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caTissue eLearning Materials May 2008

caTissue Suite v1.0 Overview. caTissue eLearning Materials May 2008. Session Overview. 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

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caTissue eLearning Materials May 2008

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  1. caTissue Suite v1.0Overview caTissue eLearning Materials May 2008

  2. Session Overview • 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

  3. 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

  4. 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

  5. Chapter 1: Introduction 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

  6. Chapter 2: Getting Started 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

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

  8. Chapter 2: Getting StartedSimple caTissue Suite Workflow The following image outlines a simple caTissue Suite workflow:

  9. 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 Chapter 2: Getting StartedOverview The key features of caTissue Suite are:

  10. Chapter 2: Getting StartedOverview (continued) The key features of caTissue Suite are continued as follows: • 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

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

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

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

  14. Chapter 2: Getting StartedLogin Details 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: http://catissuecore.wustl.edu/catissuecore • Login: admin@admin.com • Password: Login123

  15. 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:

  16. Chapter 3: Administrative Data 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.

  17. Chapter 3: Administrative DataFunctional Outline of the Administrative Data Tab 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. • 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

  18. Chapter 3: Administrative DataCollection Protocol 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: • 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 The following diagram outlines the workflow involved in creating a Collection Protocol:

  19. Chapter 3: Administrative DataCollection Protocol Information Model The following diagram outlines the Collection Protocol information model:

  20. Chapter 3: Administrative DataStorage Containers 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:

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

  22. 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 DataLocal Extensions

  23. Chapter 4: Biospecimen Data 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

  24. Chapter 4: Biospecimen DataFunctional 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. • 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

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

  26. 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

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

  28. Chapter 4: Biospecimen DataCP Based Data View (continued) • The icons indicate: • Anticipated Event Point • Completed Event Point • Anticipated Specimen • Collected Specimen

  29. 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” Chapter 4: Biospecimen DataSpecimen Status Change: Anticipated to Collected The following diagram outlines the CP based data entry feature:

  30. 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 DataTracking Consents The following list outlines the features of consent tracking:

  31. Chapter 4: Biospecimen DataSurgical Pathology Report (SPR) Support) The following diagram outlines the workflow of a SPR:

  32. Chapter 4: Biospecimen DataDeidentified Report with Highlighted Concept Codes The following diagram outlines the de-identified report:

  33. 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 DataAnnotations: Clinical and Pathology Introduction The features of annotation are:

  34. Chapter 4: Biospecimen DataClinical and Pathology Annotations The following table outlines the clinical and pathology annotations: 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

  35. Chapter 4: Biospecimen Data Forms Hooked to Different Entities The following table outlines the forms hooked to various entities:

  36. Chapter 4: Biospecimen Data Forms Hooked to Different Entities(continued) The following table outlines the forms hooked to various entities:

  37. Chapter 5: Query 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

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

  39. 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.

  40. Chapter 5: QuerySimple Query 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

  41. 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: QueryAdvanced 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:

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

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

  44. Chapter 6: Ordering Specimens 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

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

  46. 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

  47. 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

  48. 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

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

  50. 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. • 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

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