Interaction/Pathway/Network data with various formats can be directly imported into VisANT, either copy/paste (CTRL-C/CTRL-V) the data into Your Data Text Area in the ToolBox Panel in VisANT, or directly load them from a local file (for local application and web start only). Different formats are recognized by VisANT automatically, here is the list of supported format:

To ensure the performance, except for VisML, the Fine Arts option under Option Menu will be turned off when the total size of nodes and edges > 12000. You can, of course, turn this option back on if necessary.


One nice feature of KGML is that it keeps the visual properties. However, the name of the nodes will need to be resolved using the MetaGraph-->Resolve All Nodes Name menu (NOT  the Nodes-->Resolve Selected Nodes Name menu because there are many nodes hidden in collapsed metanode) when data integration is required, such as the case where expression data need to be mapped to the nodes. Here is a macro file illustrates the steps to use KEGG pathway for expression enrichment analysis. Click here to try out.


hsa04310 [ xml | graphics ] Wnt signaling pathway. Click the graphics will load the KGML of the pathway at http://www.genome.jp/kegg/xml/hsa/hsa04310.xml


Please contact VisANT@zlab.bu.edu if you find bugs.


Tip: a KEGG pathway can be easily loaded into VisANT if the searched term starts with the "map", such "map04110" where 04110 is the pathway id (cell cycle pathway), the pathway for the current species will be loaded into VisANT. VisANT supports many different ways to load KEGG pathway, which are detailed in our publication VisANT 3.0: new modules for pathway visualization, editing, prediction and construction.


VisANT has primary support of GML. Here is a GML example file, it can be loaded into VisANT directly, here is the network looks like:




Here is a macro file that will loop through 5 GML files for animation purpose,  Click here to try out.

Note: per user request, VisANT renders the shape circle in GML with VBALL shape, as shown above.

Please contact VisANT@zlab.bu.edu if you find bugs, or you have suggestions/comments.


The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification. The PSI-MI format is a data exchange format for protein-protein interactions.


VisANT supports importing of PSI-MI data file. Here are two sample files in the format PSI-MI 1.0:
psi_sample.xml   Load this file in VisANT    |   Ito_expand.xml    Load this file in VisANT
Here is a sample file of PSI-MI 2.5:
BIOGRID-GENE-113010-2.0.32.psi25.xml   Load this file in VisANT

Please contact VisANT@zlab.bu.edu if you find bugs.
Note: if the interaction involves two interactors that belong to the different organisms, it will be ignored in the current implementation.

BioPAX is a collaborative effort to create a data exchange format for biological pathway data. VisANT supports importing data file of BioPAX format, both Level 1 and Level 2.


Level 1:BioPAX Level 1 represents metabolic pathway information. Here are two sample files (so far our parser only supports BioPAX file with only one pathway, we are working on to enhance it) :


The right show the result of VisANT visualization of this short demo provided by BioPAX group, which involves two pathway steps: the first step invloves two small molecules for both reactors and products, which are grouped to indicate this situation. The biochemical reaction is catalyzed (activation) by protein glucokinase; while the 2nd step only involves one reactor and product, and is catalyzed by protein phosphoglucose. All the participants are grouped into one pathway group. biopax-short-demo-pathway.owl   Load this file in VisANT  



The is a real pathway from BioCyc, which enable us to examine the VisANT visualization schema of BioPAX pathway. The detailed annotation of the comparison is shown in the right figure, click on the image to get the full-size one in a new window. biopax-example-ecocyc-glycolysis.owl  Load this file in VisANT original pathway in BioCyc


We apply the graphic annotation similar to KEGG pathway. For a given bio-chemical reaction A ---> B, if a catalysis C is presented, then the reaction will look similar to A ---> C ---> B. Same rule has been applied to modulation.

The pathway's layout is based on their pathways steps using a top-down manner. If there are more than one reactors/products in one Biochemical reaction, they are grouped; if one of the reactors is also one of the products in the previous pathway step, it is duplicated and grouped separately. For example, for two given reactions: R1+R2 ---> P1+P2, and P1+R3 ---> P3, then R1 will be grouped with R2, and P1 will be grouped with P2, P1 is then duplicated and grouped with R3. Each modulation and catalysis is counted separately.

Level 2:BioPAX Level 2 expands BioPAX to cover molecular interactions which are compatible with PSI-MI format supported by VisANT. In addition, the featured invention of Meta-Network in VisANT makes it nature for us to support unique features of BioPAX Level 2, including Pathway Hierarchy and Black-Box pathway. In fact, VisANT is so far the only network software that is capable to support visualization of network hierarchy. However, because Level 2 has not been finalized yet, sample files are not available. We are contacting BioPAX group in an effort to get earlier release of sample files.

