Pharmaceutical Software Development: GxP Software, 21 CFR Part 11 Controls and Biotech Software Development

Updated October 2026 · Written and maintained by the Progression Agency strategy team

Pharmaceutical software development is building the custom systems drug and biotech companies run their labs, trials, quality and manufacturing on, where every record may one day be read by an inspector. Pharma software development differs from ordinary business software because the predicate rules decide which records matter, 21 CFR Part 11 sets the controls for electronic records and signatures, and the regulated company’s quality unit, not the developer, decides when a system is validated. This page covers the pharmaceutical software we build, what GxP software means, the Part 11 software requirements, validation support, data integrity and what projects cost. We build GxP-aware software for pharma and biotech teams, starting with a free proposal and a written scope.

What is pharmaceutical software development?

Pharmaceutical software development is the design, build and support of custom software for drug, biologic and biotech companies, and for the labs, contract organizations and distributors around them. The software usually creates, changes or stores records that a regulator can ask to see, which is why the build comes with requirements, test evidence and change control that an ordinary business app would not need. Pharma software development sits beside our work on healthcare software development for providers and payers, but the buyers, the records and the rules are different.

Who buys it

The buyers are drug sponsors, contract manufacturers and development organizations, contract research organizations, testing labs, biotech startups and distributors. A sponsor may want a quality workflow tool; a contract lab may want a client portal on top of its LIMS; a startup may want a data platform for its assays. What they share is a quality unit that will ask how the software was specified, tested and changed.

Pharma software, pharmacy software and device software are different jobs

Pharma software supports discovery, development, manufacturing, quality and distribution of drugs; the records are lab data, batch records, trial data and safety reports. Pharmacy software supports dispensing and patient-facing pharmacy operations, and it is a separate job covered by our pharmacy app development page. Software that is itself a medical device, or sits inside one, follows device life cycle standards, which we cover under embedded software development. This page covers the first.

Custom software beside the platforms you already license

Many pharma companies already license a LIMS, a quality system, an ERP and a clinical platform. Custom work fills the gaps between them: an integration that stops re-keying, a portal for a client, a dashboard across systems, a workflow no vendor product covers. We name vendors only as categories because we build around whatever you already run, and we claim no partnership with any of them.

Pharmaceutical software we build

Pharmaceutical software we build falls into eight areas. Each can sit inside or outside GxP scope depending on what its records are used for, and the customer’s quality unit makes that call. The plant-floor side shares ground with our manufacturing software development work, the field side with HCP marketing, and companies that sell a LIMS or quality product and need it marketed can read about life sciences marketing.

LIMS software development and lab data tools

LIMS software development covers extending a laboratory information management system you already license, building a lightweight one for a young lab, and writing the tools around it: sample intake, instrument file parsers, review dashboards and client portals. The design question that matters is where the authoritative record lives. We keep that single, make every transfer traceable and leave existing instruments and the LIMS in place wherever possible.

Quality workflows: deviations, CAPA, change control and training records

Deviation, corrective and preventive action, change control and training workflows are routing problems with strong record rules. The software needs roles, due dates, escalation, attachment handling, e-signatures where the process calls for them and a history no one can edit quietly. A gap-filling tool beside a purchased quality system is common, such as a trend dashboard or a supplier portal.

Manufacturing and batch record integrations

Batch data lives in manufacturing execution systems, historians, ERP and paper. Integrations move recipe parameters, weights, equipment states and results between them. The risk is mismatched data, so each interface carries the source, the user or system that sent it and the time, and unmatched records are flagged and not dropped.

Clinical operations tools and integrations

Clinical teams run electronic data capture, a clinical trial management system, an electronic trial master file and many smaller tools. Custom work covers study dashboards, site communication portals, document routing and data feeds between systems. Where the software handles study records, the sponsor’s data governance and the guidance covered below apply.

Pharmacovigilance intake and case routing

Safety teams receive adverse event reports by email, phone, web forms and partners. Software can capture each report once, check for missing fields, route it to the right reviewer and keep a time-stamped trail of who did what. The medical coding and the safety database stay with the system of record; our tool feeds and tracks the work around it.

