GxP Software Development

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Updated October 20, 2026

• Evidence is a pipeline output Requirements, commits, builds, test runs and deployments each leave a record, and the pipeline links those records into a release the client's QA can review.
• Trace every requirement ID to code and tests A stable ID travels from the user requirement through stories, commits and tagged tests, and the pipeline generates the trace matrix with a gap report on every build.
• Scale testing to documented risk Annex 11, FDA's Part 11 guidance and ICH Q9(R1) tie validation effort to risk, so each requirement gets a risk rating and a test method that the client's QA approves.
• Build data integrity into the product Audit trails, electronic signatures, access control and trusted time map to Part 11 and Annex 11 as engineering controls, with ALCOA+, a data integrity guidance term, as the design checklist.
• The client's QA owns validation Qualification and release approval stay with QA too, while the development partner supplies evidence under a quality agreement that records the split.

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In short: GxP software development is building software that a life sciences company uses for regulated work, such as batch records or laboratory results, in a way that lets the company validate it and keep it validated. The company's quality assurance (QA) team owns validation. In the model this guide proposes, the development team produces much of the validation evidence inside its delivery pipeline: requirement IDs traced to code and tests, test depth set by documented risk, attributable test records, controlled changes and a release record per version. Audit trails, electronic signatures and other data integrity controls are built into the product and mapped to 21 CFR Part 11 and EU GMP Annex 11.

For system owners and QA leads who commission custom or integrated systems as part of pharmaceutical software development, this guide takes the builder's side: how a development team can make validation a review of records rather than a reconstruction.

What GxP Software Development Means

GxP is shorthand for the good practice rules of the life sciences, with the x standing for the field, as in good manufacturing practice (GMP) or good clinical practice (GCP). A system falls under it when the rules require its records or it supports a regulated activity. The regulated company draws that line for its own systems, and a justified and documented risk assessment, the basis Annex 11 sets for the extent of validation, decides how much evidence the build must produce.

In the US, 21 CFR Part 11 treats electronic records and signatures that meet its controls as generally equivalent to paper records and handwritten signatures, with controls for closed systems in section 11.10 that include validation, audit trails and authority checks. In the EU, Annex 11 of the EU GMP guide covers computerized systems, and its principle is that the application should be validated and the IT infrastructure qualified. Part 11 addresses the persons who use the systems, and Annex 11 makes the regulated user check that a system was developed under an appropriate quality management system. No product delivers compliance on its own, so the supplier's development process ends up in the company's evidence.

FDA's Part 11 scope and application guidance says the agency intends to exercise enforcement discretion on specific Part 11 requirements for validation (11.10(a)), audit trails (11.10(e) and (k)(2)), copies of records (11.10(b)) and record retention (11.10(c)), while it enforces all predicate rule requirements; the regulation text is unchanged.

Status snapshot (checked 2026-09-30): the EudraLex Volume 4 index lists "Annex 11 Computerised Systems (revision January 2011)" and no Annex 22, and that Annex 11 text had June 30, 2011 as its deadline for coming into operation. The European Commission's consultation on revised versions of Chapter 4 and Annex 11 and on a new Annex 22 ran from July 7, 2025 to October 7, 2025. No adopted text had been published. FDA's Computer Software Assurance guidance is final: the version issued on February 3, 2026, titled Computer Software Assurance for Production and Quality Management System Software, supersedes the final guidance of September 24, 2025. ISPE published the GAMP 5 Second Edition in July 2022.

Validation Evidence as a Pipeline Output

When computer system validation runs as a document project at the end of development, the trace matrix is assembled by hand before go-live. That breaks down when software ships in small increments. The alternative makes evidence a by-product of work the team already does: every requirement, commit, build, test run and deployment leaves a record, and the pipeline links those records so QA can review a release instead of reconstructing it. The method assumes the builder owns the pipeline, so it does not fit a configured or SaaS product whose vendor runs its own; there QA relies on supplier assessment instead.

A pipeline can run the V-model's paired specification and test levels on every change, which is one way agile delivery and validation can fit together. The table is Pharos Production's engineering mapping, and its last column is our reading, not a structure any regulator prescribes.

