Frequently Asked Questions about BIGR®

This page answers some common questions that we hear from our clients about the BIGR® Biospecimen Management System. Should you have any further questions, please consult our Contact Us page.

Registration

Does the system support multiple sample types?

Yes, BIGR® currently provides support for more than 20 different sample types, including frozen tissue, paraffin tissue, blood, serum, etc. Additional sample types can be defined and added easily through system configuration.

Does the system support flexible collection procedures, such as samples arriving at the biorepository prior to sample or donor annotation?

Yes, BIGR® supports registering samples by simply scanning their barcode, allowing samples to be added to your biorepository as quickly as possible, preserving their quality. Conversely, BIGR® allows samples and their donors to be registered and fully annotated before samples are physically received at the biorepository. In both situations the sample is safely registered in BIGR®.

Does the system limit the amount of information I can enter when registering a sample?

Beside a few necessary details such as the sample type, the amount of information to be entered when registering a sample is completely up to each client. BIGR® allows registration forms to be associated with samples that dictate the data elements that are to be captured and whether they are required, and these registration forms can contain as many or as few data elements as desired. For clients who work with multiple IRB protocols and/or consent versions, BIGR® provides even greater flexibility, providing the ability to specify different registration forms for each IRB protocol/consent version. This flexibility ensures that regardless of the scenario under which a sample is collected, our clients have complete control over the information that is collected.

Can the system be configured to allow different information to be entered for different sample types?

Yes, BIGR® has customizable rules that determine the appropriate registration form for each type of sample. Each collected sample type can have a different registration form, or similar sample types can share a registration form.

Does the system allow multiple samples to have the same identifier?

Yes, samples may be assigned an alias, or alternate identifier, designated by the client, alongside the unique identifier BIGR® assigns to each sample that is registered in the system. The same alias value may be assigned to any number of samples (e.g. a row of samples in a rack, or any grouping scheme desired by the client). Further, the system supports searching for samples by both the unique BIGR® identifier as well as by the client designated alias.

Can a user quickly register multiple samples in the system?

Yes, BIGR®’s sample registration transaction allows a user to register similar samples for the same collection event or donor with ease, remembering the data element values of the previous sample. In fact, if the sample barcode is being generated and its label printed at the time of registration, a sample with the same data element values as the previously registered sample can be registered with a single click.

What does the system do with samples when a donor revokes their consent?

BIGR® has a transaction that allows samples associated with a consent to be pulled from the system for a variety of reasons, including revocation of consent. This transaction provides the user with a pick list of inventory locations for the samples to allow them to be removed from inventory. If a sample is not in inventory then that is noted as well. Further, if a sample is received at a remote location using BIGR® and that sample cannot be used because of revocation of consent, BIGR® will note that the sample cannot be used.

Does the system allow for external identifiers for donors and collection events?

Yes, each donor and collection event may be assigned an alias, or alternate identifier, designated by the client, alongside the unique identifier BIGR® assigns to each donor and collection event that is registered in the system.

Label Printing

Does the system allow both pre-printing and on-demand printing of barcoded labels?

Yes, label printing is an integral part of BIGR®. Labels can either be preprinted to allow a supply of labels to be available within a lab, a biorepository, or wherever they are needed, or labels can be printed on demand when a sample is registered. When printing a label, the user has the ability to select the label template, the printer, and the number of times to print the label.

Does the system allow a label to be printed multiple times?

Yes, this can be accomplished in two ways in BIGR®. First, when printing a label multiple copies of the label can be printed. Second, a label that was previously printed can be reprinted as many times as necessary, which allows labels that have become unusable for any reason to be reprinted.

How much flexibility is available with respect to designing labels with the system?

BIGR® allows labels to be completely customized to contain 1D, 2D and Data Matrix barcodes along with the value of any data element captured by a registration form or annotation form. BIGR® integrates with the industry leading BarTender® label software to support an unlimited number of label templates along with an unlimited number of label printers.

