Blogs

Ontology Development and Management

Ontologies are a foundation of FAIRification, data exploration and reuse in AI and ML. They are an extension of Master Data Management (MDM) taking taxonomies and vocabularies and adding a layer of context and real-world relationships to the data. Defining ontologies is not simple and requires a combination of deep scientific domain knowledge and data management understanding. Coupled with the definition is their ongoing management and governance to ensure the scientific and business needs are met.

Zifo has experience in ontology development and various commercial and open-source ontology definition and management platforms alongside deep domain and technical knowledge to support your FAIR and semantic data journey.

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Data Readiness for AI/ML

Getting the most from data requires extraction, transformation and piping to and from platforms both on-prem and in the cloud – data wrangling. During this ETL data is transformed to alternate formats and structures to support downstream consumption like loading to data lakes, data warehouses. There are many nuances to this process and no two projects are ever identical due to the variability of data source and end state data structures.

Zifo has experience with many “data wrangling” approaches, extraction automation and scaling, ETL tools, data formats and enrichment techniques that all support the data re-use and FAIR data journey.

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Data Modelling Consulting

We ensure compliance with the FAIR principles (Findable, Accessible, Interoperable, Reusable) while being mindful of data maturity and readiness.

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MLOps: Reliable, Scalable, Explainable ML

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Generative AI in Drug Discovery and Protein Engineering

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Data Readiness for AI/ML

From quality checks and normalization to feature engineering and data enrichment, Zifo prepares your data to drive impactful AI and ML outcomes.

We provide services such as:

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Scientific Expertise Domain

Our Scientific expertise domain spans from Discovery (e.g. Cell and Gene Therapy, NGS, Structural/Medicinal Chemistry, HTS and HCS), Pre-clinical Development (e.g. Biomarker and Metabolite analysis, DMPK, In vitro/in vivo Studies, Biologics development, Translational studies), Clinical Trials (e.g. Regulatory Submission Reporting (IND, NDA, BLA), SEND, CDISC, SDTM, ADAM standards 21 CFR Part 11, GLP, GCP, Clinical Supply & Clinical Sample Management, etc.) and Manufacturing (Digitation, QA, Knowledge maps, GxP).

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Digital Transformation

We provide the Digital transformation strategies that are essential to get your business into the new digital era of AI-driven drug discovery. Our approach is designed to address every facet of your specialized business needs by utilizing our 3-pillar approach of Science, Technology, and Data, with People at the core.

At Zifo, we have deep expertise at each of these pillars to provide an end-to-end support and results including developing a comprehensive Business Strategy for the entire organization to drive the Pipeline through work process changes and potential technology and process solutions at any stage of your journey.

Final Deliverables may include: Benchmarking analysis, Data governance strategy and implementation, FAIR data transformation, Data science and workflow orchestration, Data architecture, Product Configuration and implementation, Project and change management definition, etc.

Science Technology

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Business Systems Analysis

All our Business Analysts are scientists with lab experience and empathy, who truly understand the scientific workflows and pain points of transforming data into breakthroughs.

Our methodologies include: Business Process Mapping, Current and Future State visualizations, VoC and Gap Analysis reports, User and Functional Requirements Specifications, Data Governance and Management Strategies, Use Cases and User Stories, Data Flow Mapping and Data Modeling, FAIR Data Assessment, UATs, User adoption documentation and Training, etc.

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Platform Implementation, Change Management, and User Adoption

We provide an end-to-end service to meet your every need. We know that people are at the core of any successful change. Our change management approach is focused on engaging stakeholders and end-users by capturing their vision, understanding their processes and data needs, with empathic communication and program success monitoring.

Final results/deliverables may include: Development of Business Strategy for the entire R&D IT organization, 4R Analysis Report, VoC and User Requirements, Process Harmonization & System Standardization Opportunities Report, Project Management services, FAIR and Data Governance Opportunities Reports, Technical Configuration, Customization & Implementation of any scientific platform, DB and Server Configuration, Instrument integration/Lab automation services, UAT and Validation services, Training and Hypercare, and well as continued Application Support services.