Regulatory document and submission tracking

Regulatory teams track submissions, commitments, health authority questions and the documents behind them. A custom tracker can link each commitment to its owner and due date, pull status from document systems and give leadership a single view. It does not replace the submission itself or the system a company uses to publish it.

Supply chain and serialization data

FDA describes the Drug Supply Chain Security Act as outlining steps to achieve an interoperable and electronic way to identify and trace certain prescription drugs at the package level as they move through the supply chain. For software, that means data exchange with trading partners and clean serial number records. We build the connectors, exception queues and reporting around the company’s serialization platform.

Field and HCP apps

Field teams use apps for call notes, sample requests, content sharing and consent capture. These are usually closer to commercial than to GxP records, but privacy, consent and promotional review rules still apply. The outreach strategy itself is the subject of our HCP marketing page; we build the app a field team carries.

GxP software: what the term covers

GxP is the shorthand for the good practice quality rules, with the letter standing for the practice: manufacturing, clinical, laboratory and others. GxP software is software that creates, changes, stores or reports records governed by those rules. Calling a product GxP software describes how its records are used, not a badge it carries. Many GxP software systems sit in one company, each with its own risk.

GMP, GCP, GLP and the predicate rules

The underlying requirements are what FDA’s scope guidance calls predicate rules, meaning the requirements other than Part 11 that say which records must be kept. Examples include 21 CFR Part 211, current good manufacturing practice for finished pharmaceuticals; 21 CFR Part 58, good laboratory practice for nonclinical laboratory studies; and the ICH guideline for good clinical practice. Part 11 then governs how those records are kept when they are electronic. The first question for any system is therefore which predicate rule creates the record.

GxP and non-GxP systems on one project

A single project often touches both kinds of record. A lab dashboard may show results from a GxP system alongside purely operational data. The usual approach is to scope controls by risk: put the full controls where regulated records are created or changed, and keep the rest simpler. FDA’s data integrity guidance says that when one system performs both GMP and non-GMP functions, the chance that the non-GMP functions affect GMP operations should be assessed and mitigated.

What makes software GxP-ready, and what does not

Software is ready for GxP use when its design, evidence and change history let the regulated company show that it does what it is meant to do. That comes from architecture and records: unique accounts, audit trails, controlled changes, tested requirements. It does not come from a label. We build GxP-aware software, and the customer’s quality unit decides when it is fit for use.

Is every system in a pharma company GxP software?

No. A company also runs finance, human resources, marketing and facilities systems that create no regulated records. The test is the record: a system that creates, changes, stores or reports a record required under a predicate rule is in scope for the controls, and one that does not is not. The quality unit makes and documents that decision, and a system used for both kinds of work needs its non-regulated functions assessed for their effect on the regulated ones, as FDA’s data integrity guidance says.

21 CFR Part 11 software requirements

The 21 CFR Part 11 software requirements are the criteria under which FDA considers electronic records and electronic signatures trustworthy, reliable and generally equivalent to paper records and handwritten signatures, as section 11.1 of the regulation puts it. Software teams meet them through design choices and procedures. In plain words, 21 CFR Part 11 software is software that creates or keeps records the rule covers, and the FDA 21 CFR Part 11 software requirements are a handful of short sections, summarized below.

Controls for closed systems (11.10)

A closed system is one where access is controlled by the people responsible for the records on it. Section 11.10 asks for procedures and controls designed to ensure authenticity, integrity and, when appropriate, confidentiality of electronic records, and that the signer cannot readily repudiate the signed record. They include: validation of systems; accurate and complete copies in human readable and electronic form; protection of records for retrieval throughout retention; limiting access to authorized individuals; secure, computer-generated, time-stamped audit trails that do not obscure previously recorded information and are retained at least as long as the records; operational system checks to enforce permitted sequencing; authority checks; device checks; education, training and experience for the people who develop, maintain and use the systems; written policies that hold individuals accountable for actions under their electronic signatures; and controls over systems documentation.

Open systems (11.30)

An open system is one where access is not controlled by the people responsible for the records. Section 11.30 requires procedures and controls designed to ensure authenticity, integrity and confidentiality from the point of creation to receipt, including the 11.10 controls as appropriate and additional measures such as document encryption and appropriate digital signature standards. A system that exchanges records with outside parties across the internet is the case to think about.

