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From: Sarah K. <ske...@ca...> - 2018-09-18 09:39:14
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Please note the current SBML Editors will continue to work on this publication and it will proceed as planned. SBML Editors |
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From: Sarah K. <ske...@ca...> - 2018-09-18 08:33:13
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Sorry I was perhaps not completely clear. Nicolas Le Novere has withdrawn from the paper and has handed over all notes/comments etc to the remaining SBML Editors. There will be a slight hiatus in the timing, but we are close to having a manuscript for submission, and we will proceed with this. Thank you to everyone who has commented so far and I hope this completely clarifies the situation. Sarah Coordinator of SBML Editors On 18/09/2018 09:04, Sarah Keating wrote: > Please note the current SBML Editors will continue to work on this > publication and it will proceed as planned. > > SBML Editors > |
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From: Nicolas Le N. <n.l...@gm...> - 2018-08-04 14:12:28
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Dear Colleagues, We are in the process of submitting a manuscript describing SBML Level 3 for publication in Molecular Systems Biology as a perspective (current version attached). The manuscript has been written by past and current SBML editors and both its content and structure discussed with MSB editors. Although the structure and the main messages of the paper have been settled, we would welcome any suggestion you would have in relation with the manuscript. Best regards The SBML editors. |
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From: Andreas D. <and...@un...> - 2017-05-12 07:34:37
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> Am 11.05.2017 um 23:13 schrieb Haoran Yu <hal...@gm...>: > > Dear SBML layout team, > > My name is Haoran Yu, I will be working on a SBML and SBGN-ML bidirectional converter project. I have recently signed up for the mailing list because I will be using layout to generate diagrams. However, I'm not sure if I can receive email from this mailing lists because there were issues previously. Could someone manually add me hal...@gm... to the mailing lists and send me a reply to this message please? > > My second question is: are there example files for SBML that has layout? Should I be searching in BioModels for example files? > > Thank you for your help. > > Sincerely, > Haoran Dear Haoran, Welcome in this list! It seems your subscription worked very well. If you want to obtain examples for SBML layout models, you can easily create your one examples. I am here describing now two alternative tools that will yield very different layouts. 1) Escher at http://escher.github.io. Download one of the example maps in JSON format and convert it with EscherConverter to SBML with Layout or to SBGN-ML https://github.com/SBRG/EscherConverter. 2) CellDesigner at http://www.celldesigner.org. Create a model, save it to CellDesigner's SBML and use the converter from a previous GSoC at https://github.com/funasoul/celldesigner-parser to create SBML+Layout out of it. CellDesigner by itself can export SBGN-ML. I hope this helps! Happy coding! With best regards Dr. Andreas Draeger Principal Investigator --- University of Tübingen Center for Bioinformatics Tübingen (ZBIT) Applied Bioinformatics Group Sand 14 · Office #C320 · 72076 Tübingen · Germany Phone: +49-7071-29-70459 · Fax: +49-7071-29-5152 Web: http://draeger-lab.org · Twitter: @dr_drae YouTube: https://www.youtube.com/channel/UCp7fWtXGFOIjV35u7ONiVbg |
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From: Haoran Yu <hal...@gm...> - 2017-05-11 21:13:24
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Dear SBML layout team, My name is Haoran Yu, I will be working on a SBML and SBGN-ML bidirectional converter project <https://summerofcode.withgoogle.com/projects/#6351966180474880>. I have recently signed up for the mailing list because I will be using layout to generate diagrams. However, I'm not sure if I can receive email from this mailing lists because there were issues previously. Could someone manually add me hal...@gm... to the mailing lists and send me a reply to this message please? My second question is: are there example files for SBML that has layout? Should I be searching in BioModels for example files? Thank you for your help. Sincerely, Haoran |
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From: Frank T. B. <fbe...@ca...> - 2016-06-30 14:01:33
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Hello Andreas, not according to the layout specification, you are free to draw the curves as you like them. (They would not even have to connect at all). That was done to provide the most freedom to implement any kind of lines connecting elements. best Frank On Wed, Jun 29, 2016 at 5:38 PM, Andreas Dräger < and...@un...> wrote: > Dear all, > > When drawing a reaction like the one in the example attached, is it > necessary to always let a connection from a speciesGlyph end in the > reactionGlyph or would it also be correct if the edge starting at node B > would end at its intersection point with the red edge? > > In other words, is it necessary to provide two curve segments to connect B > to the reaction glyph or is the first one sufficient? > > With best regards > > Dr. Andreas Dräger > Center for Bioinformatics Tuebingen (ZBIT), Dept. Cognitive Systems, > University of Tuebingen, Sand 1, Office #A313, 72076 Tübingen, Germany > Phone: +49-7071-29-78982, Fax: +49-7071-29-5091, twitter: @dr_drae > > > > > ------------------------------------------------------------------------------ > Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San > Francisco, CA to explore cutting-edge tech and listen to tech luminaries > present their vision of the future. This family event has something for > everyone, including kids. Get more information and register today. > http://sdm.link/attshape > _______________________________________________ > sbml-layout mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-layout > > |
