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Context-sensitive creation of kinetic equations in biochemical networks

Home Page: https://draeger-lab.github.io/SBMLsqueezer/

License: GNU General Public License v3.0

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biological-networks information-extraction mathematical-modelling metabolic-engineering regulatory-network computational-biology systems-biology andreas-zell biochemical-networks andreas-dr-ger

sbmlsqueezer's Introduction

SBMLsqueezer

Context-sensitive creation of kinetic equations in biochemical networks

License (GPL version 3) Latest version DOI:10.1186/s12918-015-0212-9 Build Status

Authors: Eike Pertuch, Andreas Dräger

Alumni: Alexander Dörr, Sebastian Nagel, Roland Keller, Sandra Saliger, Simon Schäfer, Sarah R. Müller vom Hagen, Johannes Pfeuffer, Hannes Borch, Dieudonné Motsou Wouamba, Lisa Falk, Thomas M. Hamm, Clemens Wrzodek, Stefanie Hoffmann

Short description

SBMLsqueezer generates kinetic equations for biochemical networks according to context of each reaction. When used as a plug-in for CellDesigner it uses the information from the SBGN representation of all network components. In the stand-alone mode, SBMLsqueezer evaluates the Systems Biology Ontology (SBO) annotations to extract this information. An online version of SBMLsqueezer is available that runs without instally any software on the local machine. The rate laws that can be produced by SBMLsqueezer include several types of generalized mass action; detailed and generalized enzyme kinetics, various types of Hill equations, S- and H-systems, and additive models for gene regulation. User defined settings specify which equation to apply for any type of reaction and how to ensure unit consistency of the model. Equations can be created using contextual menus. All newly created parameters are equipped with the derived unit and annotated with SBO terms if available and meaningful textual names. MathML is inserted directly into the SBML file. LaTeX or text export of ordinary differential equations is provided.

Please cite

  1. Andreas Dräger, Daniel C. Zielinski, Roland Keller, Matthias Rall, Johannes Eichner, Bernhard O. Palsson, and Andreas Zell. SBMLsqueezer 2: Context-sensitive creation of kinetic equations in biochemical networks. BMC Systems Biology, 9(1):1-17, September 2015. [ DOI | link | pdf ]
  2. Andreas Dräger. Computational Modeling of Biochemical Networks. Ph.D. thesis, University of Tübingen, Tübingen, Germany, January 2011. [ link ]
  3. Andreas Dräger, Adrian Schröder, and Andreas Zell. Systems Biology for Signaling Networks, volume 1 of Systems Biology, chapter Automating mathematical modeling of biochemical reaction networks, pages 159-205. Springer-Verlag, July 2010. [ DOI | link ]
  4. Andreas Dräger, Nadine Hassis, Jochen Supper, Adrian Schröder, and Andreas Zell. SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks. BMC Systems Biology, 2(1):39, April 2008. [ DOI | link | pdf ]

Users' Guide

For more information, see the Users' Guide

sbmlsqueezer's People

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alexander-doerr avatar clemens82 avatar dependabot[bot] avatar draeger avatar eikept avatar greenwenny avatar hannesborch avatar jpfeuffer avatar lisafalk avatar mariahei avatar mvhsara avatar rolandkeller5 avatar simonhs87 avatar thecodingdad avatar tmhamm avatar

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sbmlsqueezer's Issues

Problems with a recent SBML file for yeast metabolic reconstruction

Hello,

I have downloaded the most recent yeast genome-scale metabolic reconstruction as an SBML file from GitHub: https://github.com/SysBioChalmers/yeast-GEM.

My goal is to add reaction kinetic parameters using SBMLsqueezer. I have opened the file and tried running Squeeze. I'm using default options, except that I've disabled the setting "Consider all reactions to be enzyme-catalyzed" (it was turned on by default). After clicking Next, the Squeeze operation starts running and quickly jumps from around 10% to 100%. When checking the results, it looks like from one point on, the reactions have missing values ( " - " ) for the KineticLaw and Formula fields. When clicking on one of these missing values, the program mentions a Java exception: (java.lang.NullPointerException). Here as a screenshot with the error and the missing parameter values: https://imgur.com/a/6aONNU6.

Assuming that this was a problem with parsing the SBML file, I converted it from SBML L3V1 to SBML L2V4 using COPASI. This time, the Squeeze operation appears to run fine. However, after clicking "Finish", I am unable to save the modifications to the SBML file. If I click "Save as", then no file is being generated. If I click "Save", the SBML file has a size of 0 bytes.

I am attaching a ZIP file with the two SBML files (L2V4 and L3V1).

yeastGEM.zip

I also tried running the SBMLsqueezer CLI. However, I ran into troubles with this as well.