Electronic signatures (11.50, 11.70, 11.100 to 11.300)

Signed records must show the printed name of the signer, the date and time of signing and the meaning of the signature, such as review, approval, responsibility or authorship, and those items get the same controls as the record (11.50). Signatures must be linked to their records so they cannot be excised, copied or transferred to falsify a record by ordinary means (11.70). Each signature must be unique to one individual and not reused, and the organization must verify identity before issuing one (11.100). Signatures not based on biometrics need at least two distinct identification components such as an identification code and a password, and must be administered so that attempted use by anyone but the owner requires collaboration of two or more individuals (11.200). Controls for codes and passwords cover uniqueness, periodic checks or revision such as password aging, loss management, transaction safeguards and testing of tokens and cards (11.300).

How we build those controls

Our manufacturing software page says it this way: “We implement electronic record and signature controls when required, with validation support.” In a build, that means named accounts and roles, an audit trail the application writes whenever a regulated record is created, changed or deleted, signature screens that capture the meaning of the signature, records and signatures stored together and a way to produce a readable copy. The regulated company still decides which records are in scope, which procedures surround the software and when the system is validated.

What should an audit trail screen show?

At minimum the record, the field changed, the old and new values, the user, the date and time, and the reason where the process asks for one. Section 11.10(e) requires that changes not obscure previously recorded information, so the screen shows history and never overwrites it. Filters by record, user and date let a reviewer work through changes quickly, and an export gives an inspector a readable copy. FDA’s data integrity guidance gives an HPLC example: the audit trail includes the user name, the date and time of the run, the integration parameters used and details of any reprocessing, with a change justification.

What FDA’s Part 11 scope guidance changed

Many teams read Part 11 as broader than FDA intends. FDA’s Part 11 scope and application guidance, issued in September 2003, explains how the agency interprets the rule’s scope and where it uses enforcement discretion. It is guidance, which FDA says describes its current thinking and is a recommendation unless a regulatory requirement is cited.

Narrow scope and enforcement discretion

The guidance says FDA intends to interpret the scope of Part 11 narrowly and to exercise enforcement discretion for the Part 11 requirements for validation, audit trails, record retention and record copying as the guidance explains. Records must still be maintained or submitted under the underlying predicate rules, and FDA can take action for noncompliance with those. It treats records required under predicate rules and kept in electronic format in place of paper as Part 11 records, and recommends deciding and documenting which records those are. Systems that were operational before August 20, 1997, the effective date of Part 11, can fall under enforcement discretion for all Part 11 requirements if a list of conditions is met, including that the system met and still meets the predicate rules and that there is documented evidence it is fit for its intended use.

Why many teams still build full audit trails

The same guidance says that even where no predicate rule calls for a given audit trail, it may still be important to have audit trails or other measures to ensure the trustworthiness and reliability of records, and that audit trails can be particularly appropriate when users create, modify or delete regulated records during normal operation. FDA’s data integrity questions and answers add that audit trail review is similar to assessing cross-outs on paper. For a new build, the reasoning is practical: adding an audit trail while designing the data model is simpler than adding it later. This is reasoning about a software project, not legal advice.

GxP software validation: who does what

GxP software validation is the documented demonstration that a system does what it is intended to do for its intended use. The party that owns the intended use owns the decision. The sections below say how that splits when a vendor builds the software and a regulated company uses it. Pharma software validation, and 21 CFR Part 11 software validation under section 11.10(a), both start from the customer’s intended use.

The regulated company validates; we support it

The rules put the responsibility on the user of the system. Section 11.10(a) lists validation of systems to ensure accuracy, reliability, consistent intended performance and the ability to discern invalid or altered records among the controls for persons who use closed systems. ICH E6(R3) says the responsible party is responsible for the validation status of a system throughout its life cycle. FDA’s data integrity guidance says a workflow is an intended use of a computer system to be checked through validation, in proportion to risk, and that qualifying a platform alone does not show a given workflow is correct. We support all of that with requirements, tests and records. We do not describe any system as validated.

Can a software vendor validate a system for the customer?

