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From: Chris J. M. <my...@ec...> - 2015-01-30 14:37:22
|
Hmm, I don’t think “ignored” implies the same thing as optional. Ignored implies there is something to ignore. I think it would be more clear to state that bounding box changes from required to optional for ReactionGlyph. However, even this is a bit odd. A better approach I think would be to have an abstract class where BoundingBox is optional then have other classes individually make it required, if needed. Kind of the same approach we are taking with id in L3V2. Chris > On Jan 30, 2015, at 12:07 AM, Frank Bergmann <fbe...@ca...> wrote: > > Hello Chris, > > the spec says: If a “ReactionGlyph” specifies a curve, the bounding box is to be ignored (page 16, just before 3.10.1). The same goes for the SpeciesReferenceGlyph. So this is in accordance with the specification. Please let me know if you need more detail on this. > > best > Frank > > >> On Jan 30, 2015, at 1:02 AM, Chris J. Myers <my...@ec...> wrote: >> >> Hi, >> >> ReactionGlyph inherits from GraphicalObject. GraphicalObject has a required BoundingBox. A BoundingBox has a required Point and Dimension. However, the ReactionGlyph in Example 4.3.1 is simply a curve and does not have a BoundingBox. Is this valid or am I missing something? It seems like it would be nice to not require a bounding box for a reaction represented by a curve. If we do require this, what would it be in this example, a box enclosing the curve? >> >> Thanks, >> >> Chris >> >> >> ------------------------------------------------------------------------------ >> Dive into the World of Parallel Programming. The Go Parallel Website, >> sponsored by Intel and developed in partnership with Slashdot Media, is your >> hub for all things parallel software development, from weekly thought >> leadership blogs to news, videos, case studies, tutorials and more. Take a >> look and join the conversation now. http://goparallel.sourceforge.net/ >> _______________________________________________ >> sbml-layout mailing list >> sbm...@li... >> https://lists.sourceforge.net/lists/listinfo/sbml-layout > > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming. The Go Parallel Website, > sponsored by Intel and developed in partnership with Slashdot Media, is your > hub for all things parallel software development, from weekly thought > leadership blogs to news, videos, case studies, tutorials and more. Take a > look and join the conversation now. http://goparallel.sourceforge.net/ > _______________________________________________ > sbml-layout mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-layout |
From: Nicolas R. <rod...@eb...> - 2015-01-30 10:56:00
|
On 01/30/2015 12:15 AM, Chris J. Myers wrote: > One more thing about this example. The ReactionGlyph in the example has a curve, but for the class ReactionGlyph in JSBML, I don’t see a createCurve method. You have some more details taken directly from the specs on the libsbml docs. http://sbml.org/Software/libSBML/docs/java-api/index.html?org/sbml/libsbml/GeneralGlyph.html Although in the section 3.10 of the specs, on the description of the Curve, it is said that if a curve is defined, the BoundingBox is to be ignored. I will add a createCurve method to jsbml. Nico >> On Jan 29, 2015, at 5:02 PM, Chris J. Myers <my...@ec...> wrote: >> >> Hi, >> >> ReactionGlyph inherits from GraphicalObject. GraphicalObject has a required BoundingBox. A BoundingBox has a required Point and Dimension. However, the ReactionGlyph in Example 4.3.1 is simply a curve and does not have a BoundingBox. Is this valid or am I missing something? It seems like it would be nice to not require a bounding box for a reaction represented by a curve. If we do require this, what would it be in this example, a box enclosing the curve? >> >> Thanks, >> >> Chris >> > _______________________________________________ > jsbml-team mailing list > jsb...@ca... > https://lists.caltech.edu/listinfo/jsbml-team |
From: Frank B. <fbe...@ca...> - 2015-01-30 07:07:53
|
Hello Chris, the spec says: If a “ReactionGlyph” specifies a curve, the bounding box is to be ignored (page 16, just before 3.10.1). The same goes for the SpeciesReferenceGlyph. So this is in accordance with the specification. Please let me know if you need more detail on this. best Frank > On Jan 30, 2015, at 1:02 AM, Chris J. Myers <my...@ec...> wrote: > > Hi, > > ReactionGlyph inherits from GraphicalObject. GraphicalObject has a required BoundingBox. A BoundingBox has a required Point and Dimension. However, the ReactionGlyph in Example 4.3.1 is simply a curve and does not have a BoundingBox. Is this valid or am I missing something? It seems like it would be nice to not require a bounding box for a reaction represented by a curve. If we do require this, what would it be in this example, a box enclosing the curve? > > Thanks, > > Chris > > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming. The Go Parallel Website, > sponsored by Intel and developed in partnership with Slashdot Media, is your > hub for all things parallel software development, from weekly thought > leadership blogs to news, videos, case studies, tutorials and more. Take a > look and join the conversation now. http://goparallel.sourceforge.net/ > _______________________________________________ > sbml-layout mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-layout |
