Conversion of SBML files into human-readable reports

Publications on SBML2L^AT_EX

[1]	Andreas Dräger. Computational Modeling of Biochemical Networks. PhD thesis, University of Tuebingen, Tübingen, Germany, January 2011. [ details | link ]
[2]	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 | details | link ]
[3]	Andreas Dräger, Hannes Planatscher, Dieudonné Motsou Wouamba, Adrian Schröder, Michael Hucka, Lukas Endler, Martin Golebiewski, Wolfgang Müller, and Andreas Zell. SBML2LATEX: Conversion of SBML files into human-readable reports. Bioinformatics, 25(11):1455--1456, April 2009. [ DOI | details | link | pdf ]
[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 | details | link | pdf ]

Export list of publications as BibTeX / Endnote / Rich Text Format (RTF)

Availability of SBML2L^AT_EX

SBML2L^AT_EX is available in two different forms:

1. As a stand-alone application that converts SBML files into L^AT_EX files. Since release 0.9.8, SBML2L^AT_EX comes as a convenient JAR file that does not require the installation of any other software and that can directly be used. Earlier versions include a script displaySBML.sh, which allows further processing of the L^AT_EX files.
2. As a online version, which allows users to directly create various human-readable files including PDF and TeX without installation of any software on the local computer.

The stand-alone version

The stand-alone tool provides a Graphical User Interface (GUI) mode and a command-line mode. All options (see section options) to customize the output (layout, SBML properties to be included) are available through both modes. This allows users to use SBML2L^AT_EX in a batch mode or with user interaction. The GUI can be started by passing the --gui option to the program. Since version 0.9.8, the GUI will be displayed automatically upon launching of the JAR file. In order not to use the graphical user interface, it is necessary to pass at least the SBML input file and the name of the output file to the program (see a detailed description of the command line options below) and not to use the option --gui. It is also possible to combine the option --gui with all other options in order to change the behavior of the graphical user interface or to define pre-selected values.

An API documentation can be found for the following versions:

• version 0.9.9
• version 0.9.8
• version 0.9.6

which allows users to costumize SBML2L^AT_EX or to access its methods from their own programs. To this end, a light-weight minimal version of SBML2L^AT_EX can be downloaded that does not include the library JSBML.

To process the results of this stand-alone program to obtain, e.g., PDF files, an installation of L^AT_EX and several additional packages on your system is required. For details see the L^AT_EX section.

SBML2L^AT_EX command line arguments

For an overview of the command line arguments in earlier versions of SBML2L^AT_EX, please visit the documentation for the version of interest:

• version 0.9.7
• version 0.9.8

This overview does not necessarily consider versions of SBML2L^AT_EX prior to release 0.9.9.

Program usage

java org.sbml.tolatex.SBML2LaTeX [options]
	Starts the program SBML2LaTeX.
--help, -?
	Lists all available options.

L^AT_EX Options IO

Configure input and output files

Here you can specify the SBML input file and the location of the LaTeX file for output.

--sbml-input-file[ |=]<File>
	The SBML source file to be converted to LaTeX. Accepts sBML files (*.sbml, *.xml). Default value: /local/draeger/workspace/SBML2LaTeX
--report-output-file[ |=]<File>
	The file where to save the generated LaTeX report. The standard way is to let SBML2LaTeX generate a TeX file, which the user can then compile to a different format, or from which parts can be easily extracted to support scientific writing. Additionally, SBML2LaTeX may be used to directly generate a PDF file if the LaTeX compiler pdfLaTeX is specified. Accepts Report files (*.tex, *.pdf). Default value: /local/draeger/workspace/SBML2LaTeX
--latex-dir[ |=]<File>
	Standard directory where LaTeX files can be stored Accepts directories only. Default value: /home/draeger

L^AT_EX Options

LaTeX compiler location

Here you can specify the location of the LaTeX compiler on your operating system.

--load-latex-compiler[ |=]<File>
	The path to the LaTeX compiler to generate PDF, DVI or other files from the created LaTeX report file. Accepts All files (*). Default value: /usr/bin/pdflatex

Report options

Configure the layout of the LaTeX reports, what to be included, and if to remove temporary files afterwards.

