportedBy: [EMAIL PROTECTED] The reaction element in the core CellML specification needs to be deprecated. -- Configure bugmail: http://bowmore.elyt.com/bugzilla/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the tracker item. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] [Tracker Item 49] New: Removal of the reaction element
http://bowmore.elyt.com/bugzilla/show_bug.cgi?id=49 Summary: Removal of the reaction element Product: CellML Core Specifications Version: Future versions Platform: All OS/Version: All Status: NEW Severity: feature Priority: Moderately high priority Component: Reactions AssignedTo: [EMAIL PROTECTED] ReportedBy: [EMAIL PROTECTED] The reaction element in the core CellML specification needs should be made obsolete. -- Configure bugmail: http://bowmore.elyt.com/bugzilla/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the tracker item. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] CellML Tracker being tested athttp://bowmore.elyt.com/bugzilla/
David Nickerson wrote: Clicking the Submit a problem report link under the most common actions leads to a page where the user must choose a product on which to enter a tracker item. It is not very obvious what to do on this page as the instructions are hidden in the page title sitting above the navigation bar - maybe its just me, but that is the last place I looked for instructions on what to doperhaps the instructions could be placed in the main body of the page? Hi Andre, Do you like the new template I just put up, which adds in Choose the area of the CellML project to which this relates: as a paragraph above the list of products? If I then choose, for example, CellML core specifications I get a bunch of stuff and a big red banner telling me There are no duplicate statistics for today (2007-07-20) or yesterday. followed by Please press Back and try again. and what looks like the standard footer navigation bar. This is an iframe with the list of duplicates (which doesn't come up with anything at the moment) not the main page. The template on which this in is configurable (I copied the IFRAME code from the bugzilla.mozilla.org submission temlate). The idea of the iframe is that embedded in the main page is a sub-page that lets you search for duplicates so you don't have to go elsewhere to check for duplicates and then come back. However, you are the second person to be confused by it, so perhaps it isn't worth it? I press Back and try again with the same result. How should I submit a new tracker item? Just ignore the iframe (or ideally, use the search box below it which will update it to search for the terms you enter), and once you are finished just scroll down past it. However, I think we are going to have to change this - I am just not sure how to make it less confusing - perhaps once we have at least one duplicate in statistics for the database it won't be as confusing? Best regards, Andrew Thanks, David. Andrew Miller wrote: Hi all, Following discussions with the IT group yesterday, we have arranged to set up the Bugzilla based CellML tracker for testing on an externally hosted site. The URL is http://bowmore.elyt.com/bugzilla/ This will not be the final tracker URL (and may not be the final tracker technology), as there is currently a process underway to evaluate the best tracker. However, part of this process will require actually using a tracker to see what the final result is. Users are encouraged to try out the tracker to submit and view real questions and bugs (at this point in time, this tracker is the best place at least to report PCEnv and CellML API bugs, because at the very least the correct person should get an e-mail about your submission). You feedback on using the tracker will also be valuable, as it will help inform future decisions on what tracker technology to use and/or improvements to the tracker resources. If you are able to do so, putting it on the tracker would be a good way to handle such comments, otherwise they could also be e-mailed directly to the list. Note that all new tracker items are sent to this list (unless you choose one of the private question / security issue options), and you also have the option when commenting on an issue to send your comment to the list. Best regards, Andrew Miller ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] [Tracker Item 60] New: Tracker integration with cellml.org
http://bowmore.elyt.com/bugzilla/show_bug.cgi?id=60 Summary: Tracker integration with cellml.org Product: cellml.org site Version: unspecified Platform: All OS/Version: All Status: NEW Severity: feature Priority: Very high priority Component: CellML Tracker AssignedTo: [EMAIL PROTECTED] ReportedBy: [EMAIL PROTECTED] For this tracker to be useful it must integrate into the current cellml.org Plone-based portal. What are the issues involved in this? -- Configure bugmail: http://bowmore.elyt.com/bugzilla/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the tracker item. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] [Tracker Item 61] New: Tracker look-and-feel
