caTissue Suite v1.0 Overview caTissue eLearning Materials May 2008

Training Topic Statement This section of the training provides an overview of caTissue Suite. 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 Session Overview

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

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

In this topic, you will be introduced to: The basic overview of caTissue Suite  caTissue Suite is a tissue banking application, which integrates the functionality of the existing caBIG™ TBPT (Tissue Bank and Pathology Tools). The three applications, outlined in the following diagram, developed by the TBPT Workspace are integrated with caTissue Suite Chapter 1: Introduction

In this topic, you will be introduced to: The terminologies used in caTissue Suite The simple caTissue Suite workflow The overview of the application 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 Suite application The user interface organization of the application Chapter 2: Getting Started

The following table outlines the terminologies used in caTissue Suite: TerminologyDefinition ParticipantAn individual from whom biospecimens are collected. Collection ProtocolA set of attributes that dictate how biospecimens can be collected. Participant Protocol RegistrationThe registering of a participant to a Collection Protocol indicates that the participant has agreed to the terms of the Collection Protocol by signing a consent form. Specimen Collection GroupOne or more specimens collected at one point in time from a participant enrolled in a Collection Protocol. SpecimenThe tissue or fluid collected from a participant. Chapter 2: Getting Started Terminologies

The following image outlines a simple caTissue Suite workflow: Chapter 2: Getting Started Simple caTissue Suite Workflow

 Web-based, open source  Role-based security  Configurable storage container hierarchy  Supports protocols, patient registry, and specimens  Supports pathology reports upload  Supports clinical and pathology annotations  Facilitates ordering and distributing specimens  Provision to define local extensions The key features of caTissue Suite are: Chapter 2: Getting Started Overview

 Facilitates querying, exporting results, and saving query  Certified for: JBoss Application Server Oracle and MySQL databases Windows and Linux servers Internet Explorer and Mozilla, and Safari for Mac  Well defined caBIG compatible API  Ability to interface with external IT systems  Facilitates label & barcode printing and generation Chapter 2: Getting Started Overview (continued) The key features of caTissue Suite are continued as follows:

The following table outlines the various user roles and the tasks performed by them: RoleDescription Administrator An Administrator registers new users, sites, containers, and collection and distribution protocols in the system. Supervisor A Supervisor adds participants and registers them to collection protocols. TechnicianA Technician adds specimens in the system. Scientist A Scientist performs a query on the specimens and orders the specimens. Chapter 2: Getting Started User Roles

The following diagram outlines the tasks performed by various users: Chapter 2: Getting Started Functional Block Diagram

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

The demo site provides you with the publicly available caTissue Suite application. You can use the following login details to access the site and familiarize yourself with the various features.  Demo Site URL:  Login:  Password: Login123 Chapter 2: Getting Started Login Details

Chapter 2: Getting Started User 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:

In this topic, you will be introduced to: The functional outline of the Administrative Data tab Collection Protocols Collection Protocol information model Storage Containers Storage Container Map Local Extensions 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. Chapter 3: Administrative Data

Actions Add and 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 View Reported Problems Add or Edit Local Extensions View Conflicting Reports 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 carried out using the Administrative Data tab. Chapter 3: Administrative Data Functional Outline of the Administrative Data Tab

A Collection Protocol contains a set of guidelines that describes what, how, and when the biospecimens will be collected. The Collection Protocol structure allows you to: The following diagram outlines the workflow involved in creating a Collection Protocol: Define consent questions, time points, and specimens collected per time point Define specimens, and derivatives and aliquots Create anticipated specimens for each participant registration Support complex protocols with arms and phases Chapter 3: Administrative Data Collection Protocol

The following diagram outlines the Collection Protocol information model: Chapter 3: Administrative Data Collection Protocol Information Model

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

The Storage Container hierarchy can be viewed using the map feature. The following diagram outlines the Storage Container hierarchy: 21 Chapter 3: Administrative Data Storage Container Map

You can add new forms in caTissue Suite based on your additional data capture requirements. This feature is called as Dynamic Extensions or Local Extensions. Using this feature you can: Add new forms without any programming efforts Create new forms using the form building User Interface (UI) or importing XMI (XML Metadata Interchange) Collect data Query data using the caTissue interface, caBIG API, and over caGrid Chapter 3: Administrative Data Local Extensions

In this topic, you will be introduced to: The tasks performed in the Biospecimen Data tab of the caTissue Suite application  The functional outline of the Biospecimen Data tab  The biospecimen data workflows  Collection Protocol based view  CP based data view  Specimen status change: Anticipated to collected  Tracking consents  Surgical Pathology Report (SPR) support  Deidentified report with highlighted concept codes  Annotations: Clinical and pathology introduction  Clinical and pathology annotations  Forms hooked to different entities Chapter 4: Biospecimen Data

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 Chapter 4: Biospecimen Data Functional Outline of the Biospecimen Data Tab The Biospecimen Data tab provides Supervisor and Technician specific activities. 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.

