charite.christo.metannogen
Class MetannogenMain

java.lang.Object
  java.awt.event.MouseAdapter
      charite.christo.metannogen.MetannogenMain

All Implemented Interfaces:

ChRunnable, ActionListener, MouseListener, MouseMotionListener, MouseWheelListener, EventListener

public class MetannogenMain
extends MouseAdapter
implements ActionListener, ChRunnable

HELP Metannogen requires Java version 1.5 or higher. It consists of a single WIKI:Jar-file metannogen.jar. Further data-files or program parts are automatically downloaded at runtime from the Web-server. The file metannogen.jar can be started in two different ways:

1. Using the java-command:

     java -Xmx200M -jar metannogen.jar  [options]

   The option -Xmx200M increases the maximum amount of memory allocated by the Java Virtual Machine to 200 MBytes.
2. Using (WIKI:Java_webstart): The command javaws acts on the WIKI:JNLP file metannogen.jnlp. The JNLP file may be inspected with any text editor. It contains the command line parameters.

     javaws http://www.charite.de/bioinf/strap/metannogen/metannogen.jnlp

Web proxy
In some institutions all Internet connections are going through a Web proxy (see WIKI:Proxy_server). In this case the proxy must be set correctly, otherwise downloading of files from the Web will fail. Detailed explanation is found in "Menu-bar>Options>Internet settings" or by clicking the button "Test Web Proxy" in the start frame of Metannogen.

Command line parameters of Metannogen
Metannogen takes a number of optional command line parameters. If Metannogen is started using the Java-Web-Start mechanism, the command line options are defined in a the JNLP file. Some command line options are followed by one or more text files. Files can be given as a relative or absolute file path or in form of an URL.

• -networks List of WIKI:SBML files
  The given SBML files are loaded into Metannogen. "KEGG" is a symbol for the WIKI:KEGG database, "PHM" stands for http://www.charite.de/bioinf/strap/metannogen/data/Palsson_human_2007_04_ascii.sbml.gz "EHM" designates STRING:MetannogenStatics#URL_EHM.
• -dictionaryOfSpecies List of text files containing ID replacements
  Example:

        ...
        C00124 C01582 C00984 C00962 # D-Galactose
        C00159 C02209 C00936  # D-Mannose
        ...
      

  The IDs are separated by white space. The SBML output will contain C00936 even if C00159 or C02209 appear in the biochemical equation.
• -dictionaryOfCompartments List of text files translating compartment names.
  Example:

        ...
        nucleus   cytoOrNuc
        cytosol   cytoOrNuc
        ...
                                  

  The IDs are separated by white space. The SBML output will contain cytoOrNuc even if the biochemical equation is written for "nucleus" or "cytosol".
• -names List of text files for associating a human readable name to metabolite IDs
  The two columns are separated by tab.

        ...
        C05928\t10-Formyltetrahydrofolyl
        C05931\tN-Succinyl-L-glutamate
        ...
                                  

• -replaceWhileTyping List of text files providing a dictionary for metabolite replacements.
  The replacement is applied in the text-field for the biochemical equation. When biochemical equations are typed, the specified replacements will be applied automatically after the user has finished typing a metabolite. This is triggered by inserting a white space character after the identifier or by inserting longer text using Ctrl-V or the middle mouse button. In the example below C00022 is the Kegg identifier for Pyruvate and pyr my be a display name for pyruvate. If the user types "pyr" and hits the space bar, "pyr" would be replaced by "C00001".

        ...
        H2O water C00001
        pyr C00022
        ...
                                  

  Loading networks like KEGG or PHM automatically activates replacement of names by IDs. This replacement works independent of the option "-replaceWhileTyping". The IDs and names are separated by white space.
• -dictionaryOfSimilarSpecies List of text files associating a representative ID to similar compound IDs
  Example:

        ...
        C01342  C00014  #  Ammonia NH3 NH4+
        C01353  C00288 C00011 #  H2CO3 HCO3-  CO2
        ...
      

  Biochemical reactions are sometimes written in different ways as a question of taste: Either with NH3 or NH4⁺ or either with CO2 or HCO3^-. As a consequence, Metannogen may fail to recognize that two biochemical equations denote the same catalytic process. This is avoided by providing a dictionary of similar species metabolites and by ignoring H+. Including NH3/NH4⁺ and HCO3^-/CO2 into the dictionary, for 53 more reactions in KEGG an identical counterpart is found in Palsson. The IDs and names are separated by white space.
  This dictionary does not affect network output. It is only used in the GUI to determine whether two reactions are identical.
• -proton List of IDs designating protons. This is used for the method Reaction.equals(Reaction, long options) with the flag Reaction.EQUALS_IGNORE_PROTON. Considering equivalent reactions in Palsson human metabolite network and Kegg, the equation often differes by one H+. This is the case for currently 58 reactions. To recognize that two reactions are equal if they differ only by one H⁺, the metabolite identifiers for H⁺ must be known.
• -datasetForms List of input masks for datasets. Input masks are free text containing empty variable declarations to be filled in by the curator. This allows to enter information in a structured form. All information written in variables are accessible with the API and can be used for the output file.
• -listOfCompartments File with a list of compartments.. This list is used for the compartment selector menu.
• -mapAffymetrixRid file or URL
  Mappings of ENSG- or Affymetrix IDs to reaction IDs.