A vendor can test its own software and supply evidence, but validation is shown against the customer’s intended use, in the customer’s environment, under the customer’s quality system. FDA’s data integrity guidance makes the point about intended use: qualifying a platform does not show that a given workflow produces correct results. So we write the tests and supply the records, and the customer’s quality unit approves the validation.

GAMP 5 Second Edition

ISPE’s public page for the GAMP 5 Guide, Second Edition, published in July 2022, describes ISPE GAMP 5: A Risk-Based Approach to Compliant GxP Computerized Systems. It says the edition reflects the greater role of service providers, software development approaches that are not only linear but also iterative and incremental, and wider use of software tools and automation, and that it stresses critical thinking by experienced subject matter experts. We can work inside a GAMP 5 based approach your quality system uses. We rely only on ISPE’s public page, and we claim no GAMP credential.

What we hand over

Validation support is documents and evidence your quality unit can review: the requirements, the design specifications, traceability from each requirement to its tests, the test scripts and results, release notes for every version and the configuration records for each environment. You decide how much of that goes into your validation package and what you add.

Computer software assurance

FDA’s guidance Computer Software Assurance for Production and Quality Management System Software (February 2026) describes computer software assurance as a risk-based approach to establish confidence in the automation used for production or quality management systems. It was issued by the device and biologics centers, its scope is software used in medical device production or the device quality management system, and it supersedes the September 24, 2025 version. For drug and biologic teams, whether to apply similar risk-based thinking to a GxP system is the quality unit’s call. ISPE’s page says the second edition of GAMP 5 added discussion of current FDA activity on computer software assurance.

Data integrity built into the architecture

Data integrity is easier to design in than to retrofit. The record lifecycle below is the spine of most regulated systems, and each stage leaves evidence for the next.

FDA’s data integrity questions and answers

FDA’s December 2018 guidance, Data Integrity and Compliance With Drug CGMP: Questions and Answers, says its purpose is to clarify the role of data integrity in current good manufacturing practice for drugs, and that FDA expects all data to be reliable and accurate. It defines data integrity as the completeness, consistency and accuracy of data, which should be attributable, legible, contemporaneously recorded, original or a true copy, and accurate, shortened to ALCOA. It defines an audit trail as a secure, computer-generated, time-stamped electronic record that allows reconstruction of the course of events relating to creation, modification or deletion of an electronic record. It also says shared login accounts prevent a unique individual from being identified, which is why a build gives every user a personal account.

Computer controls under 21 CFR 211.68

Section 211.68 covers automatic, mechanical and electronic equipment, including computers. It requires routine calibration, inspection or checking under a written program, controls so that changes to master production and control records are made only by authorized personnel, checks of the accuracy of input and output with a frequency based on complexity and reliability, and backup data that is exact, complete and secure from alteration, inadvertent erasure or loss. Software designs answer those points with permissions, input validation, reconciliation and tested backups.

Backups, time sync, roles and the audit trail review

Four habits do most of the work. Back up on a schedule and test restores. Keep server clocks in sync so time stamps mean something. Give roles the least access that works. And make audit trail review a normal screen with filters; who reviews it and how often is covered next.

Who reviews the audit trail, and how often?

FDA’s data integrity guidance says the personnel responsible for record review should review the audit trails that capture changes to the data as they review the rest of the record, comparing it to assessing cross-outs on paper. It adds that production and control records, which include audit trails, must be reviewed and approved by the quality unit. Where the regulations set a review frequency for the data, the same frequency applies to the audit trail; where they do not, it is set by knowledge of the process and a risk assessment that weighs data criticality, controls and effect on product quality.

Clinical software, ICH E6(R3) and electronic records in trials

Clinical software carries two overlapping expectations: the regulator’s rules for electronic records in investigations, and the sponsor’s own data governance. Both affect how a trial tool is specified and tested.

FDA’s Q&A on electronic systems in clinical investigations

FDA’s final guidance of October 2024, Electronic Systems, Electronic Records, and Electronic Signatures in Clinical Investigations: Questions and Answers, provides information for sponsors, clinical investigators, institutional review boards, contract research organizations and others on using electronic systems, records and signatures in clinical investigations. It gives recommendations on the regulations under which FDA considers such systems and records trustworthy, reliable and generally equivalent to paper. For any project that touches investigation records, read the full text with the customer’s clinical quality lead.

