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From: SourceForge.net <no...@so...> - 2010-11-18 14:30:26
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SED-ML L1V1 item #3111557, was opened at 2010-11-18 14:30 Message generated for change (Tracker Item Submitted) made by otter606 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3111557&group_id=293618 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: SED-ML issues Group: Release Candidate 1 Status: Open Resolution: None Priority: 5 Private: No Submitted By: Richard Adams (otter606) Assigned to: Nobody/Anonymous (nobody) Summary: Stronger typing for Model 'source' attribute Initial Comment: The 'source' attribute for Model is currently just a string in the schema. Given that the spec requires the value to be an XLink, preferably a URI, how about either 1) Altering the type to anyURI in the schema 2) Add source as a subelement with xlink attributes. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3111557&group_id=293618 |
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From: SourceForge.net <no...@so...> - 2010-11-16 14:16:59
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SED-ML L1V1 item #3088359, was opened at 2010-10-15 22:33 Message generated for change (Comment added) made by otter606 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088359&group_id=293618 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Specification content Group: Release Candidate 1 Status: Open Resolution: None Priority: 3 Private: No Submitted By: Richard Adams (otter606) Assigned to: Nobody/Anonymous (nobody) Summary: Figure 12 subclasses missing attributes Initial Comment: The 'Task' box is missing modelReference and simulationReference attributes ---------------------------------------------------------------------- >Comment By: Richard Adams (otter606) Date: 2010-11-16 14:16 Message: And if we're just listing attributes here, then mathML in datagenerator is now an element, not a na ttribuet, and should be removed? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088359&group_id=293618 |
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From: Richard A. <ric...@ed...> - 2010-11-16 10:21:36
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The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. |
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From: SourceForge.net <no...@so...> - 2010-11-10 22:15:38
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SED-ML L1V1 item #3106339, was opened at 2010-11-10 00:09 Message generated for change (Settings changed) made by otter606 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3106339&group_id=293618 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Specification content Group: Release Candidate 1 >Status: Closed Resolution: None Priority: 5 Private: No Submitted By: Richard Adams (otter606) Assigned to: Nobody/Anonymous (nobody) Summary: newXML schema error Initial Comment: <xs:any namespace="http://www.w3.org/1999/xhtml" processContents="skip" minOccurs="1" maxOccurs="unbounded"/> needs to be changed to <xs:any processContents="skip" minOccurs="1" maxOccurs="unbounded"/> since any XML can be contained here. ---------------------------------------------------------------------- Comment By: Richard Adams (otter606) Date: 2010-11-10 22:14 Message: edited description in newXML.tex to reflect it doesn't inherit SEDBase ---------------------------------------------------------------------- Comment By: Richard Adams (otter606) Date: 2010-11-10 19:47 Message: fixed Unique_Particle_Attribution problem by making newXML not inherit from SEDBase. ---------------------------------------------------------------------- Comment By: Richard Adams (otter606) Date: 2010-11-10 01:23 Message: Removal of a 'namespace' and allowing xs:any violates the Unique_Particle_Attribution rule. http://en.wikipedia.org/wiki/Unique_Particle_Attribution Since notes and annotation elements are optional, the schema validator cannot tell if an <annotation> element in a newXML element should be considered an annotation, or an xs:any. Since we don't know in advance what namespace the XML in newXML element is going to be, some solutions appear to be: 1) Have newXML not inherit from SEDBase, then any model XML subelement can be unambiguously attributed to xs:any. We could probably get away with this as notes/annotation could be added to the parent change/addXML element? 2) Include a placeholder namespace in the schema for newXML content, which at least allows the schema to be parsed, and get software libraries to ignore schema validation errors due to unexpected content 2) Insert a ---------------------------------------------------------------------- Comment By: Richard Adams (otter606) Date: 2010-11-10 00:10 Message: fixed ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3106339&group_id=293618 |
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From: SourceForge.net <no...@so...> - 2010-11-10 22:14:07