Pipeline activity	Evidence it produces	Requirement it supports (our reading)
Requirement intake with an ID and a risk rating	Versioned requirements with ID, risk rating and approval	Annex 11 sections 1 and 4.4: risk management and risk-based user requirements
Specification and design review	Specifications linked to requirement IDs, with review records	Annex 11 section 4.1: validation documentation across the life cycle
Commit and peer review	Commits citing a requirement or change ID, approved by a second engineer	Annex 11 section 10: controlled changes under a defined procedure
Build	Source revision, dependency versions and artifact checksum	Annex 11 section 10, which extends to system configurations
Automated testing at the depth the risk rating sets	Results per requirement ID with build, environment, executor and time	Part 11 section 11.10(a) on validation, under FDA enforcement discretion, scaled to risk as ICH Q9(R1) describes
Infrastructure as code	Environment definition, deployment log and configuration checks	Annex 11 principle that IT infrastructure is qualified
Documentation in version control	Time-sequenced revision history of specifications and manuals	Part 11 section 11.10(k) on documentation and its change control, (k)(2) under FDA enforcement discretion
Trace matrix generation	Requirement to specification, code, test and result for each release	Annex 11 section 4, feeding the client's validation report
Release packaging	Change list, risk impact, test summary, known issues and approvals	Annex 11 section 10, feeding the client's release decision
Operation and monitoring	Audit trail and access reviews, incident records and regression runs	Annex 11 sections 9, 11, 12 and 13 on audit trails, periodic evaluation, security and incidents

Some of what validation needs never passes through a pipeline. Part 11 section 11.10(i) asks the company to determine that the people who develop, maintain or use the system are qualified for their tasks, and 11.10(j) asks for written policies that hold individuals accountable for actions under their electronic signatures. User training, those policies, operating procedures and any performance qualification with users stay with the client.

Requirements Traceability From ID to Code and Test

In GxP work, requirements start as user requirements, and Annex 11 sets the bar for them: "User Requirements Specifications should describe the required functions of the computerised system and be based on documented risk assessment and GMP impact." Each requirement gets a stable ID when it is written. Its wording is versioned while the ID stays fixed, and QA approves a specific version.

In the delivery model we propose, the ID travels with the work. Stories and acceptance criteria reference it, commits and merge requests cite it and automated tests carry it as a tag. On every build the pipeline assembles the trace matrix and reports three kinds of gap: a requirement with no test, a test with no requirement and a requirement whose latest tests failed. A release candidate with an open gap on a high-risk requirement would not reach the validated environment.

An illustration of the proposed model, with invented IDs: requirement URS-042 asks for a documented reason before a GMP-relevant result changes, and the client's QA approves it as high risk. Three tests tagged URS-042 check that a change with a reason is logged, a change without one is refused and nobody can edit the log. On build 142 its trace row links specification FS-12, two commits and the three passing tests, and the release record lists it as new, high risk, three tests passed, no open deviation.

After go-live, the same links show which requirements and tests a change request touches, the input the client's change control needs for impact assessment. Annex 11 expects validation documentation to cover the relevant steps of the life cycle, and a matrix regenerated per release keeps that coverage current.

Risk-Based Testing Under GxP

Testing every function alike wastes effort, and the texts below ask for a risk-based approach instead. Annex 11 bases the extent of validation on a justified and documented risk assessment, FDA's Part 11 scope and application guidance recommends the same basis and ICH Q9(R1) states the principle for the drug side: "The level of effort, formality and documentation of the quality risk management process should be commensurate with the level of risk."

FDA's Computer Software Assurance (CSA) guidance details a risk-based method, but its scope comes first: "This guidance provides recommendations regarding computer software assurance for computers or automated data processing systems used as part of production or the quality management system for medical devices." It gives no recommendations for verifying or validating device software functions, the software that is itself a device. Within its scope, a feature is high process risk when its failure could cause a quality problem that foreseeably compromises safety, meaning a medical device risk, and assurance effort scales to that answer. Its testing runs from unscripted and exploratory testing to scripted tests run manually or by an automated tool, and it calls its listed activities neither prescriptive nor exhaustive.

