[cellml-discussion] Include_in_CellML_1.2 requested: [Tracker Item 167] Should dissallow multiple references to same component within single import element
Andrew Miller [EMAIL PROTECTED] has asked for Include_in_CellML_1.2: Tracker Item 167: Should dissallow multiple references to same component within single import element http://bowmore.elyt.com/bugzilla/show_bug.cgi?id=167 ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] Include_in_CellML_1.2 requested: [Tracker Item 153] Allow multiple connections between the same pair of components
Andrew Miller [EMAIL PROTECTED] has asked for Include_in_CellML_1.2: Tracker Item 153: Allow multiple connections between the same pair of components http://bowmore.elyt.com/bugzilla/show_bug.cgi?id=153 --- Additional Comments from Andrew Miller [EMAIL PROTECTED] Section 3.2.4 of CellML 1.1 states, in the second sentence of the second paragraph: Only one connection may be created between any given pair of components in a model. This is a fairly pointless restriction from all fronts: * From a model authors perspective, it creates a burden on the author to consolidate all their connections which may have been created for different purposes, and current model authors claim that such consolidation is time consuming and error prone. * From a model readability perspective, it is also burdensome because connections between variables may not be in a logical order (this is less of an issue if tools are used, but the point still holds). * Implementation experience suggests that it is no harder to allow multiple connections between the same pair of components when writing simulation software, but the extra constraint imposes more work on developers when writing tools which try to validate the model. To fix this, we could simply drop the first two sentences of the second paragraph of Section 3.2.4, and perhaps replace them with a short explanation. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] CellML Tracker Change Password Request
You have (or someone impersonating you has) requested to change your CellML Tracker password. To complete the change, visit the following link: http://bowmore.elyt.com/bugzilla/token.cgi?t=CJnHxg1unEa=cfmpw If you are not the person who made this request, or you wish to cancel this request, visit the following link: http://bowmore.elyt.com/bugzilla/token.cgi?t=CJnHxg1unEa=cxlpw If you do nothing, the request will lapse after 3 days (at precisely 11:24 on the 1st of September, 2007) or when you log in successfully. ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
[cellml-discussion] [Tracker Item 88] New: Should we have a tracker component for the tracker?
http://bowmore.elyt.com/bugzilla/show_bug.cgi?id=88 Summary: Should we have a tracker component for the tracker? Product: Using CellML Version: unspecified Platform: All OS/Version: All Status: NEW Severity: question Priority: Moderate priority Component: General Enquiries AssignedTo: [EMAIL PROTECTED] ReportedBy: [EMAIL PROTECTED] CC: [EMAIL PROTECTED] I know this sounds a little strange, but there are plenty of issues that people have with the tracker that I'm sure would be best handled by the tracker... Like for example, this issue could go in the 'tracker issues' part of the tracker. -- 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 89] New: 'bug mirroring' between 'realms' of Bugzilla
http://bowmore.elyt.com/bugzilla/show_bug.cgi?id=89 Summary: 'bug mirroring' between 'realms' of Bugzilla Product: Using CellML Version: unspecified Platform: All OS/Version: All Status: NEW Severity: question Priority: Moderate priority Component: General Enquiries AssignedTo: [EMAIL PROTECTED] ReportedBy: [EMAIL PROTECTED] CC: [EMAIL PROTECTED] Is there a way that bugs can be categorised in two or more different 'realms' of Bugzilla? For example, a curation feature that I would like to implement could be proposed and discussed in my realm, under the auspices of a model repository / curation issue, and then once it has been decided on, then it would be useful to have it in Tommy's Cellml.org site realm. However, it would be most useful to have the same bug in both regions, so that someone tracking the progress could see everything in one place. Perhaps a better example is just an issue that simply needs to be in more than one category. -- 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 84] New: Locale differences for real number formats
http://bowmore.elyt.com/bugzilla/show_bug.cgi?id=84 Summary: Locale differences for real number formats Product: CellML Core Specifications Version: Future versions Platform: All OS/Version: All Status: NEW Severity: feature Priority: Moderate priority Component: Model structure AssignedTo: [EMAIL PROTECTED] ReportedBy: [EMAIL PROTECTED] CC: [EMAIL PROTECTED] Andrew Miller [EMAIL PROTECTED] changed: What|Removed |Added Flag||Include_in_CellML_1.2? The CellML Specification says that several different attributes must be real numbers, but doesn't specify the format in which these real numbers are expressed. The common computer formats for representing real numbers in text differ from locale to locale, and so a valid real number in one locale may be invalid in another, therefore harming the interoperability of CellML models. I propose that we provide a basic specification of allowable real number representations in text for use in attributes such as exponent, initial_value, and so on. MathML 2.0 already deals with this through the following text: The cn element is used to specify actual numerical constants. The content model must provide sufficient information that a number may be entered as data into a computational system. By default, it represents a signed real number in base 10. Thus, the content normally consists of PCDATA restricted to a sign, a string of decimal digits and possibly a decimal point, or alternatively one of the predefined symbolic constants such as pi;. -- 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 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
[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
[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
