Inputs

MIND json file:

Drag&drop one or more files to the network panel, or load the file(s) using the menu File-->Open.... The files can be any formats supported by the platform, including MIND data JSON format, as well as MIND worksapce JSON format that stores all the information of the workspace.

Microbe of interest:

Enter the name or taxonomy ID in the search box of the Toolbox. For the node already shown in the network, double-clicking will alos query its interactions.
Note: Auto-complete starts when the 3rd char is entered
Note: Use the enter or , to complete the name/ID.
Note: Uncheck the Search database to achieve the screen-only searching.

Network of interest:

The network can be searched by entering the keywords in the context search box, and the whole network for a givencontextcan be loaded by click the All button of the correspondingcontext in the Toolbox panel.

Outputs

MIND workspace:

Save the current workspace using the menu File-->Save the Network. The file allows user starting the analysis of the network based on what left last time.

SVG file:

Save the current network in the format of Support Vector Graph (SVG) using the menu File-->Export as the SVG File. SVG file save the network high resolution image.

Image file:

Save the current network in the format of PNG image using the menu File-->Export as the Image File.

Graph operation

Zooming:

Scroll mouse wheel to zoom in/out the network, or you may click the +/- button on the Toolbox (left side) to achieve the same operation.

Panning:

Drag the mouse with the right mouse key (press the right mouse key down and drag the mouse) to move the network around.

Reset:

Click the button Reset on the Toolbox to set the zooming and panning to the default size.

Fit the page:

Click the button    to fit the network to the size of graph panel. If the option Auto Fit on the Toolbox is on, the network will always fit to the page whenever the interaction is queried.

Selection

Single node:

Use the the left mouse-clicking to make single node selection.

Multiple nodes:

• Left mouse dragging over the area of interested nodes to make the selection.
• Hold the CTRL key and use left mouse-clicking to add/remove a node to the selections
• Use the menu Edit-->Select All Nodes to select all nodes of the current network
• Use the menu Edit-->Invert Node Selection to select nodes except current selection

Editing

Network deletion:

Click the Clear button on the Toolbox, or the menu Edit-->Remove All to delete all nodes and edges of the current network.

Node deletion:

• Use the menu Edit-->Delete Selected Nodes to delete all selected nodes
• Use the menu Edit-->Delete Nodes Have NO Links to delete nodes that have no links

Undo/Redo:

Use the menu Edit-->Undo to undo the previous operation; use the menu Edit-->Redo to redo the previous operation.
Note:Not all operations can be undo or redo, name of the specific opteration to undo/redo will be shown in the menu.
Note:The default Undo/Redo limit is 10, you can change it as part of global options at Options (near the Toolbox tag)

Nodes:

The size and color of the nodes, as well as the size and color of the node label, can be changed under the Options tag. Select the checkbox Label, or use the menu Nodes-->Label to turn on the label of selected nodes.
Note:The menu Nodes is activated when there is at lease one selected node.
Note:The change only applies to the selected nodes.
Note:The default node color is determined by its taxonomy ranking, which can be changed by clicking the color button of the corresponding ranking in the Toolbox panel.
Note:The default color of the node label is same as the as the one of the node.

Edges:

The color of the edges is determined by the context of the network, which can be changed by clicking the color button of the corresponding context in the Toolbox panel.

Global controls:

• The checkbox Tooltips in the Toolbox panel turns on/off the tooltips of nodes and edges when mouse-over them.
• The checkbox Labels on the Toolbox panel turns on labels of all nodes.
• The edge opacity can be changed by the field Edge Opacity under the tag Options
• The edge thickness can be changed by the field Edge Thickness under the tag Options
• The node opacity can be changed by the field Node Opacity under the tag Options

Layout

Force layout:

Use the menu Layout-->Force-directed to start the forace layout.
Note:The running time of force layout varies avvroding to the number of nodes and edges of the network, it stops automatically.
Note:You can activate force layout mutiple times
Note:The parameter alpha can be changed under Options tag. The layout will apply the change if force layout is running.

Circle layout:

Use the menu Layout-->Circle to start the circle layout. The layout puts all nodes around a circle with minimum radius without node overlapping.

Nodes

Taxonomy ranking:

The nodes can be filtered by their raxonomy ranking, uncheck the checkbox for each ranking will hide corresponding nodes.
Note:Check/uncheck the All will select/unselect all taxonomy rankings.

Oral microbes:

Integrated with eHOMD (expanded Human Oral Microbiome Database), the menu Filters --> Select Oral Microbes will select all oral microbes in the current network, making it easier for studies such as the transmission of microbes along the gastrointestinal tract.

Edges

Edge weight:

All edges are associated with a weight in MIND database. Edges whose weight is less than the value indicated by the Weight cutoff field in the Toolbox panel are invisible.
Note:Mind support context-specific weight cutoff, which can be found in the line for the corresponding context.

Number of links:

This filter hides the links if the number of visiable links between a pair of nodes is less than the number specified in the field Number of Links.

Context:

The edges can be filtered out by specific contexts, just uncheck the checkbox in the line of each context, all edges specified by the context will be invisible.

A context in MIND database basically is the combination of the network with its associated meta data. The context panel in the Toolbox list all contexts that are available in MIND database. In addition, when users load their own networks, the corresponding contexts will also available there. Follwing are the filters to help to find specific contexts:

Category:

MIND database separates all contexts into two categories: Human microbiome and Marine microbiome. More categories may coming in the near future.

Keywords:

Any words used in the context's metadata can be searched. And the search box supports auto-complete.

Conditions:

Contexts may be filtered by conditions. For Human microbiome, the condition points to the health state.

Interaction type:

Filter the contexts based on the type of interactions, e.g., co-occurrence correlation etc.

Habitats:

Filter the contexts based on the location where microbes live.

Carts:

Carts can be used to store your pick of contexts. If a user is logged in, the contexts picked by the user will be stored on-line.

Current contexts:

It is useful to find out contexts only involved in the current network, which can be achieved through the menu Filters --> Show only contexts in the current network.

Edge merging:

MIND database uses NCBI taxonomy ID as the primary key for microbes while OTU(operational taxonomic unit) are often used in microbial studies, resulting many different OTUs being mapped to the same taxonomy ID. Therefore it is often that there are many links between a given pair of microbes even under the same context. By default, these links are merged with their weight averaged. This can be changed in the Edge merging field under Options tag.

Abundance integration:

Each context may be associated with an abundance profile. By default the adundance button associated with the context is disabled. It will be enabled as if the adundance of the context is available. Click the button will map the node size to its abundance value, and the button will be changed to

Degree mapping:

The node degree (the number of links of the node) can be mapped to it size using the menu Edit-->Map Node Size to Its Degree.
Note:Abundance mapping has higher priority than the degree mapping.

Register:

Click the button Register on the Menubar and follow the instruction.

Login:

Click the button Login on the Menubar and follow the instruction

After the login, following functions will be available:

Cart:

The contexts stored in the cart will be saved in the server.

Network submission:

When a context is loaded in MIND-web by the user, the button associated with the the context will be replace by the upload button , and only the login user can submit the context to MIND server.

Online saving&sharing:

A login user may save the network on the server and may share the saved network to friends.