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From: Andreas D. <and...@un...> - 2016-06-29 15:38:11
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Dear all, When drawing a reaction like the one in the example attached, is it necessary to always let a connection from a speciesGlyph end in the reactionGlyph or would it also be correct if the edge starting at node B would end at its intersection point with the red edge? In other words, is it necessary to provide two curve segments to connect B to the reaction glyph or is the first one sufficient? With best regards Dr. Andreas Dräger Center for Bioinformatics Tuebingen (ZBIT), Dept. Cognitive Systems, University of Tuebingen, Sand 1, Office #A313, 72076 Tübingen, Germany Phone: +49-7071-29-78982, Fax: +49-7071-29-5091, twitter: @dr_drae |
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From: kieran <kie...@ma...> - 2015-03-17 19:28:15
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Great thanks Sarah. One point: >> The spec allows the SpeciesReferenceGlyph role to be explicitly set to >> “undefined”, but libSBML doesn’t allow me to do that. >> http://sbml.org/Software/libSBML/5.11.0/docs/formatted/python-api/classlibsbml_1_1_species_reference_glyph.html#a4f0f02cd9e4a966d142d9eafe324099d > > If you use setRole("") or indeed any string that does not represent one of the allowed values libsbml will set the role to "undefined". We could certainly improve the documentation for this :-) This didn’t work for me. setRole('substrate’) results in layout:role=“substrate”, but setRole(‘undefined’) does not give me a layout:role=“undefined” in my SBML. Am I doing something wrong? |
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From: Sarah K. <ske...@ca...> - 2015-03-17 10:57:36
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Hi Kieran Thanks for the detailed feedback. It is always useful to have feedback on this very low level as it highlights all sorts of things. > > rule layout-21004 states that "A SpeciesReferenceGlyph object must have > the required attributes layout:id..” I think this is a mistake; other > similar elements are not required to have an id, and the main text > doesn't mention the requirement. I think the only required attribute > should be speciesGlyph. The SpeciesReferenceGlyph derives from a GraphicalObject - where in fact the 'id' attribute is required. So the rule is perfectly correct. Maybe the text could reiterate the attributes on an object that stem from its inheritance but it would make for a lot of repetitive text (and alot of work for people writing specifications!) > > The spec allows the SpeciesReferenceGlyph role to be explicitly set to > “undefined”, but libSBML doesn’t allow me to do that. > http://sbml.org/Software/libSBML/5.11.0/docs/formatted/python-api/classlibsbml_1_1_species_reference_glyph.html#a4f0f02cd9e4a966d142d9eafe324099d If you use setRole("") or indeed any string that does not represent one of the allowed values libsbml will set the role to "undefined". We could certainly improve the documentation for this :-) > > I got very confused by the BoundingBox.x() method. I thought that this > page meant I could use this to get the offset. > http://sbml.org/Software/libSBML/5.11.0/docs/formatted/python-api/classlibsbml_1_1_bounding_box.html#a620a83678622ecea12962007ecc6c152 > But there was no such method (?), I instead have to use > BoundingBox.getPosition().getXOffset(). Maybe this final issue is just > my not knowing my way round python and/or the documentation. This is a bug. That function does exist in the C++ API and should be available in python. However as you discovered it is not. Filed on the To Do list :-) Thanks Sarah |
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From: Kieran S. <Kie...@ma...> - 2015-03-12 10:39:00
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Hey folks, I’ve stumbled across some small issues with some aspects of the layout package this week. rule layout-21004 states that "A SpeciesReferenceGlyph object must have the required attributes layout:id..” I think this is a mistake; other similar elements are not required to have an id, and the main text doesn't mention the requirement. I think the only required attribute should be speciesGlyph. The spec allows the SpeciesReferenceGlyph role to be explicitly set to “undefined”, but libSBML doesn’t allow me to do that. http://sbml.org/Software/libSBML/5.11.0/docs/formatted/python-api/classlibsbml_1_1_species_reference_glyph.html#a4f0f02cd9e4a966d142d9eafe324099d I got very confused by the BoundingBox.x() method. I thought that this page meant I could use this to get the offset. http://sbml.org/Software/libSBML/5.11.0/docs/formatted/python-api/classlibsbml_1_1_bounding_box.html#a620a83678622ecea12962007ecc6c152 But there was no such method (?), I instead have to use BoundingBox.getPosition().getXOffset(). Maybe this final issue is just my not knowing my way round python and/or the documentation. k |
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From: Chris J. M. <my...@ec...> - 2015-02-06 19:54:12