From: Chris J. M. <my...@ec...> - 2015-01-30 00:15:46
|
One more thing about this example. The ReactionGlyph in the example has a curve, but for the class ReactionGlyph in JSBML, I don’t see a createCurve method. Chris > On Jan 29, 2015, at 5:02 PM, Chris J. Myers <my...@ec...> wrote: > > Hi, > > ReactionGlyph inherits from GraphicalObject. GraphicalObject has a required BoundingBox. A BoundingBox has a required Point and Dimension. However, the ReactionGlyph in Example 4.3.1 is simply a curve and does not have a BoundingBox. Is this valid or am I missing something? It seems like it would be nice to not require a bounding box for a reaction represented by a curve. If we do require this, what would it be in this example, a box enclosing the curve? > > Thanks, > > Chris > |
From: Chris J. M. <my...@ec...> - 2015-01-30 00:02:21
|
Hi, ReactionGlyph inherits from GraphicalObject. GraphicalObject has a required BoundingBox. A BoundingBox has a required Point and Dimension. However, the ReactionGlyph in Example 4.3.1 is simply a curve and does not have a BoundingBox. Is this valid or am I missing something? It seems like it would be nice to not require a bounding box for a reaction represented by a curve. If we do require this, what would it be in this example, a box enclosing the curve? Thanks, Chris |
From: Chris J. M. <my...@ec...> - 2014-10-28 18:37:03
|
Are there "test suite" like examples for the layout package available somewhere? Would like to test my import of layout. Thanks, Chris |
From: Chris J. M. <my...@ec...> - 2014-09-09 15:35:55
|
Thanks for the clarifications. I found a nasty bug due to the way I was handling these types of reactions that JSBML was not forgiving of while libsbml was (duplicate ids). I think I see the path forward now. Chris On Sep 9, 2014, at 8:11 AM, Frank T. Bergmann <fbe...@ca...> wrote: > Yes the bounding box can be empty. And no, it was meant to be the bounds of whatever connector you have between substrate and product. > > Frank > > From: my...@en... [mailto:my...@en...] On Behalf Of Chris J. Myers > Sent: Tuesday, September 9, 2014 3:36 PM > To: Frank T. Bergmann > Cc: The SBML L3 Layout package discussion list; LibSBML Team > Subject: Re: [libsbml-team] [sbml-layout] Proper form of implicit reaction > > Isn't the bounding box required: > > Each object of class 24 GraphicalObject has a mandatory BoundingBox, which specifies the position and the size of the object. > Can the bounding box be empty? Should it encapsulated all the arcs making up the reaction? > > Chris > > On Sep 9, 2014, at 6:56 AM, Frank T. Bergmann <fbe...@ca...> wrote: > > > What about the reactionGlyph? Bounding box or curve? Should be nothing I > think since specieReferenceGlyphs should handle the curve unless I'm > mistaken? > > > It could be empty. In graphical languages like SBGN PD, this bounding box > can represent the middle piece (or the actual process glyph). But it is not > required. You could just have your product start at the end of the reactant > arc and it would be fine. > > Frank > > > Chris > > Sent from my iPhone > > On Sep 9, 2014, at 2:08 AM, "Frank T. Bergmann" <fbe...@ca...> > wrote: > > > If I want to connect two species directly where the edge between > represents a reaction, what is the proper form? > > For example, species S0 is reactant and S1 is product of a reaction > R0. I > want > > this as arc between species labeled R0. Note if a second reactant s2 > is > added > > then another arc is added from S0 to S2 also labeled R0. > > In the layout you would have > > - two species glyphs for sg0, sg1 > - two text glyphs that position the label for s0 and s1 > - one reaction glyph rg0 > - one text glyph positioning the label r0 > - two species reference glyphs indicating that s0 is the reactant, s1 > the product (if you add the second reactant, you would add a new > species reference glyph for the new reactant) > > At the bare minimum those should all have bounding boxes, but extra > points are awarded for actually specifying the arc for each species > reference glyph. > > Does that answer your question? > > Frank > > > Thanks for the advice. > > Chris > > Sent from my iPhone > ---------------------------------------------------------------------- > ------ > -- > > Want excitement? > Manually upgrade your production database. > When you