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SED-ML L1V1 item #3106339, was opened at 2010-11-10 00:09 Message generated for change (Comment added) made by otter606 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3106339&group_id=293618 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Specification content Group: Release Candidate 1 >Status: Open Resolution: None Priority: 5 Private: No Submitted By: Richard Adams (otter606) Assigned to: Nobody/Anonymous (nobody) Summary: newXML schema error Initial Comment: <xs:any namespace="http://www.w3.org/1999/xhtml" processContents="skip" minOccurs="1" maxOccurs="unbounded"/> needs to be changed to <xs:any processContents="skip" minOccurs="1" maxOccurs="unbounded"/> since any XML can be contained here. ---------------------------------------------------------------------- >Comment By: Richard Adams (otter606) Date: 2010-11-10 22:14 Message: edited description in newXML.tex to reflect it doesn't inherit SEDBase ---------------------------------------------------------------------- Comment By: Richard Adams (otter606) Date: 2010-11-10 19:47 Message: fixed Unique_Particle_Attribution problem by making newXML not inherit from SEDBase. ---------------------------------------------------------------------- Comment By: Richard Adams (otter606) Date: 2010-11-10 01:23 Message: Removal of a 'namespace' and allowing xs:any violates the Unique_Particle_Attribution rule. http://en.wikipedia.org/wiki/Unique_Particle_Attribution Since notes and annotation elements are optional, the schema validator cannot tell if an <annotation> element in a newXML element should be considered an annotation, or an xs:any. Since we don't know in advance what namespace the XML in newXML element is going to be, some solutions appear to be: 1) Have newXML not inherit from SEDBase, then any model XML subelement can be unambiguously attributed to xs:any. We could probably get away with this as notes/annotation could be added to the parent change/addXML element? 2) Include a placeholder namespace in the schema for newXML content, which at least allows the schema to be parsed, and get software libraries to ignore schema validation errors due to unexpected content 2) Insert a ---------------------------------------------------------------------- Comment By: Richard Adams (otter606) Date: 2010-11-10 00:10 Message: fixed ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3106339&group_id=293618 |
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From: SourceForge.net <no...@so...> - 2010-11-10 19:47:51
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SED-ML L1V1 item #3106339, was opened at 2010-11-10 00:09 Message generated for change (Settings changed) made by otter606 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3106339&group_id=293618 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Specification content Group: Release Candidate 1 >Status: Closed Resolution: None Priority: 5 Private: No Submitted By: Richard Adams (otter606) Assigned to: Nobody/Anonymous (nobody) Summary: newXML schema error Initial Comment: <xs:any namespace="http://www.w3.org/1999/xhtml" processContents="skip" minOccurs="1" maxOccurs="unbounded"/> needs to be changed to <xs:any processContents="skip" minOccurs="1" maxOccurs="unbounded"/> since any XML can be contained here. ---------------------------------------------------------------------- Comment By: Richard Adams (otter606) Date: 2010-11-10 19:47 Message: fixed Unique_Particle_Attribution problem by making newXML not inherit from SEDBase. ---------------------------------------------------------------------- Comment By: Richard Adams (otter606) Date: 2010-11-10 01:23 Message: Removal of a 'namespace' and allowing xs:any violates the Unique_Particle_Attribution rule. http://en.wikipedia.org/wiki/Unique_Particle_Attribution Since notes and annotation elements are optional, the schema validator cannot tell if an <annotation> element in a newXML element should be considered an annotation, or an xs:any. Since we don't know in advance what namespace the XML in newXML element is going to be, some solutions appear to be: 1) Have newXML not inherit from SEDBase, then any model XML subelement can be unambiguously attributed to xs:any. We could probably get away with this as notes/annotation could be added to the parent change/addXML element? 2) Include a placeholder namespace in the schema for newXML content, which at least allows the schema to be parsed, and get software libraries to ignore schema validation errors due to unexpected content 2) Insert a ---------------------------------------------------------------------- Comment By: Richard Adams (otter606) Date: 2010-11-10 00:10 Message: fixed ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3106339&group_id=293618 |
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From: SourceForge.net <no...@so...> - 2010-11-10 19:47:21
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SED-ML L1V1 item #3106339, was opened at 2010-11-10 00:09 Message generated for change (Comment added) made by otter606 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3106339&group_id=293618 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Specification content Group: Release Candidate 1 Status: Open Resolution: None Priority: 5 Private: No Submitted By: Richard Adams (otter606) Assigned to: Nobody/Anonymous (nobody) Summary: newXML schema error Initial Comment: <xs:any namespace="http://www.w3.org/1999/xhtml" processContents="skip" minOccurs="1" maxOccurs="unbounded"/> needs to be changed to <xs:any processContents="skip" minOccurs="1" maxOccurs="unbounded"/> since any XML can be contained here. ---------------------------------------------------------------------- >Comment By: Richard Adams (otter606) Date: 2010-11-10 19:47 Message: fixed Unique_Particle_Attribution problem