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Platform Evaluation Decisions

We utilize our extensive methodology and solutions expertise in R&D Informatics of wide-range informatics technologies in a comprehensive vendor-agnostic, quantitative approach to decision-making. Our Product evaluation methodology includes Functional evaluation, Technical evaluation, GxP evaluation and Supplier evaluation, to bring a comprehensive solution to address your business need.

Following your selection of optimal technology solution, we offer a full Implementation Roadmap and Implementation Support, spanning from data governance transformation and technology adoption (e.g. server and DB architecture), to change management and user adoption & training.

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Strategic Roadmap and Market Research

At Zifo, we leverage our knowledge of industry best practices and experiences from 20+ years of engagements across pharma and biotech industries. Our long-standing vendor-agnostic provide optimal and customized solutions to your unique business needs.

Final deliverables may include: Industry Positioning and Best Practices; Business Process Recommendations; Standardization and Harmonization Opportunities; Technology and Digitalization Opportunities; Implementation Roadmap Solutions and Recommendations, Data strategy goals, Data harmonization, AI Readiness, etc.

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Optimizations and Extensions

Zifo’s CLEAR and LEI products boost lab efficiency and compliance. We understand lab workflows and tailor Empower configurations (custom fields, reports) to your needs, including validation.

CLEAR accelerates reviews by 70%, enhances documentation, and moves you toward a paperless lab. LEI simplifies bidirectional data exchange between LabX and Empower, minimizing errors and manual intervention.

As an Empower Toolkit application, LEI offers quick, intuitive implementation even for complex lab setups, often without requiring SOP changes. These future-proof solutions provide flexibility and efficiency for labs of any size.

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Data Integrity

Zifo ensures data correctness, completeness, and consistency through validated CDS system settings, comprehensive SOPs, and targeted training. We optimize system configurations for robust documentation and traceability, implementing user roles to enforce process adherence and prevent unauthorized actions.

Our SOPs detail all processes, including CDS application, administration, and review procedures. Training reinforces these processes, minimizing errors and unnecessary data generation. Consultants help reduce manual work by enabling direct CDS calculations and reporting, creating and validating custom fields and reports.

Our CLEAR extension for Empower enhances data security by guiding users through double-check and audit trail reviews, optimizing the process and providing paperless documentation. This comprehensive approach enables successful CDS implementation and operation, with options for optimizing individual areas.

Whether you’re updating an existing system or streamlining sample processing, Zifo offers cost-effective, high-quality solutions based on years of global CDS expertise.

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Support and Helpdesk

Incident Management: With 25+ years of CDS experience, Zifo supports your CDS implementation from planning and requirements gathering to testing and ongoing operation. We offer flexible integration, from project management support to fully managed services. 

Lab Support: Our comprehensive approach considers user, quality management, and IT perspectives, enabling support at all levels of your CDS installation. We collaborate with your IT, utilize your ticketing system, or work directly with your key users. 

Managed Services: Zifo’s Service Desk optimizes laboratory software operations, providing tailored solutions. We assist with Empower custom fields, reports, and project structuring. Our managed services deliver organized IT solutions for a defined period under a comprehensive contract.

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Validation

Our services encompass a comprehensive approach to system validation, beginning with thorough system analysis and risk assessment of your CDS-based processes. Based on this assessment, we develop detailed test plans and execute comprehensive tests to ensure system functionality and reliability. Finally, we deliver comprehensive documentation and reports covering all aspects of the validation process, ensuring compliance with regulatory requirements.

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Implementation (Rhizomer)

For large-scale Empower installations, Zifo’s Rhizomer 2.0 enables central management of LAC/E computers, eliminating on-site configuration. This reduces administrative workload, costs, and the need for on-site personnel. Updates are quick — typically 20 minutes –, minimizing downtime and boosting productivity.

Rhizomer facilitates rapid restoration in case of computer failure. Key features include rollback options, automatic change documentation, customizability, and configuration backup. It’s a future-proof solution designed for efficient lab management.

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Training and Workshops

Every laboratory has its own processes, objectives, and challenges — and thus, very individual training needs. As a leading provider of classroom training for Empower users, Zifo addresses this with specific training plans that optimally fit your laboratory’s requirements. We offer all our Empower training modules in German and English. Our training provides an optimal balance of theory and practice, suitable for beginners and system administrators alike.

