Center for Complexity and Self-Management of Chronic Disease (CSCD): Core 2: Methods and Analytics Progress (2014-2015)

The main 2014-2015 accomplishments of the Methods and Analytics core include: publications, infrastucrture and high-throughput data analytics.

I. Research Publications

PMCID: PMC4310910: This study examined cognitive decline in early-onset Alzheimer's Disease patients. Chronicity and complexity of cognitive impairment drive the need for development of innovative methods and protocols for fusing multi-source data to derive biomarkers that capture the progression of neurodegeneration and identify associations between neuroimaging, genetics and clinical observations. We developed a complex pipeline workflow protocol for modeling, analysis and visualization of the data and showed significant associations between genetics (e.g., SNP/rs7718456) and various morphometry measures of regional brain anatomy (e.g., left hippocampal volume).

II. Infrastructure

Deployed and continuously expanding the CSCD Center web-infrastructure.

III. High-Throughput Data Analytics Workflows

CSCD MACORE investigators develop efficient and reliable end-to-end computational workflow solutions for advanced data analytics (see CSCD shared resources). One example of such complex computational protocol is described below.

ISB TPP Pipeline Workflow

The Trans-Proteomics Pipeline (TPP) tutorial is shown below. We developed a distributed workflow, based on the Pipeline Environment that efficiently implements the TPP pipeline.


Workflow Protocol

These steps illustrate the complete pipeline users can follow to start the Pipeline client, load the Pipeline graphical representation of the TPP workflow, as a network, execute the workflow and retrieve intermediate and final results:

Read the TPP Documentation


Open a web-browser

Load the Pipeline TPP in your browser, or directly go to


Workflow Controls

Use the “View Source”, “Open”, “Download”, or “Run” options (bottom) to see, load, retrieve or start the TPP pipeline workflow (using guest-user credentials) on the LONI/INI/USC Pipeline Try-It-Now server.


Run the pipeline

Click the Run button to initiate the execution of the workflow. Depending on the server utilization, the workflow may take up to 2 hours to complete. See the times for completing each of the steps (modules) in the image below. Different modules will take different amount of time to complete based on the complexity of the processing they represent.


Workflow Interface

The Pipeline client user interface has three main components. The left hand panel contains a hierarchy of software tools and services already described within the environment. The main canvas displays the details of the pipeline workflow as a graph network showing the flow of data between nodes, which represent atomic or composite processing steps. The bottom horizontal panel contains the controls for starting (playing), stopping, and pausing a workflow execution, a server monitor, and sessions manager (important of multiple workflows are executed in parallel).


Inputs and Controls

The sample datasets used in the TPP tutorial are already available in in the pipeline server (or can be downloaded locally from the TPP web-site). These are represented by:


Monitoring Workflow Status

After initiating the workflow execution (by pressing the Run button) you will see visual clues illustrating the status of the execution. Moving Blue circles indicate ongoing execution, Green circles indicate complete execution of a module, Orange circles for incomplete jobs, or Red circles show failing execution.


Inspect the Results

To inspect intermediate, or final results of the workflow, right-click on a module and select “View Execution”. Then go to the Output Files and either Download or View the results.



Users can further share the pipeline workflow or its results with colleagues, as necessary.

Workflow Modification

Users can further modify the workflow by replacing specific processing steps with other software modules, generally modifying the protocol or expanding the workflow to include additional processing or analytic steps.

See also