by making newXML not inherit from SEDBase. ---------------------------------------------------------------------- Comment By: Richard Adams (otter606) Date: 2010-11-10 01:23 Message: Removal of a 'namespace' and allowing xs:any violates the Unique_Particle_Attribution rule. http://en.wikipedia.org/wiki/Unique_Particle_Attribution Since notes and annotation elements are optional, the schema validator cannot tell if an <annotation> element in a newXML element should be considered an annotation, or an xs:any. Since we don't know in advance what namespace the XML in newXML element is going to be, some solutions appear to be: 1) Have newXML not inherit from SEDBase, then any model XML subelement can be unambiguously attributed to xs:any. We could probably get away with this as notes/annotation could be added to the parent change/addXML element? 2) Include a placeholder namespace in the schema for newXML content, which at least allows the schema to be parsed, and get software libraries to ignore schema validation errors due to unexpected content 2) Insert a ---------------------------------------------------------------------- Comment By: Richard Adams (otter606) Date: 2010-11-10 00:10 Message: fixed ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3106339&group_id=293618 |
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From: Frank T. B. <fbe...@ca...> - 2010-11-10 17:32:45
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Hello Richard, I agree, referencing the xhtml namespace is wrong. And I agree, newXML should not inherit from SEDBase. Annotations can already be added to the addXML element, so we are covered. Best Frank From: Richard Adams [mailto:ric...@ed...] Sent: Wednesday, November 10, 2010 2:17 AM To: Frank T. Bergmann Subject: sed-ml schema Hi Frank I just came across some issues with the newXML element as it is defined in the schema. Previously the schema defined new XML as <xs:any namespace="http://www.w3.org/1999/xhtml" processContents="skip" minOccurs="1" maxOccurs="unbounded"/> which is clearly wrong as newXML should hold any XML, not HTML. But changing to <xs:any processContents="skip" minOccurs="1" maxOccurs="unbounded"/> violates the Unique_Particle_Attribution rule. http://en.wikipedia.org/wiki/Unique_Particle_Attribution Since notes and annotation elements are optional, the schema validator cannot tell if an <annotation> element in a newXML element should be considered an annotation, or an xs:any, so SEDML validation fails as the schema itself is considered invalid. I can only think of altering newXML to *not* inherit from SEDBase, then any model XML subelement can be unambiguously attributed to xs:any. But just wondered if you might have any alternative solutions. This is in the tracker 3106339. Cheers Richard Dr Richard Adams Software Development Team Leader, Centre For Systems Biology Edinburgh University of Edinburgh Tel: 0131 651 9019 email : ric...@ed... Web: http://csbe.bio.ed.ac.uk/adams.php |
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From: SourceForge.net <no...@so...> - 2010-11-10 01:23:10
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SED-ML L1V1 item #3106339, was opened at 2010-11-10 00:09 Message generated for change (Comment added) made by otter606 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3106339&group_id=293618 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Specification content Group: Release Candidate 1 >Status: Open >Resolution: None Priority: 5 Private: No Submitted By: Richard Adams (otter606) Assigned to: Nobody/Anonymous (nobody) Summary: newXML schema error Initial Comment: <xs:any namespace="http://www.w3.org/1999/xhtml" processContents="skip" minOccurs="1" maxOccurs="unbounded"/> needs to be changed to <xs:any processContents="skip" minOccurs="1" maxOccurs="unbounded"/> since any XML can be contained here. ---------------------------------------------------------------------- >Comment By: Richard Adams (otter606) Date: 2010-11-10 01:23 Message: Removal of a 'namespace' and allowing xs:any violates the Unique_Particle_Attribution rule. http://en.wikipedia.org/wiki/Unique_Particle_Attribution Since notes and annotation elements are optional, the schema validator cannot tell if an <annotation> element in a newXML element should be considered an annotation, or an xs:any. Since we don't know in advance what namespace the XML in newXML element is going to be, some solutions appear to be: 1) Have newXML not inherit from SEDBase, then any model XML subelement can be unambiguously attributed to xs:any. We could probably get away with this as notes/annotation could be added to the parent change/addXML element? 2) Include a placeholder namespace in the schema for newXML content, which at least allows the schema to be parsed, and get software libraries to ignore schema validation errors due to unexpected content 2) Insert a ---------------------------------------------------------------------- Comment By: Richard Adams (otter606) Date: 2010-11-10 00:10 Message: fixed ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3106339&group_id=293618 |
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From: SourceForge.net <no...@so...> - 2010-11-10 00:10:11