http://bowmore.elyt.com/bugzilla/show_bug.cgi?id=61 Summary: Tracker look-and-feel Product: cellml.org site Version: unspecified Platform: All OS/Version: All Status: NEW Severity: feature Priority: Moderate priority Component: CellML Tracker AssignedTo: [EMAIL PROTECTED] ReportedBy: [EMAIL PROTECTED] Blocks: 60 This tracker should use the standard cellml.org look-and-feel. -- Configure bugmail: http://bowmore.elyt.com/bugzilla/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the tracker item. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] [Tracker Item 62] New: User authentication
http://bowmore.elyt.com/bugzilla/show_bug.cgi?id=62 Summary: User authentication Product: cellml.org site Version: unspecified Platform: All OS/Version: All Status: NEW Severity: feature Priority: Moderate priority Component: CellML Tracker AssignedTo: [EMAIL PROTECTED] ReportedBy: [EMAIL PROTECTED] Blocks: 60 This tracker should share common user authentication with the cellml.org portal. -- Configure bugmail: http://bowmore.elyt.com/bugzilla/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the tracker item. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] [Tracker Item 63] New: Tracker should not CC cellml-discussion
http://bowmore.elyt.com/bugzilla/show_bug.cgi?id=63 Summary: Tracker should not CC cellml-discussion Product: cellml.org site Version: unspecified Platform: PC OS/Version: Windows Status: NEW Severity: normal Priority: Moderate priority Component: CellML Tracker AssignedTo: [EMAIL PROTECTED] ReportedBy: [EMAIL PROTECTED] CC all new tracker items and changes to the mailing list is creates a lot of litter on the list. One of the aims of the tracker is to allow the list to be used for things that won't fit into the tracker. I suggest that an all open tracker items search be shared, and its RSS feed URL be placed somewhere on the front page. I just tried this for a saved search of my own, and the feed works just like an e-mail inbox, will all recent changes showing up as new feed items, virtually in real time. I couldn't share the search at this time (See also tracker items 58 and 59). -- Configure bugmail: http://bowmore.elyt.com/bugzilla/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the tracker item. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] [Tracker Item 65] New: cellml.org site searches of tracker items
http://bowmore.elyt.com/bugzilla/show_bug.cgi?id=65 Summary: cellml.org site searches of tracker items Product: cellml.org site Version: unspecified Platform: All OS/Version: All Status: NEW Severity: feature Priority: Moderate priority Component: CellML Tracker AssignedTo: [EMAIL PROTECTED] ReportedBy: [EMAIL PROTECTED] Blocks: 60 We should be able to do searches using the cellml.org site search and have the search delve into to tracker items for possible matches. -- Configure bugmail: http://bowmore.elyt.com/bugzilla/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the tracker item. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] [Tracker Item 60] Tracker integration with cellml.org
http://bowmore.elyt.com/bugzilla/show_bug.cgi?id=60 Andre [EMAIL PROTECTED] changed: What|Removed |Added Depends on||65 -- Configure bugmail: http://bowmore.elyt.com/bugzilla/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the tracker item. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] [Tracker Item 66] New: Dependency graphs not working
http://bowmore.elyt.com/bugzilla/show_bug.cgi?id=66 Summary: Dependency graphs not working Product: cellml.org site Version: unspecified Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: Moderately high priority Component: CellML Tracker AssignedTo: [EMAIL PROTECTED] ReportedBy: [EMAIL PROTECTED] Dependency graphs do not appear to work - at least all I seem to get is a blue dot. -- Configure bugmail: http://bowmore.elyt.com/bugzilla/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the tracker item. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] [Tracker Item 67] New: MathML 3.0
http://bowmore.elyt.com/bugzilla/show_bug.cgi?id=67 Summary: MathML 3.0 Product: CellML Core Specifications Version: Future versions Platform: PC OS/Version: Linux Status: NEW Severity: feature Priority: Moderate priority Component: Mathematics AssignedTo: [EMAIL PROTECTED] ReportedBy: [EMAIL PROTECTED] The MathML version 3.0 specification is currently under development. We need to follow the specification's progress and decide if and when to switch to the new specification. See this thread on cellml-discussion: http://article.gmane.org/gmane.text.xml.cellml.general/375 -- Configure bugmail: http://bowmore.elyt.com/bugzilla/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the tracker item. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] [Tracker Item 64] New: Cross-referencing from description and comments does not seem to be working .