For a drug GMP system we would apply the same feature-level logic by analogy; that is our interpretation, not FDA's position. ICH Q9(R1) and the Part 11 guidance anchor it on the drug side. We propose a risk rating and a test method for each requirement, and the client's QA approves them. By default we would give high-risk requirements scripted automated tests with negative cases, medium-risk ones automated tests or recorded scenario sessions and low-risk ones exploratory testing with a session record.

ISPE's GAMP 5 guide, industry guidance written for regulated companies, suppliers and regulators, adds a second axis. It groups software into categories 1, 3, 4 and 5 by how much of it is standard, configured or custom-built. Validation effort grows toward custom code. ISPE describes the Second Edition as giving more weight to service providers and to software tools and automation. In the model we propose, the client's QA confirms each category.

What Makes Automated Test Evidence Acceptable

A green pipeline badge is not evidence. For production or quality management system software used by medical device manufacturers, FDA's CSA guidance says what the record should capture: "When establishing the record, the manufacturer should capture sufficient objective evidence to demonstrate that the software feature, function, or operation was assessed and performs as intended." The record also names the intended use, the risk analysis result and the testing done. Outside that scope the guidance does not apply, but in our view a similar test suits any record: a reader who was not there should see what was tested, on which build, by whom and with what result. On a GxP engagement, our QA services team would write that test into the pipeline as rules:

• Each result names the requirement ID and risk rating it covers.
• Each run is pinned to an exact build: source revision, artifact checksum, environment and configuration version.
• The record keeps actual results and logs, not only a pass flag.
• The executing pipeline identity, the reviewer and a time from a synchronized clock make every run attributable.
• Evidence goes to write-once storage.
• Failures stay in the record, and an intermittent failure is a deviation to investigate rather than a retry that hides it.
• Test code and test tools sit under the same change control as the product, with the tool versions recorded for each run.

Where IQ, OQ and PQ Fit

Installation, operational and performance qualification (IQ, OQ and PQ) are a common industry way of organizing qualification. Neither Part 11 nor the Annex 11 text in force names them, nor does FDA's CSA guidance; PIC/S inspectorate guidance lists them among the tests computerized system validation should include as necessary, and Annex 11 asks that IT infrastructure be qualified. Where a client's procedures call for them, continuous delivery changes when they run.

In the model we propose, installation evidence comes from infrastructure as code: each environment is built from a versioned definition and checked against it automatically, which gives the client's IQ a repeatable record per environment. Operational evidence comes from automated functional and regression suites run against the specification for each release candidate. Performance qualification stays with the client's users under their own procedures, and QA decides per release what to repeat from the risk of the change and the trace of what it touched.

Change and Configuration Control in CI

After the first release, change control keeps or loses the validated state. Annex 11 is brief: "Any changes to a computerised system including system configurations should only be made in a controlled manner in accordance with a defined procedure." Part 11 section 11.10(k)(2), a clause under FDA's enforcement discretion, suits teams that keep documentation next to code, since it asks for "Revision and change control procedures to maintain an audit trail that documents time-sequenced development and modification of systems documentation." In our reading, documentation held in version control with reviewed revisions can produce that trail, provided written revision and change control procedures govern it. In the pipeline we propose, which is engineering practice rather than a list either text contains:

• Every change starts from an approved change record naming the requirements and risk it affects.
• Merges to the protected main branch need a passing pipeline and review by an engineer other than the author.
• Pipeline definitions are code, reviewed like code.
• The artifact that passed testing is the one promoted to production, identified by checksum and never rebuilt.
• Environment configuration lives in version control, with drift checks against the approved definition.
• Libraries are pinned, each build carries a software bill of materials and a dependency update is a change like any other.
• Deployment to a validated environment waits for the client's recorded release approval, and emergency fixes follow the client's fast path.