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SED-ML L1V1 item #3106339, was opened at 2010-11-10 00:09 Message generated for change (Comment added) made by otter606 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3106339&group_id=293618 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Specification content Group: Release Candidate 1 >Status: Closed >Resolution: Fixed Priority: 5 Private: No Submitted By: Richard Adams (otter606) Assigned to: Nobody/Anonymous (nobody) Summary: newXML schema error Initial Comment: <xs:any namespace="http://www.w3.org/1999/xhtml" processContents="skip" minOccurs="1" maxOccurs="unbounded"/> needs to be changed to <xs:any processContents="skip" minOccurs="1" maxOccurs="unbounded"/> since any XML can be contained here. ---------------------------------------------------------------------- >Comment By: Richard Adams (otter606) Date: 2010-11-10 00:10 Message: fixed ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3106339&group_id=293618 |
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From: SourceForge.net <no...@so...> - 2010-11-10 00:09:26
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SED-ML L1V1 item #3106339, was opened at 2010-11-10 00:09 Message generated for change (Tracker Item Submitted) made by otter606 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3106339&group_id=293618 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Specification content Group: Release Candidate 1 Status: Open Resolution: None Priority: 5 Private: No Submitted By: Richard Adams (otter606) Assigned to: Nobody/Anonymous (nobody) Summary: newXML schema error Initial Comment: <xs:any namespace="http://www.w3.org/1999/xhtml" processContents="skip" minOccurs="1" maxOccurs="unbounded"/> needs to be changed to <xs:any processContents="skip" minOccurs="1" maxOccurs="unbounded"/> since any XML can be contained here. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3106339&group_id=293618 |
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From: Richard A. <ra...@st...> - 2010-10-27 13:09:17
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Hi guys, I've been through the spec several times for typos & inconsistencies etc., The remaining 9 open issues on the tracker are also (I think) relatively minor and have proposed solutions https://sourceforge.net/tracker/?group_id=293618&atid=1345549 but please see what you think. If OK I can make the changes in spec and schema, except for 3088359 as I don't know how the UML diagrams are generated. Cheers Richard -- Dr Richard Adams Software Development Team Leader, Centre For Systems Biology Edinburgh University of Edinburgh Tel: 0131 650 8285 email : ric...@ed... -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. |
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From: SourceForge.net <no...@so...> - 2010-10-27 12:58:54
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SED-ML L1V1 item #3082434, was opened at 2010-10-06 21:16 Message generated for change (Comment added) made by otter606 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3082434&group_id=293618 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Richard Adams (otter606) Assigned to: Dagmar Waltemath (dagwa) Summary: Discrepancy between spec and schema on ListOf Initial Comment: Section 3.8 - "All listOf* elements are optional in a SED-ML document" but only ListofOutputs has minOccurs=0 - all other other top-level listofXXX lack a minOccurs - default is 1. Is there any reason for ListOf to be optional? -it's much easier to have ListOf as it keeps structure of document consistent ---------------------------------------------------------------------- >Comment By: Richard Adams (otter606) Date: 2010-10-27 13:58 Message: How about following the SBML solution for this: all listOfXXXs are optional, but if included, they must have at least one child XXX element ? ---------------------------------------------------------------------- Comment By: Richard Adams (otter606) Date: 2010-10-06 21:32 Message: Also : ListOfVariables/PArameters : if can be empty then declarations in schema need 'minOccurs=0". Some listOf descriptions in the spec lack a statement of cardinality. Is it correct to allow the ListOfModels to have 0 models? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3082434&group_id=293618 |
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From: SourceForge.net <no...@so...> - 2010-10-15 22:14:47
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SED-ML L1V1 item #3088381, was opened at 2010-10-15 23:13 Message generated for change (Comment added) made by otter606 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088381&group_id=293618 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. >Category: Specification content >Group: Release Candidate 1 Status: Open Resolution: None Priority: 5 Private: No Submitted By: Richard Adams (otter606) >Assigned to: Richard Adams (otter606) Summary: section 3.4.6 Algorithm Initial Comment: add syntax description for correct defn of kisaoID ---------------------------------------------------------------------- >Comment By: Richard Adams (otter606) Date: 2010-10-15 23:14 Message: committed proposed addition of sentence ' and should be defined in the correct syntax, as defined by the regular expression \code {KISAO:[0-9]\{7\}}." ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088381&group_id=293618 |
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From: SourceForge.net <no...@so...> - 2010-10-15 22:13:30