--check-consistency
	If true, the automatic model consistency check is performed and the results are written in the appendix of the model report file. Default value: false
--miriam-annotation[ |=]<Boolean>
	If true (default), MIRIAM annotations are included into the model report if there are any. In this case, SBML2LaTeX generates links to the resources for each annotated element. Default value: true
--show-predefined-units[ |=]<Boolean>
	If true (default), all predefined unit declarations of the SBML are made explicit in the report file as these are defined by the corresponding SBML Level and Version. Otherwise only unit definitions from the model are included. Note that this option is only available if the option 'INCLUDE_UNIT_DEFINITIONS_SECTION' is active. Default value: true
--print-full-ode-system
	If set to true, the entire rate of change will be written for each species. By default, SBML2LaTeX only prints the sum of the individual reaction rates, which are hyper-linked but displayed at a different position of the report. Note that this option is only available if the option 'INCLUDE_REACTIONS_SECTION' is active. Default value: false
--clean-workspace
	If this option is set to true, all temporary files will be deleted after running SBML2LaTeX. In case of PDF creation, for instance, this will cause even the TeX file to be deleted. However, this option can be meaningful to remove all the temporary files created by your system's LaTeX compiler. Default value: false

Layout options

These options allow you to influence layout and style of the LaTeX report.

--landscape
	This option decides whether to set the LaTeX document in landscape or portrait mode. By default most pages are in portrait format. Default value: false
--print-names-if-available
	If selected, the names of SBML elements (NamedSBase) are displayed instead of their identifiers. This can only be done if the element has a name. Default value: false
--title-page
	If true, a separate title page will be created. By default the title is written as a simple heading on the first page. Default value: false
--typewriter[ |=]<Boolean>
	This option decides whether a typewriter font should be applied to highlight SBML identifiers. This is particularly important when these occur in mathematical equations. Default value: true
--reactants-overview-table
	If true, the details (identifier and name) of all reactants, modifiers and products participating in a reaction are listed in one table. By default a separate table is created for each one of the three participant groups including its SBO term. Note that this option is only available if the option 'INCLUDE_REACTIONS_SECTION' is active. Default value: false

Typographical options

Here you can specify general properties such as paper size and font styles.

--font-headings[ |=]<String>
	Allows to select the font of captions and other (by default sans serif) text. All possible values for type <String> are: avant, cmss, and helvetica. Default value: helvetica
--font-size[ |=]<Short>
	This option allows you to select the size of the standard text font. Headings appear with a larger font. All possible values for type <Short> are: 8, 9, 10, 11, 12, 14, and 17. Default value: 11
--font-text[ |=]<String>
	Allows to select the font of continuous text. Choosing 'times' is actually not recommended because in some cases equations might not look as nicely as they do when using 'mathptmx'. Default: Times font mathptmx. All possible values for type <String> are: chancery, charter, cmr, mathptmx, palatino, times, and utopia. Default value: mathptmx
--font-typewriter[ |=]<String>
	Select a typewriter font that can be used for identifiers if option 'TYPEWRITER' is selected. URLs and other resources are also marked with this font. All possible values for type <String> are: cmt and courier. Default value: cmt
--paper-size[ |=]<String>
	The paper size for LaTeX documents. With this option the paper format can be influenced. Default paper size: DIN A4. All sizes a?, b?, c? and d? are European DIN sizes. Letter, legal and executive are US paper formats. All possible values for type <String> are: letter, legal, executive, a0, a1, a2, a3, a4, a5, a6, a7, a8, a9, b0, b1, b2, b3, b4, b5, b6, b7, b8, b9, c0, c1, c2, c3, c4, c5, c6, c7, c8, c9, d0, d1, d2, d3, d4, d5, d6, d7, d8, and d9. Default value: a4

Content of the report

Select sections to be included in the report.

--include-compartment-types-section[ |=]<Boolean>
	This option decides whether or not a section about compartment types should be included in the resulting model report. Note that this option only causes an effect if the model contains compartment type declarations. Default value: true
--include-compartments-section[ |=]<Boolean>
	This option decides whether or not a section about compartments should be included in the resulting model report. Note that this option only causes an effect if the model contains compartment declarations. Default value: true
--include-constraints-section[ |=]<Boolean>
	This option decides whether or not a section about constraints should be included in the resulting model report. Note that this option only causes an effect if the model contains constraint declarations. Default value: true
--include-events-section[ |=]<Boolean>
	This option decides whether or not a section about events should be included in the resulting model report. Note that this option only causes an effect if the model contains event declarations. Default value: true
--include-function-definitions-section[ |=]<Boolean>
	This option decides whether or not a section about function definitions should be included in the resulting model report. Note that this option only causes an effect if the model declares any function definitions. Default value: true
--include-initial-assignments-section[ |=]<Boolean>
	This option decides whether or not a section about initial assignments should be included in the resulting model report. Note that this option only causes an effect if the model declares any initial assignments. Default value: true
--include-parameters-section[ |=]<Boolean>
	This option decides whether or not a section about parameters should be included in the resulting model report. Note that this option only causes an effect if the model declares any parameters. Default value: true
--include-reactions-section[ |=]<Boolean>
	This option decides whether or not a section about reactions should be included in the resulting model report. Note that this option only causes an effect if the model declares any reactions. Furthermore, this option also decides if a summary of the differential equation system that is implied by the given model should be generated. Again, this will only cause an effect if the model contains any species. Default value: true
--include-rules-section[ |=]<Boolean>
	This option decides whether or not a section about rules should be included in the resulting model report. Note that this option only causes an effect if the model declares any rules, no matter if these are of algebraic, assignment or rate rule type. Default value: true
--include-species-section[ |=]<Boolean>
	This option decides whether or not a section about the species in the given model should be included in the resulting model report. Note that this option only causes an effect if the model declares any species. Default value: true
--include-unit-definitions-section[ |=]<Boolean>
	This option decides whether or not a section about the unit definitions of the given model should be included in the resulting model report. Note that this option only causes an effect if the model declares any unit definitions. However, in some level/version combinations SBML models contain predefined unit definitions which might be included in the model report if this option is active. Default value: true

