caTissue Core v1.2.2 (LSD) Overview

1. caTissue Core v1.2.2 (LSD) Overview caTissue eLearning Materials May 2008

2. Session Overview • Training Topic Statement This section of the training provides an overview of caTissue Core. • Target Audience This training program is designed for: • Directors of tissue banks • CIOs of cancer centers • Senior management team of tissue banks • Training Prerequisites • The user should be familiar with basic cancer related terminology and tissue bank related activities • The user should have basic computer literacy

3. Session Goals By the end of this training, you will: • Gain high level introduction to caTissue Core • Be able to evaluate caTissue Core based on your tissue bank requirements

4. Contents Chapter 1: Introduction Chapter 2: Getting Started Chapter 3: Administrative Data Chapter 4: Biospecimen Data Chapter 5: Query Chapter 6: Sharing Data Over caGrid Chapter 7: Hardware and Software Requirements Chapter 8: Release History Chapter 9: References and Current Adopters Chapter 10: Support Information

5. Chapter 1: Introduction In this topic, you will be introduced to: • The basic overview of caTissue Core. caTissue Core is a web-based application for: • Managing biospecimen inventory • Tracking biospecimen related activities • Adding basic annotations The adjacent image outlines the basic features of caTissue Core.

6. Chapter 2: Getting Started In this topic, you will be introduced to: • The terminologies used in caTissue Core • The simple caTissue Core workflow • The various role-based users and the tasks performed by them • The functional block diagram that outlines the tasks performed by various role-based users • The publicly available demo site • The login details to access the caTissue Core application • The user interface organization of the application

7. Chapter 2: Getting StartedTerminologies The following table outlines the terminologies used in caTissue Core:

8. Chapter 2: Getting StartedSimple caTissue Core Workflow The following diagram outlines a simple caTissue Core workflow:

9. Chapter 2: Getting StartedUser Roles The following table outlines the various user roles and the tasks performed by them:

10. Chapter 2: Getting StartedFunctional Block Diagram The following diagram outlines the tasks performed by various users:

11. Chapter 2: Getting StartedPublic Demo Site The following image displays the home page of the caTissue Core application. Visit the home page and access the publicly available demo sites.

12. Chapter 2: Getting StartedLogin Details The demo site provides you with the publicly available caTissue Core application. You can use the following login details to access the site and familiarize yourself with the various features. • Demo Site URL: http://testserver3.wustl.edu:8080/catissuecore • Login: admin@admin.com • Password: Login123

13. Chapter 2: Getting StartedUser Interface Organization • The application is categorized into the following tabs: • Administrative Data Tab: This section is used by the Administrators • Biospecimen Data Tab: This section is used by the Technicians and Supervisors • Search Tab: This section is primarily used by the Scientists The following diagram outlines the organization of the application:

14. Chapter 3: Administrative Data In this topic, you will be introduced to: • The functional outline of the Administrative Data tab • Collection Protocols • Storage Containers • Storage Container Maps Although the Administrative Data tab comprises of features like adding Users, Institutions, Departments, Cancer Research Groups, and so on; this presentation covers only the important topics like Collection Protocols, Storage Containers, and Storage Container Maps.

15. Chapter 3: Administrative DataFunctional Outline of the Administrative DataTab You can perform Administrator specific tasks using the Administrative Data tab. For example, setting up new user accounts, creating collection protocols, setting up storage hierarchy, and so on. The adjacent diagram outlines the actions you can perform using the Administrative Data tab. • Actions • Add or Approve Users • Add or Edit Sites • Add or Edit Institutions • Add or Edit Departments • Add or Edit Storage Types • Add or Edit Storage Containers • Add or Edit Collection Protocols • Add or Edit Distribution Protocols

16. Chapter 3: Administrative DataCollection Protocols A Collection Protocol contains a set of guidelines that describes what, how, and when the biospecimens are to be collected. The following diagram outlines the caTissue Core Collection Protocol structure:

17. Chapter 3: Administrative DataStorage Containers A Storage Container represents a physically discrete repository that is used to store specimens, specimen arrays, or other containers. Storage Containers examples include: -80º C freezer, liquid nitrogen freezer, -20º C freezer, 4º C freezer, and so on. The following workflow outlines the steps involved in creating a Storage Container:

18. Chapter 3: Administrative DataStorage Container Map The Storage Container hierarchy is viewed using the map feature. The following diagram outlines the Storage Container hierarchy:

19. Chapter 4: Biospecimen Data In this topic, you will be introduced to: • The functional outline of the Biospecimen Data tab • The Collection Protocol based view • The biospecimen data workflows

20. Chapter 4: Biospecimen Data Functional Outline of the Biospecimen DataTab • You can perform Supervisor and Technician specific activities using the • Biospecimen Data tab. This tab allows: • Supervisors to register participants to Collection Protocols • Technicians to perform steps associated with biospecimen management and accessioning • The following diagram outlines the actions performed using the Biospecimen • Data tab. • Actions • Add or Edit Participants • Register Participants • Add Specimen Collection Groups • Add Specimens • Derive and Aliquot Specimens • Add Event to Specimens • Distribute Specimens and Specimen • Arrays

21. Chapter 4: Biospecimen DataCollection Protocol Based View • It is convenient to add biospecimen data using the Collection Protocol • based view, also known as the CP based view. The CP based view: • Displays hierarchical information of the participant and biospecimen • Allows free-flowing navigation • Provides visual clues while performing complex workflows within a tissue bank

