High Level Requirements

Centralized inventory system

• A database to track each specimen stored in the freezers, including details about the specimen, owner (researcher or group), date of entry, and expiration or intended disposal date.

• Classify and catalogue specimens

• Searchable specimen catalogue.

• Track specimen movement to long-term storage.

F12: Specimen Catalogue

• Fields to identify and flag samples based on specific criteria like GMO status, quarantine status, and mycoplasma testing results. (Charles Perkins Centre (CPC) and Charles Perkins Centre (CPC))

Quantity tracking for samples

• Track the exact quantity of samples stored in each box / packet.

• Updates when portions are taken out for experiments.

• Updates when samples are replenished.

• Alerts when samples (e.g. seeds) require replenishment.

F30: Sample Inventory Alerts - Critical Level Alerts

• This will prevent situations where empty packets remain in the seed stores without records, which is a current issue.

Critical Sample Identification

• A system to identify and label critical samples within cold storage environments

• The system should allow for the classification of samples based on criticality, so in case of incidents (e.g., freezer failure), the most critical samples are prioritized for saving

Advance search functionality

• Allows users to search and locate specific samples.

• The search should cover standard attributes, as well as fields like sample type, owner, GMO status, and other compliance-related fields

• Allows users to save the search criteria for future use.

F40: Data Extraction Based on Filters and Complex Operators

F41: Saves Queries for Future Use

This feature is particularly useful for CPC and BMC for locating shared resources like cell lines, facilitating researcher collaboration.

Inventory sharing and communication

• Inventory visibility across teams so that researchers can identify existing samples in shared storage when looking to source specific samples.

• Streamline communication to prevent redundant sample storage.

F2: Support for Multiple Studies

Specimen labelling

• Unique identifiers (such as barcodes or RFID tags) for specimens, enabling consistent and accurate tracking within BIMS.

• Sample description, criticality, expiration date.

• Capability to generate and print specimen labels directly from the system.

F34: Supports Barcoding

• For example, unique identifier linking it to general details about the samples, including genetic lineage, phenotype, and sequence data for seed stores.

Specimen location mapping

• Assign a precise location for each specimen within a freezer (site, room, rack /shelf, box, packet), allowing efficient retrieval.

F35: Tracks the Physical Storage Location of Each Specimen

Tracking Across Multiple Sites

• Support for multi-location tracking of samples to facilitate efficient inventory management.

F25: Tracking Specimens for Multi-Site Clinical Studies

• e.g. same seed samples might be stored at Camden or Narrabri

F8: Allows for Multiple Diagnoses at Sample and Patient Level

• Track and associate multiple diagnoses for individual samples and patients.

Useful for complex clinical studies where a single patient or sample may have multiple linked diagnoses.

F24: Supports Hospital-Based Unplanned Collections

• BIMS should manage and track biospecimens collected in unplanned scenarios, such as emergency procedures or urgent patient care.

F28: Bulk Processing for Specimens

• Allow batch updates to specimen records (e.g., updating storage locations, ownership, or status) to streamline high-volume operations.

F29: Sample Custody Tracking

• Track and log specimen custody / ownership changes, including handovers between researchers, transport personnel, or storage facilities.

F33: Different and Multi-Study Specimen Distribution

• Enable the allocation and tracking of specimens across multiple studies

Specimen Disposal and Lifecycle Management

Disposal workflow

• A workflow to mark specimens for disposal, with notifications to researchers to confirm disposal or request an extension.

Lifecycle management

• A retention policy to manage long-term storage. This will help with decisions on when samples can be disposed of, especially when researchers or students have left the university.

• Track each specimen’s lifecycle, from entry to disposal, with prompts for review at defined intervals.

Reminders for expiring specimens

• Notifications to researchers and TSS staff when specimens have reached the end of their storage period, triggering a disposal or renewal process.

Handling abandoned or unused samples

• A workflow for managing samples left behind by former researchers, with options to:

• Notify current researchers of available samples.

• Reduce the size of stored samples if needed.

• Dispose of samples based on retention policies or researcher input

User Profile Management

User Registration and Profile Creation

• The system should allow new users to register and create profiles with personal information, affiliation (e.g., research group), and contact details.

• User profiles should include required fields such as name, email, position, and department, as well as optional fields like phone number or secondary contacts.

Role-Based Access Control

• The system should support role-based access levels, allowing different permissions for users such as TSS Admin, Researcher, Technician, and Guest.

• Permissions should be configurable based on the user’s role, defining access to specific freezers, specimen data, and BIMS features.

F16: Customizable Level of Access

Training and induction tracking

• BIMS should track each user’s training and induction status, with fields indicating completion dates and types of training (e.g., freezer induction, compliance training).

• The system should restrict access to certain functionalities or freezer areas for users who have not completed required training.