want reliability, choose Perforce Perforce version control. > Predictably reliable. > > http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg > > .cl > ktrk > _______________________________________________ > sbml-layout mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-layout > > > ---------------------------------------------------------------------- > -------- > Want excitement? > Manually upgrade your production database. > When you want reliability, choose Perforce. > Perforce version control. Predictably reliable. > > http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg. > > clktrk _______________________________________________ > sbml-layout mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-layout |
From: Frank T. B. <fbe...@ca...> - 2014-09-09 14:12:22
|
Yes the bounding box can be empty. And no, it was meant to be the bounds of whatever connector you have between substrate and product. Frank From: my...@en... [mailto:my...@en...] On Behalf Of Chris J. Myers Sent: Tuesday, September 9, 2014 3:36 PM To: Frank T. Bergmann Cc: The SBML L3 Layout package discussion list; LibSBML Team Subject: Re: [libsbml-team] [sbml-layout] Proper form of implicit reaction Isn't the bounding box required: Each object of class 24 GraphicalObject has a mandatory BoundingBox, which specifies the position and the size of the object. Can the bounding box be empty? Should it encapsulated all the arcs making up the reaction? Chris On Sep 9, 2014, at 6:56 AM, Frank T. Bergmann <fbe...@ca... <mailto:fbe...@ca...> > wrote: What about the reactionGlyph? Bounding box or curve? Should be nothing I think since specieReferenceGlyphs should handle the curve unless I'm mistaken? It could be empty. In graphical languages like SBGN PD, this bounding box can represent the middle piece (or the actual process glyph). But it is not required. You could just have your product start at the end of the reactant arc and it would be fine. Frank Chris Sent from my iPhone On Sep 9, 2014, at 2:08 AM, "Frank T. Bergmann" <fbe...@ca... <mailto:fbe...@ca...> > wrote: If I want to connect two species directly where the edge between represents a reaction, what is the proper form? For example, species S0 is reactant and S1 is product of a reaction R0. I want this as arc between species labeled R0. Note if a second reactant s2 is added then another arc is added from S0 to S2 also labeled R0. In the layout you would have - two species glyphs for sg0, sg1 - two text glyphs that position the label for s0 and s1 - one reaction glyph rg0 - one text glyph positioning the label r0 - two species reference glyphs indicating that s0 is the reactant, s1 the product (if you add the second reactant, you would add a new species reference glyph for the new reactant) At the bare minimum those should all have bounding boxes, but extra points are awarded for actually specifying the arc for each species reference glyph. Does that answer your question? Frank Thanks for the advice. Chris Sent from my iPhone ---------------------------------------------------------------------- ------ -- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191 <http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg> &iu=/4140/ostg .cl ktrk _______________________________________________ sbml-layout mailing list sbm...@li... <mailto:sbm...@li...> https://lists.sourceforge.net/lists/listinfo/sbml-layout ---------------------------------------------------------------------- -------- Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce. Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191 <http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg> &iu=/4140/ostg. clktrk _______________________________________________ sbml-layout mailing list sbm...@li... <mailto:sbm...@li...> https://lists.sourceforge.net/lists/listinfo/sbml-layout |
From: Chris J. M. <my...@ec...> - 2014-09-09 13:36:05
|
Isn't the bounding box required: Each object of class 24 GraphicalObject has a mandatory BoundingBox, which specifies the position and the size of the object. Can the bounding box be empty? Should it encapsulated all the arcs making up the reaction? Chris On Sep 9, 2014, at 6:56 AM, Frank T. Bergmann <fbe...@ca...> wrote: >> What about the reactionGlyph? Bounding box or curve? Should be nothing I >> think since specieReferenceGlyphs should handle the curve unless I'm >> mistaken? >> > > It could be empty. In graphical languages like SBGN PD, this bounding box > can represent the middle piece (or the actual process glyph). But it is not > required. You could just have your product start at the end of the reactant > arc and it would be fine. > > Frank > >> Chris >> >> Sent from my iPhone >> >> On Sep 9, 2014, at 2:08 AM, "Frank T. Bergmann" <fbe...@ca...