Introduction

caTissue OpenSpecimen Suite is the next-generation tissue banking application which integrates the functionality of the existing caBIG™ TBPT (Tissue bank and pathology Tools). The tool will make it easier for researchers to locate and analyze tissue specimens for use in cancer research that is based on tissue, clinical, and genomic characteristics. As part of the initial goal, the following three applications were developed in year 1 and year 2:

• caTissue Core: This application is used to track multiple specimens from the same patient or participant, create and track refined materials (RNA, DNA) that are used for molecular analysis, and distribute specimens.
• caTissue Clinical Annotations (CA): Stores and queries pathology annotations for breast, prostate, and melanoma cases. Future iterations would also cover other cancer types and information systems, for example, clinical pathology information systems, tumor registry, and so on.
• caTIES: Automates the process of coding, storing, and retrieving data from free-text pathology reports. caTissue Suite is an integrated system that can seamlessly perform tasks across the three applications mentioned above. All three applications have been independently developed and have their own UML (Unified modeling language) and data models. In addition, while caTissue Core and CAE are web based applications, caTIES is a Java thick client application. Thus, in the integrated solution, caTIES has been re-engineered to utilize the common object model and the existing caTIES user interface will be utilized for administrative functions. For example: QA or QC of de-identification and concept coding), and the essential functionality required for end user researchers will be provided through the integrated web interface.

Licensing

All caTissue , clinical, and genomic characteristics.Licensing

All OpenSpecimen source and pre-built binaries are provided under the caTissue OpenSpecimen Open Source License

The

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OpenSpecimen Community

The caTissue OpenSpecimen community exists primarily through discussion groups/forums, the issue tracker and, to a lesser extent, the source control repository. You are encouraged to contribute to the discussion and you can also help us to keep the effectiveness of the groups high by following and promoting the guidelines listed here.

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Showing courtesy and respect to others is a vital part of the NCI culture, and we strongly encourage everyone participating in caTissue OpenSpecimen development to join us in accepting nothing less. There's never a reason to be antagonistic or dismissive toward anyone who is sincerely trying to contribute to a discussion.

Where to Discuss

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OpenSpecimen

Refer to the discussion groups/forums. Specifically the caTissue OpenSpecimen development forum.

How to Report a Bug

See issue tracker for details on how issues are reported and tracked for caTissueOpenSpecimen.

Working with the Code

If you want to get your hands dirty with the code inside caTissueOpenSpecimen, the Community Code Contribution is the right place to start. 

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Testing is very important to maintaining the quality of caTissueOpenSpecimen. Unit Tests must be written for any new code, and changes must be verified to not break existing tests before they are submitted for code review. Please see sections below for a more detailed description of caTissue OpenSpecimen Testing approach.

Ensuring Code Quality

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You may use any IDE (or even a simple text editor) to do caTissue OpenSpecimen development. Please refer to the Community Code Contribution document for details about setting up the Eclipse environment.

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OpenSpecimen Architecture

The caTissue OpenSpecimen Technical Administration Guide describe the caTissue OpenSpecimen architecture. The guide focuses on administrative tasks associated with the use of caTissue OpenSpecimen Suite and mainly focuses on using the application program interface in the caTissue OpenSpecimen Suite application for data entry and query operations. New developers should read over the guide first to make sure they understand the big picture of caTissue OpenSpecimen development.

Contributing Code

As caTissue OpenSpecimen is open source, we're excited that to make it possible for our users to fix bugs and create new features, and we hope to get great patches from the community. Before you fire up your favorite IDE and begin hammering away at that new feature, though, please take the time to read this section and understand the process. While it seems rigorous, we want to keep a high standard of quality in the code base. Also, please be aware that the code contributors must sign a Contributor License Agreement before we can accept any code.

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