        ...
  ENSG00000049860 ENSG00000049860\tR00022 R06141
  ENSG00000135697\tR00032
       ...
                                  

  In the left column are one or several WIKI:Ensembl or WIKI:Affymetrix IDs. In the right column are one or several reaction IDs. This is used to display expression profiles graphically which are provided by the user in text files where each line contains an Ensembl or Affymetrix ID and one or several floating point numbers. A respective mapping is already automatically generated from the Kegg database via Kegg-orthologies. This option allows to extend this mapping.

The reaction network can be exported in different file formats like SBML. Though the file export function is accessible in the GUI (Menu-bar>File), the prefered way is to run Metannogen as a command line tool without GUI. This allows Metannogen to be included in shell scripts. Complex pipelines can be constructed to directly couple Metannogen with data analysis. The option "-datasets" and an option like "-toSBML1" are required. The other options are optional.

• -datasets File with datasets
  Loads the dataset files from the given file or URL. The URL usually points to a Perl or PHP script which concatenates the single text files of each dataset to one text files. Two possible applications:
  1. When Metannogen is used from another program to access the data programmatically. In this case the other program invokes:

     charite.christo.Metannogen.main("-datasets","file.txt"); 

  2. To export the data in non-interactive mode. Here it is used together with an option like -toSBML1 output-file
• -toSBML1 OutputFile
  The customizable output script No 1 is used to generate WIKI:SBML output. The dataset source must be specified with the -datasets option.
  Different versions of export scripts: The user may also refer to Export_SBML2.java by using the option -toSBML2. Each export script Export_SBML[number].java can be modified at runtime using the GUI. Without restarting Metannogen, the modified export script can be run to export the file. The following options are analogous: -toSBML2, -toSBML3 ... or -toTXT2 or -toSQL2 or -toLIBSBML2. The latter requires installation of the program library libsbml (http://sbml.org/Software/libSBML). Detailed instructions are found in the source code of the export script.
• -attributes List of text files with variable declarations
  The two columns are separated by tab. The first column contains the dataset ID, the second column contains one or several variable declarations separated by white space. Content with white space must be quoted with double quotes.

        ...
        R00959\t$VAR1="variable one for dataset R00959 "   $VAR2_cyto="This is only valid for cytosol"
        R00960\t$VAR1="variable one for Dataset R00960 "   $VAR2_cyto="This is only valid for cytosol"
        ...
                                  

• -useReactionAttributes List of attribute names for WIKI:SBML export.
  Attributes contain additional information for WIKI:XML elements (Also see http://www.w3schools.com/Xml/xml_attributes.asp). In SBML several standard attributes for reaction and species elements are well defined. Nevertheless, the possibility for additional (non-standard) attributes had been included for two reasons.
  • The set of standard attributes may be extended in future SBML versions.
  • A computer program that takes SBML as input may accept information in form of non-standard attributes.
  Attributes are defined by the user in the comment text area of datasets using a syntax which is similar to variable declarations in WIKI:Perl. They may also be defined in text files given in the command line after the "-useReactionAttributes" option.
• -useSpeciesAttributes Equivalent to "-useReactionAttributes".
• -attributesOverride List of text files with variable declarations
  Same as "-attributes" with the difference that the variables override the variables defined in the comment text of datasets.
• -exportReactionIDs List of text files providing a set of reaction IDs to be exported
  

    R01271
    R00301
    HR05020.*
    

  Tokens containing asterisk are treated as WIKI:Regular_expression. The compartment suffix like "@cyto" ist optional. If this option is given, only the specified reactions are included in the output. All other reactions are skipped.

The following command line options are only important under very special circumstances:

• -noExit
  Metannogen will not terminate the Java-process. This option is only important when the main-method charite.christo.Metannogen.main(String[]) is called from another program.

Field Summary

Fields inherited from interface charite.christo.interfaces.ChRunnable

APPEND, DOWNLOAD_FINISHED, INTERPRET_LINE, LOG, SET_ICON_IMAGE

Constructor Summary

MetannogenMain()

Method Summary

void	actionPerformed(ActionEvent ev)
static void	arraysEqul(String[] ss1, String[] ss2)
static JComponent	newPnlServer()
Object	run(String id, Object arg)

Methods inherited from class java.awt.event.MouseAdapter

mouseClicked, mouseDragged, mouseEntered, mouseExited, mouseMoved, mousePressed, mouseReleased, mouseWheelMoved

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MetannogenMain

public MetannogenMain()

Method Detail

actionPerformed

public void actionPerformed(ActionEvent ev)

Specified by:

actionPerformed in interface ActionListener

run

public Object run(String id,
                  Object arg)

Specified by:

run in interface ChRunnable

newPnlServer

public static JComponent newPnlServer()

arraysEqul

public static void arraysEqul(String[] ss1,
                              String[] ss2)