Can a user create barcoded collection kits with the system?

Yes, BIGR® allows users to preprint barcoded labels that can be assembled into a collection kit. The user can specify the number of labels to be printed, and sets of labels can be printed using different templates and on different printers if desired. At the time of registration in BIGR, the barcodes are affixed to samples and associated with a donor and a collection event.

Does the system support any type of label printer?

Our experience is with Zebra 600dpi thermal transfer printers that print 1D, 2D and data matrix barcodes. However, BIGR® is not limited to any specific brand of printer.

Does the system support any type of barcode scanner?

Our experience is with Symbol scanners. However, BIGR® is not limited to any specific brand of scanner.

Sample Derivative Operations

Does the system support tracking the genealogy of derived samples?

Yes, BIGR® provides support for sample derivative operations and records the genealogy of samples. Customizable rules allow specification of valid derived sample types and data inheritance and default values for derived samples. Integration with the Label Printing module allows labels for all derivatives to be printed on demand at the time they are created in the system.

How many different derivative operations are supported by the system?

BIGR® currently provides support for more than 10 different derivative operations, including aliquoting, subdividing, and blood separation. Additional operations can be defined and added easily through system configuration.

Does the system allow a batch of derivative operations to be recorded at the same time, or must derivative operations be entered one at a time?

BIGR® supports a batch mode for derivative operations, where multiple operations of the same type can be recorded at the same time. In conjunction with customizable data inheritance and default values, this mode allows for efficient recording of multiple operations in a minimum amount of time.

Does the system automatically update the volume or weight of a parent sample when performing derivative operations?

Yes, BIGR® updates the volume or weight of a parent sample if necessary to reflect the amount of used material, and even marks the sample consumed if appropriate. However, the user is always free to override the decision of the system and adjust the weight, volume or consumed state of a parent sample manually.

Data Annotation

Does the system allow for flexible design of annotation forms?

Yes, BIGR®’s ultra-flexible annotation engine, KnowledgeCapture™, allows our clients to design annotation forms that can contain data elements of their choosing, and to associate these annotation forms with samples, collection events and donors. This technology, and associated library, was initially developed over a three year period with a research grant from the U.S. National Institute of Standards and Technology. Consult our Overview of KnowledgeCapture™ for more information on this powerful feature.

Does the system provide a pre-defined library of relevant data elements?

Yes, the pre-defined library of data elements from which to choose when designing annotation forms currently contains over 3000 data elements and 7000 data values across 75 disease groups. The library can be amended to add data elements to meet virtually any requirements.

How easy is it for a user to evolve annotation forms once they are in use?

Any aspect of an annotation form can be changed through an administrative transaction in BIGR®, including adding new data elements from the library and removing existing data elements. Once the annotation form changes are saved the updated annotation form can be used immediately by all users.

Does the system’s annotation capabilities conform to industry standard terminologies?

Yes, BIGR®’s annotation engine was built around standards such as SNOMED-CT, CAP Synoptic Reports, AJCC6, HUGO, and LOINC, among others.

Sample Search and Request

How does the system allow a user to search for samples?

BIGR®’s Sample Search and Request module, designed by scientists and researchers from diverse disciplines, is a powerful query tool used to locate, evaluate and compare samples. Its broad range of criteria allows precise filtering to enable users to quickly determine how many samples of interest are available in the biorepository.

What limitations exist for search criteria in the system?

There are essentially no limitations for search criteria. BIGR®’s query engine allows a broad range of criteria to be specified, including any data element from any data annotation form in the system, using the same powerful KnowledgeCapture technology that powers the annotation engine. This allows limitless flexibility in forming queries, allowing users to use their data elements of interest for both data annotation and querying.

Does the system allow search criteria to be saved?

Yes, search criteria are defined through query forms, which are similar to data annotation forms. Query forms include the data elements that comprise the search criteria for the query, and can also include the values of those data elements that should be used when performing the search.