ICH E6(R3)

The ICH E6(R3) guideline for good clinical practice reached Step 4 on January 6, 2025, the stage at which the final text is recommended for adoption by the regulatory bodies of the ICH regions; the sponsor’s regulatory team confirms where it applies. Its section 4 on data governance covers the data life cycle, including metadata and audit trails, and computerized systems. Its validation section says the approach should be based on a risk assessment, that systems should be validated before use and that later changes are validated on risk.

Integrating EDC, CTMS and eTMF data

Trial teams rarely replace their data capture, trial management or trial master file systems; they connect them. Integrations carry study, site and subject identifiers, document status and milestones. We design the interfaces to preserve the source system’s record and its history, and to make mismatches visible to the study team.

Selling into Europe: EU GMP Annex 11

A company that manufactures for the European market has a second rulebook. The European Commission’s EudraLex Volume 4 page describes the volume as containing references to the applicable legislation and guidance for interpreting the principles and guidelines of good manufacturing practice for medicinal products for human and veterinary use, and its list of annexes includes Annex 11, on computerized systems, with a January 2011 revision. We build to the requirements the customer’s quality system sets, which may include Annex 11. The current text on the Commission’s page should be read with the customer’s quality team at the start of a project, and we do not quote it here.

Integrations: LIMS, ERP, MES, QMS and identity

Many regulated projects are integration projects. The application itself is the work of our software development company, and the extra care in pharma goes into the interfaces and the data movement.

System categories we connect

We connect laboratory systems, quality systems, enterprise resource planning, manufacturing execution, clinical data capture and trial management, document management, safety databases and identity providers. These are categories, not partnerships; we work with the APIs and file exchanges the customer’s platforms offer, including data pipelines when volumes are large.

Interfaces that keep the audit trail intact

An interface should never be a silent edit. Each transfer records the source system, the user or service account, the time and the values sent, and the receiving system keeps its own audit trail. Reconciliation reports compare counts and checksums so a missing or changed record is found. Failures go to a queue a person must clear and sign off.

AI features in regulated workflows

AI can help with drafting, classification and search, and our AI integration work can add it to a workflow. In regulated work the rule is that a person reviews and owns the result. The software records the prompt, the model and version, the output and the reviewer’s decision, and keeps AI suggestions out of the regulated record until a user accepts them. We make no claim that an AI feature is validated; the customer’s quality unit decides on that.

Security, hosting and supplier assessments

Pharma companies assess their software suppliers, and a supplier should be ready to answer. Hosting, access and change controls are part of the build, and our DevOps services cover pipelines, environments and monitoring.

Answering a supplier audit questionnaire

A supplier audit asks how the software is developed, tested, secured and changed. We answer with what exists for the project: the written scope, the requirements and test records, the access list and the change history. We do not claim certifications, and we say so on the questionnaire when it asks.

Cloud hosting under the customer’s quality system

The software can run in the customer’s cloud account, in a hosted environment or on premises, whichever the quality system has qualified. A regulated setup needs separate environments for development, test and production, access that follows the customer’s rules and logged administrator actions. Moves between hosts are covered by our cloud migration work.

Is Progression certified or validated?

No, and we do not claim to be. We hold no ISO 13485, ISO 27001, SOC 2 or GAMP credential, and we do not call any system validated. Those statements belong to your quality system and your products. Our job is to work inside your process: following your procedures, producing the records they require and giving your quality unit the evidence it needs to decide.

Biotech software development for early-stage companies

Biotech software development for a young company is a different brief from a validated plant system. The needs are data capture, analysis and sharing, and the aim is not to over-build. A biotech software development company should be able to say which controls are worth adding now and which can wait. Biotechnology software development of this kind often starts as a single tool, and biotech software development services should leave a path to add controls later. Teams that plan to productize a platform can also look at our SaaS development page.

Research tools that may become GxP later

A tool used in discovery today may feed a regulatory filing in three years. Design it with unique accounts, a basic audit trail and clean data export from the first release. Adding signatures, formal change control and validation evidence later is far easier on that base than on a spreadsheet.

