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From: Augustin L. <ca...@gm...> - 2018-01-17 18:32:35
|
Dear SBGN Community, The election for two new members of the SBGN Editorial Board in replacement of Augustin Luna, Robin Haw and Tobias Czauderna has the following result. Four of the nominees chose to stand in the election. 20 voters participated in the election, all were eligible to vote according to the SBGN Editorial Board Election Rules. The results were close and as follows: Vasundra Toure: 17 Andreas Draeger: 15 Adrien Rougny: 14 Guanming Wu: 7 Thanks to all candidates and everyone who participated in the vote. Congratulations to Vasundra, Andreas, and Adrien who are elected SBGN Editors for the term 2018 to 2020! Happy New Year 2018! |
|
From: Augustin L. <ca...@gm...> - 2018-01-10 14:32:52
|
This is a last reminder. Please remember to vote for SBGN editors by this Friday, January 12, using this form: https://goo.gl/forms/LUpaK9zbZ7GuKi4t2 See details below. Thank you very much ---------- Forwarded message ---------- From: Augustin Luna <ca...@gm...> Date: Wed, Dec 20, 2017 at 8:54 AM Subject: SBGN Election 2017 To: SBGN Discussion List <sbg...@go...>, libSBGN Development and Technical Issues <sbg...@li...>, The SBGN editors internal mailing list <sbg...@go...>, List for all SBGN Editors past and present <sbg...@li...> Dear SBGN Community, At the core of SBGN governance sits a body of five editors, elected by the community. Editors are in charge of coordinating the discussions pertaining to the specifications, and write the specifications themselves. Editors will serve terms of three years that cannot been served consecutively. This year Augustin Luna, Robin Haw and Tobias Czauderna will step-down as editors, and we need to elect three new editors for a three year term. The SBGN community has recently been asked who could be potential SBGN Editors. Sixteen people have been nominated and 4 have accepted to stand in the election. The details of the electoral procedure are as follows: * The election is being organized by Augustin Luna who will not vote in the election. * Only subscribers of sbgn-discuss are eligible to vote and must have been subscribed to the list at the time the election was announced on sbgn-discuss. * Each subscriber of sbgn-discuss has three votes for this election. However, you can only use one vote for a nominee, and you don't have to use all your votes. * Subscribers are eligible on an individual basis, i.e., if you are subscribed with multiple e-mail addresses you should only complete the voting form once. * In the case of a tie, there will be a subsequent run-off election between the tied nominees. If you have any problems or questions contact Augustin Luna (aluna AT jimmy.harvard.edu) and NOT the SBGN Editorial Board. You can now vote for your favorite nominees. Voting for yourself, if you are one of the nominees, is perfectly fine. The three top-scorers will be elected as editors. In order to avoid multiple votes, the vote is authenticated and you have to provide your name and e-mail address. However, this information will not be made public. To vote, please complete the form https://goo.gl/forms/LUpaK9zbZ7GuKi4t2 Nominees (in alphabetical order by last name): * Andreas Draeger: Andreas has served as editor for SBML and worked on tools using the SBGN notation. * Adrien Rougny: Adrien has helped in the development of the SBGN PD specification and has developed tools around the SBGN notation. * Vasundra Toure: Vasundra has helped in several areas of SBGN in the past few years, including the specifications, website, and has worked on tools involving SBGN. * Guanming Wu: Guanming works on the Reactome project that has made use of the SBGN notation for a number of years. Due to an extension in the nomination process and the holiday season, the deadline for the election will be Friday January 12, 2017 23:59 EST. A reminder will be sent out the first week of 2018. Voting for the SBGN Editorial Board is important. It is one of the means you have of ensuring the project is well maintained. Thank you very much for your help! |
|
From: Augustin L. <ca...@gm...> - 2018-01-05 17:07:45
|
Dear SBGN Community, A reminder to please vote for SBGN editors, using this form: https://goo.gl/forms/LUpaK9zbZ7GuKi4t2 See original email below for more details. Thank you very much for your help! ---------- Forwarded message ---------- From: Augustin Luna <ca...@gm...> Date: Wed, Dec 20, 2017 at 8:54 AM Subject: SBGN Election 2017 To: SBGN Discussion List <sbg...@go...>, libSBGN Development and Technical Issues <sbg...@li...>, The SBGN editors internal mailing list <sbg...@go...>, List for all SBGN Editors past and present <sbg...@li...> Dear SBGN Community, At the core of SBGN governance sits a body of five editors, elected by the community. Editors are in charge of coordinating the discussions pertaining to the specifications, and write the specifications themselves. Editors will serve terms of three years that cannot been served consecutively. This year Augustin Luna, Robin Haw and Tobias Czauderna will step-down as editors, and we need to elect three new editors for a three year term. The SBGN community has recently been asked who could be potential SBGN Editors. Sixteen people have been nominated and 4 have accepted to stand in the election. The details of the electoral procedure are as follows: * The election is being organized by Augustin Luna who will not vote in the election. * Only subscribers of sbgn-discuss are eligible to vote and must have been subscribed to the list at the time the election was announced on sbgn-discuss. * Each subscriber of sbgn-discuss has three votes for this election. However, you can only use one vote for a nominee, and you don't have to use all your votes. * Subscribers are eligible on an individual basis, i.e., if you are subscribed with multiple e-mail addresses you should only complete the voting form once. * In the case of a tie, there will be a subsequent run-off election between the tied nominees. If you have any problems or questions contact Augustin Luna (aluna AT jimmy.harvard.edu) and NOT the SBGN Editorial Board. You can now vote for your favorite nominees. Voting for yourself, if you are one of the nominees, is perfectly fine. The three top-scorers will be elected as editors. In order to avoid multiple votes, the vote is authenticated and you have to provide your name and e-mail address. However, this information will not be made public. To vote, please complete the form https://goo.gl/forms/LUpaK9zbZ7GuKi4t2 Nominees (in alphabetical order by last name): * Andreas Draeger: Andreas has served as editor for SBML and worked on tools using the SBGN notation. * Adrien Rougny: Adrien has helped in the development of the SBGN PD specification and has developed tools around the SBGN notation. * Vasundra Toure: Vasundra has helped in several areas of SBGN in the past few years, including the specifications, website, and has worked on tools involving SBGN. * Guanming Wu: Guanming works on the Reactome project that has made use of the SBGN notation for a number of years. Due to an extension in the nomination process and the holiday season, the deadline for the election will be Friday January 12, 2017 23:59 EST. A reminder will be sent out the first week of 2018. Voting for the SBGN Editorial Board is important. It is one of the means you have of ensuring the project is well maintained. Thank you very much for your help! |
|
From: Augustin L. <ca...@gm...> - 2017-12-20 13:55:06
|