How are the results of a search displayed in the system?

BIGR®’s search results are displayed in a tabular format that allows for quick review and comparison of pertinent data elements. This format was designed in conjunction with scientists who require the ability to rapidly evaluate a potentially large result set by simply scrolling through it.

Does the system allow the results of a search to be configured such that a user can see exactly the data elements of interest?

Yes, BIGR® allows complete control over the search results by each user. Any combination of data elements that comprise query criteria, along with any data elements that have been captured in any data annotation form, can be displayed in the tabular search results. In addition, this tabular view is completely customizable by the user, including how many data elements are displayed and the order in which they are displayed, and the user may create and select from multiple tabular views.

Can the results of a search be exported?

Yes, the results of a BIGR® search can be saved on the clipboard or exported into Excel.

Does the system allow additional information to be retrieved for each sample in a search result set, above and beyond what is displayed in the tabular results?

While any data element can be displayed in the tabular results for quick review, and there is no limit on the number of data elements that can be displayed in the tabular results view, it is often impractical for all details to be displayed in this fashion. Therefore a more detailed inspection can always be performed via drilldown pages that include all data annotation forms for each sample. This allows the complete set of annotations for each sample to be viewed.

How can a particular researcher reserve samples in the system?

The most common mechanism for reserving samples in BIGR® is to assign the samples to an inventory group to which only the researcher has access.

Does the system allow a researcher to request samples be delivered to a lab?

Yes, Part of BIGR®’s core request functionality includes the ability for a researcher to request samples directly from the search results screen.

If samples are requested by a user, can another user request the same samples?

Once samples are placed on a request, they are no longer available for subsequent requests. One exception to this is if a repository manager exercises the option to reject the request, in which case the samples are made available again for future requests.

Request Management

Does the system track each request and its status towards fulfillment?

BIGR® provides for comprehensive management and fulfillment of requests. A repository manager can view open requests along with all request details, and either accept and fulfill or reject the request. A sortable picklist can be displayed and printed to allow the repository manager to locate samples in inventory in an optimal manner. A wizard-like interface guides the repository manager through the request fulfillment process, performing numerous validations to ensure each request is fulfilled accurately.

Can a user request samples from remote biorepositories?

Yes, BIGR® supports both local and remote biorepositories. If a request is made for samples from a remote biorepository, BIGR® supports the shipping of those samples from the remote location.

Does the system provide alerts during the request process?

Yes, BIGR® provides email alerts to keep both the requestor and repository manager informed of the creation and progress of a request.

Inventory and Logistics

Does the system track samples using barcode IDs and scanners?

Yes, barcode IDs are used throughout BIGR® to track samples, and all transactions that require a barcode ID support scanning of the barcode.

Can a user perform batch storage of samples using your system, or must samples be stored one at a time?

BIGR®’s default method of storage is batch mode, in which a user scans multiple samples into a container, such as a box, and then places the container into a storage unit. A single sample can just as easily be stored, though, by scanning it into an empty or partially filled container.

Does your system suggest the next available inventory location when adding samples to inventory? Can this be overridden by the user?

Yes, BIGR® suggests an available location for the container that holds samples, but also allows the user to override the suggested location to use any empty location. BIGR® guides the user during the override procedure by only allowing an available and suitable location to be selected.

Does your system ensure that samples are stored in appropriate storage units?

Yes, when adding samples to a storage unit their storage type (e.g. -80C, LN2, etc) is specified, and BIGR® only allows samples to be stored in storage units that were configured to hold samples of the specified storage type. This ensures that samples are always stored in appropriate storage units.

Does your system record the status of a sample as it is processed?

Yes, BIGR® records the status of each sample to determine its general availability for requests, its inventory state, and where it is in the shipping pipeline if it is shipped to a remote location, and whether it is consumed. This enables BIGR® to keep track and report on the state of every sample under its control.

What happens to a sample record in the system when a sample is consumed?

