Visualization of metabolic networks in VisANT

VisANT 5.0 supports the visualization of genome-scale and ecosystem-level metabolic networks. Each metabolic model will be encapsulated by an expandable metanodes. While expanded model metanodes display the complete metabolic network of single organisms, by collapsing the organism metanodes one can hide intracellular details, and view overall community structure and interaction.

Several file formats are supported (see: supported file formats). For example, you can build an ecosystem-level metabolic network by importing multiple COMETS model files into VisANT. However, it is highly recommended to working with a manifest. A manifest file is a plain text file which contains all required information for building a metabolic network. Users can assemble a manifest by himself/herself or use the one created by COMETS.

Different set of features will be enable depending on the supplied files. Here is a complete list

Features Required input file(s)
A. Visualization of a genome-scale metabolic network (without flux)
Option 1
  1. A manifest file
  2.  
Option 2
  1. A model file
B. Visualization of a genome-scale metabolic network (with flux)
Option 1
  1. A manifest file
Option 2
  1. A model file
  2. A flux file
Option 3
  1. A metabolic network from (A)
  2. A flux file
C. Visualization of an ecosystem-level metabolic network (without flux)
Option 1
  1. A manifest file
Option 2
  1. A layout file
Option 3
  1. Multiple model files
D. Visualization of an ecosystem-level metabolic network (with flux)
Option 1
  1. A manifest file
Option 2
  1. A metabolic network from Step (C)
  2. A flux file
Comparative Analysis
Option 1
  1. A metabolic constructed by step (B) or (D)
  2. The flux file(s)

Work with COMETS

By default, COMETS will not produce any output files. Be sure to enable ‘Write flux log’ in COMETS (see: http://www.bu.edu/segrelab/comets-e-coli-simulation-example/). A COMETS manifest (usually named COMETS_manifest.txt) will be automatically generated in the output folder after every run. To visualize the COMETS result in VisANT,

  1. click [Symbiosis] -> [Open] -> [Open a COMETS manifest file]
  2. Pick up the manifest file
  3. Decide if you want to visualize the flux distribution of the whole model world, or just the distribution in a specific location. If you choose “Load the entire world’, VisANT will average the flux distribution over the different spatial locations.
  4. VisANT will process the layout file, model file(s) and flux file, then and project the flux distribution onto the metabolic network.

Work with your own data.

The best way to import your own data into VisANT is to create a custom manifest file. Details of how to prepare a manifest file can be found in the supported file formats. A user defined manifest file should work as a COMETS manifest file. Alternatively, you may import your files one by one to build your own metabolic network from scratch. For instance, you can first import several model files to build a metabolic networks of a community and later on append an additional flux data to enable the dynamic flux visualization on your network.

Open/append a model file

The metabolic mode can be uploaded from a SBML file or a COMETS model file. To import a model file

  1. clock [Symbiosis] -> [Open] -> [Open/Append a COMETS model file]
  2. Select a model file (either a SBML file or a COMETS model file) from the open dialog.
  3. The metabolic mode will be imported and encapsulated by an model metanode.

You can repeat the above procedure to ‘append’ additional metabolic model to your existing network. Each new added metabolic mode will form a mode metanode and receives an unique ID from the system.

Open COMETS Layout file

COMETS layout file specifics the medium composition, the initial condition and the spatial information of a model world. A ecosystem level metabolic network can be built form a COMETS layout file. To important a COMETS layout file

  1. click [Symbiosis] -> [Open] -> [Open a COMETS Layout file]
  2. Pick up a COMETS layout file
  3. VisANT will process the layout file and corresponding models.

The resulting network doesn’t have any flux information. However, you may project the flux distribution into your existing network by importing a flux file.

Comparative analysis

You would be able to compare the flux distribution under different conditions or under different locations in VisANT. When performing a comparative analysis, there are two ways to show the differences.

  • By default, each edge will be divided into several segments. The number of segments will equal to the number of conditions/locations. Each segment represents the flux of corresponding conditions or locations, and the thickness of each segment is proportional to the amount of flux. The below figure shows an example where the red is for the condition X and the blue is for the condition Y. In this toy example, the flux in the condition X is stronger than the flux in the condition Y.
  • When the number of conditions/locations users want to compare is 2, users can choose to only show the difference of fluxes. In this representation, the edge thickness will be proportional to the differences between two (2nd condition/location - 1st condition/location).
  • To perform a comparative analysis

    1. Build a metabolic network (with the flux distribution).
    2. click [Symbiosis] -> [Compare] -> [Compare with the fluxes in another location] or [Compare with the fluxes in diff. condition].
      1. If you select [Compare with the flux in another location],specific the X-, Y- and Z-coordinate in the following dialog. Check [Show the differences of the fluxes] if you want VisANT to calculate the differences between two locations. Click the [Next, select a flux file] to go to the next step.
      2. If you select [Compare with the flux in diff. condition], you won’t be able to specific the X-, Y- and Z-coordinate in the following dialog. VisANT will compare the existing fluxes with the average fluxes over the different spatial locations in the second condition. Check [Show the differences of the fluxes] if you want VisANT to calculate the differences between two conditions. Click the [Next, select a flux file] to go to the next step.
    3. Select the flux file from the file choice dialog.
    4. The VisANT will process the flux data and build a comparative network.

    Customize the color code schema

    By default, when the flux distribution is available, VisANT will color the environmental metabolites based on the following rules

    To change the color code schema:

    1. Mouse over the “Properties” tab to open the “PropertySheets”
    2. Scroll down to the “COMETS Plug-in”
    3. Use the color chooser to change the color accordingly.

    Layout your metabolic network

    In VisANT 5.0, we implemented a special layout (named Symbiotic Layout) for the ecosystem level metabolic network. The new layout aims to reduce the network complexity and highlight the underlying metabolic exchanges which are biological relevant to community dynamics. To apply the Symbiotic Layout to your network, simply click [Symbiosis] -> [Symbiotic Layout]]

    The Symbiotic Layout only works when the number of model metanodes is equal or greater than two. For each model metanode, the internal metabolites and reactions, except the exchange reactions, will form two circles inside the model. The inner circle is metabolite and the outer circle is biochemical reactions. If there are only two model metanodes in the network, two models will be placed in the same line and the environmental metabolites connecting to both models will be placed in between two model metanodes. Other extracellular metabolites are placed on the external side of the model they are part of. If the network contains more than two model metanode, all model metanode will be arranged in a big circle, while the metabolites involved in the inter-species interactions will be in the middle.