> >> wrote: >> >>>> If I want to connect two species directly where the edge between >>>> represents a reaction, what is the proper form? >>>> >>>> For example, species S0 is reactant and S1 is product of a reaction >>>> R0. I >>> want >>>> this as arc between species labeled R0. Note if a second reactant s2 >>>> is >>> added >>>> then another arc is added from S0 to S2 also labeled R0. >>> >>> In the layout you would have >>> >>> - two species glyphs for sg0, sg1 >>> - two text glyphs that position the label for s0 and s1 >>> - one reaction glyph rg0 >>> - one text glyph positioning the label r0 >>> - two species reference glyphs indicating that s0 is the reactant, s1 >>> the product (if you add the second reactant, you would add a new >>> species reference glyph for the new reactant) >>> >>> At the bare minimum those should all have bounding boxes, but extra >>> points are awarded for actually specifying the arc for each species >>> reference glyph. >>> >>> Does that answer your question? >>> >>> Frank >>> >>>> Thanks for the advice. >>>> >>>> Chris >>>> >>>> Sent from my iPhone >>> ---------------------------------------------------------------------- >>> ------ >>> -- >>>> Want excitement? >>>> Manually upgrade your production database. >>>> When you want reliability, choose Perforce Perforce version control. >>>> Predictably reliable. >>>> >> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg >>>> .cl >>>> ktrk >>>> _______________________________________________ >>>> sbml-layout mailing list >>>> sbm...@li... >>>> https://lists.sourceforge.net/lists/listinfo/sbml-layout >>> >>> >>> ---------------------------------------------------------------------- >>> -------- >>> Want excitement? >>> Manually upgrade your production database. >>> When you want reliability, choose Perforce. >>> Perforce version control. Predictably reliable. >>> >> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg. >>> clktrk _______________________________________________ >>> sbml-layout mailing list >>> sbm...@li... >>> https://lists.sourceforge.net/lists/listinfo/sbml-layout |
From: Frank T. B. <fbe...@ca...> - 2014-09-09 12:57:15
|
> What about the reactionGlyph? Bounding box or curve? Should be nothing I > think since specieReferenceGlyphs should handle the curve unless I'm > mistaken? > It could be empty. In graphical languages like SBGN PD, this bounding box can represent the middle piece (or the actual process glyph). But it is not required. You could just have your product start at the end of the reactant arc and it would be fine. Frank > Chris > > Sent from my iPhone > > On Sep 9, 2014, at 2:08 AM, "Frank T. Bergmann" <fbe...@ca...> > wrote: > > >> If I want to connect two species directly where the edge between > >> represents a reaction, what is the proper form? > >> > >> For example, species S0 is reactant and S1 is product of a reaction > >> R0. I > > want > >> this as arc between species labeled R0. Note if a second reactant s2 > >> is > > added > >> then another arc is added from S0 to S2 also labeled R0. > > > > In the layout you would have > > > > - two species glyphs for sg0, sg1 > > - two text glyphs that position the label for s0 and s1 > > - one reaction glyph rg0 > > - one text glyph positioning the label r0 > > - two species reference glyphs indicating that s0 is the reactant, s1 > > the product (if you add the second reactant, you would add a new > > species reference glyph for the new reactant) > > > > At the bare minimum those should all have bounding boxes, but extra > > points are awarded for actually specifying the arc for each species > > reference glyph. > > > > Does that answer your question? > > > > Frank > > > >> Thanks for the advice. > >> > >> Chris > >> > >> Sent from my iPhone > > ---------------------------------------------------------------------- > > ------ > > -- > >> Want excitement? > >> Manually upgrade your production database. > >> When you want reliability, choose Perforce Perforce version control. > >> Predictably reliable. > >> > http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg > >> .cl > >> ktrk > >> _______________________________________________ > >> sbml-layout mailing list > >> sbm...@li... > >> https://lists.sourceforge.net/lists/listinfo/sbml-layout > > > > > > ---------------------------------------------------------------------- > > -------- > > Want excitement? > > Manually upgrade your production database. > > When you want reliability, choose Perforce. > > Perforce version control. Predictably reliable. > > > http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg. > > clktrk _______________________________________________ > > sbml-layout mailing list > > sbm...@li... > > https://lists.sourceforge.net/lists/listinfo/sbml-layout |
From: Chris J. M. <my...@ec...> - 2014-09-09 12:42:20
|
