Gaggle Workspace   

Data Files  
Select an organism from the portal to see available data:
Network Portal Files - Select All | Group | Delete | Delete Unselected
NameType DescriptionOperations

User Files - Upload Data | Select All | Group | Open | Save | Delete | Delete Unselected
NameType DescriptionOperations
Gaggle Workflow

Modules

Workflows
KBase
Firegoose
Generic
Cytoscape
MeV

Workflow Canvas

This is your workflow canvas. Start adding workflow components from the left, open a saved workflow or read our quick start guide.

Workflow Help

Quick Start Guide

1  Start the Gaggle Boss by clicking on the Start the Boss link and click on the "Gaggle" link in the firegoose toolbar to connect to Gaggle.

2  Add workflow modules from left sidebar and connect them.

3  Select an organism to analyze if you would like to use Network Portal organisms in your workflow. This will automatically create necessary attributes specific for the selected organism. Otherwise you can leave this field unselected and enter your custom specifications for each module.

4  Click "Run" to start the workflow

Running custom workflows

If you would like to use your own cytoscape or mev files it is possible to create custom workflows. For the initial setup you will need to download and install custom workflow modules.

1  Install each goose by using the links on the left (if this is your first time). This will download the updated goose.

2  Start the Gaggle Boss by clicking on the Start the Boss link

3  Click on the Gaggle toolbar in Firefox and Connect to Gaggle

4  Drag and drop the goose you want into your workflow canvas

5  For each module (except firegoose), workflow will automatically capture path to the executable file in your computer if you open the module (cytoscape or mev) after the gaggle boss has already started.Alternatively, "Enter the url of the executable in your computer" e.g for cytoscape: "C:\Program Files\Cytoscape_v2.8.3\Cytoscape.exe" in Windows or "/Applications/Cytoscape_v2.8.3" in Mac OSX.

6  Select any subactions for your modules from the dropdown menu.

7  If your workflow requires additional files, enter path to data files in your desktop or on the web. For example, this could be link to the expression file in your desktop or web.

8  In order to connect to components in the workflow drag the circle from the input goose to square of the next workflow component

9  Save your workflow

Running the Workflow

1  Create a new workflow or open a saved one

2  Click "Run" to start the workflow

3  For Firegoose, this will open a new tab and will take you to the page you specified in your workflow

4  Select the type of the data you want for the next component from the Firegoose toolbar and select "Next"

5  Your data will be broadcast to the next component in your workflow and your next application or webpage will be opened.

6  For each workflow component you need to select specific data and click "Next"

Recording the Workflow

1  Gaggle can follow your actions and record them into your workflow for automated tasks

2  Before recording make sure that the Gaggle bos has started

3  Click on "Record" button to start recording

4  Create workflow and follow the steps to complete your analysis

5  Go back to your workspace and "Stop" your recording Once you are done

6  Workflow components and connections will be automatically created and placed into your workspace.

7  You can "Pause" workflow anytime

API documents for developing Boss and Goose that supports workflow

Sample

A sample workflow

Sample2

Another sample

Sample 4

windows version of Sample 3

Case 3

Assigning functions to hypothetical proteins

Case 2

Analyzing gene expression data

Case 1

Discovering detailed regulon information

6.21.13

Name:

Description:

Save as a new workflow

Do you want to login and save the workflow?

Do you really want to delete the workflow?

You haven't selected a data application method. Do you want to proceed?

Workflow finished. Do you want to execute the next one in the batch?

Do not ask for this batch

Configure the Path of Gaggle Geese Applications

There are two ways to configure the execution path of a goose:

    If you already know the path of the goose (e.g for cytoscape: "C:\Program Files\Cytoscape_v2.8.3\Cytoscape.exe" in Windows or "/Applications/Cytoscape_v2.8.3" in Mac OSX), simply add the path to the input field.

    Alternatively, Gaggle can automatically detect the path for you. Here is how it works: First, click the "Start Gaggle boss" button to start the boss. Next, start the goose application and connect to the boss. (most geese connect to boss automatically. MeV, however, needs to be connected manually) and that's it! The Gaggle boss will remember the paths for ALL the workflows.

How to Build a Workflow

Important: Go to the Java Test Page and verify that the version of your Java is at least Java SE 6 (or 1.6).