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Ah, I see. In that case, there should be good reasons to make the change. I think at the very least the specification could be a bit more clear about the fact that a BoundingBox is not always required when there is a Curve. Also, the assigning of defaults difference is not a specification issue, but an implementation issue. So, I think it is something which should be considered. It seems a bit out-of-character for no defaults. Perhaps, there could be an option to assign defaults or not to make it a little more clear this is what it does. Just a thought. That being said, I’m not sure how many people deal with both libsbml and jsbml, but making them as identical as possible will help any that do. Cheers, Chris > On Feb 6, 2015, at 10:48 AM, Lucian Smith <luc...@gm...> wrote: > > Actually, a new release is not required for L3v2--there's a caveat in the L3v2 spec that says that L3v1 packages may still be used, but that they must behave as they did in L3v1, and cannot take advantage of L3v2 constructs and changes, such as the id-on-everything. Not that we can't talk about it; just wanted to confirm that an L3v2 version is not strictly necessary. > > I agree that the differences between libsbml and jsbml should always be minimized, regardless of the statuses of specifications. I don't know if the libsbml unit tests can be converted easily to jsbml or not, but it definitely seems worth it to do so. I think that's the only way to reliably find these cases where they behave differently from one another. > > -Lucian > > On Fri, Feb 6, 2015 at 9:36 AM, Chris J. Myers <my...@ec... <mailto:my...@ec...>> wrote: > Well, I think a new release is required for L3V2, so we could at least discuss this. > > My point though is more about difference in libsbml/jsbml. I think we should try to avoid these when possible. I don’t think there are many places (correct me if I’m wrong) where libsbml actually fills in defaults for required values. This behavior seems to be a bit out-of-character for the no defaults philosophy. I guess layout has this weird history, since it was developed before L3. However, we may want to discuss this too. > > Chris > > > On Feb 6, 2015, at 10:30 AM, Frank Bergmann <fbe...@ca... <mailto:fbe...@ca...>> wrote: > > > >> > >> We can do that but I would be more in flavour of relaxing the validation > >> rule for ReactionGlyph and SpeciesReferenceGlyph and > >> in the long run making the boundingBox not mandatory on GraphicalObject > >> as you proposed and make it mandatory only on objects > >> that need it. > >> > > > > I don’t know … i see the release of a new specification as much more problematic, as a new release of JSBML. We argued for years about the values for the specification and I’m for one am not looking forward to open that box again. Since layout pretty much contains just bounds and curves, i really don’t think there is a necessity to make all the elements in the bounds optional. > > > > Frank > > > > > >>> For now, I’ve added a BoundingBox at the end point of size 0,0. No more validation errors :-). > >>> > >> > >> > >> ------------------------------------------------------------------------------ > >> 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/ <http://goparallel.sourceforge.net/> > >> _______________________________________________ > >> sbml-layout mailing list > >> sbm...@li... <mailto:sbm...@li...> > >> https://lists.sourceforge.net/lists/listinfo/sbml-layout <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/ <http://goparallel.sourceforge.net/> > > _______________________________________________ > > sbml-layout mailing list > > sbm...@li... <mailto:sbm...@li...> > > https://lists.sourceforge.net/lists/listinfo/sbml-layout <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/ <http://goparallel.sourceforge.net/> > _______________________________________________ > sbml-layout mailing list > sbm...@li... <mailto:sbm...@li...> > https://lists.sourceforge.net/lists/listinfo/sbml-layout <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 |
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From: Frank B. <fbe...@ca...> - 2015-02-06 18:50:52
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Let me rephrase … even if there is a new release of the layout package, the current release is not going anywhere, it is approved, and as such the validation rules stand as they are (even if a future version might change them). As such it is much easier for a library writing that version to change or the tools supporting that version, than to retroactively try and amend the specification. But sure … lets discuss this at HARMONY … All the best Frank > On Feb 6, 2015, at 6:36 PM, Chris J. Myers <my...@ec...> wrote: > > Well, I think a new release is required for L3V2, so we could at least discuss this. > > My point though is more about difference in libsbml/jsbml. I think we should try to avoid these when possible. I don’t think there are many places (correct me if I’m wrong) where libsbml actually fills in defaults for required values. This behavior seems to be a bit out-of-character for the no defaults philosophy. I guess layout has this weird history, since it was developed before L3. However, we may want to discuss this too. > > Chris > >> On Feb 6, 2015, at 10:30 AM, Frank Bergmann <fbe...@ca...> wrote: >> >>> >>> We can do that but I would be more in flavour of relaxing the validation >>> rule for ReactionGlyph and SpeciesReferenceGlyph and >>> in the long run making the boundingBox not mandatory on GraphicalObject >>> as you proposed and make it mandatory only on objects >>> that need it. >>> >> >> I don’t know … i see the release of a new specification as much more problematic, as a new release of JSBML. We argued for years about the values for the specification and I’m for one am not looking forward to open that box again. Since layout pretty much contains just bounds and curves, i really don’t think there is a necessity to make all the elements in the bounds optional. >> >> Frank >> >> >>>> For now, I’ve added a BoundingBox at the end point of size 0,0. No more validation errors :-). >>>> >>> >>> >>> ------------------------------------------------------------------------------ >>> 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 > > > ------------------------------------------------------------------------------ > 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 |
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From: Lucian S. <luc...@gm...> - 2015-02-06 17:48:18