What about the reactionGlyph? Bounding box or curve? Should be nothing I think since specieReferenceGlyphs should handle the curve unless I'm mistaken? Chris Sent from my iPhone On Sep 9, 2014, at 2:08 AM, "Frank T. Bergmann" <fbe...@ca...> wrote: >> If I want to connect two species directly where the edge between >> represents a reaction, what is the proper form? >> >> For example, species S0 is reactant and S1 is product of a reaction R0. I > want >> this as arc between species labeled R0. Note if a second reactant s2 is > added >> then another arc is added from S0 to S2 also labeled R0. > > In the layout you would have > > - two species glyphs for sg0, sg1 > - two text glyphs that position the label for s0 and s1 > - one reaction glyph rg0 > - one text glyph positioning the label r0 > - two species reference glyphs indicating that s0 is the reactant, s1 the > product > (if you add the second reactant, you would add a new species reference > glyph for the new reactant) > > At the bare minimum those should all have bounding boxes, but extra points > are awarded for actually specifying the arc for each species reference > glyph. > > Does that answer your question? > > Frank > >> Thanks for the advice. >> >> Chris >> >> Sent from my iPhone > ---------------------------------------------------------------------------- > -- >> Want excitement? >> Manually upgrade your production database. >> When you want reliability, choose Perforce Perforce version control. >> Predictably reliable. >> http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.cl >> ktrk >> _______________________________________________ >> sbml-layout mailing list >> sbm...@li... >> https://lists.sourceforge.net/lists/listinfo/sbml-layout > > > ------------------------------------------------------------------------------ > Want excitement? > Manually upgrade your production database. > When you want reliability, choose Perforce. > Perforce version control. Predictably reliable. > http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk > _______________________________________________ > sbml-layout mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-layout |
From: Frank T. B. <fbe...@ca...> - 2014-09-09 08:08:34
|
> If I want to connect two species directly where the edge between > represents a reaction, what is the proper form? > > For example, species S0 is reactant and S1 is product of a reaction R0. I want > this as arc between species labeled R0. Note if a second reactant s2 is added > then another arc is added from S0 to S2 also labeled R0. > In the layout you would have - two species glyphs for sg0, sg1 - two text glyphs that position the label for s0 and s1 - one reaction glyph rg0 - one text glyph positioning the label r0 - two species reference glyphs indicating that s0 is the reactant, s1 the product (if you add the second reactant, you would add a new species reference glyph for the new reactant) At the bare minimum those should all have bounding boxes, but extra points are awarded for actually specifying the arc for each species reference glyph. Does that answer your question? Frank > Thanks for the advice. > > Chris > > Sent from my iPhone > ---------------------------------------------------------------------------- -- > Want excitement? > Manually upgrade your production database. > When you want reliability, choose Perforce Perforce version control. > Predictably reliable. > http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.cl > ktrk > _______________________________________________ > sbml-layout mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-layout |
From: Chris J. M. <my...@ec...> - 2014-09-08 23:24:42
|
If I want to connect two species directly where the edge between represents a reaction, what is the proper form? For example, species S0 is reactant and S1 is product of a reaction R0. I want this as arc between species labeled R0. Note if a second reactant s2 is added then another arc is added from S0 to S2 also labeled R0. Thanks for the advice. Chris Sent from my iPhone |
From: Frank T. B. <fbe...@ca...> - 2013-08-13 13:56:31
|
Dear SBML community, We are pleased to announce the availability of the final Version 1 specification of the SBML Level 3 Layout Package. You can find the document at its resolvable URI: http://identifiers.org/combine.specifications/sbml.level-3.version-1.layout. version-1.release-1 The Layout ('layout') specification activity page is: http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/Layout_%28lay out%29 Please report any errors, issues or questions either to the Package Working Group for 'layout' (sbm...@li...) or to the authors directly. The authors thank all of the people who have contributed to the development of the 'layout' package and its specification over the years. Frank (on behalf of all the authors: Ralph Gauges, Ursula Rost, Sven Sahle, Katja Wengler and Frank T. Bergmann) |
From: Nicolas R. <rod...@eb...> - 2013-07-29 14:57:32
|