Dear SBGN Community, At the core of SBGN governance sits a body of five editors, elected by the community. Editors are in charge of coordinating the discussions pertaining to the specifications, and write the specifications themselves. Editors will serve terms of three years that cannot been served consecutively. This year Augustin Luna, Robin Haw and Tobias Czauderna will step-down as editors, and we need to elect three new editors for a three year term. The SBGN community has recently been asked who could be potential SBGN Editors. Sixteen people have been nominated and 4 have accepted to stand in the election. The details of the electoral procedure are as follows: * The election is being organized by Augustin Luna who will not vote in the election. * Only subscribers of sbgn-discuss are eligible to vote and must have been subscribed to the list at the time the election was announced on sbgn-discuss. * Each subscriber of sbgn-discuss has three votes for this election. However, you can only use one vote for a nominee, and you don't have to use all your votes. * Subscribers are eligible on an individual basis, i.e., if you are subscribed with multiple e-mail addresses you should only complete the voting form once. * In the case of a tie, there will be a subsequent run-off election between the tied nominees. If you have any problems or questions contact Augustin Luna (aluna AT jimmy.harvard.edu) and NOT the SBGN Editorial Board. You can now vote for your favorite nominees. Voting for yourself, if you are one of the nominees, is perfectly fine. The three top-scorers will be elected as editors. In order to avoid multiple votes, the vote is authenticated and you have to provide your name and e-mail address. However, this information will not be made public. To vote, please complete the form https://goo.gl/forms/LUpaK9zbZ7GuKi4t2 Nominees (in alphabetical order by last name): * Andreas Draeger: Andreas has served as editor for SBML and worked on tools using the SBGN notation. * Adrien Rougny: Adrien has helped in the development of the SBGN PD specification and has developed tools around the SBGN notation. * Vasundra Toure: Vasundra has helped in several areas of SBGN in the past few years, including the specifications, website, and has worked on tools involving SBGN. * Guanming Wu: Guanming works on the Reactome project that has made use of the SBGN notation for a number of years. Due to an extension in the nomination process and the holiday season, the deadline for the election will be Friday January 12, 2017 23:59 EST. A reminder will be sent out the first week of 2018. Voting for the SBGN Editorial Board is important. It is one of the means you have of ensuring the project is well maintained. Thank you very much for your help! |
|
From: Augustin L. <ca...@gm...> - 2017-11-30 16:43:38
|
A reminder to get any nominations in today. The SBGN Editors On Tue, Nov 21, 2017 at 6:55 PM, Augustin Luna <ca...@gm...> wrote: > We kindly ask you to nominate potential editors using this form: > > https://goo.gl/forms/YPKhSnhl9ZkUHdYX2 > > Self-nominations are perfectly fine. You can nominate as many people > as you wish (use one form per person). > > The deadline for nominations is November 30, 2017. > > At the core of SBGN governance sits a body of five editors, elected by > the community. Editors are in charge of coordinating the discussions > pertaining to the specifications, and write the specifications > themselves. Editors will serve terms of three years that cannot been > served consecutively. > > This year Robin Haw and Augustin Luna will complete their three year > term as an editor and will step down. Tobias Czauderna decided to > step-down as well after serving one year as an editor. Therefore, we > need to elect three new editors for a three year term. Neither > Augustin, nor Robin cannot be nominated for a new term this year. > Tobias can still be nominated since he only served for one year. > > We, the current editors, will contact the nominees and check > their willingness to stand for election. > > Then we will run the election. Each subscriber of sbgn-discuss will > have as many votes as editors to elect, which is three for this > election. > > SBGN editors thrive to serve the community and reflect your wishes and > needs. We thank you very much for your help in ensuring that the SBGN > development is coordinated in a democratic manner. > > The SBGN Editors |
|
From: Augustin L. <ca...@gm...> - 2017-11-21 23:55:58
|
We kindly ask you to nominate potential editors using this form: https://goo.gl/forms/YPKhSnhl9ZkUHdYX2 Self-nominations are perfectly fine. You can nominate as many people as you wish (use one form per person). The deadline for nominations is November 30, 2017. At the core of SBGN governance sits a body of five editors, elected by the community. Editors are in charge of coordinating the discussions pertaining to the specifications, and write the specifications themselves. Editors will serve terms of three years that cannot been served consecutively. This year Robin Haw and Augustin Luna will complete their three year term as an editor and will step down. Tobias Czauderna decided to step-down as well after serving one year as an editor. Therefore, we need to elect three new editors for a three year term. Neither Augustin, nor Robin cannot be nominated for a new term this year. Tobias can still be nominated since he only served for one year. We, the current editors, will contact the nominees and check their willingness to stand for election. Then we will run the election. Each subscriber of sbgn-discuss will have as many votes as editors to elect, which is three for this election. SBGN editors thrive to serve the community and reflect your wishes and needs. We thank you very much for your help in ensuring that the SBGN development is coordinated in a democratic manner. The SBGN Editors |
|
From: Augustin L. <ca...@gm...> - 2017-11-06 20:20:15
|
Are you still having the problem? Can you say more about the runtime error you're having? Augustin Luna On Fri, Oct 27, 2017 at 10:59 AM, Irina Balaur <ib...@ei...> wrote: > Dear All, > > I am writing you this email because I would like to kindly ask for your > advice. I have tried to get the libSBGN jar based on the repository: > https://github.com/sbgn/libsbgn, but I didn’t succeed so far since I got > several issues. I am using a Mac book, with: > > *java 9.0.1**Java(TM) SE Runtime Environment (build 9.0.1+11) * > > Please see below these issues. > First, I tried to compile it as it is in the repository, but I got the > following error message for Build failed; perhaps this is due to an > incompatibility between java from system and the version mention in the > repository. > > > > > > > * [javac] Compiling 12 source files to > /Users/iroznovat/Documents/libsbgn/org.sbgn/build [javac] warning: > [options] bootstrap class path not set in conjunction with -source 1.5 > [javac] error: Source option 1.5 is no longer supported. Use 1.6 or > later. [javac] error: Target option 1.5 is no longer supported. Use 1.6 > or later.**BUILD FAILED * > > Second, I changed the org.sbgn/build.xml file to refer to ant.build.javac > version 1.6 instead of 1.5: > line 5: <property name=“ant.build.javac.target” value=“*1.5*”/> —>1.6 > <property name=“ant.build.javac.source” value="*1.5*"/> —>1.6 > > line 103: <javac srcdir="test" debug="true" > includes="**" > destdir="build" > source=“*1.5*”> —>1.6 > > The build is successful, but there is a runtime error when I add the > resulted libsbgn.jar archive to my java project in eclipse. > > Could you please let me know if you have any suggestions on these issues? > Thank you very much. > > Best regards, > [image: EISBM logo] <http://www.eisbm.org> > * Irina BALAUR Researcher* > European Institute for Systems Biology and Medicine > > > > *E-mail:* ib...@ei... > *Website:* http://www.eisbm.org > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > sbgn-libsbgn mailing list > sbg...@li... > https://lists.sourceforge.net/lists/listinfo/sbgn-libsbgn > > |