Options for the graphical user interface

Additional options

--check-for-updates[ |=]<Boolean>
	Decide whether or not this program should search for updates at start-up. Default value: true
--gui
	If this option is given, the program will display its graphical user interface. Default value: false

Requirements for SBML2L^AT_EX

Required L^AT_EX packages

If the resulst of SBML2L^AT_EX are to be translated to DVI, PS or PDF files, an installation of L^AT_EX is required. In addition to standard L^AT_EX, SBML2L^AT_EX uses several packages, which you will need to install to your system or to copy them into the same directory as the results of SBML2L^AT_EX. Another option is to copy the following style packages into a subdirectory of your SBML2L^AT_EX installation and to set the TEXINPUTS variable to this directory (see the displaySBML.sh script for an example). For convenience, all packages listed below are already included in the SBML2L^AT_EX bundle, besides the KOMAscript. Required L^AT_EX styles and packages:

• KOMAscri pt (should already be included into your L^AT_EX installation)
• breqn introduces automatic line breaks within equations.
• flexisym is needed by breqn.
• mhchem required to typeset chemical equations.
• rccol produces fancy tables in which decimal numbers always get the same number of decimal digits.
• fltpoint is required by rccol.

Other packages you may need for a successful compilation can be downloaded from the CTAN archive as well. You also need to download the SBML2L^AT_EX logo (EPS format, PDF) of this homepage for a successful compilation of your resulting L^AT_EX file. Both files are already included in the SBML2L^AT_EX bundle in the resources directory.

Program requirements

1. Mandatory components and libraries
   • Computer: CPU 800 MHz, 128MB RAM, 1MB free disk space. SBML2L^AT_EX was successfully tested with Linux operating systems (Kernel 2.6.18). As a Java program, it may also run under different operating systems as long as a JRE is available.
   • Java VM 1.6 or later (available from Oracle) to execute the program.
   • For an up-to-date support of the Systems Biology Ontology (SBO) an SBO definition file in OBO format is required. The SBML2L^AT_EX bundle already contains a version of SBO. The current verion is available at http://www.ebi.ac.uk/sbo/main/download.do.
2. Optional components
   • LaTeX (available from LaTeX-project.org) is needed for the conversion of the LaTeX files to DVI, PS, and PDF files.
   • If desired, ImageMagick (available at http://www.imagemagick.org/www/download.html) allows for conversion of files generated by LaTeX or pdfLaTeX to the following formats: EPS, JPG, PNG, GIF. This will create one picture file per page.
   • The packing program ZIP is required by the conversion skript file to put all files created by ImageMagick into one ZIP arcive. The command line program zip must be installed on your Linux/Unix distribution.
3. Obsolete requiremenst of SBML2L^AT_EX for versions before 0.9.9: If you are still using older versions of SBML2L^AT_EX, we strongly recommend switching to the latest version, which is much simpler and easier to use. Otherwise, the following additional requirements will be important to know:
   • Older versions of SBML2L^AT_EX included the library JDom in the SBML2L^AT_EX bundle in order to parse the MIRIAM annotation file. Generally, it is available at http://www.jdom.org. SBML2L^AT_EX requriers JDom for the MIRIAM support.
   • The latest MIRIAM.xml file (see http://www.ebi.ac.uk/compneur-srv/miriam-main/mdb?section=export). The resource directory of the SBML2L^AT_EX bundle already contains such a file, which may not be the most recent one.
   • Older versions of SBML2L^AT_EX also require libSBML: An installation of libSBML version 3.3.1 or later with Java bindings (available from http://sbml.org/Software/libSBML). Note that libSBML may require to install some XML parser first (e. g., Xerces, Expat or libxml2, see the libSBML homepage for details). For your convenience SBML2L^AT_EX version 0.9.6 and higher contains an installation bash script that automatically downloads and installs libSBML 3.3.1 with Xerces 3.0.0 in the subdirectory lib. Note that since release 0.9.8 SBML2L^AT_EX does no longer require libSBML because it is now based on JSBML, which is already included in the JAR file for convenience.