On 29/07/13 15:50, Frank T. Bergmann wrote: >> <reactionGlyph id="rGlyph_4" reaction="rxn25" objectRole="SBO-0000167"> >> >> I suppose it is replace by the sboTerm from SBase ? >> >> >> Is it a convention for write the SBO ID using '-' instead of ':' ? >> >> When writing in L2 annotation, using the old namespace, when a sboTerm is >> define on a glyph should we write an sboTerm attribute, objectRole or > both. >> And again should we write the SBO term ID with the dash ? >> > Hello Nico, > > Thanks for reading so carefully. 'objectRole' is actually an attribute of > the render package, there it is used to assign render styles to a given > graphical object. 'objectRole' is a string attribute that render used to > extend layout. In my software I map sbo terms to render styles. But it has > no meaning in the layout package. I see. > I could actually find no mentioning of objectRole in the current rc2. That's why I asked if it was replaced by the sboTerm. Thanks, ignoring the objectRole attribute for layout from now. Nico |
From: Nicolas R. <rod...@eb...> - 2013-07-29 14:54:19
|
On 29/07/13 15:41, Nicolas Rodriguez wrote: > On 24/07/13 20:40, Sarah Keating wrote: >> Dear Members of the SBML community, >> >> As part of the process of developing and accepting SBML L3 packages the >> PWG are required to submit a 'release candidate' specification; together >> with information relating to two pieces of software that implement the >> specification; for approval by the SBMLEditors. >> >> The Layout package group has now >> submitted this information which is publicly available here: >> >> http://tinyurl.com/sbml-layout-rc2 >> >> The SBMLEditors (excluding those that may be authors of the Layout spec) >> will now consider the spec and the implementations and determine whether >> they meet the "Criteria for approval" as outlined in the SBML >> Development process. >> (http://sbml.org/Documents/SBML_Development_Process_for_SBML_Level_3). >> >> At this point we are opening the floor to comments from all members of >> the SBML community who have not been particularly involved with the >> development of comp. > Few questions about the 'objectRole' attribute that was existing in the > L2 version ? > > <reactionGlyph id="rGlyph_4" reaction="rxn25" objectRole="SBO-0000167"> > > I suppose it is replace by the sboTerm from SBase ? > > > Is it a convention for write the SBO ID using '-' instead of ':' ? > > When writing in L2 annotation, using the old namespace, when a sboTerm > is define on a glyph should we write an sboTerm attribute, objectRole or > both. > And again should we write the SBO term ID with the dash ? Just found out an other question about this attribute. Here is an extract of the file I am trying to parse : <speciesReferenceGlyph id="curve50" speciesReference="WID12050894_DWID86_c" speciesGlyph="sGlyph_13" role="substrate" objectRole="substrate"> There, we have a name and not an SBO ID for the objectRole attribute. Is it normal ? Is a list of string allowed on top of SBO ID ? Just for info, the layout seems to have been created using SBW : <!--Created by SBW SBML LayoutViewer/Manipulator--> Not sure if there was some modification in between, can ask the author and/or pass the file around. Thanks, Nico |
From: Frank T. B. <fbe...@ca...> - 2013-07-29 14:51:29
|
> <reactionGlyph id="rGlyph_4" reaction="rxn25" objectRole="SBO-0000167"> > > I suppose it is replace by the sboTerm from SBase ? > > > Is it a convention for write the SBO ID using '-' instead of ':' ? > > When writing in L2 annotation, using the old namespace, when a sboTerm is > define on a glyph should we write an sboTerm attribute, objectRole or both. > And again should we write the SBO term ID with the dash ? > Hello Nico, Thanks for reading so carefully. 'objectRole' is actually an attribute of the render package, there it is used to assign render styles to a given graphical object. 'objectRole' is a string attribute that render used to extend layout. In my software I map sbo terms to render styles. But it has no meaning in the layout package. I could actually find no mentioning of objectRole in the current rc2. Thanks! Frank |
From: Nicolas R. <rod...@eb...> - 2013-07-29 14:41:57
|
On 24/07/13 20:40, Sarah Keating wrote: > Dear Members of the SBML community, > > As part of the process of developing and accepting SBML L3 packages the > PWG are required to submit a 'release candidate' specification; together > with information relating to two pieces of software that implement the > specification; for approval by the SBMLEditors. > > The Layout package group has now > submitted this information which is publicly available here: > > http://tinyurl.com/sbml-layout-rc2 > > The SBMLEditors (excluding those that may be authors of the Layout spec) > will now consider the spec and the implementations and determine whether > they meet the "Criteria for approval" as outlined in the SBML > Development process. > (http://sbml.org/Documents/SBML_Development_Process_for_SBML_Level_3). > > At this point we are opening the floor to comments from all members of > the SBML community who have not been particularly involved with the > development of comp. Few questions about the 'objectRole' attribute that was existing in the L2 version ? <reactionGlyph id="rGlyph_4" reaction="rxn25" objectRole="SBO-0000167"> I suppose it is replace by the sboTerm from SBase ? Is it a convention for write the SBO ID using '-' instead of ':' ? When writing in L2 annotation, using the old namespace, when a sboTerm is define on a glyph should we write an sboTerm attribute, objectRole or both. And again should we write the SBO term ID with the dash ? Thanks, Nico |