First, when running with the SBML L3V1 file, it complained about an SBO term:

java -Xmx1500m -jar SBMLsqueezer_v2.1.jar --sbml-in-file=yeastGEM-L3V1.xml --sbml-out-file=out-L2V4.xml --all-reactions-as-enzyme-catalyzed=false --read-from-sabio-rk=false
------------------------------------------------------------
SBMLsqueezer version 2.1
Copyright ? 2006-2015 University of Tuebingen,
Center for Bioinformatics Tuebingen (ZBIT).
This program comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome
to redistribute it under certain conditions.
See http://www.gnu.org/licenses/gpl-3.0-standalone.html.
------------------------------------------------------------
Feb 10, 2020 6:13:20 PM org.sbml.squeezer.ReactionType <clinit> --- INFO: Loading kinetic equations...
Feb 10, 2020 6:13:20 PM org.sbml.squeezer.ReactionType <clinit> --- INFO: done in 19 ms.
Feb 10, 2020 6:13:21 PM org.sbml.squeezer.SBMLsqueezer initializeReaderAndWriter --- INFO: Loading library JSBML
Feb 10, 2020 6:13:21 PM de.zbit.Launcher launchCommandLineMode --- INFO: Launching command-line mode of SBMLsqueezer.
Feb 10, 2020 6:13:21 PM org.sbml.squeezer.SBMLsqueezer squeeze --- INFO: Scanning input files
Feb 10, 2020 6:13:21 PM de.zbit.io.fileformat.FormatIdentification init --- WARNING: Could not load format identification magic byte file.
Feb 10, 2020 6:13:21 PM org.sbml.squeezer.SBMLsqueezer squeeze --- INFO: Squeezing file C:\Users\amizeranschi\Desktop\yeastGEM-L3V1.xml into C:\Users\amizeranschi\Desktop\out-L2V4.xml\yeastGEM-L3V1.xml
Feb 10, 2020 6:13:21 PM org.sbml.squeezer.SBMLsqueezer readSBMLSource --- INFO: reading SBML file...
Feb 10, 2020 6:13:22 PM org.sbml.squeezer.SBMLsqueezer readSBMLSource --- INFO: done in 1,511 ms.
Feb 10, 2020 6:13:22 PM org.sbml.squeezer.SBMLsqueezer squeeze --- INFO: Creating kinetic laws.
Feb 10, 2020 6:13:24 PM org.sbml.squeezer.SBMLsqueezer squeeze --- SEVERE: input: C:\Users\amizeranschi\Desktop\yeastGEM-L3V1.xml, output: C:\Users\amizeranschi\Desktop\out-L2V4.xml/yeastGEM-L3V1.xml
java.util.NoSuchElementException: No term named 'SBO:0000655'
        at org.biojava3.ontology.Ontology$Impl.getTerm(Ontology.java:350)
        at org.sbml.jsbml.SBO.isChildOf(SBO.java:1248)
        at org.sbml.jsbml.SBO.isTranslation(SBO.java:1871)
        at org.sbml.squeezer.ReactionType.<init>(ReactionType.java:766)
        at org.sbml.squeezer.KineticLawGenerator.generateLaws(KineticLawGenerator.java:535)
        at org.sbml.squeezer.SBMLsqueezer.squeeze(SBMLsqueezer.java:500)
        at org.sbml.squeezer.SBMLsqueezer.squeeze(SBMLsqueezer.java:567)
        at org.sbml.squeezer.SBMLsqueezer.commandLineMode(SBMLsqueezer.java:253)
        at de.zbit.Launcher.launchCommandLineMode(Launcher.java:724)
        at de.zbit.Launcher.run(Launcher.java:857)
        at de.zbit.Launcher.<init>(Launcher.java:211)
        at org.sbml.squeezer.SBMLsqueezer.<init>(SBMLsqueezer.java:224)
        at org.sbml.squeezer.SBMLsqueezer.main(SBMLsqueezer.java:177)

Second, when running with the SBML L2V4 file (which I've created from the L3V1 file, using COPASI), the model was read correctly and the algorithm ran, but then it mentioned another error while writing the output file (which turned out empty):

