NetworkAnalyzer

Using the Help

Welcome to NetworkAnalyzer help!

To display information about NetworkAnalyzer, select topics in the index.

If the built-in help and built-in tutorials don't answer all your questions, please contact the development team at .

Networks

What is a Network?

A network is a hypothesis about how the systems-level behavior of a cell or cellular system arises from the physiochemical interactions of DNA, RNA, proteins, metabolites, ions, and other chemical constituents. More specifically, a network is a set of chemical components (biomolecules), a description of how those biomolecules interact, or regulate each other (edges), and a list of compartments in which those biomolecules exist. In addition, a network includes a description of how each biomolecule, compartment, and membrane should be drawn visually. Networks can be used to visualize and analyze experiments (see Experiment section), and can be exported to several formats.

Creating & Opening

To create a network select File⇒ New.

To open a network select File⇒ Open, highlight the desired network, and click Open.

Note: If another user with write permissions is currently editing the network, you will not be able to save any changes you make to the original network. In that case you will still be able to save changes to a new network.

Biomolecules

The application allows you to enumerate the proteins, genes, metabolites, and other chemicals in your hypothesis, specify their rendering styles, and annotate them with evidence. Biomolecules can be added in either the diagram of editor modes. To add biomolecules in editor mode, fill out the biomolecule form and click Add New. Biomolecules can be added in diagram mode by dragging the desired biomolecule style from the biomolecule toolbar.

Each biomolecule must have a unique name that contains only letters, digits, and underscores. Additionally, names may only start with letters, and cannot be the reserved names "null" or "undefined". Biomolecule labels support an HTML-style syntax for Greek characters, subscripts, and superscripts, eg.

Below is a table of all available Greek characters.

In editor mode, if the compartment of a biomolecule is modified, the biomolecule will be placed at the top left of the selected compartment. In diagram mode each biomolecule's compartment is automatically updated when the biomolecule is dragged.

In editor mode the name, label, rendering style, regulation, and comments of a biomolecule can be edited through the biomolecules form. A similar form can be accessed in diagram mode by double clicking on a biomolecule. See the next section for more information about regulations.

The regulation field allows you to describe interactions among biomolecules. In particular, the field allows you to use boolean algebra to describe how a biomolecule is regulated by other biomolecules. Edges are automatically drawn to the biomolecule from any biomolecule referenced in its regulation. Below are several examples of regulatory rules:

Biomolecule Styles

Biomolecule styles describe how a group of biomolecules should be rendered in diagram mode. Biomolecule styles include four attributes

• Name
• Shape
• Fill Color
• Outline Color

Note: Biomolecule style names must start with a letter and can only contain letters, numbers, and underscores. Additionally biomolecule style names cannot not be the reserved terms "null" or "undefined".

The following shapes are available:

7-Pass Transmembrane Receptor	ATPase	Centrosome	DNA	Flagellum	Golgi
Ig Receptor	Ion Channel	Mitochondrion	Pore	Y-shaped receptor	Circle
Diamond	Ellipse	Hexagon	House	Inverted House	Inverted Trapezium
Inverted Triangle	Octagon	Parallelogram	Pentagon	Rectangle	Septagon
Trapezium	Triangle

Compartments & Membranes

Compartments and membranes can be added, edited, and removed in both the editor and diagram modes using either the compartment form, the new component toolbar, or double clicking on a compartment. Membranes are similar to compartments, and are automatically created between pairs of compartments. Membranes inherit their rendering attributes from the preceding compartment. Compartments have five attributes:

• Name
• Compartment Color
• Membrane Color
• Membrane Phospholipid Body Color
• Membrane Phospholipid Outline Color

Biomolecule can be assigned to compartments either by dragging them in the diagram mode, or through the compartment combo box in editor mode.

Note: Compartment names must start with a letter and can only contain letters, numbers, and underscores. Additionally compartment names cannot not be the reserved terms "null" or "undefined".

Diagram Mode

The diagram mode displays an editable, graphical rendering of the current network. Diagram mode is the default editing mode.

To add a biomolecule to the network in diagram mode, drag and drop the desired style from the new biomolecule toolbar onto the diagram. After dropping the icon onto the diagram, a popup window will prompt you for the name, label, regulation, and comments of the new biomolecule.

In diagram mode, double clicking on a biomolecule opens a popup window which allows you to edit the name, label, style, regulation, and comments of the biomolecule.

Biomolecules can be repositioned by dragging them across the diagram; the compartment of each biomolecule will be automatically updated upon completion of dragging. To select, and then drag, cut, or copy multiple biomolecules hold either the shift or control keys while selecting biomolecules.