Please contact VisANT@zlab.bu.edu if you find bugs.


The simplest format for network in VisANT, can also be used to create new nodes (one node per line, such as ste4 below) and edges. Users can simply enter or copy/paste text in the Add textbox in VisANT's toolbox and click the Add button to add a list of edges/nodes. This simple format also supports creation of Meta-Node, and a sample is listed below:

YAL054C YLR153C 0 M0020
YAL054C YLR153C 0 M0031
YAL054C YLR049C 0 M0034
YAL054C YHL043W 0 M0046
YAL054C YNL189W 0 M0034
YAL054C YMR280C -1 M004
YAL054C YBR117C 0 M0046
YAL054C YDR216W -1 M004
YAL054C YBR046C 0 M0036
YAL054C YBR049C -1 M004
YAL054C YER061C 0 M0036
YAL054C YDR207C -1 M004
YAL054C YHR041C 0 M0034
YAL054C YKL112W -1 M004


ste4
#complex M4453
YAL054C YLR153C YLR049C YHL043W
#group xx2323
YAL054C YLR049C YHL043W
#group
YBR049C
YER061C
YHR041C
#group myGroup
YER061C
YDR207C
YHR041C


Copy/paste above sample data to the Add textbox and click the Add button, then do a circle layout with the Layout-->Circle* menu and then click the Fit to Page button, a metanetwork will be shown similar to the one shown below:



VisANT supports the weighted edge, and a complete line of a weighted edge includes 5 columns:

Node_1 Node_2 direction Method_id Weight

Here is an example:

YAL054C YDR207C 0 M0037 0.263304413189123


Above line represents a weighted binary interaction between node 1 (first column) and node 2 (second column). The integer in the third column represents the direction of the interaction, i.e., 0 signifies an undirected link, 1 indicates that the link has a direction from node 1 to node 2 (we support KEGG notation for edge type, try out number 0-9 to see different type of edge), and negative sign "-" indicates the direction is from node 2 to node 1. The forth column represents the method id as can be viewed from method table in VisANT. The user can also add their own method in VisANT. The last column indicates the weight of this edge.

 

Starting from V5.16, the Edge-List supports the specification of node type as shown below:


			R00001[reaction]
            D08559[drug] ESR2 2 M6001
            D08559[drug] ESR1 2 M6001
            C02174[compound] R00001[reaction] 1 M6002
            R00001[reaction] C00404[compound] 1 M6002
            R00001[reaction] C00001[compound] 1 M6002
			
The default node type is gene\protein. The available node types include compound, drug, complex, reaction, disease. therapy, and more will come in the future. As always, above data can be copy/paste to Add text field for quick teste.


If you forgot the format, simply export a network in the format of edge-list using the File-->Export as Tab-Delimited File-->All menu.

VisANT 5.0 supports the visualization of genome-scale or ecosystem-level metabolic networks. The involving formats are listed below:

Manifest File (optional)

This file specifies all files required for building a metabolic network, especial for the networks involving multiple models. VisANT will load files and build a network accordingly. It is highly recommended to have a manifest file for your data. Two types of manifest files are supported: COMETS manifest file and VisANT FBA manifest file. Both are a simple text file enumerates the files and attributes required for the data visualization. Each row indicates a property-file(s) or property-value(s) pair separated by a colon. When a property is associated with more than one files or values, then the files or values must be separated by a single space. The first line of the VisANT FBA manifest file must be

#!FBA_Manifest

Here is an example:
#!FBA_Manifest
ModelFileName: model_CSP.mod model_CSP.mod model_2.mod
ModelLabel: model1 model2 mode3
FluxFileName: flux.txt

The required properties are

The optional properties are

Property Value
ModelFileName A list of model files separated by a single space. VisANT accepts
  • Simple file name: model_CSP.mod
  • Absolute path: /home/user1/models/model_CSP.mod
  • Relative path: ../../model_CSP.mod
  • URL: http://yourdomain.edu/models/model_CSP.mod
ModelLabel A list of model names separated by a single space. A model name must be unique and the order of the names here must match the order of files that you specified in the ModelFileName.
FluxFileName The flux file.

 

VisANT also supports formats specified by COMETS software. A COMETS manifest file is auto-created by COMETS and usually named as COMETS_manifest.txt, which can be directly imported into VisANT. Here is an example of the COMETS manifest file


LayoutFileName: petri_dish_circles.txt
ModelFileName: model_CSP.mod model_2.mod
FluxFileName: flux_log_20140404155741.txt

Notes: be sure all file paths are correct.