From: Frank T. B. <fbe...@ca...> - 2013-07-24 15:44:49
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Dear Package Working Group, Thank you again for all the valuable feedback on the last release candidate. Since no major problems occurred I went ahead and just mailed the release candidate to the editors. I also attach it to this email and you can find it online under: http://tinyurl.com/sbml-layout-rc2 Changes in this version are mostly cosmetic in nature, but do include some reformatting (you will be glad to know that the figure in the background section on page 5 now fits neatly with the text, thanks Mike!) and editing (thanks to Lucian, Sarah and Mike). Apart from that typos (like the missing layout prefix nico spotted, along with the outrageous numbering of the validation rules are corrected, thanks Sarah!). No class names were changed in this round, let's leave that to version 2, when we can also talk about a broader restructuring of the package. Thank you all again, and let's hope we hear from the editors soon! Frank Bergmann on behalf of the authors Ralph Gauges, Ursula Rost, Sven Sahle, Katja Wengler and Frank Bergmann |
From: Sarah K. <ske...@ca...> - 2013-07-22 09:45:02
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Hi Frank These are comments relating to the numbering of the validation rules: 1. Rules on GeneralGlyph layout-20708 should be layout-20808 2. The validation rules for Dimensions repeat the number of the previous section. Could I ask you change these to 21701-21704 rather than renumber other following rules ? (Although it would not matter if you want to leave it here - it just messes up my references; which can be changed :-) 3. Rules on Curve skips numbers 21404-21406 and then uses 21407-21409 any reason ?? Sarah |
From: Sarah K. <ske...@ca...> - 2013-07-22 09:08:00
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Hi Andreas I agree that the names and types etc are confusing. However at this point I am going to make the "layout has historical roots" argument (again!). If these names got changed now then we would break all the implementations that currently use layout. I would suggest that these changes are held off for a version2 of the specification; which would require all implementations to make changes and thus they could be expected to change element names etc. I know I have used this argument for a couple of things - but again layout was mostly designed long before the L3 process was outlined and has been in use for so long that it has be treated slightly differently :-) Sarah On 16/07/2013 00:30, Andreas Dräger wrote: > Hi everybody, > > Just a short question about Figure 5 in the new manuscript: Why does the > Curve element have a sub-element "listOfCurveSegments", but the > associated entity is called ListOfLineSegments? Since the > ListOfLineSegments has again sub-elements that are referred to as > "curveSegment", the list should probably be renamed to > ListOfCurveSegments? Note that the name of the actual entity within the > list is in turn called LineSegment. From my perspective, this is a bit > confusing. I therefore propose to unify the names here. > > Best > Andreas > |
From: Andreas D. <and...@un...> - 2013-07-15 23:31:06
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Hi everybody, Just a short question about Figure 5 in the new manuscript: Why does the Curve element have a sub-element "listOfCurveSegments", but the associated entity is called ListOfLineSegments? Since the ListOfLineSegments has again sub-elements that are referred to as "curveSegment", the list should probably be renamed to ListOfCurveSegments? Note that the name of the actual entity within the list is in turn called LineSegment. From my perspective, this is a bit confusing. I therefore propose to unify the names here. Best Andreas -- Dr. Andreas Draeger University of California, San Diego, La Jolla, CA 92093-0412, USA Bioengineering Dept., Systems Biology Research Group, Office #2506 Phone: +1-858-534-9717, Fax: +1-858-822-3120, twitter: @dr_drae |
From: Chris J. M. <my...@ec...> - 2013-07-11 14:42:01
