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About

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Getting started

MetaNetX.org is an online platform for accessing, analyzing and manipulating genome-scale metabolic networks (GSM) as well as biochemical pathways. To this end, it integrates a great variety of data sources and tools.

The metabolic models

MetaNetX.org treats each model (i.e., metabolic network or pathway) as an object constituted by different entities:
  • chemical compounds (chem)
  • subcellular compartments (comp)
  • species (spec): chemical compounds that are assigned to a subcellular compartment
  • metabolic reactions (reac): reactions that transform species into another
  • genes or peptides (pept)
  • enzymes (enzy): sets of peptides (or genes) linked to a reaction with information on bounds (maximal and minimal bounds) defining the directionality such that the maximum flux can be carried by this reaction with these enzymes
Depending on the studied model (GSM or pathway), it may contain biomass production reaction(s) (identified by the identifier "BIOMASS" in the corresponding reaction equation), or uptake or secretion reactions (external/boundary reactions; identified by chemical species associated with the artificial "BOUNDARY" compartment).


Import/Export

Select a model from the repository

MetaNetX.org includes a repository of models from, for example, BiGG or the Model SEED, networks from BioCyc, and metabolic pathways from UniPathway; all reconciled in a common namespace defined by MNXref.
The "Pick from repository" menu allows you to select one or more models from this repository. It is possible to search for specific models using the Search field. Search criteria can comprise taxonomy, lineage (that can be displayed using the show/hide button), or identifiers.

Upload your own model

The "Upload user model" menu allows a user to upload models in various formats (such as SBML or Excel) by following the detailed instructions. In the same way, a list of reactions constituting a metabolic model can be specified using the text field of the "Upload reactions" menu. Depending on the user's choice, these uploaded models can be automatically translated into the MNXref common namespace, for comparison purpose or, on the contrary, they can be kept unchanged if the goal is only to perform analyses on them.

Download

A model and its corresponding analyses can be downloaded by clicking on the model's name in the "My selection" summary table (NB: this table only appears when you have selected or imported at least one model). Here various export formats such as SBML, Excel, or tab-separated are available.

Visualize

Tables

Information concerning the models as well as results of analyses performed on them, are provided in the form of tables. All these tables follow the same scheme:
  • a header row: each column's content is shown by an abbreviation; on mouse over, a more detailed description of the column properties is provided.
  • a body: one line per item. For example, when selecting the reaction table for one or more models, each row corresponds to one reaction.
Elements within a table are typically links to additional information. For example, when clicking on an entry in the #reac column within the "My selection" table, a new table with information concerning the reactions of the previously selected model(s) is displayed. Similarly, clicking on the name of a chemical compound redirects to information describing the compound in more detail, like structure, chemical formula, or charge; it may also provide links to external databases.

The Show/hide field allows one to select or deselect columns to be displayed in a table. With increasing number of models or analyses, the number of columns increases. In this case, the column properties are abbreviated by the numeric model identifier or the analysis type followed by abbreviated analysis characteristics for the corresponding model.
To ease the inspection of large tables, each column can also be sorted in increasing or decreasing order by clicking on the arrows of the respective column headers. NB: it is possible to subsequently combine sorting orders.

All tables with a "Search" text field in the top left corner can be filtered. For example, the term "reversible" or the symbol "<==>" can be used to only display reversible reactions.

The "My selection" table

Once you have selected or imported at least one model to work on, a "My selection" summary table will be displayed at the top of each page. This table displays information about the models in the current workspace as well as information about the performed analyses or modifications: number of reactions, compartmentalized metabolites, decompartmentalized metabolites, compartments, and different types of completed analyses. Further details are typically accessible when following links. This either refreshes the bottom part of the site or redirects to a new page with the corresponding information. For example, when selecting BC (basic classification) it is possible to examine the basic model properties such as enzymatic, transport, or irreversible reactions in detail.
The Analysis column in the top table links to the basic model properties (BC) as well as to the performed analyses. Here, we currently distinguish between:
  • BC: basic classification
  • DE: dead end analysis
  • GCR: groups of coupled reactions
  • FBA: flux balance analysis
  • RKO: single reaction knockouts
  • PKO: single peptide or gene knockout

Furthermore, from this "My selection" table, it is possible to compare selected models with respect to reactions, metabolites, compartments, or performed analyses by choosing the respective Overall link. However, when looking at more than one model, the content of some column can be model dependent. For this reason, each selected model is assigned a short numeric identifier (for example, #1 or #2) and the header of the columns of the comparison tables refers to these identifiers. (NB: The link between the numeric identifier of a model and its name is provided in the "My selection" table). In these comparison tables, a "+" symbol denotes that the individual reaction, metabolite, ... is present in the respective model whereas the "-" symbol indicates that it is absent.

Applet

In addition to the tabular information, MetaNetX.org allows you to inspect metabolic networks dynamically using a Java applet. Each time the view in applet symbol is shown, the applet can be launched to visually inspect the corresponding element within its network context.

NB: The website and the applet are dynamically linked so that every time the applet symbol of a new object is clicked on within the website, this automatically updates the applet view by centering on the corresponding object. Similarly, adding or removing a model to your selection automatically adds or removes it from the applet view.

Analyze

MetaNetX.org allows you to perform various analyses (structural analyses and simulations) that are accessible through the "Analyze" section of the menu. A description of each analysis is available within its respective page. For each analysis, it is possible to select one or more models from the workspace simultaneously. The results of each analysis are displayed using a specific page for further inspection as soon as the analysis has finished. In addition, they can subsequently be inspected using the Summary/Delete view by selecting the respective analysis ID, for example, DE for dead end analysis, or by selecting, for example, the reactions or metabolites view where results are then displayed per reaction or metabolite (depending on the analysis).
NB: some analyses, like FBA, require both boundary reactions and a unique biomass reaction. If a model does not fulfill either of the requirements a warning message is displayed, or the user is requested to, for example, select a biomass reaction if more than one is associated with the given model.

Create/Modify

This section of the menu allows you to modify existing models or to create new models based on models in the workspace and on previously performed analyses. Hence, it is possible to create, for example, a consensus model or to reduce an existing model to its functional part only.
Not all types of modifications are accessible through this section. If you want to modify a model in detail, it is usually easier to export, modify, and re-import a model.