Release Records and Periodic Review

Each release closes with the record listed in the table above. GMP software validation does not end at go-live. Annex 11 states: "Computerised systems should be periodically evaluated to confirm that they remain in a valid state and are compliant with GMP." A well-instrumented system can supply several inputs for that evaluation, such as change history, incident records, audit trail and access reviews, restore tests and regression runs on platform updates. The evaluation and its conclusion belong to the client's QA.

Cloud and SaaS Releases

Cloud platforms and SaaS products change on the provider's schedule. In the model we propose, the client's infrastructure is defined as code, which gives cloud qualification a repeatable baseline, and a regression suite runs per integration against each provider release before it reaches the validated environment. The Annex 11 consultation draft cites the increased use of cloud services in its introduction.

Data Integrity Controls Built Into the Software

Some controls cannot be added by procedure after delivery: audit trails, electronic signatures, access and time become engineering here.

Audit Trails

Section 11.10(e) of Part 11 lists the control: "Use of secure, computer-generated, time-stamped audit trails to independently record the date and time of operator entries and actions that create, modify, or delete electronic records." Changes must not obscure earlier entries, and the trail is kept at least as long as the records it covers. FDA has announced enforcement discretion for this clause while it enforces all predicate rule requirements.

Annex 11 section 9 asks that "Consideration should be given, based on a risk assessment, to building into the system the creation of a record of all GMP-relevant changes and deletions", with the reason for each change or deletion of GMP-relevant data documented and the trail available in an intelligible form and regularly reviewed.

In the design we propose, that means an append-only log written by the server for every create, change and delete of a GxP record. Each entry holds the user, the time, the old and new values and, for GMP-relevant data, a reason captured at the moment of change. Administrators can read the trail but cannot edit or disable it.

Review decides whether the trail is usable. FDA's data integrity questions and answers expect that "Personnel responsible for record review under CGMP should review the audit trails that capture changes to data associated with the record as they review the rest of the record", so in the design we propose the trail opens from the record screen and the review itself is recorded. The Annex 11 consultation draft also encourages tools for audit trail review, which argues for review reports and exception filters inside the product.

Electronic Signatures

In the design we propose, each signature is stored as its own record with the signer's identity, the meaning, the server time and a hash of the exact record version signed; the hash is how the design binds each signature to its record, the link section 11.70 asks for. Signing outside a continuous session asks for all components again, and a change to a signed record needs a new signature. The company itself verifies each signer's identity and certifies to FDA that its electronic signatures are intended to be the legally binding equivalent of handwritten ones.

A Part 11 electronic signature is a data structure with rules. Signed records show the signer's printed name, the date and time of signing and "The meaning (such as review, approval, responsibility, or authorship) associated with the signature." Signatures are linked to their records so they cannot be excised, copied or transferred by ordinary means, each signature belongs to one person and a non-biometric signature uses at least two components, such as an identification code and a password. Annex 11 section 14 adds that signatures are permanently linked to their record and carry the time and date they were applied.

Access and Identity

In the design we propose, sign-in goes through the client's identity provider, and roles mirror the client's procedures. There are no shared accounts, repeated failed attempts raise alerts, every grant and revocation lands in the audit trail and an access review report shows who can do what.

Part 11 limits access to authorized individuals, adds authority checks on who may sign or alter a record and, for signatures based on identification codes and passwords, asks for transaction safeguards that detect and urgently report attempts at their unauthorized use. Annex 11 section 12 asks for access controls and a record of who entered, changed, confirmed or deleted data with the date and time. The consultation draft proposes unique personal accounts for all users.

Time

Both texts want the date and time of each audited action and signature, and how that time stays trustworthy is an engineering choice. In the design we propose, that means server clocks synchronized to a trusted source, time stamps stored in UTC and shown with the user's time zone, drift monitored like any other control and never a time taken from a user's device.

ALCOA+ as a Design Checklist

Neither Part 11 nor the Annex 11 text in force uses the term ALCOA+, which appears in data integrity guidance. FDA's drug CGMP questions and answers use the five-letter ALCOA: attributable, legible, contemporaneously recorded, original or a true copy and accurate. PIC/S and MHRA guidance describe the plus as complete, consistent, enduring and available. PIC/S also states that "Companies should implement technical solutions that improve compliance with ALCOA+". The Annex 11 consultation draft would bring the term into the annex: "As defined by the ALCOA+ principles, data integrity covers many topics". So ALCOA+ works best as a design checklist, not a legal test.