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Actually, a new release is not required for L3v2--there's a caveat in the L3v2 spec that says that L3v1 packages may still be used, but that they must behave as they did in L3v1, and cannot take advantage of L3v2 constructs and changes, such as the id-on-everything. Not that we can't talk about it; just wanted to confirm that an L3v2 version is not strictly necessary. I agree that the differences between libsbml and jsbml should always be minimized, regardless of the statuses of specifications. I don't know if the libsbml unit tests can be converted easily to jsbml or not, but it definitely seems worth it to do so. I think that's the only way to reliably find these cases where they behave differently from one another. -Lucian On Fri, Feb 6, 2015 at 9:36 AM, Chris J. Myers <my...@ec...> wrote: > Well, I think a new release is required for L3V2, so we could at least > discuss this. > > My point though is more about difference in libsbml/jsbml. I think we > should try to avoid these when possible. I don’t think there are many > places (correct me if I’m wrong) where libsbml actually fills in defaults > for required values. This behavior seems to be a bit out-of-character for > the no defaults philosophy. I guess layout has this weird history, since > it was developed before L3. However, we may want to discuss this too. > > Chris > > > On Feb 6, 2015, at 10:30 AM, Frank Bergmann <fbe...@ca...> > wrote: > > > >> > >> We can do that but I would be more in flavour of relaxing the validation > >> rule for ReactionGlyph and SpeciesReferenceGlyph and > >> in the long run making the boundingBox not mandatory on GraphicalObject > >> as you proposed and make it mandatory only on objects > >> that need it. > >> > > > > I don’t know … i see the release of a new specification as much more > problematic, as a new release of JSBML. We argued for years about the > values for the specification and I’m for one am not looking forward to open > that box again. Since layout pretty much contains just bounds and curves, i > really don’t think there is a necessity to make all the elements in the > bounds optional. > > > > Frank > > > > > >>> For now, I’ve added a BoundingBox at the end point of size 0,0. No > more validation errors :-). > >>> > >> > >> > >> > ------------------------------------------------------------------------------ > >> 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 > > > > ------------------------------------------------------------------------------ > 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 > |
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From: Chris J. M. <my...@ec...> - 2015-02-06 17:37:14
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Well, I think a new release is required for L3V2, so we could at least discuss this. My point though is more about difference in libsbml/jsbml. I think we should try to avoid these when possible. I don’t think there are many places (correct me if I’m wrong) where libsbml actually fills in defaults for required values. This behavior seems to be a bit out-of-character for the no defaults philosophy. I guess layout has this weird history, since it was developed before L3. However, we may want to discuss this too. Chris > On Feb 6, 2015, at 10:30 AM, Frank Bergmann <fbe...@ca...> wrote: > >> >> We can do that but I would be more in flavour of relaxing the validation >> rule for ReactionGlyph and SpeciesReferenceGlyph and >> in the long run making the boundingBox not mandatory on GraphicalObject >> as you proposed and make it mandatory only on objects >> that need it. >> > > I don’t know … i see the release of a new specification as much more problematic, as a new release of JSBML. We argued for years about the values for the specification and I’m for one am not looking forward to open that box again. Since layout pretty much contains just bounds and curves, i really don’t think there is a necessity to make all the elements in the bounds optional. > > Frank > > >>> For now, I’ve added a BoundingBox at the end point of size 0,0. No more validation errors :-). >>> >> >> >> ------------------------------------------------------------------------------ >> 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 |
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From: Frank B. <fbe...@ca...> - 2015-02-06 17:30:34
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> > We can do that but I would be more in flavour of relaxing the validation > rule for ReactionGlyph and SpeciesReferenceGlyph and > in the long run making the boundingBox not mandatory on GraphicalObject > as you proposed and make it mandatory only on objects > that need it. > I don’t know … i see the release of a new specification as much more problematic, as a new release of JSBML. We argued for years about the values for the specification and I’m for one am not looking forward to open that box again. Since layout pretty much contains just bounds and curves, i really don’t think there is a necessity to make all the elements in the bounds optional. Frank >> For now, I’ve added a BoundingBox at the end point of size 0,0. No more validation errors :-). >> > > > ------------------------------------------------------------------------------ > 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 |
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From: Chris J. M. <my...@ec...> - 2015-02-06 16:07:19
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>> >> JSBML folks: you might consider copying this behavior. > > We can do that but I would be more in flavour of relaxing the validation > rule for ReactionGlyph and SpeciesReferenceGlyph and > in the long run making the boundingBox not mandatory on GraphicalObject > as you proposed and make it mandatory only on objects > that need it. > I agree. I think we should try to avoid having behaviors like the one you describe Frank as they are not part of the specification. Or at the very least we need to have them well documented, so we can be more sure that libsbml and jsbml behave consistently. Chris |
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From: Nicolas R. <rod...@eb...> - 2015-02-06 15:45:42