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SED-ML L1V1 item #3088381, was opened at 2010-10-15 23:13 Message generated for change (Tracker Item Submitted) made by otter606 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088381&group_id=293618 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Richard Adams (otter606) Assigned to: Nobody/Anonymous (nobody) Summary: section 3.4.6 Algorithm Initial Comment: add syntax description for correct defn of kisaoID ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088381&group_id=293618 |
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From: SourceForge.net <no...@so...> - 2010-10-15 22:04:26
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SED-ML L1V1 item #3088351, was opened at 2010-10-15 22:17 Message generated for change (Settings changed) made by otter606 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088351&group_id=293618 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Specification content Group: Release Candidate 1 >Status: Closed Resolution: Fixed Priority: 5 Private: No Submitted By: Richard Adams (otter606) Assigned to: Richard Adams (otter606) Summary: Section 2.1 MathMl typos Initial Comment: various spellings + example aggregate function listings mixed up ---------------------------------------------------------------------- Comment By: Richard Adams (otter606) Date: 2010-10-15 22:17 Message: fixed ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088351&group_id=293618 |
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From: SourceForge.net <no...@so...> - 2010-10-15 22:02:48
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SED-ML L1V1 item #3088376, was opened at 2010-10-15 23:02 Message generated for change (Tracker Item Submitted) made by otter606 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088376&group_id=293618 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Specification content Group: Release Candidate 1 Status: Open Resolution: None Priority: 6 Private: No Submitted By: Richard Adams (otter606) Assigned to: Nobody/Anonymous (nobody) Summary: Section 4.2.1 table 8 missing element? Initial Comment: NewXML class can have anyXML as a nested element, this should be added as a sub-element in table 8? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088376&group_id=293618 |
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From: SourceForge.net <no...@so...> - 2010-10-15 22:00:52
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SED-ML L1V1 item #3088353, was opened at 2010-10-15 22:20 Message generated for change (Settings changed) made by otter606 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088353&group_id=293618 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Specification content Group: Release Candidate 1 >Status: Closed Resolution: Fixed Priority: 5 Private: No Submitted By: Richard Adams (otter606) Assigned to: Richard Adams (otter606) Summary: typos in uri scheme 2.2 Initial Comment: various typos ---------------------------------------------------------------------- Comment By: Richard Adams (otter606) Date: 2010-10-15 22:21 Message: fixed ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088353&group_id=293618 |
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From: SourceForge.net <no...@so...> - 2010-10-15 21:33:28
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SED-ML L1V1 item #3088359, was opened at 2010-10-15 22:33 Message generated for change (Tracker Item Submitted) made by otter606 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088359&group_id=293618 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Specification content Group: Release Candidate 1 Status: Open Resolution: None Priority: 3 Private: No Submitted By: Richard Adams (otter606) Assigned to: Nobody/Anonymous (nobody) Summary: Figure 12 subclasses missing attributes Initial Comment: The 'Task' box is missing modelReference and simulationReference attributes ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088359&group_id=293618 |
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From: SourceForge.net <no...@so...> - 2010-10-15 21:30:50
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SED-ML L1V1 item #3088178, was opened at 2010-10-15 16:46 Message generated for change (Settings changed) made by otter606 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088178&group_id=293618 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. >Category: SED-ML issues >Group: Release Candidate 1 Status: Open >Resolution: Fixed Priority: 7 Private: No Submitted By: Richard Adams (otter606) >Assigned to: Richard Adams (otter606) Summary: xmlns attributes in SED-ML elements Initial Comment: Currently in description of the Notes element, it has a mandatory xmlns attribute to define the namespace as xhtml. But, since an xmlns attribute applies the namespace to the element it appears in, this sets the namespace of 'Notes' to the xhtml namespace - I think this is incorrect, as Notes is an element in the SED-ML namespace. Instead, the top-level xhtml element should declare its namespace. I.e., Notes should be like annotation. In SBML, notes elements are in SBML namespace e.g.,as described section 3.2.3 of SBML l3v1 spec. Propose we update listing 11 to: 1 < s e d M L [ . . ] > 2 < n o t e s > 3 < p x m l n s = h t t p : / / w w w . w 3 . o r g / 1 9 9 9 / x h t m l> T h e e n c l o s e d s i m u l a t i o n d e s c r i p t i o n s h o w s t h e o s c i l l a t i n g b e h a v i o u r o f 4 t h e R e p r e s s i l a t o r m o d e l u s i n g d e t e r m i n i s t i c a n d s t o c h a s t i c s i m u l a t o r s . < / p > 5 < / n o t e s > and edit section 3.3.2 to explain this < / s e d M L > ---------------------------------------------------------------------- >Comment By: Richard Adams (otter606) Date: 2010-10-15 22:30 Message: Committed proposed changes into notesClass.tex ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088178&group_id=293618 |