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Medical Device Validation

Validation of Medical Devices involving Mobile Applications, Software-based, AI/ML-based devices is critical to gaining regulatory approval and marketing. Regulatory constraints are wide-reaching and deep knowledge and up to date awareness of Quality System Regulations (QSR), CSA/CSV process, and cybersecurity regulations are needed to ensure compliant medical devices. Zifo has extensive experience in this domain and experience with SaMD development and validation approaches.

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Testing and QA Services

Zifo provides comprehensive application testing services, including functional, performance, and security testing. We leverage test automation to streamline testing and accelerate delivery. Additionally, we conduct usability and accessibility testing to enhance user experience and ensure compliance with accessibility standards.

We also establish and manage Testing Centers of Excellence (TCoEs) to help organizations centralize testing capabilities, adopt best practices, and maximize testing efficiency. TCoEs enable consistent quality delivery across projects and drive continuous improvement through the adoption of advanced methodologies and tools.

Whether you need end-to-end testing services or specialized testing support, Zifo ensures that your systems meet operational, regulatory, and user expectations.

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Commissioning, Qualification and Validation (CQV)

Zifo provides comprehensive lab compliance support, from procurement to ongoing maintenance. We excel in validation, ensuring compliance with regulatory and customer requirements. Our expertise encompasses Data Integrity (DI) within GLP/GMP environments and robust documentation. We offer periodic compliance services, including reviews, audits, and CAPA support. Additionally, we specialize in Enterprise Application Validation, including SDLC Qualification, instrument integrations, and end-user training.

Zifo boasts years of CQV leadership in the GxP space, partnering with global pharma and biotech. We ensure regulatory compliance with deep knowledge of 21 CFR Part 11, EU Annex 11, and GAMP 5. Our ISO 9001:2015 and ISO 27001:2013 certified QMS supports successful FDA and EMA audits. We offer scalable CQV services with a focus on ownership and innovation, covering a wide range of laboratory instruments.

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Digital Validation and Assurance (CSV/CSA)

At Zifo, we bring extensive expertise in Computer System Validation (CSV) and Computer Software Assurance (CSA), ensuring that computer systems work as intended and comply with regulatory standards. With proven experience across the life sciences domain, we specialize in delivering solutions tailored to meet the requirements of GLP, GCP, GMP and GMLP domains.

We provide end-to-end services, from devising the validation strategy and conducting risk assessments to executing validation activities, including IQ, OQ, PQ test script development, test execution, issue resolution and summary reporting. Our approach aligns with the latest CSA guidance, emphasizing a risk-based validation framework that prioritizes critical thinking over excessive documentation.

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IT Quality and Compliance Consultation

Our experts can help you with new quality system design, delivery, and maintenance; auditing against regional regulatory guidelines (21 CFR Part 11/EU Annex 11/Japanese ERES, HIPAA, GLP, GCP, GMP, GMLP, GDPR, QSR); quality system audits and recommendations; and quality system best practice adoption.

Zifo consultants engages with industry consortiums (RAPS, ISPE, Pistoia, KENX etc.) to stay ahead in regulatory advancements and implement agile, risk-based, and paperless validation strategies, including CSA and GMLP.

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AI Software Assurance

Implementation of AI/ML in GxP areas require strong understanding of Good Machine Learning Principles (GMLP) and concepts of AI/ML Validation. Zifo’s GxP AI Experts can help you design the quality framework for your AI journey with necessary creation of policies and procedures as well as help with building AI Software Assurance practice.

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Scientific Cloud and Enterprise Architecture

Our Scientific Cloud and Enterprise Architecture Consulting services empower life sciences organizations with scalable, secure, and cost-optimized cloud solutions on AWS, Azure, and GCP. We specialize in modernizing IT infrastructure, enhancing cloud security, and optimizing platforms for scientific workloads.

Key Capabilities:

Solution Architecture: Strategic cloud-native design for scientific computing.
Cloud Modernization: Seamless transition to scalable cloud environments.
Cloud Security: Proactive risk identification and compliance alignment.
DevSecOps and FinOps: Secure, cost-efficient operations with automated governance.
Observability: End-to-end visibility into cloud performance and security.
COTS Integration: Integrate commercial off-the-shelf solutions.
Platform Modernization: Upgrade legacy infrastructure to cloud-native architectures.

