CPAS Overview (v1.4)

The help topics in this section cover CPAS version 1.4.

CPAS is a set of web-based bioinformatics and project management tools to help scientists store, analyze, and share data from high-throughput experiments and clinical trials. To get started with CPAS, you'll want to be familiar with the following parts of the system:

Projects and Folders

CPAS organizes your data and information in a hierarchy of projects and folders. A project is the top level of organization in CPAS, and your CPAS system can contain any number of projects. Beneath a project, you can have any number of folders and subfolders to further organize your project. Projects and their folders show up in the left navigation page, and you can click on their links in the navigation pane or in the breadcrumb links at the top of the page to move up or down in the hierarchy.

In general a project corresponds to an area of work. For example, you might create a project for each study laboratory that is collaborating on your research. The CPAS security model allows you to secure a project or a folder, so that you can strictly control which users can access which parts of your project if you need to.

You can structure your project however you like; any project or folder can contain any CPAS module. In terms of how you design them, there's no difference between a project and a folder – either can display a Wiki page, or a message board, or the results of an MS2 run. So you can create as many folders as you need beneath your project, but you also don't have to create subfolders unless you have a need for further organization.

For more information, see Projects and Folders.

Modules and Web Parts

CPAS modules are the functional units which you can use to build your CPAS system. Modules store and display data and content. CPAS provides two types of modules: Bioinformatics Modules, which process, analyze, and display experiment data; and Project Management Modules, which provide collaborative features for sharing information.

When you install CPAS, all of the available modules are installed, but you only use the ones you need. To use a module, you add the user interface part of that module to a project or folder in CPAS. That user interface part is called a web part. The web part displays the data or information that's stored in the module and provides the user interface for working with it. You can think of a web part as a window onto your data.

Currently CPAS includes the following modules; others will be added in the future:

Bioinformatics Modules

  • Data Pipeline: The Data Pipeline module uploads experiment data files to CPAS. You can track the progress of uploads and view log and output files with more detail about the data’s trip through the pipeline, from file conversion to the final location of the analyzed runs.
  • Experiment Module: The Experiment module provides experiment annotation based on FuGE-OM standards. It defines the XAR (eXperimental ARchive) file format for importing and exporting experiment data and annotations, and allows user-defined custom annotations for specialized protocols and data.
  • MS2 Module: The MS2 module (also sometimes called the MS2 Viewer) provides MS2 data mining for individual runs and across multiple experiments. It supports multiple search engines, including X!Tandem, SEQUEST, and Mascot. The MS2 module integrates with existing analytic tools like PeptideProphet and ProteinProphet.
  • Study Module: The Study module manages parameters for human studies involving distributed sites, multiple visits, standardized assays, and participant data collection. The study module provides specimen tracking for samples collected at site visits.
  • Flow Cytometry Module: The Flow module manages compensated, gated flow cytometry data, and generates dot plots of cell scatters.
  • Mouse Models Module: The Mouse Models module tracks mouse samples for experiments, and links sample source information (e.g., breeding pair, cage, treatment date, genotype) to analysis results.

Project Management Modules

  • Announcements Module: The Announcements module is a ready-to-use message board where users can post announcements and files and participate in threaded discussions.
  • Wiki Module: The Wiki module provides a simple publishing tool for creating and editing web pages on the CPAS site. The Wiki module includes the Wiki, Narrow Wiki, and Wiki TOC web parts.
  • Issue Tracker Module: The Issues module provides a ready-to-use workflow system for tracking tasks and problems across a group.


If you're setting up CPAS for a group to use, then one of the first things you will need to do is to add users and specify their permissions for the resources in your project.

The CPAS security model lets you specify which users have access to which projects and folders. A given user belongs to a specific group, which has a designated set of permissions for a project or folder. When you set up your project, you should think carefully about which users should be able to view or modify the data in any given project or folder. The default security settings are conservative, so that if you do not modify them at first, your data will be protected from anonymous viewers.

It's a good idea to familiarize yourself with the CPAS security model if you are managing a project in CPAS. For more information, see the Security help topic.


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