Comparison of SMBL models

getting a software tool

After retrieving the different .xml-files we aimed to crosscheck its contents. We therefore used the open source software Notepad ++, V8.1, which can be downloaded here.

pimping the software tool

The software is a free (as in “free speech” and also as in “free beer”:beer:) source code editor and Notepad replacement that supports several languages. Running in the MS Windows environment, its use is governed by GNU General Public License (GNU is a recursive acronym of 'GNU’s Not Unix'). What you might want to additionally install is a plugin called "compare".

Simply navigate to 'plugins' --> 'plugins admin' and search for 'compare'. After installing the plugin and opening two of the -xml-files you will be able to check out the differences between both files.

compare

Having both .xml-files open in the comparison view we are now able to start a first comparison.

File metrics

BIOMD0000000347_url.xml:

1968 lines, length 77.493

bachmann2011.xml:

3686 lines, length 156.362

Ok, there might be a slight difference between the content, friendo! Yes, man, there is! The bachmann2011.xml contains a lot of additional 'Copasi'-information. Although we were not able to decipher all of the additional / missing Information there is metainformation in addition to the core-model information. E.g. there are Meta-IDs provides for Species in the BIOMD0000000347_url.xml, that we could not find in bachmann2011.xml where as obseravtions for stoichomertry could not be made in the BIOMD0000000347_url.xml.

just for fun

Attempt to compare files with web-API of bives

Sendig POSTv request to http://bives.bio.informatik.uni-rostock.de/ with body:
{ "files": [ "https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000861.2?filename=Bachmann2011.xml", "https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000347.2?filename=BIOMD0000000347_url.xml" ], "commands": [ "SBML" ] }
Short abstract of response:
{"xmlDiff":"<?xml version=\"1.0\" encoding=\"UTF-8\"?>\r\n <bives type=\"fullDiff\" id=\"bivesPatch\">\r\n \r\n <update>\r\n <attribute name=\"version\" id=\"2\" oldValue=\"1\" newValue=\"4\" oldPath=\"\/sbml[1]\" newPath=\"\/sbml[1]\" \/>\r\n <attribute name=\"metaid\" id=\"3\" oldValue=\"COPASI0\" newValue=\"_229114\" oldPath=\"\/sbml[1]\/model[1]\" newPath=\"\/sbml[1]\/model[1]\" \/>\r\n <attribute name=\"name\" id=\"4\" oldValue=\"Bachmann2011 - Division of labor by dual feedback regulators controls JAK2\/STAT5 signaling over broad ligand range\" newValue=\"Bachmann2011_JAK2-STAT5_FeedbackControl\" oldPath=\"\/sbml[1]\/model[1]\" newPath=\"\/sbml[1]\/model[1]\" \/>\r\n <attribute name=\"id\" id=\"5\" oldValue=\"jak2_stat5_feedbacks\" newValue=\"Bachmann2011_JAK2STAT5_FeedbackControl\" oldPath=\"\/sbml[1]\/model[1]\" newPath=\"\/sbml[1]\/model[1]\" \/>\r\n
Response was not intuitively understandble, therefore the compare plugin of notepad++ was used