The currently selected biomolecules can be cut or copied from the diagram by selecting Edit⇒ Cut or Edit⇒ Copy. Similarly, to paste the last cut or copied biomolecules select Edit⇒ Paste.

To undo or redo any action select Edit⇒ Undo or Edit⇒ Redo.

The diagram can be panned either by dragging the diagram across the screen or by dragging the red rectangle in the overview window which indicates the currently visible portion of the diagram. To zoom in or out on the diagram select View⇒ Zoom from the main menu or use your mouse wheel.

To view the diagram in fullscreen mode select View⇒ Fullscreen from the main menu. In fullscreen mode, by default only the diagram is visible. Two toolbars are accessible in fullscreen mode by mousing over the top and bottom portions of the screen. Mousing over the top portion of the screen will reveal a toolbar with controls for zooming. Mousing over the bottom portion of the screen reveals a toolbar with play, pause, and stop controls. Editing is disabled in fullscreen mode.

The overview window displays a small preview of the entire diagram and indicates the currently visible portion of the diagram. Dragging the red rectangle in the overview window will pan the diagram across the screen. To toggle the overview window select View⇒ Overview.

To find a specific biomolecule by either name or label, open the find biomolecule popup window (Edit⇒ Find), enter the name or label of the biomolecule you wish to find, and click Find.

Editor Mode

Editor mode displays a form-based way to edit a diagram. Editor mode also displays several additional advanced rendering and animation options not available in diagram mode.

The advanced options tabs provides you with additional control over the rendering of a network:

Exporting & Importing

To export a network select File⇒ Export, and choose the desired export format. Note: The only importable export format is the XML. Additionally, networks can be transloaded from KEGG. To import a network select File⇒ Import.

The following export formats are available:

• Images
  • dot
  • gif
  • jpg
  • png
  • pdf
  • svg
• Animation
  • multipage pdf
  • swf
• Simulation
  • Boolean Simulation (m)
• Exchange Formats
  • BioPax
  • CellML
  • SBML
  • XML (can be imported)

Saving

To save a network select File⇒ Save, or Save As.

Note: Write privileges (see User Privileges & Publishing section) are required to save a network.

Renaming & Deleting

The Network Manager (Network⇒ Manage Networks) can be used to edit the names and descriptions of networks as well as edit user privileges over networks. The Network Manager can also be used to delete networks. See User Privileges & Publishing section for more information about user privileges.

Note: Write privileges are required edit a network's name or description; Owner privileges are recurred to edit user privileges or delete a network.

User Privileges & Publishing

User privileges are the way user access to networks is controlled to enable multiple users to view and edit networks.

Four privilege levels are defined:

• Owner — Can edit and save changes to a network as well as manager user privileges over the network and delete the network.
• Write — Can edit and save changes to a network.
• Read — Can only read a network. Cannot save changes to a network.
• None — Used to remove user privileges to a network.

User privileges to a network can be edited using the Network Manager (Network⇒ Manage Networks).

Note: Owner privileges are required to edit user privileges over a network.

At this time real-time collaborative editing is not supported. Collaborative editing is supported through network locking, whereby at any given time at most one user can edit and save changes to a network. All other users with privileges over the network will be blocked from saving changes to the network when a network is locked.

Publishing is a way to share a network with all registered users. All users have "Read"-level privileges on published networks.

Networks can be published and unpublished through the Network Manager (Network⇒ Manage Networks).

Experiments

What is an Experiment?

An experiment is a dataset of high-dimensional measurements of a biological system. One dimension of the dataset must correspond to biomolecules. The other dimensions may correspond to time points, individuals, cell types, and experimental conditions.

Currently, experiments can only be loaded from CytoBank, a public repository of flow cytometry data. Please contact to discuss integrating additional data sources.

Opening

To open an experiment with the current network, first open the Experiment Manager (Experiment⇒ Manage Experiments). Next select an experiment from the list on the left and associate biomolecules in the current network with experimental conditions and observed channels. Click Save to commit your changes. Finally, to open the experiment with the current network select Experiment⇒ Visualize Experiment and select the desired experiment from the list of linked experiments. A measurement will be opened according to the currently selected axes (see Configuring Axes section), and the network will be animated with experimental data.

Note: A CytoBank user account is required to load experiments from CytoBank. To create a CytoBank user account see CytoBank⇒ Creating an Account.

NetworkAnalyzer imports experiment statistics (median, mean, percentile, etc. fluorescent activity) from CytoBank for each population annotated in an experiment.