|
From: Irina B. <ib...@ei...> - 2017-10-27 15:22:58
|
Dear All, I am writing you this email because I would like to kindly ask for your advice. I have tried to get the libSBGN jar based on the repository: https://github.com/sbgn/libsbgn, but I didn’t succeed so far since I got several issues. I am using a Mac book, with: java 9.0.1 Java(TM) SE Runtime Environment (build 9.0.1+11) Please see below these issues. First, I tried to compile it as it is in the repository, but I got the following error message for Build failed; perhaps this is due to an incompatibility between java from system and the version mention in the repository. [javac] Compiling 12 source files to /Users/iroznovat/Documents/libsbgn/org.sbgn/build [javac] warning: [options] bootstrap class path not set in conjunction with -source 1.5 [javac] error: Source option 1.5 is no longer supported. Use 1.6 or later. [javac] error: Target option 1.5 is no longer supported. Use 1.6 or later. BUILD FAILED Second, I changed the org.sbgn/build.xml file to refer to ant.build.javac version 1.6 instead of 1.5: line 5: <property name=“ant.build.javac.target” value=“1.5”/> —>1.6 <property name=“ant.build.javac.source” value="1.5"/> —>1.6 line 103: <javac srcdir="test" debug="true" includes="**" destdir="build" source=“1.5”> —>1.6 The build is successful, but there is a runtime error when I add the resulted libsbgn.jar archive to my java project in eclipse. Could you please let me know if you have any suggestions on these issues? Thank you very much. Best regards, <http://www.eisbm.org/>Irina BALAUR Researcher European Institute for Systems Biology and Medicine E-mail: ib...@ei... <mailto:ib...@ei...> Website: http://www.eisbm.org |
|
From: Alexander M. <am...@ei...> - 2017-10-25 11:40:50
|
Hi Martijn, Thank you for your reply. I guess we will have to find resources to make the annotation support implemented in some universal standard way in libSBGN. As Frank wrote previously there is a solution already https://github.com/sbgn/sbgn/wiki/SBGN-ML_Extensions. In fact, Ludovic uses this one for a translation from CellDesigner. If I undestand correctly it is not quite standardised yet. We hope this is to be used in translators and in MINERVA. Best regards, Alexander On Wed, Oct 25, 2017 at 11:59 AM, Martijn van Iersel <mva...@gm...> wrote: > Hey Alexander, > > I'm no longer active in the field of LibSBGN (not really active in the > field of Bioinformatics even). So I'm afraid I can't help you there. > > regards, > Martijn > > > On Tue, Oct 24, 2017 at 5:53 PM, Alexander Mazein <am...@ei...> > wrote: > > > Hello, > > > > I was wondering who is working with libsbgn currently? Martijn? Are there > > any plans to support IDs and colours in libsbgn? > > > > Ludovic (cc) has developed a js version that supports this. The > > implementation was discussed at one of COMBINE/HARMONY meetings. > > > > We have a request from Piotr (cc) so we could support annotation import > > from sbgnml files in MINERVA (https://www.ncbi.nlm.nih.gov/ > pubmed/28725475 > > ). > > > > Newt (http://newteditor.org/; http://web.newteditor.org/) will be > > supporting annotation and colours via libsbgn.js. > > > > Relevant links: > > > > https://github.com/sbgn/libsbgn > > https://www.ncbi.nlm.nih.gov/pubmed/22581176 > > > > https://github.com/eisbm/libsbgn.js > > > > Best regards, > > > > Alexander > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > sbgn-editors mailing list > sbg...@li... > https://lists.sourceforge.net/lists/listinfo/sbgn-editors > |
|
From: Frank T. B. <fra...@gm...> - 2017-10-25 09:39:57
|
Hello Alexander, You ought to be able to make use of libSBGNs extension object, to encode colors or to store any other kind of annotation within the sbgn-ml. An example can be found here: https://github.com/sbgn/sbgn/wiki/SBGN-ML_Extensions Best Frank From: Martijn van Iersel [mailto:mva...@gm...] Sent: Wednesday, October 25, 2017 11:00 AM To: Alexander Mazein <am...@ei...> Cc: The SBGN Editors internal mailing list <sbg...@li...>; Nicolas Le Novere <n.l...@gm...>; Piotr Gawron <pio...@un...>; Professor Schreiber Falk <fal...@mo...>; Falk Schreiber <fal...@gm...>; libSBGN Development and Technical Issues <sbg...@li...> Subject: Re: [sbgn-libsbgn] Support for annotation in libsbgn Hey Alexander, I'm no longer active in the field of LibSBGN (not really active in the field of Bioinformatics even). So I'm afraid I can't help you there. regards, Martijn On Tue, Oct 24, 2017 at 5:53 PM, Alexander Mazein <am...@ei... <mailto:am...@ei...> > wrote: Hello, I was wondering who is working with libsbgn currently? Martijn? Are there any plans to support IDs and colours in libsbgn? Ludovic (cc) has developed a js version that supports this. The implementation was discussed at one of COMBINE/HARMONY meetings. We have a request from Piotr (cc) so we could support annotation import from sbgnml files in MINERVA (https://www.ncbi.nlm.nih.gov/pubmed/28725475). Newt (http://newteditor.org/; http://web.newteditor.org/) will be supporting annotation and colours via libsbgn.js. Relevant links: https://github.com/sbgn/libsbgn https://www.ncbi.nlm.nih.gov/pubmed/22581176 https://github.com/eisbm/libsbgn.js Best regards, Alexander |
|
From: Martijn v. I. <mva...@gm...> - 2017-10-25 09:00:01
|
Hey Alexander, I'm no longer active in the field of LibSBGN (not really active in the field of Bioinformatics even). So I'm afraid I can't help you there. regards, Martijn On Tue, Oct 24, 2017 at 5:53 PM, Alexander Mazein <am...@ei...> wrote: > Hello, > > I was wondering who is working with libsbgn currently? Martijn? Are there > any plans to support IDs and colours in libsbgn? > > Ludovic (cc) has developed a js version that supports this. The > implementation was discussed at one of COMBINE/HARMONY meetings. > > We have a request from Piotr (cc) so we could support annotation import > from sbgnml files in MINERVA (https://www.ncbi.nlm.nih.gov/pubmed/28725475 > ). > > Newt (http://newteditor.org/; http://web.newteditor.org/) will be > supporting annotation and colours via libsbgn.js. > > Relevant links: > > https://github.com/sbgn/libsbgn > https://www.ncbi.nlm.nih.gov/pubmed/22581176 > > https://github.com/eisbm/libsbgn.js > > Best regards, > > Alexander > |
|
From: Alexander M. <am...@ei...> - 2017-10-24 15:53:13
|
Hello, I was wondering who is working with libsbgn currently? Martijn? Are there any plans to support IDs and colours in libsbgn? Ludovic (cc) has developed a js version that supports this. The implementation was discussed at one of COMBINE/HARMONY meetings. We have a request from Piotr (cc) so we could support annotation import from sbgnml files in MINERVA (https://www.ncbi.nlm.nih.gov/pubmed/28725475 ). Newt (http://newteditor.org/; http://web.newteditor.org/) will be supporting annotation and colours via libsbgn.js. Relevant links: https://github.com/sbgn/libsbgn https://www.ncbi.nlm.nih.gov/pubmed/22581176 https://github.com/eisbm/libsbgn.js Best regards, Alexander |
|
From: Haoran Yu <hal...@gm...> - 2017-03-30 11:06:15
|
Thank you for your response, I managed to fix the issue. I had no problem
building libsbgn. It turns out that the issue is not with libsbgn, it's
another library I am using that included the wrong libsbgn jar (paxtools).
I'm sorry for the confusion.