The following diagrams outline a high level overview of the various workflows performed using the Biospecimen Data tab of the caTissue Suite application: Chapter 4: Biospecimen Data Biospecimen Data Workflows

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 Chapter 4: Biospecimen Data Collection Protocol Based View

Register Participants and Accession Specimens Collection Protocol short title Participants registered under Lung Cancer Collection Protocol Chapter 4: Biospecimen Data CP Based Data View The following diagram outlines the various elements of a CP based view:

The icons indicate: Anticipated Event Point Completed Event Point Anticipated Specimen Collected Specimen Chapter 4: Biospecimen Data CP Based Data View (continued)

 The system creates anticipated specimens as per the Collection Protocol definition when a participant is registered to the CP  At each time point, the Technician or Supervisor marks the specimens as collected and at this time point, the system changes the status of the anticipated specimens to real, that is status changes from “Pending” to “Collected” The following diagram outlines the CP based data entry feature: Chapter 4: Biospecimen Data Specimen Status Change: Anticipated to Collected

 Consents are defined at the Collection Protocol level  Consents are recorded at participant registration, specimen collection group, and each specimen level  Consents are verified during each specimen distribution Chapter 4: Biospecimen Data Tracking Consents The following list outlines the features of consent tracking:

The following diagram outlines the workflow of a SPR: Chapter 4: Biospecimen Data Surgical Pathology Report (SPR) Support)

The following diagram outlines the de-identified report: Chapter 4: Biospecimen Data Deidentified Report with Highlighted Concept Codes

 They are based on the checklist provided by the CAP (College of American Pathologists)  They support querying for participants and specimens based on annotations  They can be edited and new attributes required for data collection can be added as per your local needs Chapter 4: Biospecimen Data Annotations: Clinical and Pathology Introduction The features of annotation are:

Clinical Smoking and Alcohol Use Family History Lab Values Treatment Information Comorbidities Follow-up Information Pathology Breast CNS Colorectal Heme Kidney Lung Melanoma Pancreas Prostate The following table outlines the clinical and pathology annotations: Chapter 4: Biospecimen Data Clinical and Pathology Annotations

Chapter 4: Biospecimen Data Forms Hooked to Different Entities ParticipantSpecimen Collection GroupSpecimen 1.Lab Annotation 2.Family History Annotation 3.Treatment Annotation 4.Rad RX Annotation 5.Chemo RX Annotation 6.Treatment Regimen 7.Environmental Exposure Health Annotation 8.Alcohol Health Annotation 9.Smoking Health Annotation 10.Health Examination Annotation 11.New Diagnosis Health Annotation 12.No Evident Disease Health Annotation 1.Base Solid Tissue Pathology Annotation 2.Base Hematology Pathology Annotation 3.Radical Prostatectomy Pathology Annotation 4.Needle Biopsy Prostate Pathology Annotation 5.Retropubic Enucleation Pathology Annotation 6.Transurethral Prostatic Resection Pathology Annotation 7.Pancreas Pathology Annotation 8.Lung Biopsy Pathology Annotation 9.Lung Resection Based Pathology Annotation 1.Specimen Based Solid Tissue Pathology Annotation 2.Colorectal Specimen Pathology Annotation 3.Pancreas Specimen Pathology Annotation 4.Melanoma Specimen Pathology Annotation 5.CNS Specimen Pathology Annotation 6.Prostate Specimen Pathology Annotation 7.Kidney Specimen Pathology Annotation 8.Lung Specimen Pathology Annotation 9.Breast Specimen Pathology Annotation The following table outlines the forms hooked to various entities:

Chapter 4: Biospecimen Data Forms Hooked to Different Entities (continued) ParticipantSpecimen Collection GroupSpecimen 13.Recurrence Health Examination Annotation 14.Local Recurrence Health Examination Annotation 15.Distant Recurrence Health Examination Annotation 10.Kidney Biopsy Based Pathology Annotation 11.Kidney Nephrectomy Pathology Annotation 12.Melanoma Pathology Annotation 13.CNS Pathology Annotation 14.Breast Pathology Annotation 15.Local Excision Based Colorectal Pathology Annotation 16.Excisional Biopsy Based Colorectal Pathology Annotation 17.Resection Based Colorectal Pathology Annotation The following table outlines the forms hooked to various entities:

In this topic, you will be introduced to: The functional outline of the Search tab The overview of the Query operation A simple query Advanced query: Features Perform advanced query Advanced query: View results Chapter 5: Query

Actions Simple Search Advanced Search My List Export Results The following diagram outlines the actions performed using the Search tab. Chapter 5: Query Functional Outline of the Search Tab

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

A Simple Query is ideal for queries based on a few parameters. A query can be performed as outlined in the following diagrams: Perform Simple Search View Simple Search Results Chapter 5: Query Simple Query

 Query any data  Security safeguard for regulatory (HIPPA) and proprietary data  View results in any form – drill down mechanism  Save query with parameterization  Export data into CSV  Add specimens to shopping cart to order Chapter 5: Query Advanced Query: Features An Advanced Query is performed on queries based on a complex parameters. A query can be performed as outlined in the following diagrams:

The following diagram outlines the steps to perform an advanced query. Chapter 5: Query Perform Advanced Query

Send requests for specimen Export data to Excel Select data elements to display The following diagram outlines the advanced query result screen. Chapter 5: Query Advanced Query: View Results

In this topic, you will be introduced to: The features of ordering specimen. You can:  Query for specimens or specimen arrays, add them to the shopping cart, and place an order  Order specimens, derivatives, specimen arrays, and specimens from pathological reports Chapter 6: Ordering Specimens

The following diagram outlines the biospecimen order screen: Derivative specimen Chapter 6: Ordering Specimens (continued)

Chapter 7: Hardware Requirements In this topic, you will be introduced to:  The hardware requirements for installing caTissue Suite 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

 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 Chapter 7: Hardware Requirements (continued)

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

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

Chapter 9: References and Current Adopters In this topic, you will be introduced to: References and adopters that will help you in obtaining more information on caTissue Suite.  This wiki link allows users and developers of caTissue to post questions and share tips about its deployment and use  This link provides you with a forum for discussion on caTissue questions

Chapter 9: References and Current Adopters (continued)  This link gives you a brief introduction to the caTissue Suite 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 Suite v1.0  directory/: This link allows you to view a list of all the adopters directory/

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, listserv, and Face- to-Face meetings)  The NCICB Applications Support 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

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 Chapter 10: Support Information (continued)