User profile updates and audits

• The system should allow users and administrators to update profile details as necessary (e.g., change in department or role) while maintaining a log of profile changes for auditing.

• User profile history should be accessible to administrators, including modifications to roles, permissions, and access levels.

Integration with University’s access management system

• The system should integrate with existing University’s access management system to synchronize user details.

• The system should enable Single Sign-On (SSO) and MFA.

Patient and Consent Management

Patient Information Capture and Storage

• The system should enable the capture and storage of patient information, including key identifiers (e.g., name, ID number, date of birth) and relevant health data.

Consent Collection and Storage

• BIMS should allow the collection of consent in both electronic and paper-based formats (scanned copies).

• Each consent instance should be linked to the respective patient record and include metadata such as consent date, purpose, and expiry (if applicable).

F20: Consent Form Tracking

Consent Form Templates

• BIMS should support the creation, editing, and version control of consent form templates to standardize the consent collection process.

Consent Form Printing and Electronic Capture

• The system should allow users to print consent forms directly from BIMS.

• BIMS should support digital signature capture for electronic consent collection.

F21: Multiple Consent Forms per Study

• Allow researchers to associate multiple consent forms with a single study, with metadata specifying the form’s purpose and scope.

Enable tracking of different consent levels (e.g., for biospecimen use, genetic testing) within a single research study.

Specimen Storage Management

Specimen storage requests

• An online form or application workflow within BIMS for researchers to formally request freezer space. Forms should capture required details, such as intended storage duration, specimen type, and researcher contact information.

Allocation tracking

• Ability to track which research group or individual owns each section of freezer space, with an expiration or review date to prompt space reassignment or specimen disposal if no longer needed.

Availability monitoring

• Real-time visualization of available freezer space across all units, accessible to TSS staff and researchers as appropriate.

Reminder notifications

• Reminders to researchers when their storage duration is nearing its end, prompting specimen disposal or renewal of space if necessary.

Workflow Management for Specimen Access

Specimen Access Request Submission

• The system should allow researchers to submit access requests for specific specimens, specifying details such as specimen type, purpose of access, and requested access duration.

• BIMS should provide a standardized request form, capturing necessary information to streamline the review and approval process.

• BIMS should allow the requester to attach any relevant documents with the access request.

Access Management and Approval Workflow

• BIMS should implement an approval workflow for specimen access requests, allowing designated approvers (e.g., lab managers, principal investigators, TSS Team) to review and approve or deny requests.

• The system should support a multi-step approval process, including optional secondary approvals, where necessary.

F38: Managing and Tracking Requests

Approval Notification and Communication

• The system should send automated notifications to researchers when their access requests are approved, denied, or require additional information.

• BIMS should facilitate communication between researchers and approvers during the review process, allowing researchers to clarify details or submit additional documentation.

Lab Manager View for Approved Requests

• Lab managers should have a dedicated view within BIMS displaying all approved specimen access requests, showing key details such as the requesting researcher, specimen identifiers, and access timelines.

• This view should include filtering and sorting options, allowing lab managers to easily track active, expired, or upcoming requests (request history).

Sample access and usage logs

• Detailed access log for each sample stored in the storage.

• This will include tracking who, when and why accessed the samples.

F31: Sample/Biospecimen Usage Tracking

Logistics Management

Capture logistics information

• Manage logistics related information when the specimen is transported (collection location and next destination).

• Track movement of specimens between locations.

F32: Shipping Specimens to Offsite Locations

F27: Bulk Transfer of Specimens Between Locations

• support tracking and recording bulk specimen transfers between sites or facilities.

Access and Security Controls

Building and Freezer induction records

• Maintain induction forms and training completion records for all personnel authorized to access freezers, linking to individual user profiles in BIMS.

• BIMS should record induction completion and authorized access for each individual.

User role permissions

• Define roles and permissions within BIMS for researchers, TSS staff, and administrators, ensuring that only authorized personnel can access or modify specimen records.

Audit trails

• Track every change made to specimen data, space allocations, and freezer status to maintain accountability and data integrity.

F18: Audit Trail Support

• Freezer status might already be maintained and audited in RampX

Data Analytics and Reporting

Usage and inventory reports

• Generate reports on freezer occupancy and specimen types stored, etc.

F10: Dashboard Reporting

F6: Batch Export of Data

• BIMS should allow the batch export of specimen and associated metadata in various formats (e.g., CSV, Excel, JSON).

F37: Samples and Data Validation + Validation Reports

• Validate specimen data for completeness, accuracy, and compliance, generating validation reports to identify discrepancies.

Integration Capabilities

Integration with RampX (Cold storage management system)

• Integration with the existing Rampax system to display freezer temperature data, operational status, and alarm notifications in BIMS.

