Trial coordinators tracking patient visits, protocol deviations, and site milestones in spreadsheets with no central visibility for the sponsor -- database locks delayed because the status of every site is a phone call?
Regulatory inspection findings on data integrity because source data verification records were in email threads with no audit trail?
Clinical Trial Management Software Development
Trial coordinators tracking patient visits, protocol deviations, and site milestones in spreadsheets have no central visibility -- and the sponsor is always a phone call behind the actual status. Database locks get delayed because no one has a real-time view of where every site stands.
We build custom clinical trial management software for pharma companies, biotech firms, and CROs. Trial setup, site management, patient enrolment tracking, deviation management, and regulatory documentation in one system -- with an audit trail that holds up under inspection.
Trial setup -- protocol, arms, visits, and eligibility criteria
Site and investigator management with performance dashboards
Patient enrolment, visit scheduling, and deviation tracking
Audit trail and regulatory document management (ICH E6)
A clinical trial management system (CTMS) is purpose-built software for tracking the operational and regulatory aspects of clinical trials -- site activation, patient enrolment, visit compliance, protocol deviations, and regulatory document collection. RaftLabs builds custom CTMS platforms for pharma companies, biotech firms, and CROs that need trial operations management and audit-ready documentation built to ICH E6 and 21 CFR Part 11 requirements.
100+Products shipped
·24+Industries served
·FixedCost delivery
·12-14Week delivery cycles
Why trial operations break down without a dedicated CTMS
Clinical trials generate a large volume of operational data across sites, coordinators, and timelines. Protocol version changes affect eligibility criteria and visit schedules. Investigator staff turns over. Sites activate and close at different times. Patients miss visits, deviate from protocol, and withdraw consent. Each of these events needs to be documented, reviewed, and tracked -- not managed through email threads and site-level spreadsheets.
The inspection risk is the most direct consequence. Regulatory agencies expect to see a controlled record of every site activation decision, every deviation, and every change to the trial master file. When that record exists in email folders and shared drives with no version control or access log, the finding is data integrity -- one of the costliest inspection outcomes in terms of delay and remediation cost.
A custom CTMS gives the sponsor a single view of operational status across all sites without coordinator phone calls. It gives each site a structured workflow for the tasks they are responsible for. And it produces the audit trail that inspection readiness requires -- not as an export, but as a live record of every action taken in the system.
What we build
Protocol and study setup
Trial configuration covering study arms, visit schedules, inclusion and exclusion criteria, and randomisation schemes. Protocol amendment management that updates visit schedules and eligibility criteria across all active sites when an amendment is approved. Investigational product management with dosing schedule, storage requirements, and dispensing record structure. Study calendar view showing visit windows, required assessments, and allowed deviation ranges. Protocol version history so the current criteria and schedule at any point in the trial are retrievable for inspection review.
Site management
Site qualification and initiation tracking from feasibility through IRB approval, regulatory submission, and activation. Investigator and study staff records with role assignments, training records, and delegation of authority log. Regulatory document collection -- IRB or IEC approval, 1572 forms, financial disclosure, and CVs -- with expiry tracking and renewal reminders. Site performance dashboard showing enrolment against target, visit compliance rate, query rate, and deviation count by site. Site visit scheduling and report management for monitoring activities.
Patient enrolment and tracking
Screening log with screen fail reason capture and eligibility criteria verification. Informed consent tracking with version and date recorded per patient. Enrolment status by site and study-wide with projection against target. Visit scheduling with allowed window calculation from the protocol calendar. Visit compliance tracking with overdue visit flagging and lost-to-follow-up identification. Withdrawal and early termination recording with reason categorisation for safety and statistical reporting.
Protocol deviation management
Deviation capture linked to the patient record, the protocol section, and the visit where the deviation occurred. Deviation classification by severity -- minor, major, or important -- with the classification workflow requiring review and sign-off. CAPA assignment and tracking with effectiveness review at the defined review date. Deviation trend reporting by site, investigator, category, and protocol section so patterns are visible before they become inspection findings. Sponsor and CRO review workflow with approval tracking and response documentation.
Data management integration
Integration with EDC systems -- Medidata Rave, Veeva Vault EDC, and others -- so visit data entered in the EDC is reflected in the CTMS without dual entry. Data query status surfaced in the operational view alongside visit compliance so coordinators see open queries alongside upcoming visits. Data reconciliation alerts when the EDC record and CTMS enrolment record are inconsistent. Database lock workflow tracking -- query resolution, data freeze, and lock status by site -- replacing the email chain that typically manages the lock process.
Regulatory documentation
Trial master file index aligned to ICH E8 and sponsor TMF reference model. Document version control with upload, review, and approval workflow. Inspection readiness checklist that identifies missing or out-of-date TMF documents before an audit. Audit trail covering every system action -- document upload, approval, deviation entry, and enrolment change -- with user identification and timestamp. 21 CFR Part 11 electronic signature implementation for documents requiring sponsor or investigator sign-off. TMF health reporting showing completeness by section and site.
Frequently asked questions
A CTMS is operational software for managing the conduct of a clinical trial -- not the scientific data, which is handled by an EDC, but the operational record: which sites are active, how many patients are enrolled at each site, whether visits are happening on schedule, what deviations have occurred, and whether the regulatory documents at each site are current. It is the tool that gives the sponsor visibility into trial operations without relying on individual site coordinator reports. It also produces the audit trail and TMF documentation that inspection readiness requires under ICH E6 Good Clinical Practice guidelines.
EDC systems capture clinical data from patient visits -- the structured data entered against the protocol data collection requirements. The CTMS captures operational data -- enrolment status, visit compliance, deviations, and site management records. Integration between the two systems means the CTMS shows visit completion status based on EDC data entry, and query counts from the EDC appear in the site performance view without dual entry. We integrate with Medidata Rave, Veeva Vault EDC, and OpenClinica through their APIs. For EDC systems without a standard API, we integrate through file-based exchange. Integration scope and approach is confirmed during discovery.
The primary standards for clinical trial management systems are ICH E6 (Good Clinical Practice) for trial conduct and documentation, 21 CFR Part 11 for electronic records and signatures in FDA-regulated trials, and EU Annex 11 for computer system validation in EMA-regulated trials. ICH E6 defines what records must be maintained and what the audit trail must capture. 21 CFR Part 11 defines how electronic signatures must be implemented and what system access controls are required. We design the system to meet these requirements from the start. Your validation team performs the formal computer system validation process. We support that process with documentation and test protocols.
A CTMS covering trial setup, site management, patient enrolment and visit tracking, deviation management, and regulatory document management for a single active trial programme typically takes 16 to 20 weeks from requirements sign-off to go-live. EDC integration adds four to six weeks depending on the EDC system and integration complexity. Multi-programme platforms covering several trials concurrently, or systems requiring formal IQ/OQ/PQ validation documentation, take longer. We scope the timeline and milestone plan at the start of the engagement so your clinical operations and validation teams can plan around it.
Talk to us about your clinical trial management project.
Tell us your trial programme, the systems you are currently using, and where the operational gaps are. We will scope a CTMS built around how your trials run.