• Unique accounts, server time stamps and entry at the moment of the action make data attributable and contemporaneous.
• Human-readable views and exports of a record with its audit trail and signatures keep data legible and available for the retention period, as Part 11 section 11.10(b) and (c) require, both under FDA's enforcement discretion.
• Original data is kept as captured, and copies come from a verified process.
• Accuracy, completeness and consistency come from validation rules at entry, a second check on critical manual entries as Annex 11 section 6 asks, no silent deletes and enforced step sequencing, which Part 11 section 11.10(f) calls operational system checks.
• Enduring data survives migrations. Restore tests prove the backups, archives are checked as Annex 11 section 17 asks and a legacy modernization project verifies migrated records before the old system is retired.

Annex 11 section 5 expects built-in checks when systems exchange data electronically, so each integration between GxP systems would get message validation, reconciliation counts and its own audit entries.

Supplier Documentation for Your QA Team

Annex 11 reaches suppliers through the regulated user: "The regulated user should take all reasonable steps, to ensure that the system has been developed in accordance with an appropriate quality management system." It also bases the need for a supplier audit on a risk assessment and has the manufacturer sign formal agreements that state each third party's responsibilities. Part 11 section 11.10(i) brings the development team into scope, since the controls a regulated company must employ include "Determination that persons who develop, maintain, or use electronic record/electronic signature systems have the education, training, and experience to perform their assigned tasks." The determination is the company's, and the supplier supports it with its team's records.

For its supplier assessment, QA can reasonably ask for a written description of the delivery lifecycle and for named team members with their roles, access and training. It can also ask for a security statement naming any certificates or audit reports the supplier holds, disclosure of subcontractors and agreement to host an audit and support an inspection.

AI Features in GxP Systems

We would treat an AI feature inside a GxP system, such as document classification, as validated software with an intended use, a risk rating, test evidence and change control. The model version, training data reference, prompts and thresholds would become configuration items versioned with the evaluation set, so a model update would be a change with its own evidence. In our approach, where a wrong output could affect a GxP decision, a trained reviewer stays between the output and the decision.

PIC/S cited the implementation of AI systems in pharmaceutical manufacturing as a reason to update the GMP guidelines, and ISPE's description of GAMP 5 lists appendices on AI and machine learning. The snapshot above gives the status of the Annex 22 that the same consultation proposed.

Who Does What: A RACI for Validation-Ready Delivery

The split below is the delivery model we propose, in which the client's QA owns validation and qualification. No regulation assigns these letters, so the table belongs in the formal agreement with the supplier that Annex 11 section 3 expects. R is responsible, A accountable, C consulted and I informed. On the qualification row, supplier-run suites produce evidence and the client's QA decides what counts as qualification.

Activity	Client QA	Client system owner and users	Pharos Production
GxP assessment, validation plan and approach	A, R	C	C
User requirements and GxP risk assessment	A	R	C
Risk rating and test method per requirement	A	C	R
Functional and design specifications	A	C	R
Development, code review, automated testing and trace matrix	C	I	A, R
Environment definition and installation records	C	I	A, R
Assessment of the CI server, pipeline definitions and test tools	A	I	R, supplies the evidence
Qualification, including IQ, OQ and PQ	A	R	C
Validation report and release approval	A, R	C	I
Change control and impact assessment after go-live	A	R	C
Audit trail review during record review	A	R	I
Periodic evaluation	A	R	C
Supplier assessment and audit of the development partner	A, R	C	C

The same agreement should settle evidence custody: in the model we propose, the write-once evidence store sits in the client's cloud account or receives each release's evidence there. At contract end the supplier hands over the complete store and its index, and the client keeps the records retrievable through the retention period, as Part 11 section 11.10(c) asks, under FDA's enforcement discretion, with archived data checked under Annex 11 section 17.