Haoran
-------------------------------------------------------------
Buildfile: C:\Users\HY\Documents\SBML2SBGN\libsbgn_new\build.xml
dist:
prepare:
[mkdir] Created dir:
C:\Users\HY\Documents\SBML2SBGN\libsbgn_new\org.sbgn\build
[mkdir] Created dir:
C:\Users\HY\Documents\SBML2SBGN\libsbgn_new\org.sbgn\gensrc
[mkdir] Created dir: C:\Users\HY\Documents\SBML2SBGN\libsbgn_new\docs
[mkdir] Created dir: C:\Users\HY\Documents\SBML2SBGN\libsbgn_new\dist
jaxb:
[xjc] Compiling
file:/C:/Users/HY/Documents/SBML2SBGN/libsbgn_new/resources/SBGN.xsd
[xjc] Writing output to
C:\Users\HY\Documents\SBML2SBGN\libsbgn_new\org.sbgn\gensrc
build:
[javac]
C:\Users\HY\Documents\SBML2SBGN\libsbgn_new\org.sbgn\build.xml:40: warning:
'includeantruntime' was not set, defaulting to build.sysclasspath=last; set
to false for repeatable builds
[javac] Compiling 12 source files to
C:\Users\HY\Documents\SBML2SBGN\libsbgn_new\org.sbgn\build
[javac] warning: [options] bootstrap class path not set in conjunction
with -source 1.5
[javac] warning: [options] source value 1.5 is obsolete and will be
removed in a future release
[javac] warning: [options] target value 1.5 is obsolete and will be
removed in a future release
[javac] warning: [options] To suppress warnings about obsolete options,
use -Xlint:-options.
[javac] 4 warnings
[javac]
C:\Users\HY\Documents\SBML2SBGN\libsbgn_new\org.sbgn\build.xml:45: warning:
'includeantruntime' was not set, defaulting to build.sysclasspath=last; set
to false for repeatable builds
[javac] Compiling 11 source files to
C:\Users\HY\Documents\SBML2SBGN\libsbgn_new\org.sbgn\build
[javac] warning: [options] bootstrap class path not set in conjunction
with -source 1.5
[javac] warning: [options] source value 1.5 is obsolete and will be
removed in a future release
[javac] warning: [options] target value 1.5 is obsolete and will be
removed in a future release
[javac] warning: [options] To suppress warnings about obsolete options,
use -Xlint:-options.
[javac] 4 warnings
[copy] Copying 4 files to
C:\Users\HY\Documents\SBML2SBGN\libsbgn_new\org.sbgn\build
jar:
[jar] Building jar:
C:\Users\HY\Documents\SBML2SBGN\libsbgn_new\dist\org.sbgn.jar
dist:
BUILD SUCCESSFUL
Total time: 9 seconds
On Thu, Mar 30, 2017 at 12:20 AM, Matthias König <kon...@go...>
wrote:
> Hi Haoran,
> could you please file an issue on
> https://github.com/sbgn/libsbgn/issues
> with the problems you have and the errors you get in the build
>
> I just pulled the repository and build the develop version without
> problems. So can not reproduce your issue
>
> git clone https://github.com/sbgn/libsbgn.git
> cd libsbgn
>
> ant
>
> -------------------------------------------------------------
> Buildfile: /home/mkoenig/git/libsbgn/build.xml
>
> dist:
>
> prepare:
>
> jaxb:
> [java] parsing a schema...
> [java] compiling a schema...
> [java] org/sbgn/bindings/Arc.java
> [java] org/sbgn/bindings/Arcgroup.java
> [java] org/sbgn/bindings/Bbox.java
> [java] org/sbgn/bindings/Glyph.java
> [java] org/sbgn/bindings/Label.java
> [java] org/sbgn/bindings/Map.java
> [java] org/sbgn/bindings/ObjectFactory.java
> [java] org/sbgn/bindings/Point.java
> [java] org/sbgn/bindings/Port.java
> [java] org/sbgn/bindings/SBGNBase.java
> [java] org/sbgn/bindings/Sbgn.java
> [java] org/sbgn/bindings/package-info.java
>
> build:
> [javac] Compiling 12 source files to /home/mkoenig/git/libsbgn/org.
> sbgn/build
> [copy] Copying 1 file to /home/mkoenig/git/libsbgn/org.sbgn/build
>
> jar:
> [jar] Building jar: /home/mkoenig/git/libsbgn/dist/org.sbgn.jar
>
> dist:
>
> BUILD SUCCESSFUL
> Total time: 1 second
> -------------------------------------------------------------
>
>
> On Wed, Mar 29, 2017 at 8:52 PM, Haoran Yu <hal...@gm...> wrote:
>
>> I'm wondering if the Sbgn class is autogenerated. Is there any resource
>> that I can use to generate the class files. I looked at the developer's
>> guide and the documentation and I couldn't find anything.
>>
>> Thank you,
>> Haoran
>>
>> On Mar 28, 2017 3:11 PM, "Tobias Czauderna" <tob...@mo...>
>> wrote:
>>
>>> Hi Haoran,
>>>
>>> I just figured out that you couldn't receive my reply because you have
>>> not subscribed to the mailing list yet.
>>> Please see my reply below.
>>>
>>> Cheers,
>>> Tobias
>>>
>>> Hi Haoran,
>>>
>>> I assume you want to use the latest stable version and not the development
>>> version, right?
>>>
>>> Since the migration from subversion to git it probably hasn't been apparent
>>> what the latest stable version is.
>>> On the subversion repository we have used tags to indicate versions which
>>> are also supported by git.
>>> However, I have just created two branches for the two releases
>>> "milestone-1" and "milestone-2".
>>> If you checkout "milestone-2" you should be able to build the jar.
>>> Depending on how you build the jar (shell or IDE) there might be some
>>> warnings about dependencies.
>>> I think you are safe if you just want to build the library jar but you
>>> might have to fix the warnings for validation I guess.
>>> The warning for org.sbgn.jar should disappear anyway once you have built
>>> the library.
>>>
>>> On the other hand if you don't want to build the library you could just
>>> download the releasehttps://github.com/sbgn/libsbgn/releases
>>>
>>> Cheers,
>>> Tobias
>>>
>>>
>>>
>>>
>>> On 28 March 2017 at 04:42, Haoran Yu <hal...@gm...> wrote:
>>>
>>>> Dear libSBGN,
>>>>
>>>> I'm new to libSBGN, I tried to build the project to create a JAR file,
>>>> so that I can include it in another project I'm working on. But it seems
>>>> that the Sbgn class is missing, so anything that needs Sbgn cannot compile.
>>>> I'm not sure if it's something I did incorrectly, I cloned the source from
>>>> the git repository.
>>>>
>>>> Thanks,
>>>>
>>>> Haoran
>>>>
>>>> ------------------------------------------------------------
>>>> ------------------
>>>> Check out the vibrant tech community on one of the world's most
>>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>> _______________________________________________
>>>> sbgn-libsbgn mailing list
>>>> sbg...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/sbgn-libsbgn
>>>>
>>>>
>>>
>>>
>>> --
>>> Dr Tobias Czauderna
>>> Faculty of Information Technology
>>> Monash University, Clayton, Australia
>>> Office: Rm 318.7, New Horizons Building, 20 Research Way
>>> Phone: +61 3 990 50518
>>>
>>>
>> ------------------------------------------------------------
>> ------------------
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>> _______________________________________________
>> sbgn-libsbgn mailing list
>> sbg...@li...
>> https://lists.sourceforge.net/lists/listinfo/sbgn-libsbgn
>>
>>
>
>
> --
> Matthias König
> Junior Group Leader LiSym - Systems Medicine of the Liver
> Humboldt-University Berlin, Institute for Theoretical Biology
> https://www.livermetabolism.com
> kon...@go...
> Tel: +49 30 20938450
> Tel: +49 176 81168480 <+49%20176%2081168480>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> sbgn-libsbgn mailing list
> sbg...@li...
