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From: Matthias K. <kon...@go...> - 2015-03-09 22:13:18
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Dear SBGN development team, how can I create SBGN maps with python? I could not find any python bindings. My workflow is based on python bindings to libsbml, libsedml, antimony, roadrunner, ... Python bindings to SBGN would be very helpful. The best Matthias --------------------------------------------------- Matthias König Computational Systems Biochemistry Institute of Biochemistry Charité - Universitätsmedizin Berlin http://www.charite.de/sysbio/people/koenig/ Tel: + 49 30 450 528 197 Tel: + 49 176 81168480 --------------------------------------------------- |
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From: Martijn v. I. <mva...@gm...> - 2015-03-10 07:57:50
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Hi Matthias So far we have c++ and java bindings. There are no bindings for python yet. However, both C++ and Java bindings consist of code that is automatically generated from the XML Schema (plus a few utility functions). You could easily do the same for python. From google I found a python tool called generateDS. You should be able to run it on SBGN.xsd and get somewhere. Do let us know how it goes! regards, Martijn On 09/03/15 23:13, Matthias König wrote: > Dear SBGN development team, > > how can I create SBGN maps with python? > I could not find any python bindings. > My workflow is based on python bindings to libsbml, libsedml, > antimony, roadrunner, ... Python bindings to SBGN would be very helpful. > > The best > Matthias > > --------------------------------------------------- > Matthias König > Computational Systems Biochemistry > Institute of Biochemistry > Charité - Universitätsmedizin Berlin > http://www.charite.de/sysbio/people/koenig/ > Tel: + 49 30 450 528 197 > Tel: + 49 176 81168480 > --------------------------------------------------- > > > ------------------------------------------------------------------------------ > 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/ > > > _______________________________________________ > sbgn-libsbgn mailing list > sbg...@li... > https://lists.sourceforge.net/lists/listinfo/sbgn-libsbgn |
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From: Tobias C. <tob...@mo...> - 2015-03-10 10:22:25
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Hi Matthias, Another solution might be to use PyXB http://pyxb.sourceforge.net/ Kind regards, Tobias *From:* Martijn van Iersel [mailto:mva...@gm...] *Sent:* Tuesday, 10 March 2015 6:58 PM *To:* sbg...@li... *Subject:* Re: [sbgn-libsbgn] Python API for libSBGN Hi Matthias So far we have c++ and java bindings. There are no bindings for python yet. However, both C++ and Java bindings consist of code that is automatically generated from the XML Schema (plus a few utility functions). You could easily do the same for python. From google I found a python tool called generateDS. You should be able to run it on SBGN.xsd and get somewhere. Do let us know how it goes! regards, Martijn On 09/03/15 23:13, Matthias König wrote: Dear SBGN development team, how can I create SBGN maps with python? I could not find any python bindings. My workflow is based on python bindings to libsbml, libsedml, antimony, roadrunner, ... Python bindings to SBGN would be very helpful. The best Matthias --------------------------------------------------- Matthias König Computational Systems Biochemistry Institute of Biochemistry Charité - Universitätsmedizin Berlin http://www.charite.de/sysbio/people/koenig/ Tel: + 49 30 450 528 197 Tel: + 49 176 81168480 --------------------------------------------------- ------------------------------------------------------------------------------ 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/ _______________________________________________ sbgn-libsbgn mailing list sbg...@li... https://lists.sourceforge.net/lists/listinfo/sbgn-libsbgn |
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From: Andreas D. <and...@en...> - 2015-03-10 16:13:44
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Am 10.03.15 um 03:22 schrieb Tobias Czauderna: > > Hi Matthias, > > > > Another solution might be to use PyXB > > http://pyxb.sourceforge.net/ > > > Or use Jython and the Java bindings: http://www.jython.org/ -- Dr. Andreas Draeger University of California, San Diego, La Jolla, CA 92093-0412, USA Bioengineering Dept., Systems Biology Research Group, Office #2506 Phone: +1-858-534-9717, Fax: +1-858-822-3120, twitter: @dr_drae |
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From: Augustin L. <ca...@gm...> - 2015-03-10 16:54:50
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I was able to generate the API with generateDS easily. sudo easy_install https://pypi.python.org/packages/2.7/g/generateDS/generateDS-2.15a-py2.7.egg generateDS.py -o libsbgn.py -s libsbgnSubs.py SBGN.xsd I haven't tried it out, but I would start there. The resulting methods then look like: class glyphSub(supermod.glyph): def __init__(self, notes=None, extension=None, id=None, compartmentRef=None, class_=None, compartmentOrder=None, orientation='horizontal', label=None, state=None, clone=None, callout=None, entity=None, bbox=None, glyph_member=None, port=None): super(glyphSub, self).__init__(notes, extension, id, compartmentRef, class_, compartmentOrder, orientation, label, state, clone, callout, entity, bbox, glyph_member, port, ) supermod.glyph.subclass = glyphSub # end class glyphSub It seems to only require lxml and might create less dependencies in your own code. Augustin Luna On Tue, Mar 10, 2015 at 12:13 PM, Andreas Dräger <and...@en...> wrote: > Am 10.03.15 um 03:22 schrieb Tobias Czauderna: >> >> Hi Matthias, >> >> >> >> Another solution might be to use PyXB >> >> http://pyxb.sourceforge.net/ >> >> >> > > Or use Jython and the Java bindings: http://www.jython.org/ > > -- > Dr. Andreas Draeger > University of California, San Diego, La Jolla, CA 92093-0412, USA > Bioengineering Dept., Systems Biology Research Group, Office #2506 > Phone: +1-858-534-9717, Fax: +1-858-822-3120, twitter: @dr_drae > > > ------------------------------------------------------------------------------ > 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/ > _______________________________________________ > sbgn-libsbgn mailing list > sbg...@li... > https://lists.sourceforge.net/lists/listinfo/sbgn-libsbgn |
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From: Matthias K. <kon...@go...> - 2015-03-10 20:37:30
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Hi all, thanks a lot for the help. Unfortunately, the automatically generated python objects are not what I was looking for. These could work for someone who is very familiar with SBGN, but for a starter all the logic to get a basic understanding of the workings of SBGN, which are available in the Java API, are missing. I probably will have a look at the python-java connection suggested by Andreas. But with language integration in the other direction, i.e. trying to call the java API from python with Py4J <http://py4j.sourceforge.net/index.html> or Jpype. Matthias On Tue, Mar 10, 2015 at 5:13 PM, Andreas Dräger <and...@en...> wrote: > Am 10.03.15 um 03:22 schrieb Tobias Czauderna: > > > > Hi Matthias, > > > > > > > > Another solution might be to use PyXB > > > > http://pyxb.sourceforge.net/ > > > > > > > > Or use Jython and the Java bindings: http://www.jython.org/ > > -- > Dr. Andreas Draeger > University of California, San Diego, La Jolla, CA 92093-0412, USA > Bioengineering Dept., Systems Biology Research Group, Office #2506 > Phone: +1-858-534-9717, Fax: +1-858-822-3120, twitter: @dr_drae > > > > ------------------------------------------------------------------------------ > 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/ > _______________________________________________ > sbgn-libsbgn mailing list > sbg...@li... > https://lists.sourceforge.net/lists/listinfo/sbgn-libsbgn > -- --------------------------------------------------- Matthias König Computational Systems Biochemistry Institute of Biochemistry Charité - Universitätsmedizin Berlin http://www.charite.de/sysbio/people/koenig/ Tel: + 49 30 450 528 197 Tel: + 49 176 81168480 --------------------------------------------------- |
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