How Pharos Production Helps

Pharos Production offers validation-ready delivery, with evidence from the pipeline handed to the client's QA, and would supply every item on the supplier documentation list above. Pharos Production holds no ISO 27001 certificate and no SOC 2 report, so the security controls it offers on a pharma engagement are the ones written into the quality agreement and open to your supplier audit. The offer, with engagement options on our pharmaceutical software development services page, also includes:

• A validation-ready pack with every release: trace matrix, test evidence, change list and release record
• A quality agreement next to the master services agreement that records the split above

Sources: eCFR 21 CFR Part 11. FDA Part 11 scope and application guidance, CSA guidance, data integrity questions and answers and ICH Q9(R1). European Commission Annex 11, EudraLex Volume 4 index, consultation page and Annex 11 draft. PIC/S PI 041-1 and consultation news. MHRA data integrity guidance. ISPE GAMP 5 page. Engineering guidance, not regulatory or legal advice.

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Last updated: October 20, 2026

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• What is a GxP system?

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  A GxP system is software that handles records a good practice rule requires, such as good manufacturing or good clinical practice, or that supports a regulated activity. Laboratory information management, manufacturing execution and electronic batch record systems are typical examples.

  In the US, Part 11 reaches records kept in electronic form under FDA's records requirements, and FDA's Part 11 scope and application guidance says the agency interprets that scope narrowly. Each regulated company makes the call for its own systems, and Annex 11 bases the extent of validation on a justified and documented risk assessment.

• What is the difference between GxP and non-GxP software projects?

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  A GxP project builds or changes a system that holds regulated records or supports a regulated activity, so its requirements, tests, changes and releases should leave evidence that the client's QA can use for validation. A non-GxP project, such as a marketing website, can follow ordinary engineering practice.

  A pipeline that produces evidence by default should make it easier to move a system across that line later.

• How do you validate a computer system for GxP use?

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  The regulated company plans the validation, writes user requirements with a risk assessment, confirms through testing and qualification that the system meets them and closes with a report and a release decision. A development supplier contributes specifications, test evidence traced to the requirements and records of each change.

  Annex 11 wants validation documentation to span the life cycle, and FDA's Part 11 guidance recommends a justified and documented risk assessment as the basis for the approach.

• How do you keep a GxP system in a validated state after go-live?

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  Through change control and periodic evaluation, plus two Annex 11 duties that are easy to overlook: every incident, not only system failures and data errors, is reported and assessed, with the root cause of critical incidents identified, and systems that support critical processes need provisions for continuity. In the model we propose, the periodic evaluation can draw on regression runs after platform or vendor releases, audit trail and access reviews and incident records, while its conclusion stays with the client's QA.

• How do IQ, OQ and PQ work with agile, continuously delivered software?

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  Where a client's procedures call for IQ, OQ and PQ, they can run on evidence the pipeline produces continuously. They are a common industry way of organizing qualification, used in PIC/S inspectorate guidance but not in Part 11 or the Annex 11 text in force, which asks that IT infrastructure be qualified without naming the stages.

  In the model we propose, installation evidence comes from infrastructure defined as code and checked on every deployment, automated suites cover operational testing for each release candidate and the client's users still perform performance qualification. QA sets what to repeat from the risk of the change and its trace.

• Can software be 21 CFR Part 11 compliant out of the box?

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  A product can provide the technical controls Part 11 lists, such as access limits, signature manifestations and authority checks, but compliance also depends on the company's validation, procedures and training. A claim of out-of-the-box compliance is best read as a list of controls to verify.

  The certification to FDA that a company's electronic signatures are intended to be the legally binding equivalent of handwritten ones comes from that company, not from the vendor.

• Does FDA's CSA guidance apply to drug manufacturers?

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  Not by its own terms. The guidance addresses software that device manufacturers use in production or in their quality management system, and it makes no recommendations on validating the device software functions themselves.

  Using its feature-level, risk-based logic for a drug GMP system is an interpretation by analogy, and this guide labels it as ours. On the drug side, ICH Q9(R1) and FDA's Part 11 scope and application guidance support scaling effort to risk.

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