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On 02/06/2015 03:14 PM, Chris J. Myers wrote: >> On Feb 6, 2015, at 8:12 AM, Frank Bergmann <fbe...@ca...> wrote: >> >> >>> On Feb 6, 2015, at 3:40 PM, Chris J. Myers <my...@ec...> wrote: >>> >>>> On Feb 5, 2015, at 11:59 PM, Frank Bergmann <fbe...@ca...> wrote: >>>> >>>> >>>>> On Feb 6, 2015, at 12:49 AM, Chris J. Myers <my...@ec...> wrote: >>>>> >>>>> Hi Frank, >>>>> >>>>> Thanks for your detailed answer. >>>>>> but you would not need to contain that structure … it would also be valid to have >>>>>> >>>>>> - an empty bounding box for the reaction glyph, and only one species reference directly connecting species glyph1 with species glyph2 >>>>>> >>>>>> >>>>> This is actually what I was trying to do, but I was getting validation errors. Here is what I did: >>>>> >>>>> reactionGlyph.createBoundingBox(); >>>>> reactionGlyph.getBoundingBox().createDimensions(); >>>>> reactionGlyph.getBoundingBox().createPosition(); >>>>> >>>>> It then complains about there not being x and y position values. Perhaps, I should not create the Position or Dimension, but I think it was complaining about that too. For now, I’m duplicating the curve in both the ReactionGlyph and SpeciesReference, but this is not ideal. >>>>> >>>> This must be a different behavior of JSBML, this is not what would happen in libSBML. >>>> >>> Actually, it is libsbml validation that complains: >>> >>> Validation Problems Found by libsbml >>> 0:A <point> object must have the required attributes 'layout:x' and 'layout:y' and may have the optional attributes 'layout:id', and 'layout:z'. No other attributes from the Layout namespace are permitted on a <point>. >>> Reference: L3V1 Layout V1 Section 3.4.1 >>> Layout attribute 'x' is missing. >>> >>> >> Indeed, in libSBML, when you create a ReactionGlyph, an empty bounding box (at position 0,0, and dimension 0,0) will be created already. It will not be written out if you should choose to create a curve on the reaction glyph. >> >> i think that is the difference in behavior. >> > Ah, that makes sense. > > JSBML folks: you might consider copying this behavior. We can do that but I would be more in flavour of relaxing the validation rule for ReactionGlyph and SpeciesReferenceGlyph and in the long run making the boundingBox not mandatory on GraphicalObject as you proposed and make it mandatory only on objects that need it. > For now, I’ve added a BoundingBox at the end point of size 0,0. No more validation errors :-). > |
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From: Chris J. M. <my...@ec...> - 2015-02-06 15:14:43
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> On Feb 6, 2015, at 8:12 AM, Frank Bergmann <fbe...@ca...> wrote: > > >> On Feb 6, 2015, at 3:40 PM, Chris J. Myers <my...@ec...> wrote: >> >>> >>> On Feb 5, 2015, at 11:59 PM, Frank Bergmann <fbe...@ca...> wrote: >>> >>> >>>> On Feb 6, 2015, at 12:49 AM, Chris J. Myers <my...@ec...> wrote: >>>> >>>> Hi Frank, >>>> >>>> Thanks for your detailed answer. >>>>> >>>>> but you would not need to contain that structure … it would also be valid to have >>>>> >>>>> - an empty bounding box for the reaction glyph, and only one species reference directly connecting species glyph1 with species glyph2 >>>>> >>>>> >>>> This is actually what I was trying to do, but I was getting validation errors. Here is what I did: >>>> >>>> reactionGlyph.createBoundingBox(); >>>> reactionGlyph.getBoundingBox().createDimensions(); >>>> reactionGlyph.getBoundingBox().createPosition(); >>>> >>>> It then complains about there not being x and y position values. Perhaps, I should not create the Position or Dimension, but I think it was complaining about that too. For now, I’m duplicating the curve in both the ReactionGlyph and SpeciesReference, but this is not ideal. >>>> >>> >>> This must be a different behavior of JSBML, this is not what would happen in libSBML. >>> >> Actually, it is libsbml validation that complains: >> >> Validation Problems Found by libsbml >> 0:A <point> object must have the required attributes 'layout:x' and 'layout:y' and may have the optional attributes 'layout:id', and 'layout:z'. No other attributes from the Layout namespace are permitted on a <point>. >> Reference: L3V1 Layout V1 Section 3.4.1 >> Layout attribute 'x' is missing. >> >> > > Indeed, in libSBML, when you create a ReactionGlyph, an empty bounding box (at position 0,0, and dimension 0,0) will be created already. It will not be written out if you should choose to create a curve on the reaction glyph. > > i think that is the difference in behavior. > Ah, that makes sense. JSBML folks: you might consider copying this behavior. For now, I’ve added a BoundingBox at the end point of size 0,0. No more validation errors :-). Chris > Frank > > > > ------------------------------------------------------------------------------ > 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 |
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From: Frank B. <fbe...@ca...> - 2015-02-06 15:12:19
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> On Feb 6, 2015, at 3:40 PM, Chris J. Myers <my...@ec...> wrote: > >> >> On Feb 5, 2015, at 11:59 PM, Frank Bergmann <fbe...@ca...> wrote: >> >> >>> On Feb 6, 2015, at 12:49 AM, Chris J. Myers <my...@ec...