6 Essential Factors when Choosing a CTMS

This post is part of a Bad Rabbit series on selecting RA systems:

Clinical trial management systems (CTMS) help—you guessed it—manage the operational data involved in establishing and running clinical trials. The right CTMS will help you organize data in a secure, centralized location. It will streamline and standardize processes, increase trial status and financial transparency, and provide useful metrics. But the wrong CTMS can become a costly burden.

So, how do you evaluate features and costs to identify the right CTMS for your research institution? Read on for the essentials of evaluating a CTMS. We’ve even included a vendor list at the end to help help narrow down your choices.

System capabilities

Clinical trial management systems come with many capabilities to make your work easier. Before getting swept away by an attractive list of features, identify those which truly matter most to your organization.

Any CTMS should offer these core features:

  • Protocol calendar setup and management

  • Subject visit and procedure tracking

  • Operational reporting

From there, the additional capabilities depend on the vendor. Modern CTMS can handle everything from feasibility assessment, protocol amendments, study milestone recognition, invoicing and payment tracking to financial system integration.

Here’s a list of additional capabilities a CTMS may include (adapted from Applied Clinical Trials Online):

  • Staff effort tracking

  • Budget creation and tracking

  • Business development

  • Trial and site planning

  • Patient recruitment

  • Site management

  • Study financials and investigator grants and payment management

When starting to evaluate systems, identify your must-have features, features that would be nice to have, and those you can you live without. In addition to overarching goals, consider the goals of individuals and departments that will be impacted by the CTMS.



Integrated systems offer the best bang for your buck, ensuring research protocols run efficiently. Benefits include:

  • Fewer logins

  • Easy transitions between data collection and site operation

  • No double data entry; e.g., info entered in the patient database will be automatically replicated when they are added to a study

Financial system integrations come standard with most commercially-available CTMTS, and make invoicing easier. For example, if you complete a visit or reach a milestone in the study, the CTMS should automatically communicate that event or the existence of an invoice to the Finance system for action.

If you’re looking to enhance your CTMS integrations, Bad Rabbit can help—click here to read about a successful software integration project at one of the leading pediatric research institutions in the U.S.


System compliance & security

The biggest question in CTMS security: is it HIPPA and 21 CFR Part 11 Compliant?

Clinical trial management systems are designed to meet regulations, but maintaining compliance is dependent on institution standard operating procedures and staff practices, as well as IT infrastructure.

Additional security features to evaluate:

  • Ability to configure both group and individual security permissions

  • Existence of an audit trail

  • Data backup and recovery plans for hosted systems


System delivery models

Generally, there are three delivery models of CTMS:

1. Cloud-based software-as-a-service (SaaS)

Vendor provides cloud-based server to customers in subscription-based or pay-as-you-go pricing model. There are two types of cloud-based SaaS:

Dedicated SaaS provides a single-tenant environment managed by the vendor, hosted on vendor-owned and -managed servers. Typically, this CTMS is not customizable but allows a balance of customer control with streamlined deployment and vendor-managed maintenance.

On-demand/multitenant SaaS consist of one copy of the CTMS software with one database supporting multiple organizations on a single base of servers. Typically, the least expensive option, these web/cloud-based systems allow you to subscribe and start using the system quickly.

The distinction between dedicated and multitentant SaaS should not impact user experience, but can influence pricing models, and may be a relevant concern for compliance auditors.

Cloud-based systems are ideal for complex, multisite clinical studies because all information is stored in a central location and maintained by a third-party service provider. Study protocols, patient data, outcomes, etc. can be input from any web-based device. However, lack or difficulty of customizations may prove limiting depending on your organization’s goals.

2. Hosted SaaS

Consists of physical servers and software obtained from vendor. The client organization’s IT staff installs and maintains the software on off-premise servers.

Hosted SaaS systems typically require lower upfront investment because infrastructure needs are reduced.

3. Enterprise/on-premise model

End-users purchase software licensing based on their organizational needs and maintain it themselves.

An on-premise CTMS may allow for more advanced customizations, but requires significant configuration by the vendor and user organizations, more long-term and extensive IT support, and a longer implementation cycle.

As technology has evolved, many organizations are shifting to cloud-based models with lower implementation and maintenance costs.



Of course, budget concerns are top of mind. One of the biggest discrepancies in CTMS cost comes in pricing models, which depend on the system delivery method and hosting.

Note: Whether cloud-based or installed, most CTMS vendors charge annual fees for support and updates, and may require additional implementation and hosting fees.

This table demonstrates general pricing models and additional costs for CTMS, broken down by delivery model:

Delivery model

SaaS: On-Demand

SaaS: Dedicated or Hosted

Enterprise On-Site

Pricing Model(s)

Subscription; monthly fees per-user or per-study.

Subscription; user pays monthly or annual fee to use the software.

After setup fees, end users typically pay annual licensing fee.

Setup Fees

Typically none. System is initiated and available online; setup is user-driven.

One-time setup cost includes installation and implementation.

Implementation costs include base software installation; hardware, servers, hosting fees, and network infrastructure; internal IT services; and external/remote access.

Recurring Fees

(Per-User or Per-Study)

Monthly subscription fee per-user or per-study

Monthly hosting fees; monthly subscription fee per-user and/or per-study

Either monthly fee per user, or fixed cost + per-study fee

Per Module Fees

Covering add-ons for payments, monitoring, etc.

On-demand systems may have multiple subscription plans with more functionality in higher-cost tiers

Some vendors include all supported modules with base license and subscription fees. Others may charge monthly fee per user per module.

NOTE: This grid is intended as a general guideline only. Vendor-specific pricing is typically not public information, and prices are tailored to specific customer needs.


Additional vendor selection factors

Beyond delivery models, evaluate prospective vendors’ offerings and pricing for:

  • Training

  • Support and Maintenance

  • Software Updates

  • The existence of active user communities and vendor conferences

  • The ability to impact a vendor’s functional roadmap by providing feedback and voting on features

Support and update pricing models vary, but the existence of a roadmap and active user community indicate the vendor is making appropriate investments.


Vendor options

The right CTMS will help you efficiently manage day-to-day operations of your clinical research site, streamlining daily activities and supporting financial health.

The table below lists common CTMS vendors, and is provided for informational purposes only. Please view product webpages for details, and let us know if we missed anything!

Product Description
Allegro (Forte) Cloud-based clinical trial management system.
BioClinica CTMS A web-based end-to-end clinical trials management solution designed to control, efficiency, and quality data to every study.
Clinical Conductor CTMS (Bio-Optronics, Inc.) CTMS designed to accommodate regulatory compliance and enhance clinical research operations. Keeps track of finances, recruitment, participants and delivers comprehensive reporting and monitoring.
Clincal Studio Electronic Data Capture (EDC) system that streamlines the study build, data collection and management of clinical research. Cloud-based data management system allowing anywhere/remote access.
Intrinsic CTMS® Intrinsic CTMS® is built with native integration with Microsoft applications including Outlook, Excel, SharePoint, and Power BI. Cloud-based, with a streamlined interface, the ability to manage studies at any level, and a task-based design.
OnCore (Forte) Enterprise research system designed to help centralize, manage and gain insight into all research-related activities, including financial management, billing compliance, turnkey reporting, committee management and more.

With myriad vendors, and technology advancing every day, navigating the world of clinical trial management systems can be overwhelming. Bad Rabbit can help guide you through the product analysis and selection process, leveraging both our business domain and technical expertise. We don’t promote any particular software; we just want to help you find the right fit. Drop us a line and let’s get started.