> https://lists.sourceforge.net/lists/listinfo/sbgn-libsbgn
>
>
|
|
From: Matthias K. <kon...@go...> - 2017-03-30 07:20:26
|
Hi Haoran, could you please file an issue on https://github.com/sbgn/libsbgn/issues with the problems you have and the errors you get in the build I just pulled the repository and build the develop version without problems. So can not reproduce your issue git clone https://github.com/sbgn/libsbgn.git cd libsbgn ant ------------------------------------------------------------- Buildfile: /home/mkoenig/git/libsbgn/build.xml dist: prepare: jaxb: [java] parsing a schema... [java] compiling a schema... [java] org/sbgn/bindings/Arc.java [java] org/sbgn/bindings/Arcgroup.java [java] org/sbgn/bindings/Bbox.java [java] org/sbgn/bindings/Glyph.java [java] org/sbgn/bindings/Label.java [java] org/sbgn/bindings/Map.java [java] org/sbgn/bindings/ObjectFactory.java [java] org/sbgn/bindings/Point.java [java] org/sbgn/bindings/Port.java [java] org/sbgn/bindings/SBGNBase.java [java] org/sbgn/bindings/Sbgn.java [java] org/sbgn/bindings/package-info.java build: [javac] Compiling 12 source files to /home/mkoenig/git/libsbgn/org.sbgn/build [copy] Copying 1 file to /home/mkoenig/git/libsbgn/org.sbgn/build jar: [jar] Building jar: /home/mkoenig/git/libsbgn/dist/org.sbgn.jar dist: BUILD SUCCESSFUL Total time: 1 second ------------------------------------------------------------- On Wed, Mar 29, 2017 at 8:52 PM, Haoran Yu <hal...@gm...> wrote: > I'm wondering if the Sbgn class is autogenerated. Is there any resource > that I can use to generate the class files. I looked at the developer's > guide and the documentation and I couldn't find anything. > > Thank you, > Haoran > > On Mar 28, 2017 3:11 PM, "Tobias Czauderna" <tob...@mo...> > wrote: > >> Hi Haoran, >> >> I just figured out that you couldn't receive my reply because you have >> not subscribed to the mailing list yet. >> Please see my reply below. >> >> Cheers, >> Tobias >> >> Hi Haoran, >> >> I assume you want to use the latest stable version and not the development >> version, right? >> >> Since the migration from subversion to git it probably hasn't been apparent >> what the latest stable version is. >> On the subversion repository we have used tags to indicate versions which >> are also supported by git. >> However, I have just created two branches for the two releases >> "milestone-1" and "milestone-2". >> If you checkout "milestone-2" you should be able to build the jar. >> Depending on how you build the jar (shell or IDE) there might be some >> warnings about dependencies. >> I think you are safe if you just want to build the library jar but you >> might have to fix the warnings for validation I guess. >> The warning for org.sbgn.jar should disappear anyway once you have built >> the library. >> >> On the other hand if you don't want to build the library you could just >> download the releasehttps://github.com/sbgn/libsbgn/releases >> >> Cheers, >> Tobias >> >> >> >> >> On 28 March 2017 at 04:42, Haoran Yu <hal...@gm...> wrote: >> >>> Dear libSBGN, >>> >>> I'm new to libSBGN, I tried to build the project to create a JAR file, >>> so that I can include it in another project I'm working on. But it seems >>> that the Sbgn class is missing, so anything that needs Sbgn cannot compile. >>> I'm not sure if it's something I did incorrectly, I cloned the source from >>> the git repository. >>> >>> Thanks, >>> >>> Haoran >>> >>> ------------------------------------------------------------ >>> ------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> sbgn-libsbgn mailing list >>> sbg...@li... >>> https://lists.sourceforge.net/lists/listinfo/sbgn-libsbgn >>> >>> >> >> >> -- >> Dr Tobias Czauderna >> Faculty of Information Technology >> Monash University, Clayton, Australia >> Office: Rm 318.7, New Horizons Building, 20 Research Way >> Phone: +61 3 990 50518 >> >> > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > sbgn-libsbgn mailing list > sbg...@li... > https://lists.sourceforge.net/lists/listinfo/sbgn-libsbgn > > -- Matthias König Junior Group Leader LiSym - Systems Medicine of the Liver Humboldt-University Berlin, Institute for Theoretical Biology https://www.livermetabolism.com kon...@go... Tel: +49 30 20938450 Tel: +49 176 81168480 |
|
From: Haoran Yu <hal...@gm...> - 2017-03-29 18:52:36
|
I'm wondering if the Sbgn class is autogenerated. Is there any resource that I can use to generate the class files. I looked at the developer's guide and the documentation and I couldn't find anything. Thank you, Haoran On Mar 28, 2017 3:11 PM, "Tobias Czauderna" <tob...@mo...> wrote: > Hi Haoran, > > I just figured out that you couldn't receive my reply because you have not > subscribed to the mailing list yet. > Please see my reply below. > > Cheers, > Tobias > > Hi Haoran, > > I assume you want to use the latest stable version and not the development > version, right? > > Since the migration from subversion to git it probably hasn't been apparent > what the latest stable version is. > On the subversion repository we have used tags to indicate versions which > are also supported by git. > However, I have just created two branches for the two releases > "milestone-1" and "milestone-2". > If you checkout "milestone-2" you should be able to build the jar. > Depending on how you build the jar (shell or IDE) there might be some > warnings about dependencies. > I think you are safe if you just want to build the library jar but you > might have to fix the warnings for validation I guess. > The warning for org.sbgn.jar should disappear anyway once you have built > the library. > > On the other hand if you don't want to build the library you could just > download the releasehttps://github.com/sbgn/libsbgn/releases > > Cheers, > Tobias > > > > > On 28 March 2017 at 04:42, Haoran Yu <hal...@gm...> wrote: > >> Dear libSBGN, >> >> I'm new to libSBGN, I tried to build the project to create a JAR file, so >> that I can include it in another project I'm working on. But it seems that >> the Sbgn class is missing, so anything that needs Sbgn cannot compile. I'm >> not sure if it's something I did incorrectly, I cloned the source from the >> git repository. >> >> Thanks, >> >> Haoran >> >> ------------------------------------------------------------ >> ------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> sbgn-libsbgn mailing list >> sbg...@li... >> https://lists.sourceforge.net/lists/listinfo/sbgn-libsbgn >> >> > > > -- > Dr Tobias Czauderna > Faculty of Information Technology > Monash University, Clayton, Australia > Office: Rm 318.7, New Horizons Building, 20 Research Way > Phone: +61 3 990 50518 > > |
|
From: Tobias C. <tob...@mo...> - 2017-03-28 03:15:50
|