1. Install each goose by clicking the on the name of the goose in the "Modules" column. (If this is your first time). This will download the updated goose. You will need to install them for your application

2. Drag the box corresponding to the goose you want in your workflow and drop into the Workflow canvas.

3. For each goose "Enter the url of the executable in your computer" e.g for cytoscape: "C:\Program Files\Cytoscape_v2.8.3\Cytoscape.exe" in Windows or "/Applications/Cytoscape_v2.8.3/Cytoscape" in Mac OSX

4. Select any subactions or data you want to open.

5. Input the url (or path) to the data file to be opened by a the component.

6. In order to connect to components in the workflow drag the circle from the input goose to square of next workflow component.

7. Save your workflow.

Saved Workflows

You can save workflows into your personal workspace if you are logged in or you can save them into public workspace. Please remember that public workflows can be edited/deleted by others.

It is a good practise to provide a descriptive text for the workflow for future reference.

Clicking on the workflow title will bring workflow components into the canvas and will also list associated reports under the reports section.

The Gaggle Workspace

Important: Go to the Java Test Page and verify that the version of your Java is at least Java SE 6 (or 1.6).

The Gaggle Workspace Page consists of the following tabs:
1. The Dataspace Tab. User can capture data using Firegoose from heterogenous webpages (tutorial video here) or local files for cloud-based organization and storage of raw and processed data (tutorial video here). All the data is displayed in the Dataspace tab.

You should first select an organism from the "select organism" dropdown list. Data related to the selected organism will be displayed in two tables. First, the Network Portal Files Table. These files are automatically generated by the Network Portal. Usually they are Cytoscape network files and MeV analysis files. Second, the User Data Table. Users can upload any data related to the species and the files will be stored on the server. A video tutorial of uploading and organizing data can be found here. For each file, users can select from a list of actions from the dropdown list on each row of the tables to open, edit, and download the data file. Users can also select multiple data files and use the links on top of the table to save, delete, or group data. Tutorials can be found here.

In particular, users can group data by checking the checkboxes in the table and clicking the "Group" link on top of the tables. The newly generated group will be displayed in the "My Group" list on the right-hand side of the page. Users can select to open some or all the data in a group.

2. The Workflow Tab. The system automatically records data communication between various applications and generates workflows. Users can also manually create workflows by dragging and dropping workflow components to the canvas and connecting them to indicate directions of data communications. Users can save and rerun workflows on different data sets. A video tutorial can be viewed here.

3. The Save State Tab. It allows users to save the state of all open websites and desktop applications and reload the session later from any machine. A tutorial video can be found here.

4. The Session Reports Tab. Reports are automatically generated for workflows. A report consists of snapshots of each applications of the workflow after the workflow is finished. A video tutorial is here.

5. The History Tab. The page records the actions (e.g., open a data file, save/load states, etc.) triggered by users.

6. The Log Tab. The page contains debugging information. Users can send debugging information to us if they encounter problems.

7. An open API for community development.

How to Upload File to the Workspace

1. Select the target organism for which the files you want to upload. If you want the files to be available for all organisms, don't select any organism.

2. Click the "Browse" button and select one or more files you want to upload.

3. Type additional information in the "Description" box.

4. Select the type of files (MeV, Cytoscape, Generic) you are uploading. Later on, the files will be automatically opened by their associated applications if possible. For example, suppose you select "Mev Analysis File" as the type of a file, later on when you select the "Open" action in the User File table, MeV will be started automatically and the file will be opened.

5. You can upload application specific files as well as text(.txt) files that contain lists of genes. MeV files (.tsv) should look like the following:


Notice that the first column contains the gene names and the first row contains the name of the log ratios.

The text file include a list of genes. It should look like this:

Save/Load States

Users can save and load states. After clicking the "Save State" button, the Boss contacts each geese to save their current states (e.g., all the tabs opened in Firefox, and the associated gaggle data, all the networks opened in Cytoscape, all the expression files opened in MeV etc).

It generally takes about half to one minute to save the state. Once the state is saved, a new row will appear in the saved states table.

User can edit, delete, and load the saved states. After user clicks the "load" button, all the applications corresponding to the state will be automatically started and the state data will be loaded.

A tutorial video could be viewed here.

Workflow Report

A Workflow reports consists of snapshots of each application when workflow execution has finished. A sample report looks like the following and a video tutorial can be found here.

Broadcast Data Type

If you are opening a list of gene names (e.g., {DVU2025, DVU2028, DVU3038}, select "Namelist". If you are opening a file that contains a list of gene names, select "File".


Saved Analysis States  
Name
 Description Date Files Operations

Reports

Workflow Reports - Delete Selected
Name Workflow Date Operations

History


Log