> wrote: >>> >>> Hi Frank, >>> >>> Thanks for your detailed answer. >>>> >>>> but you would not need to contain that structure … it would also be valid to have >>>> >>>> - an empty bounding box for the reaction glyph, and only one species reference directly connecting species glyph1 with species glyph2 >>>> >>>> >>> This is actually what I was trying to do, but I was getting validation errors. Here is what I did: >>> >>> reactionGlyph.createBoundingBox(); >>> reactionGlyph.getBoundingBox().createDimensions(); >>> reactionGlyph.getBoundingBox().createPosition(); >>> >>> It then complains about there not being x and y position values. Perhaps, I should not create the Position or Dimension, but I think it was complaining about that too. For now, I’m duplicating the curve in both the ReactionGlyph and SpeciesReference, but this is not ideal. >>> >> >> This must be a different behavior of JSBML, this is not what would happen in libSBML. >> > Actually, it is libsbml validation that complains: > > Validation Problems Found by libsbml > 0:A <point> object must have the required attributes 'layout:x' and 'layout:y' and may have the optional attributes 'layout:id', and 'layout:z'. No other attributes from the Layout namespace are permitted on a <point>. > Reference: L3V1 Layout V1 Section 3.4.1 > Layout attribute 'x' is missing. > > Indeed, in libSBML, when you create a ReactionGlyph, an empty bounding box (at position 0,0, and dimension 0,0) will be created already. It will not be written out if you should choose to create a curve on the reaction glyph. i think that is the difference in behavior. Frank |
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From: Chris J. M. <my...@ec...> - 2015-02-06 14:40:27
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> On Feb 5, 2015, at 11:59 PM, Frank Bergmann <fbe...@ca...> wrote: > > >> On Feb 6, 2015, at 12:49 AM, Chris J. Myers <my...@ec...> wrote: >> >> Hi Frank, >> >> Thanks for your detailed answer. >>> >>> but you would not need to contain that structure … it would also be valid to have >>> >>> - an empty bounding box for the reaction glyph, and only one species reference directly connecting species glyph1 with species glyph2 >>> >>> >> This is actually what I was trying to do, but I was getting validation errors. Here is what I did: >> >> reactionGlyph.createBoundingBox(); >> reactionGlyph.getBoundingBox().createDimensions(); >> reactionGlyph.getBoundingBox().createPosition(); >> >> It then complains about there not being x and y position values. Perhaps, I should not create the Position or Dimension, but I think it was complaining about that too. For now, I’m duplicating the curve in both the ReactionGlyph and SpeciesReference, but this is not ideal. >> > > This must be a different behavior of JSBML, this is not what would happen in libSBML. > Actually, it is libsbml validation that complains: Validation Problems Found by libsbml 0:A <point> object must have the required attributes 'layout:x' and 'layout:y' and may have the optional attributes 'layout:id', and 'layout:z'. No other attributes from the Layout namespace are permitted on a <point>. Reference: L3V1 Layout V1 Section 3.4.1 Layout attribute 'x' is missing. >> In your example, we would represent it as two separate line segments from each reactant to the product labeled with the reactionId. Therefore, it makes the most sense to leave the curve on the SpeciesReference and put nothing on the reactionGlyph itself, but this is illegal. So, I’m a bit stumped as anything I can think of is a bit artificial. >> > > you could always create a curve containing simply the connecting point (last point of the substrate arc, first point of the product arc). or indeed an empty bounding box at the position of the last point of the substrate arc) That would be less artificial. > This seems a reasonable enough approach for me. Thanks, Chris > Cheers > Frank > >> Thanks for your help. >> >> Chris >> >>> >>> >>>> On Feb 4, 2015, at 8:33 PM, Chris J. Myers <my...@ec... <mailto:my...@ec...>> wrote: >>>> >>>> One more question about this example. The UML indicates that a ReactionGlyph and a SpeciesReferenceGlyph can both have a curve. However, in the case that the ReactionGlyph has a curve, what does the SpeciesReferenceGlyph have? The example does not show anything other than “…”. Since the SpeciesReferenceGlyph also inherits from GeneralGlyph, it is required to have a BoundingBox though I assume you may say the same thing that it can have a Curve which dismisses this requirement. However, in this case, what would the Curve be? I’ve already put the Curve on the ReactionGlyph, would I have to put an identical Curve on the SpeciesReferenceGlyph? This seems wrong to me. >>>> >>>> Let me be more specific. I would like to represent the following: >>>> >>>> Species S1, S2 >>>> Reaction R >>>> Reactant S1 >>>> Product S2 >>>> >>>> I would like to represent this as two SpeciesGlyphs for S1 and S2, and a ReactionGlyph for R which is simply a Curve connecting the two SpeciesGlyphs. What should the layout code be for this? >>>> >>>> Thanks, >>>> >>>> Chris >>>> >>>>> On Jan 30, 2015, at 12:07 AM, Frank Bergmann <fbe...@ca... <mailto: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... <mailto: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/ <http://goparallel.sourceforge.net/> >>>>>> _______________________________________________ >>>>>> sbml-layout mailing list >>>>>> sbm...@li... <mailto: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/ <http://goparallel.sourceforge.net/> >>>>> _______________________________________________ >>>>> sbml-layout mailing list >>>>> sbm...@li... <mailto: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/ <http://goparallel.sourceforge.net/> >>>> _______________________________________________ >>>> sbml-layout mailing list >>>> sbm...@li... <mailto: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/ <http://goparallel.sourceforge.net/> >>> _______________________________________________ >>> sbml-layout mailing list >>> sbm...@li... <mailto: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/_______________________________________________ <http://goparallel.sourceforge.net/_______________________________________________> >> sbml-layout mailing list >> sbm...@li... <mailto:sbm...@li...> >> https://lists.sourceforge.net/lists/listinfo/sbml-layout <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 |
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From: Frank B. <fbe...@ca...> - 2015-02-06 06:59:54