Hi Haoran, I assume you want to use the latest stable version and not the development version, right? Since the migration from subversion to git it probably hasn't been apparent what the latest stable version is. On the subversion repository we have used tags to indicate versions which are also supported by git. However, I have just created two branches for the two releases "milestone-1" and "milestone-2". If you checkout "milestone-2" you should be able to build the jar. Depending on how you build the jar (shell or IDE) there might be some warnings about dependencies. I think you are safe if you just want to build the library jar but you might have to fix the warnings for validation I guess. The warning for org.sbgn.jar should disappear anyway once you have built the library. On the other hand if you don't want to build the library you could just download the release https://github.com/sbgn/libsbgn/releases Cheers, Tobias On 28 March 2017 at 04:42, Haoran Yu <hal...@gm...> wrote: > Dear libSBGN, > > I'm new to libSBGN, I tried to build the project to create a JAR file, so > that I can include it in another project I'm working on. But it seems that > the Sbgn class is missing, so anything that needs Sbgn cannot compile. I'm > not sure if it's something I did incorrectly, I cloned the source from the > git repository. > > Thanks, > > Haoran > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > sbgn-libsbgn mailing list > sbg...@li... > https://lists.sourceforge.net/lists/listinfo/sbgn-libsbgn > > -- Dr Tobias Czauderna Faculty of Information Technology Monash University, Clayton, Australia Office: Rm 318.7, New Horizons Building, 20 Research Way Phone: +61 3 990 50518 |
|
From: Haoran Yu <hal...@gm...> - 2017-03-27 17:42:15
|
Dear libSBGN, I'm new to libSBGN, I tried to build the project to create a JAR file, so that I can include it in another project I'm working on. But it seems that the Sbgn class is missing, so anything that needs Sbgn cannot compile. I'm not sure if it's something I did incorrectly, I cloned the source from the git repository. Thanks, Haoran |
|
From: Alexander M. <am...@ei...> - 2016-10-07 11:25:30
|
Hi Nicolas and Frank, Thank you very much for your replies and examples. That clarifies the issue. Best wishes, Alexander On Fri, Oct 7, 2016 at 12:49 PM, Frank T. Bergmann <fbe...@ca...> wrote: > Hello Alexander, > > just answering about SBGN-ML ... there we have an attribute > "compartmentOrder" that does allow us to resolve this issue. > > see also the test cases: > > http://svn.code.sf.net/p/libsbgn/code/trunk/test-files/ > PD//compartmentOrder1.sbgn > http://svn.code.sf.net/p/libsbgn/code/trunk/test-files/ > PD//compartmentOrder2.sbgn > > example renderings: > > http://sysbioapps.dyndns.org/RenderComparison/Home/ProcessDescription > > cheers > Frank > > On Fri, Oct 7, 2016 at 12:11 PM, Alexander Mazein <am...@ei...> > wrote: > > Than you, Nicolas. > > > > 1. How de we know it is in cytosol? Because it is a bit more in cytosol > than > > in extracellular space? The center of the shape is within a certain > > compartment - this is how we read it? > > > > 2. SBGN-ML encodes coordinates AND depth? Would it be encoded that a) one > > compartment is on the top of another and that b) CHT1 belongs to synaptic > > button and not to synaptic cleft? Coordinates themselves do not clarify > > that? > > > > Best regards, > > > > Alexander > > > > On Fri, Oct 7, 2016 at 11:33 AM, Nicolas Le Novere <n.l...@gm... > > > > wrote: > >> > >> On 07/10/16 09:50, Alexander Mazein wrote: > >>> > >>> Hello, > >> > >> > >>> > >>> In SBGN-ML file, how parent-child relations are handled? > >> > >> > >>> > >>> Please find the diagrams attached, they are posted as examples on > >>> sbgn.org <http://sbgn.org> (http://sbgn.github.io/sbgn/examples). > >> > >> > >>> > >>> 1. In case of "Insulin signaling": how a software supposed to know > >>> where complex IGF-IGFR belongs to? The membrane location is implied > >>> but is not shown: should we avoid that? We probably should we update > >>> our examples too? > >> > >> > >> The "membrane location" is actually not part of SBGN. Here the complex > >> IGF-IGFR belong to the cytosol compartment, not the membrane. If you > want to > >> explicitly put it in a membrane, you have to create a membrane > compartment. > >> > >> Putting it anywhere does not change the semantics of the map. Think > about > >> all the maps with signalling lipids (e.g. PIP3 or DAG). In reality, > they are > >> in membrane, but are almost always represented as floating around in the > >> cytosol. Because we don't care about their location. When the location > is > >> important (for instance to represent the recruitment of Akt) people > >> generally represent a big membrane. > >> > >> However, SBGML-ML encodes the coordinates so the visual implicit > location > >> would be conserved. SBGN-ML stores all that is not SBGN :-) > >> > >>> 2. "Neuro-muscular junction": do we have depth in SBGN-ML? One > >>> compartment is shown on the top of another. > >> > >> > >> This drawing was made on purpose, to show that there is no compartment > >> nesting in SBGN. The compartment is indeed on top of the other, not > inside. > >> The respective location needs not to be conserved. For an example of map > >> with compartments in different respective locations, see: > >> > >> http://sbgn.github.io/sbgn/faq/pd#how-can-i-represent- > multi-compartment-reactions-without-multiplying-the-ugly- > compartment-boundaries > >> > >> > >> > >>> > >>> Thank you, > >>> > >>> Alexander > >>> > >>> -- You received this message because you are subscribed to the Google > >>> Groups "SBGN Discussion List" group. To unsubscribe from this group > >>> and stop receiving emails from it, send an email to > >>> sbg...@go... > >>> <mailto:sbg...@go...>. To post to this > >>> group, send email to sbg...@go... > >>> <mailto:sbg...@go...>. Visit this group at > >>> https://groups.google.com/group/sbgn-discuss. To view this discussion > >>> on the web, visit > >>> > >>> https://groups.google.com/d/msgid/sbgn-discuss/CAOPOR26AVXoGrqd1w- > 7kKcSigdGJhkhiJjG5P8MCeThhynq29Q%40mail.gmail.com > >>> > >>> <https://groups.google.com/d/msgid/sbgn-discuss/CAOPOR26AVXoGrqd1w- > 7kKcSigdGJhkhiJjG5P8MCeThhynq29Q%40mail.gmail.com?utm_ > medium=email&utm_source=footer>. > >>> > >>> > >> For more options, visit https://groups.google.com/d/optout. > >> > >> > >> -- > >> Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 > 3AT > >> Tel: +441223496433 Mob:+447833147074 n.l...@gm... > >> orcid.org//0000-0002-6309-7327 http://lenoverelab.org/perso/lenov/ > >> Skype:n.lenovere twitter:@lenovere http://nlenov.wordpress.com/ > >> > >> > >> -- > >> You received this message because you are subscribed to the Google > Groups > >> "SBGN Discussion List" group. > >> To unsubscribe from this group and stop receiving emails from it, send > an > >> email to sbg...@go.... > >> To post to this group, send an email to sbg...@go.... > >> Visit this group at https://groups.google.com/group/sbgn-discuss. > >> To view this discussion on the web, visit > >> https://groups.google.com/d/msgid/sbgn-discuss/06596e9a- > 6f9e-f741-27f3-78ce8eec17e5%40gmail.com. > >> For more options, visit https://groups.google.com/d/optout. > > > > > > -- > > You received this message because you are subscribed to the Google Groups > > "SBGN Discussion List" group. > > To unsubscribe from this group and stop receiving emails from it, send an > > email to sbg...@go.... > > To post to this group, send email to sbg...@go.... > > Visit this group at https://groups.google.com/group/sbgn-discuss. > > To view this discussion on the web, visit > > https://groups.google.com/d/msgid/sbgn-discuss/ > CAOPOR26WOKUuqpyoUgGhWRw1i4bbJ8HTMaQ3zm0qE1Kv4A98TA%40mail.gmail.com. > > > > For more options, visit https://groups.google.com/d/optout. > > -- > You received this message because you are subscribed to the Google Groups > "SBGN Discussion List" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sbg...@go.... > To post to this group, send an email to sbg...@go.... > Visit this group at https://groups.google.com/group/sbgn-discuss. > To view this discussion on the web, visit https://groups.google.com/d/ > msgid/sbgn-discuss/CAEnSYuJ5TRkC_E-0iD7PYAC5G1O4YX1rRirxi7WMCQ3cj > dyA2w%40mail.gmail.com. > For more options, visit https://groups.google.com/d/optout. > |