22. Chapter 4: Biospecimen DataBiospecimen Data Workflows The following diagrams outlines a high level overview of the various workflows performed using the Biospecimen Data tab of the caTissue Core application:

23. Chapter 5: Query In this topic, you will be introduced to: • The functional outline of the Search tab • The overview of the Query functionality • A simple query • An advanced query • The actions you can perform post display of results like defining a view, exporting data to Excel, and so on

24. Chapter 5: QueryFunctional Outline of the Search Tab The Query tab is primarily meant for Scientists to search specimens of interest. Using the Query feature, a user enters the query parameters and the system returns a matching result set. The following diagram outlines the actions that are performed using the Search tab: • Actions • Simple Search • Advanced Search • Shopping Cart • Export Results

25. Chapter 5: QueryOverview of the Query Functionality The Query feature is comprised of Simple Query and Advanced Query. The following diagram outlines the available query types.

26. Chapter 5: Query Simple Query A simple query is performed as outlined in the following diagrams: Perform Simple Search View Simple Search Results

27. Chapter 5: Query Advanced Query An advanced query is performed as outlined in the following diagrams: Perform Advanced Query View Advanced Search Results

28. Chapter 5: QueryActions Performed on Query Results Once the result set is displayed, you cancontinue to: In Advanced query, the “Add To Cart” button allows you to add the searched specimens to the “Shopping Cart”.

29. Chapter 6 – Sharing Data Over caGrid In this topic, you will be introduced to: • The caGrid features offered by caTissue Core. These features are: • Share your data on caBIG™’s caGrid infrastructure using this version of caTissue • Query data from your instance by any valid caGrid user once the grid node is deployed • Provision Grid Users: • Any valid grid user can query for data • All the grid users are statically mapped to a single caTissue user (for example, cagrid_user@wustl.edu) • The data access over the grid can be controlled by assigning or revoking privileges to the caTissue user

30. Chapter 7: Hardware Requirements In this topic, you will be introduced to: • The hardware requirements for installing caTissue Core. • The hardware configuration depends on: • The number of concurrent users • The size of the database, that is the number of participants and specimens • Suggested configuration for a test instance, new tissue bank, small tissue banks, that is with ~5K patients and ~20K specimen: • One Windows XP, Linux, or Solaris machine (any one OS) with 2 GHz CPU, 2 GB RAM and 20GB free space for caTissue • You can deploy both database and JBoss web server on the same machine

31. Chapter 7: Hardware Requirements (continued) • Suggested configuration for big tissue banks, that is 5 to 10 concurrent users, 25K patients, and ~250K specimens: • Dual server architecture: one dedicated server for database and another server for web application • Two Windows XP, Linux, or Solaris machines with 2x2 GHz CPUs (dual processor), 4 GB RAM, and 40GB free space for caTissue

32. Chapter 8: Release History In this topic, you will be introduced to: • The release history of caTissue Core and caTissue Suite. • caTissue Core 1.0 - Mar 06 • caTissue Core 1.1 - Feb 07 • caTissue Core 1.2 - May 07 • caTissue Core 1.2.2 – TBD • caTissue Suite 1.0 – April 08 • caTissue Suite 1.1 – Scheduled to be Sep 08

33. Chapter 8: Release History (continued) The following diagram outlines the release history of caTissue Core and caTissue Suite.

34. Chapter 9: References and CurrentAdopters In this topic, you will be introduced to: • References and adopters that will help you in obtaining more information on caTissue Core. • https://wiki.nci.nih.gov/display/TBPT/caTissue+Collaboration+Wiki: This wiki link allows users and developers of caTissue to post questions and share tips about its deployment and use • https://gforge.nci.nih.gov/forum/forum.php?forum_id=766: This link provides you with a forum for discussion on caTissue questions

35. Chapter 9: References and Current Adopters(continued) • https://cabig.nci.nih.gov/tools/catissuecore#early: This link gives you a brief introduction to the caTissue Core application. It provides you with links to the User Guide, Deployment Guide, and some training material. You can also download the installable zip file for caTissue Core v1.2.1 • https://cabig.nci.nih.gov/workspaces/TBPT/biospecimen-data-directory/: This link allows you to view a list of all the adopters

36. Chapter 10: Support Information In this topic, you will be introduced to: • The available and soon-to-be available support information. The following list outlines the available support for caTissue: • Participation in the Tissue Banks and Pathology Tools Workspace (teleconferences, forums, email listserv, and Face-to-Face meetings) • The NCICB Applications Support (ncicb@pop.nci.nih.gov) is available now and can provide basic application support as well as help you find links to training and documentation • caTissue section on the caBIG™ Wiki that is in the process of being populated by caTissue users at all stages of adoption

37. Chapter 10: Support Information (continued) The following list outlines the support for caTissue that will be shortly available: • caTissue training materials (to include videos and train-the-trainer packages) will be available by early June through the caBIG training portal • caBIG™Knowledge Centers which will serve as the nexus of comprehensive support for caBIG tools • caBIG™ Service Support Providers that will provide multiple categories of for-fee support • Help Desk Support • Developing and Retaining caBIG™Compatibility • Deployment Support for caBIG™ Software Applications • Documentation and Training Materials and Services