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> On Feb 6, 2015, at 12:49 AM, Chris J. Myers <my...@ec...> wrote: > > Hi Frank, > > Thanks for your detailed answer. >> >> but you would not need to contain that structure … it would also be valid to have >> >> - an empty bounding box for the reaction glyph, and only one species reference directly connecting species glyph1 with species glyph2 >> >> > This is actually what I was trying to do, but I was getting validation errors. Here is what I did: > > reactionGlyph.createBoundingBox(); > reactionGlyph.getBoundingBox().createDimensions(); > reactionGlyph.getBoundingBox().createPosition(); > > It then complains about there not being x and y position values. Perhaps, I should not create the Position or Dimension, but I think it was complaining about that too. For now, I’m duplicating the curve in both the ReactionGlyph and SpeciesReference, but this is not ideal. > This must be a different behavior of JSBML, this is not what would happen in libSBML. > In your example, we would represent it as two separate line segments from each reactant to the product labeled with the reactionId. Therefore, it makes the most sense to leave the curve on the SpeciesReference and put nothing on the reactionGlyph itself, but this is illegal. So, I’m a bit stumped as anything I can think of is a bit artificial. > you could always create a curve containing simply the connecting point (last point of the substrate arc, first point of the product arc). or indeed an empty bounding box at the position of the last point of the substrate arc) That would be less artificial. Cheers Frank > Thanks for your help. > > Chris > >> >> >>> On Feb 4, 2015, at 8:33 PM, Chris J. Myers <my...@ec... <mailto:my...@ec...>> wrote: >>> >>> One more question about this example. The UML indicates that a ReactionGlyph and a SpeciesReferenceGlyph can both have a curve. However, in the case that the ReactionGlyph has a curve, what does the SpeciesReferenceGlyph have? The example does not show anything other than “…”. Since the SpeciesReferenceGlyph also inherits from GeneralGlyph, it is required to have a BoundingBox though I assume you may say the same thing that it can have a Curve which dismisses this requirement. However, in this case, what would the Curve be? I’ve already put the Curve on the ReactionGlyph, would I have to put an identical Curve on the SpeciesReferenceGlyph? This seems wrong to me. >>> >>> Let me be more specific. I would like to represent the following: >>> >>> Species S1, S2 >>> Reaction R >>> Reactant S1 >>> Product S2 >>> >>> I would like to represent this as two SpeciesGlyphs for S1 and S2, and a ReactionGlyph for R which is simply a Curve connecting the two SpeciesGlyphs. What should the layout code be for this? >>> >>> Thanks, >>> >>> Chris >>> >>>> On Jan 30, 2015, at 12:07 AM, Frank Bergmann <fbe...@ca... <mailto: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... <mailto: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/ <http://goparallel.sourceforge.net/> >>>>> _______________________________________________ >>>>> sbml-layout mailing list >>>>> sbm...@li... <mailto: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/ <http://goparallel.sourceforge.net/> >>>> _______________________________________________ >>>> sbml-layout mailing list >>>> sbm...@li... <mailto: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/ <http://goparallel.sourceforge.net/> >>> _______________________________________________ >>> sbml-layout mailing list >>> sbm...@li... <mailto: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/ <http://goparallel.sourceforge.net/> >> _______________________________________________ >> sbml-layout mailing list >> sbm...@li... <mailto: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/_______________________________________________ <http://goparallel.sourceforge.net/_______________________________________________> > sbml-layout mailing list > sbm...@li... <mailto:sbm...@li...> > https://lists.sourceforge.net/lists/listinfo/sbml-layout <https://lists.sourceforge.net/lists/listinfo/sbml-layout> |
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From: Chris J. M. <my...@ec...> - 2015-02-05 23:49:29
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Hi Frank, Thanks for your detailed answer. > > but you would not need to contain that structure … it would also be valid to have > > - an empty bounding box for the reaction glyph, and only one species reference directly connecting species glyph1 with species glyph2 > > This is actually what I was trying to do, but I was getting validation errors. Here is what I did: reactionGlyph.createBoundingBox(); reactionGlyph.getBoundingBox().createDimensions(); reactionGlyph.getBoundingBox().createPosition(); It then complains about there not being x and y position values. Perhaps, I should not create the Position or Dimension, but I think it was complaining about that too. For now, I’m duplicating the curve in both the ReactionGlyph and SpeciesReference, but this is not ideal. In your example, we would represent it as two separate line segments from each reactant to the product labeled with the reactionId. Therefore, it makes the most sense to leave the curve on the SpeciesReference and put nothing on the reactionGlyph itself, but this is illegal. So, I’m a bit stumped as anything I can think of is a bit artificial. Thanks for your help. Chris > > >> On Feb 4, 2015, at 8:33 PM, Chris J. Myers <my...@ec...> wrote: >> >> One more question about this example. The UML indicates that a ReactionGlyph and a SpeciesReferenceGlyph can both have a curve. However, in the case that the ReactionGlyph has a curve, what does the SpeciesReferenceGlyph have? The example does not show anything other than “…”. Since the SpeciesReferenceGlyph also inherits from GeneralGlyph, it is required to have a BoundingBox though I assume you may say the same thing that it can have a Curve which dismisses this requirement. However, in this case, what would the Curve be? I’ve already put the Curve on the ReactionGlyph, would I have to put an identical Curve on the SpeciesReferenceGlyph? This seems wrong to me. >> >> Let me be more specific. I would like to represent the following: >> >> Species S1, S2 >> Reaction R >> Reactant S1 >> Product S2 >> >> I would like to represent this as two SpeciesGlyphs for S1 and S2, and a ReactionGlyph for R which is simply a Curve connecting the two SpeciesGlyphs. What should the layout code be for this? >> >> Thanks, >> >> 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 >> >> >> ------------------------------------------------------------------------------ >> 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 |