|
From: Frank T. B. <fbe...@ca...> - 2016-10-07 10:49:58
|
Hello Alexander, just answering about SBGN-ML ... there we have an attribute "compartmentOrder" that does allow us to resolve this issue. see also the test cases: http://svn.code.sf.net/p/libsbgn/code/trunk/test-files/PD//compartmentOrder1.sbgn http://svn.code.sf.net/p/libsbgn/code/trunk/test-files/PD//compartmentOrder2.sbgn example renderings: http://sysbioapps.dyndns.org/RenderComparison/Home/ProcessDescription cheers Frank On Fri, Oct 7, 2016 at 12:11 PM, Alexander Mazein <am...@ei...> wrote: > Than you, Nicolas. > > 1. How de we know it is in cytosol? Because it is a bit more in cytosol than > in extracellular space? The center of the shape is within a certain > compartment - this is how we read it? > > 2. SBGN-ML encodes coordinates AND depth? Would it be encoded that a) one > compartment is on the top of another and that b) CHT1 belongs to synaptic > button and not to synaptic cleft? Coordinates themselves do not clarify > that? > > Best regards, > > Alexander > > On Fri, Oct 7, 2016 at 11:33 AM, Nicolas Le Novere <n.l...@gm...> > wrote: >> >> On 07/10/16 09:50, Alexander Mazein wrote: >>> >>> Hello, >> >> >>> >>> In SBGN-ML file, how parent-child relations are handled? >> >> >>> >>> Please find the diagrams attached, they are posted as examples on >>> sbgn.org <http://sbgn.org> (http://sbgn.github.io/sbgn/examples). >> >> >>> >>> 1. In case of "Insulin signaling": how a software supposed to know >>> where complex IGF-IGFR belongs to? The membrane location is implied >>> but is not shown: should we avoid that? We probably should we update >>> our examples too? >> >> >> The "membrane location" is actually not part of SBGN. Here the complex >> IGF-IGFR belong to the cytosol compartment, not the membrane. If you want to >> explicitly put it in a membrane, you have to create a membrane compartment. >> >> Putting it anywhere does not change the semantics of the map. Think about >> all the maps with signalling lipids (e.g. PIP3 or DAG). In reality, they are >> in membrane, but are almost always represented as floating around in the >> cytosol. Because we don't care about their location. When the location is >> important (for instance to represent the recruitment of Akt) people >> generally represent a big membrane. >> >> However, SBGML-ML encodes the coordinates so the visual implicit location >> would be conserved. SBGN-ML stores all that is not SBGN :-) >> >>> 2. "Neuro-muscular junction": do we have depth in SBGN-ML? One >>> compartment is shown on the top of another. >> >> >> This drawing was made on purpose, to show that there is no compartment >> nesting in SBGN. The compartment is indeed on top of the other, not inside. >> The respective location needs not to be conserved. For an example of map >> with compartments in different respective locations, see: >> >> http://sbgn.github.io/sbgn/faq/pd#how-can-i-represent-multi-compartment-reactions-without-multiplying-the-ugly-compartment-boundaries >> >> >> >>> >>> Thank you, >>> >>> Alexander >>> >>> -- You received this message because you are subscribed to the Google >>> Groups "SBGN Discussion List" group. To unsubscribe from this group >>> and stop receiving emails from it, send an email to >>> sbg...@go... >>> <mailto:sbg...@go...>. To post to this >>> group, send email to sbg...@go... >>> <mailto:sbg...@go...>. Visit this group at >>> https://groups.google.com/group/sbgn-discuss. To view this discussion >>> on the web, visit >>> >>> https://groups.google.com/d/msgid/sbgn-discuss/CAOPOR26AVXoGrqd1w-7kKcSigdGJhkhiJjG5P8MCeThhynq29Q%40mail.gmail.com >>> >>> <https://groups.google.com/d/msgid/sbgn-discuss/CAOPOR26AVXoGrqd1w-7kKcSigdGJhkhiJjG5P8MCeThhynq29Q%40mail.gmail.com?utm_medium=email&utm_source=footer>. >>> >>> >> For more options, visit https://groups.google.com/d/optout. >> >> >> -- >> Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT >> Tel: +441223496433 Mob:+447833147074 n.l...@gm... >> orcid.org//0000-0002-6309-7327 http://lenoverelab.org/perso/lenov/ >> Skype:n.lenovere twitter:@lenovere http://nlenov.wordpress.com/ >> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "SBGN Discussion List" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to sbg...@go.... >> To post to this group, send an email to sbg...@go.... >> Visit this group at https://groups.google.com/group/sbgn-discuss. >> To view this discussion on the web, visit >> https://groups.google.com/d/msgid/sbgn-discuss/06596e9a-6f9e-f741-27f3-78ce8eec17e5%40gmail.com. >> For more options, visit https://groups.google.com/d/optout. > > > -- > You received this message because you are subscribed to the Google Groups > "SBGN Discussion List" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sbg...@go.... > To post to this group, send email to sbg...@go.... > Visit this group at https://groups.google.com/group/sbgn-discuss. > To view this discussion on the web, visit > https://groups.google.com/d/msgid/sbgn-discuss/CAOPOR26WOKUuqpyoUgGhWRw1i4bbJ8HTMaQ3zm0qE1Kv4A98TA%40mail.gmail.com. > > For more options, visit https://groups.google.com/d/optout. |
|
From: Alexander M. <am...@ei...> - 2016-10-07 10:11:11
|
Than you, Nicolas. 1. How de we know it is in cytosol? Because it is a bit more in cytosol than in extracellular space? The center of the shape is within a certain compartment - this is how we read it? 2. SBGN-ML encodes coordinates AND depth? Would it be encoded that a) one compartment is on the top of another and that b) CHT1 belongs to synaptic button and not to synaptic cleft? Coordinates themselves do not clarify that? Best regards, Alexander On Fri, Oct 7, 2016 at 11:33 AM, Nicolas Le Novere <n.l...@gm...> wrote: > On 07/10/16 09:50, Alexander Mazein wrote: > >> Hello, >> > > >> In SBGN-ML file, how parent-child relations are handled? >> > > >> Please find the diagrams attached, they are posted as examples on >> sbgn.org <http://sbgn.org> (http://sbgn.github.io/sbgn/examples). >> > > >> 1. In case of "Insulin signaling": how a software supposed to know >> where complex IGF-IGFR belongs to? The membrane location is implied >> but is not shown: should we avoid that? We probably should we update >> our examples too? >> > > The "membrane location" is actually not part of SBGN. Here the complex > IGF-IGFR belong to the cytosol compartment, not the membrane. If you want > to explicitly put it in a membrane, you have to create a membrane > compartment. > > Putting it anywhere does not change the semantics of the map. Think about > all the maps with signalling lipids (e.g. PIP3 or DAG). In reality, they > are in membrane, but are almost always represented as floating around in > the cytosol. Because we don't care about their location. When the location > is important (for instance to represent the recruitment of Akt) people > generally represent a big membrane. > > However, SBGML-ML encodes the coordinates so the visual implicit location > would be conserved. SBGN-ML stores all that is not SBGN :-) > > 2. "Neuro-muscular junction": do we have depth in SBGN-ML? One >> compartment is shown on the top of another. >> > > This drawing was made on purpose, to show that there is no compartment > nesting in SBGN. The compartment is indeed on top of the other, not inside. > The respective location needs not to be conserved. For an example of map > with compartments in different respective locations, see: > http://sbgn.github.io/sbgn/faq/pd#how-can-i-represent-multi- > compartment-reactions-without-multiplying-the-ugly-compartment-boundaries > > > > >> Thank you, >> >> Alexander >> >> -- You received this message because you are subscribed to the Google >> Groups "SBGN Discussion List" group. To unsubscribe from this group >> and stop receiving emails from it, send an email to >> sbg...