Model file (required)

Model files define the metabolic models. VisANT supports two different file formats,

 

SBML

Each SBML file only specifies one metabolic model, it is therefore highly recommended to use manifest file if your network have more than one models. VisANT uses JSBML library to process the SBML file. In order to keep VisANT light-weighted, this function is implemented at the server side. Therefore VisANT need internet access to process SBML files. Here are two examples:


Download this SBML file. Try out: Applet | Java Web Start.



Download this SBML file. Try out: Applet | Java Web Start.

 

COMETS Model File.

 

When working with COMETS, it is highly recommended to use the COMETS Model Files COMETS Model Files format description (http://www.bu.edu/segrelab/comets-metabolic-model-files/) Scripts for converting COBRA and SBML formats into COMET Model format http://www.bu.edu/segrelab/comets-utility-scripts/

Layout file (optional)

VisANT support COMET Layout Format: Layout Files format description (http://www.bu.edu/segrelab/comets-layout-file/). This file provides the basic information of the model world such as the grid size, extracellular metabolites etc. When a layout file does not exist, VisANT will use the information in model files to render your data.

Flux file (optional)

VisANT supports two different file formats, COMET Flux file and simple tab-delimited text file. Again, when working with COMETS, it is highly recommended to use the COMET Flux file.

COMET Flux file:

2D
fluxes{timeCycle}{Xlocation}{Ylocation}{model#} = [flux_of_reaction_1 flux_of_reaction_2 ... ];
Example:

fluxes{1}{16}{21}{1} = [0 0 -9.6E-6 -2.1E-2 0];
fluxes{2}{16}{21}{1} = [0 7E-6 0 7.3E-4 3.2E-6];
fluxes{3}{16}{122}{2} =[4.7E-8 1.6E-4 5E-2 6E-8 2.7E-9];
fluxes{3}{16}{122}{3} =[2E-3 5E-3 6.8E-8 5.7E-9 -7.6E-2];
				
3D
fluxes{timeCycle}{Xlocation}{Ylocation}{Zlocation}{model#} = [flux_of_reaction_1 flux_of_reaction_2 ... ];
Example:

fluxes{1}{16}{21}{1}{1} = [0 0 -9.6E-6 -2.1E-2 0];
fluxes{2}{16}{21}{2}{1} = [0 7E-6 0 7.3E-4 3.2E-6];
fluxes{2}{16}{71}{1}{2} = [-6E-9 0 0 5E-3 ];
fluxes{3}{16}{122}{2}{2} =[4.7E-8 1.6E-4 5E-2 6E-8];
fluxes{3}{16}{122}{1}{3} =[2E-3 5E-3 6.8E-8 5.7E-9 -7.6E-2];
				

Tab delimited flux file:

A simple tab delimited text file which contains the flux values of reactions in a matrix format. Each row includes a model name (specified in the manifest file), a reaction name, x-coordinate, y-coordinate, z-coordinate and then following by a series of flux values separated by tabs. For example:


model_1	reaction_1	16	21	1	0	0	0
model_1	reaction_2	16	21	1	0	0	0
model_1	reaction_3	16	21	1	-9.6E-6	0	0
model_1	reaction_4	16	21	1	-2.1E-2	0	0
model_1	reaction_5	16	21	1	0	0	0
model_1	reaction_1	16	21	2	0	0	0
model_1	reaction_2	16	21	2	0	7E-6	0
model_1	reaction_3	16	21	2	0	0	0
model_1	reaction_4	16	21	2	0	7.3E-4	0
model_1	reaction_5	16	21	2	0	0	0
model_2	reaction_1	16	71	1	0	-6E-9	0
model_2	reaction_2	16	71	1	0	0	0
model_2	reaction_3	16	71	1	0	0	0
model_2	reaction_4	16	71	1	0	5E-3	0
model_2	reaction_1	16	122	2	0	0	4.7E-8
model_2	reaction_2	16	122	2	0	0	1.6E-4
model_2	reaction_3	16	122	2	0	0	5E-2
model_2	reaction_4	16	122	2	0	0	6E-8
				

Metabolites Excluding List (optional)

This file provide a simple list of metabolites which are highly connected or uninteresting. They will be excluded and not shown in the output network. The file format consists of one line per metabolite, each containing the name of metabolite used in the model files. Here is an example:


cpd00002
cpd00008
cpd00063