http://bowmore.elyt.com/bugzilla/show_bug.cgi?id=64 Summary: Cross-referencing from description and comments does not seem to be working. Product: cellml.org site Version: unspecified Platform: PC OS/Version: Windows Status: NEW Severity: normal Priority: Moderate priority Component: CellML Tracker AssignedTo: [EMAIL PROTECTED] ReportedBy: [EMAIL PROTECTED] In other bugzilla installations, referencing one tracker item from another in the description text usually automatically creates a hyperlink. It may be that the term bug is sought, and we are trying to use the term tracker item. See for example text in bug 63. I mean tracker item 63. -- Configure bugmail: http://bowmore.elyt.com/bugzilla/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the tracker item. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] CellML_1.1.1 requested: [Tracker Item 48]Deprecation of the reaction element
David Nickerson wrote: What does this mean? I guess that CellML_1.1.1 is a bad name for the flag. Flags are a generic facility in Bugzilla which are requested and then granted or denied. I intended for this to be used for proposals to be requested for CellML 1.1.1 (i.e. suggested for a given version of CellML), and then granted or denied based on community consensus. How about Inclusion_CellML_1.1.1 and Inclusion_CellML_1.2 instead? Best regards, Andrew ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] CellML_1.1.1 requested: [Tracker Item48]Deprecation of the reaction element
sorry, I was more meaning what it means that you have asked for something and what we're supposed to do about it? But, yes - inclusion_CellML_1.1.1 might be better, or maybe target_CellML_version_1.1.1? for_inclusion_in_CellML_1.1.1 ? Andrew Miller wrote: David Nickerson wrote: What does this mean? I guess that CellML_1.1.1 is a bad name for the flag. Flags are a generic facility in Bugzilla which are requested and then granted or denied. I intended for this to be used for proposals to be requested for CellML 1.1.1 (i.e. suggested for a given version of CellML), and then granted or denied based on community consensus. How about Inclusion_CellML_1.1.1 and Inclusion_CellML_1.2 instead? Best regards, Andrew ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion -- David Nickerson, PhD Research Fellow Division of Bioengineering Faculty of Engineering National University of Singapore Email: [EMAIL PROTECTED] ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] [Tracker Item 75] New: Test #3
http://bowmore.elyt.com/bugzilla/show_bug.cgi?id=75 Summary: Test #3 Product: CellML Core Specifications Version: Future versions Platform: PC OS/Version: Linux Status: NEW Severity: feature Priority: Moderate priority Component: Future Improvements AssignedTo: [EMAIL PROTECTED] ReportedBy: [EMAIL PROTECTED] CC: [EMAIL PROTECTED] Sorry for the test. -- Configure bugmail: http://bowmore.elyt.com/bugzilla/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the tracker item. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] [Tracker Item 70] Delayed variables
http://bowmore.elyt.com/bugzilla/show_bug.cgi?id=70 --- Comment #2 from Andrew Miller [EMAIL PROTECTED] 2007-07-21 17:45:44 --- (In reply to comment #1) Convolution with a shifted dirac delta is really just another way of saying y(t-k), since that is essentially one approach to defining the dirac delta generalised function. Also, convolution would require us to specify the function arguments anyway. So I think convolution is not the approach we should take. Changing the specification so that y becomes y(t) (i.e. a function) seems the cleanest approach to me. I don't see the benefits of the convolution approach either. It perhaps mathematically cleaner but there are other considerations which might affect this: 1) Consistency with existing CellML specifications - how much do we want to change the specification to support this? 2) Space requirements of the representation - will this be a major show-stopper if every variable suddenly becomes applyciy/cicit/ci/apply instead of just ciy/ci? 3) Consequences for software implementations - does this provide enough data for a simulator to use - how do we define boundary conditions, and what sorts of simulation metadata do we need to make such simulations work? How will they interact with the new representation? One option might be to introduce some sort of semantics where sometimes ciy/ci is a variable meaning y, and other times it is a function, but this might cause headaches and ambiguity if we ever introduce functions as a type in CellML (although we could add attributes to the 'variables' describing their type it might be unambiguous). Also, would a variable still be called a variable in the component if it is actually a function, or do you propose that we have more than one type of element? -- Configure bugmail: http://bowmore.elyt.com/bugzilla/userprefs.cgi?tab=email --- You are receiving this mail because: --- You are on the CC list for the tracker item. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