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From: Frank B. <fbe...@ca...> - 2015-02-05 19:34:22
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Hello Chris, there is several ways you can represent this. The Layout Extension is really flexible in how to display that. Let me try to put together an illustration on how the reaction boundingbox / curve issue can be understood: https://www.dropbox.com/s/b1cnkx58babtr4w/2015-02-05_-_ReactionCurveBB.png?dl=0 The reaction glyph bounding box is meant to represent the middle piece of a reaction, such that substrate arcs do not directly bump into product arcs. To represent SBGN for example one usually just creates a rectangular bounding box, and then uses render to describe the correct process symbol for the reaction. However, you could also just use a curve that connects all your substrate arcs with the product arcs. As for your example, you have many possible ways to represent that: - you could have: - one species reference glyph, connecting species glyph1 and the reaction glyph, a reaction glyph bounding box, then a species reference glyph connecting the other end of the reaction glyph bounds to the species glyph 2 - one species reference glyph, connecting species glyph1 and the reaction glyph, a reaction glyph curve, then a species reference glyph connecting the other end of the reaction glyph bounds to the species glyph 2 but you would not need to contain that structure … it would also be valid to have - an empty bounding box for the reaction glyph, and only one species reference directly connecting species glyph1 with species glyph2 all of them are valid and it depends what is the best for you to choose one. Frank > On Feb 4, 2015, at 8:33 PM, Chris J. Myers <my...@ec...> wrote: > > One more question about this example. The UML indicates that a ReactionGlyph and a SpeciesReferenceGlyph can both have a curve. However, in the case that the ReactionGlyph has a curve, what does the SpeciesReferenceGlyph have? The example does not show anything other than “…”. Since the SpeciesReferenceGlyph also inherits from GeneralGlyph, it is required to have a BoundingBox though I assume you may say the same thing that it can have a Curve which dismisses this requirement. However, in this case, what would the Curve be? I’ve already put the Curve on the ReactionGlyph, would I have to put an identical Curve on the SpeciesReferenceGlyph? This seems wrong to me. > > Let me be more specific. I would like to represent the following: > > Species S1, S2 > Reaction R > Reactant S1 > Product S2 > > I would like to represent this as two SpeciesGlyphs for S1 and S2, and a ReactionGlyph for R which is simply a Curve connecting the two SpeciesGlyphs. What should the layout code be for this? > > Thanks, > > 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 > > > ------------------------------------------------------------------------------ > 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 |
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From: Chris J. M. <my...@ec...> - 2015-02-04 19:33:49
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One more question about this example. The UML indicates that a ReactionGlyph and a SpeciesReferenceGlyph can both have a curve. However, in the case that the ReactionGlyph has a curve, what does the SpeciesReferenceGlyph have? The example does not show anything other than “…”. Since the SpeciesReferenceGlyph also inherits from GeneralGlyph, it is required to have a BoundingBox though I assume you may say the same thing that it can have a Curve which dismisses this requirement. However, in this case, what would the Curve be? I’ve already put the Curve on the ReactionGlyph, would I have to put an identical Curve on the SpeciesReferenceGlyph? This seems wrong to me. Let me be more specific. I would like to represent the following: Species S1, S2 Reaction R Reactant S1 Product S2 I would like to represent this as two SpeciesGlyphs for S1 and S2, and a ReactionGlyph for R which is simply a Curve connecting the two SpeciesGlyphs. What should the layout code be for this? Thanks, 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 |
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From: Chris J. M. <my...@ec...> - 2015-01-30 15:28:54
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One more question about this example. The UML indicates that a ReactionGlyph and a SpeciesReferenceGlyph can both have a curve. However, in the case that the ReactionGlyph has a curve, what does the SpeciesReferenceGlyph have? The example does not show anything other than “…”. Since the SpeciesReferenceGlyph also inherits from GeneralGlyph, it is required to have a BoundingBox though I assume you may say the same thing that it can have a Curve which dismisses this requirement. However, in this case, what would the Curve be? I’ve already put the Curve on the ReactionGlyph, would I have to put an identical Curve on the SpeciesReferenceGlyph? This seems wrong to me. Let me be more specific. I would like to represent the following: Species S1, S2 Reaction R Reactant S1 Product S2 I would like to represent this as two SpeciesGlyphs for S1 and S2, and a ReactionGlyph for R which is simply a Curve connecting the two SpeciesGlyphs. What should the layout code be for this? Thanks, 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 |
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