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From: SourceForge.net <no...@so...> - 2010-10-15 21:27:26
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SED-ML L1V1 item #3088178, was opened at 2010-10-15 16:46 Message generated for change (Settings changed) made by otter606 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088178&group_id=293618 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None >Priority: 7 Private: No Submitted By: Richard Adams (otter606) Assigned to: Nobody/Anonymous (nobody) Summary: xmlns attributes in SED-ML elements Initial Comment: Currently in description of the Notes element, it has a mandatory xmlns attribute to define the namespace as xhtml. But, since an xmlns attribute applies the namespace to the element it appears in, this sets the namespace of 'Notes' to the xhtml namespace - I think this is incorrect, as Notes is an element in the SED-ML namespace. Instead, the top-level xhtml element should declare its namespace. I.e., Notes should be like annotation. In SBML, notes elements are in SBML namespace e.g.,as described section 3.2.3 of SBML l3v1 spec. Propose we update listing 11 to: 1 < s e d M L [ . . ] > 2 < n o t e s > 3 < p x m l n s = h t t p : / / w w w . w 3 . o r g / 1 9 9 9 / x h t m l> T h e e n c l o s e d s i m u l a t i o n d e s c r i p t i o n s h o w s t h e o s c i l l a t i n g b e h a v i o u r o f 4 t h e R e p r e s s i l a t o r m o d e l u s i n g d e t e r m i n i s t i c a n d s t o c h a s t i c s i m u l a t o r s . < / p > 5 < / n o t e s > and edit section 3.3.2 to explain this < / s e d M L > ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088178&group_id=293618 |
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From: SourceForge.net <no...@so...> - 2010-10-15 21:21:27
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SED-ML L1V1 item #3088353, was opened at 2010-10-15 22:20 Message generated for change (Comment added) made by otter606 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088353&group_id=293618 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. >Category: Specification content >Group: Release Candidate 1 Status: Open >Resolution: Fixed Priority: 5 Private: No Submitted By: Richard Adams (otter606) >Assigned to: Richard Adams (otter606) Summary: typos in uri scheme 2.2 Initial Comment: various typos ---------------------------------------------------------------------- >Comment By: Richard Adams (otter606) Date: 2010-10-15 22:21 Message: fixed ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088353&group_id=293618 |
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From: SourceForge.net <no...@so...> - 2010-10-15 21:20:58
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SED-ML L1V1 item #3088353, was opened at 2010-10-15 22:20 Message generated for change (Tracker Item Submitted) made by otter606 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088353&group_id=293618 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Richard Adams (otter606) Assigned to: Nobody/Anonymous (nobody) Summary: typos in uri scheme 2.2 Initial Comment: various typos ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088353&group_id=293618 |
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From: SourceForge.net <no...@so...> - 2010-10-15 21:17:56
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SED-ML L1V1 item #3088351, was opened at 2010-10-15 22:17 Message generated for change (Comment added) made by otter606 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088351&group_id=293618 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. >Category: Specification content Group: Release Candidate 1 Status: Open >Resolution: Fixed Priority: 5 Private: No Submitted By: Richard Adams (otter606) Assigned to: Richard Adams (otter606) Summary: Section 2.1 MathMl typos Initial Comment: various spellings + example aggregate function listings mixed up ---------------------------------------------------------------------- >Comment By: Richard Adams (otter606) Date: 2010-10-15 22:17 Message: fixed ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088351&group_id=293618 |
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From: SourceForge.net <no...@so...> - 2010-10-15 21:17:18
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SED-ML L1V1 item #3088351, was opened at 2010-10-15 22:17 Message generated for change (Tracker Item Submitted) made by otter606 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088351&group_id=293618 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: Release Candidate 1 Status: Open Resolution: None Priority: 5 Private: No Submitted By: Richard Adams (otter606) Assigned to: Richard Adams (otter606) Summary: Section 2.1 MathMl typos Initial Comment: various spellings + example aggregate function listings mixed up ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=1345549&aid=3088351&group_id=293618 |
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