• Log maintenance activities and repair requests, including work history for each freezer unit. BIMS should capture details of repairs, responsible persons, and associated costs. [1]

[1] Will this be required in

BIMS?

Integration with Building Management System

• A system to monitor environmental conditions (e.g., temperature, humidity).

Integration with Breeding Management System

Integration with imaging system

Integration with other external systems

• Ability to integrate with other research and lab management systems to streamline data exchange, particularly if researchers or groups use external databases for specimen data.

• Potential integration with LabArchives.

F3: Multi-source Data Integration

• Enable integration with multiple external and internal data sources for comprehensive specimen tracking and management.

This includes clinical databases, research platforms, and third-party systems, ensuring seamless data flow between BIMS and other repositories.

F7: Tissue Microarray Integration

• Support integration with tissue microarray systems for specific research needs.

Cost Tracking

Track cost for freezer space usage

• An option to track and manage cost recovery for freezer space usage.

TSS is not charging for freezer space usage currently but could be useful for future use cases.

Cold Storage Management

Cold storage monitoring (including fridges, -80 freezers)

• Real-time monitoring of freezer temperatures and conditions, with alerts for any deviations in temperature and humidity levels.

F26: Automated Freezer/Storage Management

Automated Alerts and Notifications for Incident Response

• Automated alerts to be sent to the responsible staff (TSS) and designated researchers when freezer conditions deviate from acceptable parameters (temperature and humidity levels).

Structured incident response process

• For handling cold storage failures (e.g., power outages, equipment malfunctions).

• The system should support monitoring and alerting and facilitate rapid identification of samples at risk during emergencies.

• History of potentially impacted specimens (audit logs).

• From Margaret Faedo

• Potential for capturing data from RampX/BMS and manage incidents in BIMS - TBD any duplication of functionality with RampX

Scheduled Maintenance Tracking for Freezers

• Scheduled maintenance tracking to prevent unexpected freezer failures.

• Maintain logs of any repair or service work done.

F36: Transfer Boxes from One Freezer to Another

• Allow for logging the movement of specimens between freezers, including updates to their location.

• e.g. In case of freezer failure, or a space management exercise.

Ethics and Compliance Management

Compliance tracking for samples

• Support for compliance tracking for samples, especially those involving human or animal subjects.

• Linking samples to ethics approvals and consent documentation to ensure that research is carried out in accordance with ethical guidelines

• From Margaret Faedo

Verify ethics approvals

• Audit trails and the ability to verify ethics approval for critical samples should be integrated into the system.

• Each sample should include fields for the associated ethics project, purpose, and any consent limitations on usage beyond the initial research. (CPC & BMC)

Scheduled Compliance Review Reminders

• Automated reminders should be sent to researchers and TSS staff for scheduled compliance reviews based on sample type and ethics guidelines.

• This feature is particularly useful for clinical trial samples or GMO specimens that need periodic compliance checks.

Clinical trial samples support

• Support clinical trial samples, which often come with additional compliance, ethics, and tracking requirements, such as linking patient data or clinical trial information to samples stored in cold storage.

F17: De-Identification and Anonymization

• Anonymize patient and specimen data for studies where personal identifiers are unnecessary.

Manage multiple biobanks

• Support the centralized management of specimens and operations across multiple research centers or facilities.

F1: Support for Multiple Centers

• To ensure the solution is scalable and adaptable to institutions with geographically distributed research centers or biobanking facilities, such as Camden, Narrabri, and other university-affiliated sites. It also supports decentralized operations while maintaining centralized oversight.

Administration and Configuration

F4: Batch Import of Data without IT Support

• Allow researchers and administrators to import large datasets without requiring IT involvement.

Useful for onboarding historical specimen data or managing frequent data updates.

F5: Ability to Add Features Without IT Support

• Provide configurable tools that allow adding new functionalities or modules to BIMS without technical expertise.

F9: Customizable to Meet Local Needs

• BIMS should provide configurable workflows, dashboards, and fields to adapt to the specific needs of different faculties or research groups.

Others

F22: Prospective Tracking of Clinical Data

• Enable tracking of clinical data prospectively, linking it to biospecimens.

F23: Retrospective Tracking of Clinical Data

• Allow retrospective addition of clinical data to biospecimens already in the system.

F39: Tracks Aliquots and Derivatives of Samples

• Maintain detailed tracking of aliquots (subsamples) and derivatives (processed forms) of original specimens.

F42: Pathology Report Linking and De-Identification

• Integrate pathology reports with specimen records, ensuring sensitive information is de-identified where necessary.

NFR

F11: Simplified Data Entry

• BIMS should support user-friendly, form-based interfaces for entering specimen details, including autofill suggestions and dropdowns for common values.

F19: Supports Data Encryption

• All data (in transit and at rest) to be encrypted using industry-standard encryption protocols.