@go... >> <mailto:sbg...@go...>. To post to this >> group, send email to sbg...@go... >> <mailto:sbg...@go...>. Visit this group at >> https://groups.google.com/group/sbgn-discuss. To view this discussion >> on the web, visit >> https://groups.google.com/d/msgid/sbgn-discuss/CAOPOR26AVXoG >> rqd1w-7kKcSigdGJhkhiJjG5P8MCeThhynq29Q%40mail.gmail.com >> <https://groups.google.com/d/msgid/sbgn-discuss/CAOPOR26AVXo >> Grqd1w-7kKcSigdGJhkhiJjG5P8MCeThhynq29Q%40mail.gmail.com? >> utm_medium=email&utm_source=footer>. >> >> >> For more options, visit https://groups.google.com/d/optout. > > > -- > Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT > Tel: +441223496433 Mob:+447833147074 n.l...@gm... > orcid.org//0000-0002-6309-7327 http://lenoverelab.org/perso/lenov/ > Skype:n.lenovere twitter:@lenovere http://nlenov.wordpress.com/ > > > -- > You received this message because you are subscribed to the Google Groups > "SBGN Discussion List" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to sbg...@go.... > To post to this group, send an email to sbg...@go.... > Visit this group at https://groups.google.com/group/sbgn-discuss. > To view this discussion on the web, visit https://groups.google.com/d/ms > gid/sbgn-discuss/06596e9a-6f9e-f741-27f3-78ce8eec17e5%40gmail.com. > For more options, visit https://groups.google.com/d/optout. > |
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From: Alexander M. <am...@ei...> - 2016-10-07 08:50:58
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Hello, In SBGN-ML file, how parent-child relations are handled? Please find the diagrams attached, they are posted as examples on sbgn.org ( http://sbgn.github.io/sbgn/examples). 1. In case of "Insulin signaling": how a software supposed to know where complex IGF-IGFR belongs to? The membrane location is implied but is not shown: should we avoid that? We probably should we update our examples too? 2. "Neuro-muscular junction": do we have depth in SBGN-ML? One compartment is shown on the top of another. Thank you, Alexander |
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From: Tobias C. <tob...@mo...> - 2016-06-29 12:05:42
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Hi All, During last HARMONY we started to migrate several SBGN resources from a number of sources to GitHub. For LibSBGN the code repository, the issue tracker, and the downloads have been migrated from Sourceforge to GitHub. Latest changes can be found on GitHub from now on. The code repository can be found here now https://github.com/sbgn/libsbgn The downloads (releases) can be found here now https://github.com/sbgn/libsbgn/releases The issues can be found here now https://github.com/sbgn/libsbgn/issues Until further notice the website can still be found here http://www.sbgn.org/LibSBGN and the mailing list is still sbg...@li... (archive https://sourceforge.net/p/sbgn/mailman/sbgn-libsbgn/) With kind regards, Tobias |
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From: Devesh K. <dev...@ou...> - 2016-06-20 07:41:52
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If no language attribute is present on the map element in a file, the doValidation() method throws a NullPointerException.
Stacktrace:
java.lang.NullPointerException
at org.sbgn.schematron.SchematronValidator.doValidation(SchematronValidator.java:72)
at org.sbgn.schematron.SchematronValidator.validate(SchematronValidator.java:46)
I know that a language attribute is necessary, but a better error message or a more suitable exception is thrown (with a message like "Unspecified language").
Thank You
Namaste
Devesh KhandelwalLearner
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From: Tobias C. <tob...@mo...> - 2016-04-30 00:44:21
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Hi Vasundra, Thanks! Looks good to me. Cheers, Tobias On 29 April 2016 at 19:10, Vasundra Toure <vas...@gm...> wrote: > Dear all, > > I would like to bring back the topic to support level and version in > SBGN-ML. > > There was a previous proposal and discussion that you can find here: > https://sourceforge.net/p/sbgn/mailman/message/29359274/". > > Based on this discussion, there is an improved proposal: > > PROPOSAL > -------- > To support the level and version in SBGN-ML, we would use the > identifier.org URIs and have an attribute called "version". > > The map element of a SBGN-ML would then change from: > <sbgn ...> > <map language="..."> > ... > </map> > </sbgn> > > to (here for the current version of the PD spec) > > <sbgn ...> > <map version=" > http://identifiers.org/combine.specifications/sbgn.pd.level-1.version-1.3 > "> > ... > </map> > </sbgn> > > > The language attribute will be deprecated, so we would use the version > attribute instead. > > A tool can handle the attribute by: > a) using a regex, > b) parsing the version attribute, > c) comparing against a static list of URIs > > Let us know your thoughts and if this sounds good for you. > > Thank you. > > Best regards, > Vasundra > > > ------------------------------------------------------------------------------ > Find and fix application performance issues faster with Applications > Manager > Applications Manager provides deep performance insights into multiple > tiers of > your business applications. It resolves application problems quickly and > reduces your MTTR. Get your free trial! > https://ad.doubleclick.net/ddm/clk/302982198;130105516;z > _______________________________________________ > sbgn-libsbgn mailing list > sbg...@li... > https://lists.sourceforge.net/lists/listinfo/sbgn-libsbgn > > -- Dr Tobias Czauderna Faculty of Information Technology Monash University, Clayton, Australia Office: Rm 318.7, New Horizons Building, 20 Research Way Phone: +61 3 990 50518 |
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From: Vasundra T. <vas...@gm...> - 2016-04-29 09:11:01
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Dear all, I would like to bring back the topic to support level and version in SBGN-ML. There was a previous proposal and discussion that you can find here: https://sourceforge.net/p/sbgn/mailman/message/29359274/". Based on this discussion, there is an improved proposal: PROPOSAL -------- To support the level and version in SBGN-ML, we would use the identifier.org URIs and have an attribute called "version". The map element of a SBGN-ML would then change from: <sbgn ...> <map language="..."> ... </map> </sbgn> to (here for the current version of the PD spec) <sbgn ...> <map version=" http://identifiers.org/combine.specifications/sbgn.pd.level-1.version-1.3"> ... </map> </sbgn> The language attribute will be deprecated, so we would use the version attribute instead. A tool can handle the attribute by: a) using a regex, b) parsing the version attribute, c) comparing against a static list of URIs Let us know your thoughts and if this sounds good for you. Thank you. Best regards, Vasundra |
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