All sample information, along with related donor and collection event information, is retained in BIGR®. This includes the complete audit trail with details of the transaction that consumed the sample.

Does your system provide a feedback mechanism for sample recipients to indicate the quality of received samples?

Yes, through the Data Annotation module an annotation form can easily be created that captures any desired quality metrics. This annotation form can be associated with a sample and populated by sample recipients for review by biorepository personnel.

Inventory Control Panel (ICP) and Audit History

Does the system provide an audit trail?

Yes BIGR® automatically logs every transaction that alters the state of the system, recording the transaction type, the id of the user performing the transaction, the date and time of the transaction, and the various details of the transaction.

Can a user amend the audit trail in the system?

Yes, BIGR® allows an appropriately privileged user to amend the audit trail with a note. As with all transaction logging, the id of the user and the date and time of the amendment are recorded.

Can a user view the audit trail?

Yes, through BIGR®’s Inventory Control Panel (ICP) a user with suitable privileges can easily display the history of repository elements (samples, donors, cases, boxes, requests, manifests, etc.) and track status changes and events. ICP can be accessed via a single mouse click throughout the system wherever repository elements are listed. This provides the project manager, repository manager, researcher and laboratory technician an easy to access snapshot of key information about an element, including a detailed chain-of-custody report. Note that ICP pages are also displayable in a printer-friendly mode should a hard copy be desired.

Security, Privacy and Regulatory Compliance

How does your system control access to its functionality?

A BIGR® system administrator creates users and assigns specific privileges to each user, choosing from over fifty specific transactions. This flexibility allows fine grained control over user authorization and does not limit users to pre-defined roles.

How does your system authenticate users?

BIGR® utilizes an open source component, the Common Security Module (CSM) developed for the caBIG™ initiative, that provides for authentication. HealthCare IT has coded its own module that works with the CSM to authenticate users, and through its use of CSM can also support LDAP if desired by a client.

Can restricted access be given to certain sets of inventories?

Yes, BIGR® provides this level of control through Inventory Groups. An Inventory Group is a logical grouping of samples, and they can be created to represent any desired sample grouping. A BIGR® system administrator grants individual users access to specific Inventory Groups, thereby limiting a user’s visibility to only the samples in those Inventory Groups. BIGR® supports an unlimited number of Inventory Groups, and samples can belong to multiple Inventory Groups, enabling a very flexible means of sample grouping and access control.

Is the data being transmitted from the web browser to the server secure?

Yes, BIGR® supports 128-bit SSL encryption to guarantee that the data you transmit from your browser to the server is secure. This is the same high-level encryption that is used by leading consumer web sites.

Is the system 21 CFR Part 11 compliant?

HealthCare IT recognizes that in many situations, BIGR® will need to be incorporated into an organization’s regulated process. BIGR® is developed using a Software Development Lifecycle in accordance with FDA and GAMP guidelines. HealthCare IT, Inc. will provide assistance to a client to validate our software and its operating environment in accordance with these guidelines.

Does the system adhere to the May 2007 Guidance from the FDA on Computerized Systems used in Clinical Investigations (available at http://www.fda.gov/cder/guidance/7359fnl.htm)?

Yes, BIGR® fully supports the May 2007 Guidance from the FDA on Computerized Systems used in Clinical Investigations via the following mechanisms: individual user accounts, recording unauthorized login attempts, locking a user account after an administrator-defined number of failed login attempts, password expiration after an administrator-defined number of days, strong passwords consisting of a combination of numbers and letters, an explicit logoff mechanism, expiration of a user’s session with automatic logoff after an administrator defined period of inactivity, audit trails and time synchronization with time servers.

Integration

Does the system have a set of Application Programming Interfaces (APIs)?

Yes, BIGR® provides a suite of Application Programming Interfaces (APIs) to enable access to and modification of data annotations. These APIs are designed to fit within application architectures in common usage.