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Excellent. Looks great to me. Chris On Jul 9, 2013, at 7:53 AM, Frank T. Bergmann <fbe...@ca...> wrote: > Dear Package Working Group, > > First of all let me thank you for all your feedback of the previous draft > and getting the layout specification ready to this point, where we can send > it to the editors for approval. With this mail you will find a release > candidate of the Layout specification to be sent to the SBML editors along > with a proposed cover letter. The release candidate is also online under: > > http://tinyurl.com/sbml-layout-rc > > What has changed since the last draft are the examples. Now I made > absolutely sure that there always is an L3 example available. > > We plan to send this release candidate to the editors within two weeks. > > Thank you again, > > - Frank T. Bergmann, > On behalf of the authors of the Layout specification > <2013-07-09_-_LetterToTheEditors.pdf><sbml-layout-version-1-rc-1.pdf>------------------------------------------------------------------------------ > See everything from the browser to the database with AppDynamics > Get end-to-end visibility with application monitoring from AppDynamics > Isolate bottlenecks and diagnose root cause in seconds. > Start your free trial of AppDynamics Pro today! > http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk_______________________________________________ > sbml-layout mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-layout |
From: Lucian S. <lp...@sp...> - 2013-07-09 20:28:05
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Looks good! One thing: in figure 5 (definition of 'Curve'), you have CubicBezier inherit from both SBase and LineSegment, when it should presumably inherit only from LineSegment. LineSegment itself also needs to inherit from SBase; right now, it doesn't inherit from anything (in the figure). Also, I feel like this might have been mentioned before, but all other SBML elements with id's also have name's. I know the JSBML people would prefer this, as it simplifies their class structure, but it's not otherwise a big deal. (This would affect the BoundingBox, Point, and Dimensions classes, at least.) I think you also probably need to explicitly state somewhere what the names of the 'ListOfSubGlyps' children are. For validation: you say that the layout:metaidRef of (say) a CompartmentGlyph must reference an *element* of the model, but you don't say it should reference a *Compartment*. Must it actually reference a compartment? The 'compartment' attribute has to, and it's called a CompartmentGlyph... (The same is true for SpeciesGlyphs and ReactionGlyphs, etc.) None of these are substantive changes--you should totally submit it to the editors. Good luck! -Lucian * Frank Bergmann <fbe...@ca...> [2013-07-09 14:55] writes: > Dear Package Working Group, > > First of all let me thank you for all your feedback of the previous draft > and getting the layout specification ready to this point, where we can send > it to the editors for approval. With this mail you will find a release > candidate of the Layout specification to be sent to the SBML editors along > with a proposed cover letter. The release candidate is also online under: > > http://tinyurl.com/sbml-layout-rc > > What has changed since the last draft are the examples. Now I made > absolutely sure that there always is an L3 example available. > > We plan to send this release candidate to the editors within two weeks. > > Thank you again, > > - Frank T. Bergmann, > On behalf of the authors of the Layout specification > ------------------------------------------------------------------------------ > See everything from the browser to the database with AppDynamics > Get end-to-end visibility with application monitoring from AppDynamics > Isolate bottlenecks and diagnose root cause in seconds. > Start your free trial of AppDynamics Pro today! > http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk > _______________________________________________ > sbml-layout mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-layout |
From: Frank T. B. <fbe...@ca...> - 2013-07-09 13:55:00
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Dear Package Working Group, First of all let me thank you for all your feedback of the previous draft and getting the layout specification ready to this point, where we can send it to the editors for approval. With this mail you will find a release candidate of the Layout specification to be sent to the SBML editors along with a proposed cover letter. The release candidate is also online under: http://tinyurl.com/sbml-layout-rc What has changed since the last draft are the examples. Now I made absolutely sure that there always is an L3 example available. We plan to send this release candidate to the editors within two weeks. Thank you again, - Frank T. Bergmann, On behalf of the authors of the Layout specification |