charite.christo.metannogen
Class Metannogen

java.lang.Object
  charite.christo.metannogen.Metannogen

All Implemented Interfaces:

ChRunnable

public class Metannogen
extends Object
implements ChRunnable

HELP

Overview

Metannogen is a customizable graphical work-bench to organize collections of biochemical reactions of metabolic networks. It consists of a graphical browser for metabolic networks and an editor for user defined collections of biochemical equations. The networks which are provided as SBML files can only be viewed, but not modified. The own collection of datasets, however, can be modified and exported as SBML. The program design allows efficient use of existing knowledge in form of already published metabolic networks for the reconstruction of new metabolic networks. One advantage is that biochemical reaction can be directly copied to the user data. The resulting dataset can be modified and Web-links, notes, remarks and variable declarations can be added. All reactions and datasets with equivalent biochemical equations are cross-linked. Unfortunately, different authorities such as Kegg, the Palsson group, ChEBI, HepatoNet and Reactome prefer different identifier systems for metabolites. Nevertheless, dictionaries can be provided such that reactions are recognized to be identical even if they are written with different identifiers. The equals relation of biochemical equations is important for the graphical user interface: All related reactions and datasets for a given reaction or dataset can be accessed using the context menu. It is also used in the tree-view, where all reactions which equal to a reaction in the user defined collection are highlighted. Metannogen uses the graphical pathway maps from KEGG. In the pathway maps, reactions and metabolites can be highlighted by WIKI:Marching_ants and quantitative data such as flux strength can be shown. The user interface follows conventions of typical graphical applications and implements advanced GUI concepts like browsable trees, WIKI:Cut_paste, WIKI:Word_completion, WIKI:Incremental_search and highlighting, WIKI:Spell-check and automatic Web links. Metannogen does not need to be installed because it can be directly started by clicking the Java-Web-start-button on the Metannogen page. Using a central data store, several people can work simultaneously on the same project. To evaluate Metannogen, the demo database can be selected in the start frame. The demo database is configured to accept simultaneous changes without password. Metannogen supports interprocess communication via socket connection to work in concert with other applications. allow output file formation as part of a shell script. To export the user defined network in SBML or any other format within a shell script, it can be run non-interactively.

Field Summary

static int

PORT

Fields inherited from interface charite.christo.interfaces.ChRunnable

APPEND, DOWNLOAD_FINISHED, INTERPRET_LINE, LOG, SET_ICON_IMAGE

Constructor Summary

Metannogen()

Method Summary

static Map<String,String>	getDictionaryCompartments() See command line parameter -dictionaryOfSpecies
static Map<String,String>	getDictionarySpecies() See command line parameter -dictionaryOfCompartments
static ReactionCollection	getNetwork(String id) Returns the networks with the ID for example "KEGG".
static ReactionCollection[]	getNetworks() Returns an array of all networks.
static ReactionCollection	getNetworkTranslated(ReactionCollection networkOrig) Translates a given network with the dictionaries for species and compartments.
static Reaction[]	getReactionsOfFocusedDataset() For validation after input of datasets
static void	main(String... argv)
static MReactionCollection	newReactionCollectionDatasets(long filter_options) Generates a new network object from all datasets.
static boolean	reactionIdShouldBeExported(String id)
Object	run(String id, Object arg)

Methods inherited from class java.lang.Object

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

Field Detail

PORT

public static final int PORT

See Also:

Constant Field Values

Constructor Detail

Metannogen

public Metannogen()

Method Detail

main

public static void main(String... argv)

getNetworks

public static ReactionCollection[] getNetworks()

Returns an array of all networks. Network files are given with the command shell parameter -networks=list of files/URLs.

getNetwork

public static ReactionCollection getNetwork(String id)

Returns the networks with the ID for example "KEGG". Returns null, if no network is found.

newReactionCollectionDatasets

public static MReactionCollection newReactionCollectionDatasets(long filter_options)

Generates a new network object from all datasets.

Parameters:

filter_options - zero or a bit mask from Reaction.FILTER_REJECTED_DATASETS and Reaction.FILTER_NOT_EXCLUDED

getNetworkTranslated

public static ReactionCollection getNetworkTranslated(ReactionCollection networkOrig)

Translates a given network with the dictionaries for species and compartments. The dictionaries are used that are specified by command line options.

getDictionaryCompartments

public static Map<String,String> getDictionaryCompartments()

See command line parameter -dictionaryOfSpecies

getDictionarySpecies

public static Map<String,String> getDictionarySpecies()

See command line parameter -dictionaryOfCompartments

getReactionsOfFocusedDataset

public static Reaction[] getReactionsOfFocusedDataset()

For validation after input of datasets

run

public Object run(String id,
                  Object arg)

Specified by:

run in interface ChRunnable

reactionIdShouldBeExported

public static boolean reactionIdShouldBeExported(String id)