Can your system programmatically interact with other systems that have a suitable API?

Yes, HealthCare IT is open to integration with other systems and we have performed such integration projects in the past. For once such example, see our behind-the-scenes look at BIGR®’s integration with the Aperio digital pathology system.

Does your system allow hyperlinks to be associated with samples to allow users to navigate to other sites?

Yes, BIGR® provides an administrative transaction for defining URL templates. These templates can contain any URL and insert BIGR® identifiers, such as a sample barcode, within the URL when the link is created in the user interface. Clicking the link can cause navigation to another web-based system, passing a BIGR® identifier if desired.

New Product Releases

What is the process used to determine the contents of a new release of the system? Do customers have direct input into the process?

At HealthCare IT, our software development is driven by the needs of our customers. All customer feedback, including issues, usability concerns, enhancements, and suggested new features are logged into a tracking system. A team consisting of Business Development, Product Management, Client Services, Engineering, Quality Assurance, and Informatics personnel regularly reviews and prioritizes customer input to plan software development activities for upcoming releases.

Do you communicate the contents of a planned release to your clients?

Yes, we treat our clients as partners and rely on their feedback to shape our system. Consequently, we communicate our release plans to our clients to allow them to plan for new features and enhancements and to understand when a desired feature will be available.

How often do you release new versions of the system?

We release new versions of our system between three and four times a year, based on prioritization of customer needs.

Are new releases backward-compatible with previous releases?

Yes, at HealthCare IT backward compatibility and data migration/conversion are always considered and incorporated as core components of any new release.

Technology

Is the architecture of the system scalable?

Yes, BIGR® is a web-based application built upon a scalable, modern 3-tier architecture utilizing J2EE standards-based technology. BIGR® employs a completely browser based user interface tier, J2EE application services in the application tier, and Oracle 10g to support the data tier. BIGR® can support many secure, concurrent, active user sessions.

Does your system support a “thin” client, or do I have to install software on each user’s computer.

BIGR® is completely browser-based, so there is no need to install any software on a user’s computer.

Is there a limit to the number of samples or donor records that can be stored by the system?

Since BIGR® is based on a modern architecture and uses the Oracle 10g database management system, there is virtually no limit on the number of sample or donor records that can be stored and accessed by BIGR®.

Deployment

Does your company provide a hosting option for the system?

Yes, HealthCare IT will install BIGR in our secure data center, with a dedicated application server and database for each client.

Can the system be installed in our data center?

Yes, HealthCare IT provides implementation services for installations at a client site.

Can we use your hosting service for some initial period of time and then migrate the installation to our data center?

Yes, HealthCare IT fully supports this scenario. HealthCare IT recognizes that some clients prefer to have HealthCare IT host the system in our secure data center to get up and running as quickly as possible, with a plan to ultimately install the system in their own data center.

What hardware platform (size, capacity and operating system) is required for operation of the system?

The hardware platform comprises two servers – a database server and an application server, both running the Linux operating system. The database server is nominally a server-class Intel-based computer configured with at least 2.8Ghz dual or quad Xeon processors or equivalent, 4GB memory and 2 x 36 GB and 4 x 72 GB hot-swappable hard drives in an Oracle-recommended fault-tolerant RAID configuration. The application server is nominally a server-class Intel-based computer configured with at least 2.8Ghz dual or quad Xeon processors or equivalent, 2GB memory and 2 x 72 GB hot-swappable hard drives in a fault-tolerant RAID configuration.

Do you support running your system under VMWare?

Yes, VMWare has been successfully used to deploy BIGR® and is fully supported.

Does your company provide training to users of the system?

Yes, training is provided directly by a HealthCare IT application deployment specialist. Delivered through a variety of methods to meet the client’s needs, training options include on site group and individual classroom instruction, structured exercises and supervised data entry, and online training through a web conferencing site. The HealthCare IT User Guide and related materials are distributed to each site. Release notes and revised documentation are provided with software upgrades.