Configuring Axes

The Axes Manager (Experiment⇒ Configure Axes) should be used to link experimentally observed dimensions (conditions, populations, time points, etc) to specific diagram dimensions (biomolecules, animation, comparison-x,y), as well as select the desired scaling and normalization for an experiment.

The following diagram dimensions are available:

• Biomolecules — Linked to the channel dimension by default
• Animation
• Comparison-X,Y — Displayed as small heatmaps below each linked biomolecule (see Experiment⇒ Heatmap section)

NetworkAnalyzer can import the following statistics from CytoBank:

• Median fluorescence intensity
• Arcsinh Median fluorescence intensity
• 95th percentile fluorescence intensity

The following controls are available for each of the four diagram axes:

• First
• Last
• Minimum
• Maximum
• Mean
• Median
• None

Controls are applied to dimensions in the following order:

1. Comparison-Y
2. Comparison-X
3. Animation
4. Biomolecule

The following normalizations are available:

• Difference
• Log 10 ratio
• Raw

Similar to CytoBank, if a dynamic range is specified, the data is truncated to the that range. Otherwise the data is scaled to the maximum absolute value of the normalized values.

After scaling, normalization, and truncation to the dynamic range, each dimension (except time) of a dataset is clustered, and the optimal leaf order is computed to minimize variation between successive values of each dimension. Hierarchical agglomerative clustering is computed using Euclidean distance and average linkage (Eisen et al., 1998). Optimal leaf ordering is computed as described by Bar-Joseph et al., 2001.

References:

1. Michael B. Eisen, Paul T. Spellman, Patrick O. Brown, and David Botstein (1998). Cluster analysis and display of genome-wide expression patterns. Proc Nat Acad Sci USA. 95(25):14863-8.
2. Ziv Bar-Joseph, David Gifford, and Tommi Jaakola (2001). Fast optimal leaf ordering for hierarchical clustering. Bioinformatics. 17: S22-29.

The colormap controls the color mapping between experimentally observed activities of network components and their rendered colors. The following colormaps are available:

Animation

Animations can be played, paused, and stopped using the animation toolbar. The timeline in the animation toolbar can also be used to navigate to particular frames in the animation.

The frame rate and the repeat count can be controlled through the advanced options panel in the editor mode.

To export an experiment select File⇒ Export⇒ Animation. The following export formats are available:

• multipage pdf
• swf

For instructions on embedding Adobe Flash animations in PowerPoint see:

Heatmap

The heatmap provides an alternative and more traditional view of experimental data. To view the heatmap select Experiment⇒ View Heatmap. Mouse over the heatmap to view graphs of the underlying flourescence intensity distribution.

When comparison dimensions are selected in the Axes Manager (Experiment⇒ Configure Axes) data corresponding to those dimensions will be displayed in a small heatmap below each biomolecule. The visibility of comparison heatmaps can be toggled by selecting Experiment⇒ View Comparison Heatmap.

CytoBank

What is CytoBank?

Creating an Account

To create a CytoBank account:

Uploading Data

To upload flow cytometry experiments to CytoBank log into CytoBank, select Manage Experiments⇒ Bank New Experiment, and follow the on-screen instructions.

Accessing Data

Support

Credits

User Account, Privacy & Security

Logging In & Creating a User Account

Help, I Forgot My Password!

See OpenId⇒ Help, I Forgot My Password!.

Updating Your Personal Information

To update your name, email address, organization, or password select File⇒ User Account, edit the desired fields, and click Save.

Privacy

We promise never to distribute your private information including your email address, organization, and OpenId. Your name and principal investigator will be used to enable other users to share networks with you. This information is provided to users through the Network Manager.

Security

Users are automatically logged off after 60 minutes of inactivity. Until then, other users will be blocked from editing the user's current network.

See Networks⇒ User Privileges.

OpenIds

See OpenIds section.

OpenIDs

What is an OpenId?

OpenId is a free, open source authentication protocol for gaining access to various websites. OpenId eliminates the need to create and maintain multiple usernames and passwords across different websites, simplifying your online experience.

The OpenId protocol was initially developed by Brad Fitzpatrick, and is currently maintained by the OpenId Foundation. Over ten-thousand websites support OpenId, and over 160-million OpenIds have been issued.

Registering an OpenId

Help, I Forgot My Password!

Two of the benefits of using the OpenId protocol are that you don't need to remember another username and password to use this software, and that your OpenId provider maintains the security of your password. At the same time this means that we never see your password, and don't maintain a record of your password, and thus cannot send you password reminders. Please contact your OpenId provider for password reminders.

More Information

Credits