Data platforms for assays, sequencing and screening

Assay, sequencing and screening instruments produce many files in many formats. A data platform ingests them, attaches metadata about samples and methods, makes results searchable and lets scientists share them. Storage layout, naming and permissions matter more than any dashboard, and they are the hardest things to fix once data has accumulated.

When to buy, when to build

Buy when a product matches the workflow and the company can run it; build when the workflow is unusual, the integration work dominates or the product would force the science to change. Our note on custom software vs off the shelf sets out the trade-offs, and a short discovery phase usually settles it.

Pharmaceutical app development

Pharmaceutical app development means mobile and web apps for patients, field teams and medical affairs, built for drug and biotech companies. The sections below cover three kinds. Pharma app development for pharmacies and dispensing belongs to pharmacy app development.

Patient support and adherence apps

Patient support apps offer reminders, education, symptom diaries and programs run by the sponsor. They collect health data, so privacy design matters: see our guides to HIPAA compliant software development, patient portal software and remote patient monitoring software. Records that belong in a health record can connect through EHR software development.

Apps that may be device software

Some apps are regulated as medical devices. FDA’s policy guidance Policy for Device Software Functions and Mobile Medical Applications (September 2022 revision) says FDA intends to apply its oversight to device software functions that meet the definition of a medical device and whose functionality could pose a risk to patient safety if they did not function as intended. FDA’s Software as a Medical Device page quotes the International Medical Device Regulators Forum definition: software intended to be used for one or more medical purposes that perform these purposes without being part of a hardware medical device. Whether an app meets that test depends on its function, and the customer’s regulatory team decides. Device life cycle work is on our embedded software development page.

Field force and medical affairs apps

Field and medical affairs apps handle call reports, material requests, event sign-ups and approved content. Version control of approved content, consent capture and offline use in hospitals are the common requirements. Promotional review sits with the customer’s process, and we build the approval states into the app.

How a pharmaceutical software project runs

A pharmaceutical software project follows the same cycle as other custom software, with extra documents at the gates. Our software development life cycle page covers the general stages. On our manufacturing software page we describe the rhythm in these words: map the real workflow with the people who do it, agree a first-release scope, design and test with users, build in two-week sprints with working releases and integrate with existing systems. A pharma project keeps that rhythm.

Discovery and the requirements the quality unit signs

Discovery produces the user requirements: the workflow, the records, the roles, the interfaces and the controls the quality unit wants. The unit reviews and signs them, and every later test points back to a requirement. The first-release scope is agreed in writing.

Build in increments with traceable tests

Working releases come in increments, each with tests tied to requirements. Reviewers see the software early, which finds misunderstandings while they are cheap. Test evidence is kept in a form your validation team can read.

Release, change control and support

Each release comes with notes, a list of what changed and the test results, and it goes to the customer’s test environment before production. After go-live, changes follow your change control procedure. You own the software, as our manufacturing page says of its builds.

What does pharmaceutical software development cost?

The cost of pharmaceutical software development depends on the number of workflows, the records they create, the integrations and the documentation your quality system requires. We quote after a written scope.

Our prices

We publish no fixed price for software. Every pharmaceutical software project is quoted after a written scope that lists the workflows, the interfaces, the evidence we will hand over and the support afterward. That is the free proposal.

What the market charges

The table reports what other providers publish for custom software, across the full spread of their sources. It is not a Progression quote and not a pharma rate. Regulated work adds documentation and test evidence, which the bands do not price separately.

What moves the cost in regulated software

Four things move it beyond the bands. Documentation and test evidence take time that scales with risk. Integrations multiply testing. The number of GxP workflows decides how many records carry full controls. And hosting under the customer’s controls may add environments and access work. Starting with one workflow and its integrations is the simplest way to keep early cost and risk down.

Why does regulated software cost more?

Because there is more to produce besides the code: requirements the quality unit signs, traceability, test scripts and results, release records and change control. Integrations need their own tests, and each GxP workflow adds record controls. Published bands for ordinary software do not price this separately, which is why we quote after a written scope.

Related pages on software for regulated industries:

• Healthcare software development
• Manufacturing software development
• Embedded software development
• HIPAA compliant software development
• Software development company
• Life sciences marketing

Frequently asked questions