ATiM Installation Guide

Contents 1 System Requirements 1.1 Development/Demo/Test Environments 1.2 Production Server 1.3 Client 2 Production Environment Recommendations 2.1 Security Requirements 2.2 User Access Recommendations 2.3 Server Recommendations 2.4 Backup Recommendations 3 Prospective Banks Checklist 3.1 IT Support 3.2 ATiM Hardware/Software Requirements 3.3 Application Configuration 3.4 Questions

System Requirements

Development/Demo/Test Environments

Our development/demo server has the following specifications:

• Dual 2.8GHz Intel Xeon Processors
• 1GB RAM
• 70GB Disk space

This server has provided us with ample processing power and disk space to handle multiple installations of ATiM along with other development resources including a FTP server and Subversion repository.

To setup either a development or a test or a demo installation under Windows, we highly recommend installing WAMP (wee WAMP Configuration Guide).

Production Server

As ATiM has been developed using cross-platform, open source technologies any platform capable of running MySQL, Apache and PHP should be able to host an installation.

To date we have installed and tested ATiM on:

• OS
  • RedHat Linux ES v3/v5,
  • Ubuntu 8+
  • MacOS X 10.6+
  • Windows Server 2000/2003
  • Windows XP/Vista/7
• Web Server
  • Apache 2+ (see Apache Configuration Guide)
  • IIS 6 (see IIS Configuration Guide)
• Database
  • MySQL 5+
• PHP 5.2+ (PHP 5.3+ is supported since ATiM 2.1.0 which includes CakePHP 1.3.2)

Disk space depends on the number of participants, samples and level of annotation. As a rough guide 10.0 GB of free disk space should provide ample room for any established bank (considering no picture or document has to be stored on the server).

Client

ATiM is a web application designed to be used at a resolution of 1024x768 or higher. Lower resolutions can be used but will result in a diminished user experience. Any client running a recent web browser should be able to connect and use ATiM.

CTRNet has tested and recommends the following web browsers for client workstations:

• FireFox 3 or higher
• Internet Explorer 8 or higher
• Safari 4 or higher
• Chrome ∞

Production Environment Recommendations

ATiM database is likely to house confidential health and materials information that cannot be replicated from any other source. Complete loss of this information could result in the stranding of banked biological materials.

Installation of the required computer and related network hardware are a local responsibility. CTRNet provides the following recommendations as a guideline only. They are not intended to replace institutional policy.

Security Requirements

Where ATiM is used to collect, store and present sensitive health information, qualified local expertise and resources are mandatory to ensure that installation meets or exceeds the appropriate institutional policies for handling and protecting sensitive personal data for research purposes.

User Access Recommendations

• End-user access should be managed by the login and security features provided in ATiM.
• Access to ATiM application and the related databases should be restricted to personnel trained and authorized to handle personal information on a “need-to-know” basis.
• User authorities must be documented and configured to meet local needs prior to populating the application with confidential data.

Server Recommendations

• ATiM database and application servers should run behind a managed institutional firewall intended to protect clinical data.
• ATiM database and application server accesses should be limited, secured and controlled.
• A secure connection (SSL connection (https, etc)) is recommended to connect ATiM from any workstation.

Backup Recommendations

• ATiM and the related databases should be backed up on a daily basis and treated as confidential production data.
• Off site storage should be completed on a weekly basis.
• Off site storage access should be limited, secured and controlled.

Prospective Banks Checklist

New biobanks considering use of ATiM should review the following guidelines to help ensure a successful, and timely installation.

IT Support

ATiM is a web-based and highly configurable application. Someone capable of installation, customization and ongoing support of the application will be needed. The skill set required for your IT staff will vary depending on the level of customization, data audits, and/or porting of existing data. Based on previous experience with other banks, CTRNet recommends the following qualifications for your IT support staff:

• Experience with server administration. (Only applicable if hosting on your own server).
• General database administration - Understanding of SQL, backup/restoration, ongoing maintenance.
• Understanding of PHP, specifically the CakePHP framework and/or Model-View-Controller design pattern.

When bank requirements include complex business rules, new plug-ins, or additional functionality knowledge of PHP and general web-development is imperative

ATiM Hardware/Software Requirements

Most banks choose to run ATiM on a dedicated server located in a secure server room environment. Please see section above to learn about the system requirements.

Application Configuration

ATiM was designed based on the requirements of multiple bio-respositories all with differing disease-site specialties. In most applications, the base installation will only require minor customization such as:

• Setting up dropdown lists with local data such as provider names (Doctors, local hospitals, bank staff)
• Disabling or hiding sections of the application the bank does not wish to use. For example a bank may only specialize in collecting blood products. All other sample types and related deriviates/aliquots can be hidden from the user.
• Creating users, groups and assigning appropriate permissions.
• Basic bank validation rules.

Moderate customization would include:

• Adding additional aliquot and sample types. See Inventory for a complete listing.
• Adding new storage types. See Storage Management for a complete listing.
• Adding new disease site specific events. For example a new lifestyle questionnaire for prostate cancer.

High level customization:

• Specific business logic to execute. For example complex bank data validation rules to be checked before any new record was saved.

Questions

The process of installation, customization, and loading data from existing data sources (if any) can have a significant impact on timelines for getting ATiM into a production biobank environment. To help banks better understand project timelines, CTRNet has provided a questionnaire to gather information on the prospective installation site. Upon review by CTRNet a general timeframe and project plan can be derived from the responses.

Existing data sources

Objective: Describe all existing data sources that will be ported into the ATiM.

• Format (Access, Excel, other database types)
• Data quality - Are fields controlled by constraints and validations rules?
• Number of records - Small, complex datasets can be re-entered where larger one's must be audited and loaded through scripts
• Data dictionary and/or ERD - Describe all data elements collected, permissible values for those elements, definitions, etc. An diagram of any database structure would be useful.

Disease sites collected

• DX Speciality - What types of data are collected for each disease site:
• Followup
• Path reports
• Initial Presentation
• Treatment
• Lifestyle
• Screening
• Adverse Events

Inventory

• Sample types collected + related derivatives and aliquots for each type
• Storage model described

Users Groups and Banks

• Define list of users, what roles they perform and disease site groups they work with.