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caArray is an open-source, web and programmatically accessible array data management system. caArray guides the annotation and exchange of array data using a federated model of local installations whose results are shareable across the cancer Biomedical Informatics Grid (caBIG™). caArray furthers translational cancer research through acquisition, dissemination and aggregation of semantically interoperable array data to support subsequent analysis by tools and services on and off the Grid. As array technology advances and matures, caArray will extend its logical library of assay management.
The initial generation of caArray (1.0) and subsequent point releases have provided the interface for sharing sample annotations along with the independent ability to upload and download data and programmatic data access via the MAGE-OM API and grid service. caArray 2 builds from this starting point by organizing the application around the natural workflow between investigators and the array labs that serve them, enhancing the user experience for storing and retrieving the data produced, and providing a simplified API for programmatic data query and access. For further description of the new features and improvements in caArray 2, please see Key Enhancements, below.
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Software and Documentation Links
Project Information for Developers
caArray 2 Installation at NCICB
While caArray 2 is available for local installation by any institution, the NCICB also maintains an instance of caArray for use by the community, available at https://webarchive.library.unt.edu/eot2008/20090131164926/https://array.nci.nih.gov. This instance provides the same functionality as software that is locally installed. In addition to the web application, the NCICB instance of caArray 2 provides programmatic data access via a Java API and grid service.
Key Enhancements
caArray 2 represents an important step in the evolution of caArray to address the requirements of the cancer research community.
Highlights of caArray 2 include:
- New User Interface and Navigation
The graphical user interface and the navigation through the system has been completely revised for caArray 2. Users have the ability to:
- Browse and Search through the repository for Experiments of interest. The search mechanisms lead to actionable results that are clear to the end user and incorporate their specific rights for the experiments.
- Submit and access array data and annotations based on a role-based workflow designed to support collaboration between Principle Investigators, Lab Administrators, Scientists and Statisticians. Serving as an foundation from which discrete workflow features will be added, caArray 2 provides the definition of the experiment, submission to a PI-directed and determined set of collaborators, and providing the results. The end-to-end states of an experiment are: Draft, In Progress, and Public.
- Upload, validate, and import single files or a set of zipped files. The workflow allows for the effort to be spread over time and in synch with the way work is performed in the lab but also offers the ability to perform bulk uploads of annotation and experiment data.
- Control the public visibility of an experiment. One can make Public the entire contents of an Experiment or limit public visibility to a defined set of Samples within an Experiment.
- Java API and Grid Service
The caArray Java API and corresponding caGrid service have been significantly modified for Version 2, based on feedback from the caArray API users. Both interfaces provide access to the following services: the caArray Search Service, the Data Retrieval Service, the Array Design Details Service and the File Retrieval Service. In addition, client applications can access data via domain objects packaged in the client.jar.
- MAGE-TAB support
MAGE-TAB files – IDF, SDRF, ADF – can be imported to allow bulk upload of experiment annotations and associated array data files. The original MAGE-TAB files are stored in the system intact and are available for download.
- Installation
caArray 2 provides a simplified approach to installation on Linux and Windows platforms. Much of the installation process has been automated such that, if you accept the default values, you can install caArray by typing a single command. With the exception of the database, all supporting tools are automatically installed and configured as part of the installation. The installation provides additional diagnostics to better ensure the efficacy of the installation.
External Technologies and Standards Used by caArray 2
caArray 2 leverages the following technologies and standards:
- caGrid 1.2: The Introduce Toolkit provided by caGrid was used to generate the caArray grid service
- Common Security Module (CSM): used to supply authentication, authorization and user provisioning for caArray 2.
- MIAME: Minimum Information About a Microarray Experiment that is needed to enable the interpretation of the results of a microarray experiment and potentially to reproduce the experiment.
- MAGE-TAB: A tab-delimited, spreadsheet-based format to annotate and communicate array data in a MIAME-compliant fashion.
- MGED Ontology: Ontology for describing samples used in a microarray experiment
User Information
Subscribe to the caArray Users Listserv for regular updates on caArray releases and information about caArray Users Group meetings.
Contacts
Juli Klemm - caArray Product Manager - NCICB
Anand Basu - Director, Applications Engineering - NCICB
Previous Releases
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