java -Xmx1500m -jar SBMLsqueezer_v2.1.jar --sbml-in-file=yeastGEM-L2V4.xml --sbml-out-file=out-L2V4.xml --all-reactions-as-enzyme-catalyzed=false --read-from-sabio-rk=false
------------------------------------------------------------
SBMLsqueezer version 2.1
Copyright ? 2006-2015 University of Tuebingen,
Center for Bioinformatics Tuebingen (ZBIT).
This program comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome
to redistribute it under certain conditions.
See http://www.gnu.org/licenses/gpl-3.0-standalone.html.
------------------------------------------------------------
Feb 10, 2020 6:28:03 PM org.sbml.squeezer.ReactionType <clinit> --- INFO: Loading kinetic equations...
Feb 10, 2020 6:28:03 PM org.sbml.squeezer.ReactionType <clinit> --- INFO: done in 21 ms.
Feb 10, 2020 6:28:03 PM org.sbml.squeezer.SBMLsqueezer initializeReaderAndWriter --- INFO: Loading library JSBML
Feb 10, 2020 6:28:03 PM de.zbit.Launcher launchCommandLineMode --- INFO: Launching command-line mode of SBMLsqueezer.
Feb 10, 2020 6:28:03 PM org.sbml.squeezer.SBMLsqueezer squeeze --- INFO: Scanning input files
Feb 10, 2020 6:28:03 PM de.zbit.io.fileformat.FormatIdentification init --- WARNING: Could not load format identification magic byte file.
Feb 10, 2020 6:28:03 PM org.sbml.squeezer.SBMLsqueezer squeeze --- INFO: Squeezing file C:\Users\amizeranschi\Desktop\yeastGEM-L2V4.xml into C:\Users\amizeranschi\Desktop\out-L2V4.xml\yeastGEM-L2V4.xml
Feb 10, 2020 6:28:03 PM org.sbml.squeezer.SBMLsqueezer readSBMLSource --- INFO: reading SBML file...
Feb 10, 2020 6:28:05 PM org.sbml.squeezer.SBMLsqueezer readSBMLSource --- INFO: done in 1,761 ms.
Feb 10, 2020 6:28:05 PM org.sbml.squeezer.SBMLsqueezer squeeze --- INFO: Creating kinetic laws.
Feb 10, 2020 6:28:19 PM org.sbml.squeezer.SBMLsqueezer squeeze --- INFO: done in 13,870 ms.
Feb 10, 2020 6:28:19 PM org.sbml.squeezer.SBMLsqueezer squeeze --- INFO: Saving changes and writing SBML file...
0    [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent -1.5 has been rounded to -1.
1    [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent -0.5 has been rounded to 0.
5    [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent -1.25 has been rounded to -1.
7    [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent -0.25 has been rounded to 0.
8    [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent -2.5 has been rounded to -2.
9    [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent -1.5 has been rounded to -1.
12   [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent -62.3 has been rounded to -62.
13   [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent -61.3 has been rounded to -61.
14   [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent -4.234 has been rounded to -4.
18   [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent -3.234 has been rounded to -3.
19   [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent -2.209 has been rounded to -2.
19   [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent -1.209 has been rounded to -1.
21   [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent -0.19 has been rounded to 0.
21   [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent 0.81 has been rounded to 0.
23   [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent -0.012 has been rounded to 0.
24   [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent 0.988 has been rounded to 0.
25   [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent -0.087 has been rounded to 0.
29   [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent 0.913 has been rounded to 0.
30   [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent -0.043 has been rounded to 0.
31   [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent 0.957 has been rounded to 0.
32   [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent -0.007 has been rounded to 0.
32   [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent 0.993 has been rounded to 0.
33   [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent -0.029 has been rounded to 0.
35   [main] WARN  org.sbml.jsbml.Unit  -     Loss of information because the illegal non-integer exponent 0.971 has been rounded to 0.
line 416,031 column 7 - Error: missing quotemark for attribute value
line 422,280 column 7 - Error: missing quotemark for attribute value
Feb 10, 2020 6:28:22 PM org.sbml.squeezer.SBMLsqueezer squeeze --- INFO: done in 2,936 ms.
Feb 10, 2020 6:28:22 PM org.sbml.squeezer.SBMLsqueezer squeeze --- INFO: 18.877 s needed for squeezing file yeastGEM-L2V4.xml.

It looks like the versions of SBO and JSBML that are bundled with SBMLsqueezer are outdated. Would be be possible to update these?

Not able to squeeze the rate equation in cell designer using SBML squeezer as a plugin

I am currently using the SBML squeezer plugin for squeezing the rate equations for the network drawn using cell designer 4.4.2 for my project work. I downloaded the SBML squeezer plugin.(www.cogsys.cs.unituebingen.de/software/SBMLsqueezer/downloads/jsbml-1. 1-a1-incl-libs.jar)
While using the software plugin I encountered the following issues;

  1. I am being able to get only individual rate equations for the network drawn using the cell designer but when I apply the SBML squeezer for the whole network I get no equations in the list
  2. I tried exporting the equations by clicking the tab "export changes" but no file is being created
  3. I am also unable to simulate the network because the rate equations are not getting added to the reactions in the network
  4. The model report is not generated and is showing a java.io.IOException error. (I have installed java version 8 update before all installations)
    SBMLsqueezer.docx

file extensions

When trying to save a file, the file extension is not added automatically. Without the extension, the file is not saved.

NullPointerException is thrown when trying to integrate kinetic laws into model while the node "kinetic law" is selected in the right tree in the GUI

When trying to integrate newly kinetic laws after the creation with squeezer or the search in SABIO-RK a NullPointerException is thrown if the node "Kinetic Law" is selected in the right tree in the GUI. The source of this issue is that this node has no parent node (here reaction) if selected directly from the path (via getLastPathComponent() or manually). Currently there is a workaround implemented which selects the second to last node of the path instead and then searches the children of this node for a node with the same name as the last node and then selecting the node which was found. If selected this way, the node actually contains the parent node but obviously this is not a very nice way to select the last node. Therefore the goal would be to identify the reason as for why the node has no parent when selected directly in this special case and then fix it.

4 of the junit tests are failing

The junit tests that are failing are:

  • 3 tests in SABIORKTest : testGetSuggestions, testGetKineticsLawString, testGetIDs
  • The test squeezerTests.testDirectoryForXMLFiles

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