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High Performance Computing

Zifo’s Elastic HPC Solutions enable pharma and biotech to accelerate drug discovery, genomic research, and clinical simulations using scalable cloud clusters on AWS and Azure. We design blue-green, usage-aligned HPC architectures for high availability, cost efficiency, and performance.

Key Capabilities:

HPC Cluster Deployment: Automated deployment via Ansible for AWS ParallelCluster and Azure CycleCloud.
Job Management: Integration of Slurm, SGE, PBS, MPI and PsN with approval workflows.
Performance Optimization: Low-latency computing with InfiniBand, EFA, and Accelerated Networking.
Storage Solutions: Diverse storage options including AWS FSx Lustre, Azure NetApp Files, EBS, EFS, and S3.
Operations and Security: User access management, Linux administration, patching, monitoring, and compliance.
Utilization and Cost Management: Real-time dashboards for usage and resource optimization.

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Data and AI Compute Platforms

Our cloud-native Data and AI solutions empower pharma and biotech to accelerate drug discovery, optimize operations, and enhance real-time decision-making.

Key Capabilities:

Serverless AI/ML: Managed, event-driven machine learning without infrastructure.
Edge AI: Real-time AI processing at data sources for clinical and manufacturing.
Federated Learning: Privacy-preserving AI models trained across decentralized datasets.
Generative AI in Pharma: AI-driven drug discovery, preclinical simulations, and process optimization.
Quantum AI Exploration: Complex simulations and molecular modeling using AWS Braket, Azure Quantum, and Google Quantum AI.

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Compliance Cloud

Our Qualified Hosting Services provide validated, secure, and compliant cloud infrastructure on AWS and Azure for pharma, biotech, and other regulated industries. We ensure adherence to GxP, 21 CFR Part 11, HIPAA, and GDPR through automated deployment and continuous compliance.

Key Capabilities:

Validated Environments: Pre-configured compliance controls for AWS/Azure.
Infrastructure as Code: Automated, reproducible deployments with Terraform/Ansible.
Automated Deployment: CI/CD pipelines for scalable, validated infrastructure.
Continuous Compliance: Automated checks for GxP, ISO 27001, SOC 2, and GDPR.
Security and Disaster Recovery: End-to-end data protection with backups and DR.

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Posit Services

Zifo provides comprehensive support for Posit Workbench, Posit Connect, and Posit Package Manager, ensuring a seamless, scalable, and secure infrastructure.

Key Capabilities:

Deployment: On-premise or cloud deployment of Posit products.
Scalable Compute: Optimized infrastructure for large-scale analytics.
Security and Compliance: GxP and 21 CFR Part 11 compliant environments.
MLOps and Deployment: Deploy models and applications via Posit Connect.
Interactive Applications: Build and host R/Python applications.
Package Management: Efficient package distribution and governance.
Legacy Modernization: Migrate SAS/Excel workflows to R.
Training and Support: Guidance for teams of all skill levels.

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Scientific Workflow Automation

Utilizing cutting-edge cloud technologies like Kubernetes, serverless computing, and AI-driven orchestration, Zifo offers comprehensive support in:

Compute and Orchestration: Flexible, high-performing pipelines through serverless computing, containerization, and managed workflow orchestration.
Data Integration and Management: Effective processing and management of large datasets via data lakes, ETL/ELT tools, and real-time data streaming, ensuring quality and accessibility.
Scientific Tools and Analytics: Seamless API management and integration of scientific tools with AI/ML platforms and data visualization for actionable insights.
Security and User Experience: Robust security with IAM, data encryption, and compliance, alongside intuitive front-end frameworks for enhanced accessibility and reproducibility.

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Modeling and Simulation Tools

Zifo specializes in advanced computational solutions across critical areas, including pharmacometrics (NONMEM, Monolix), molecular modeling and dynamics (GROMACS, AMBER, CHARMM), protein structure and folding (Rosetta, FoldX), and virtual screening (AutoDock, Schrödinger Suite).

Our expertise extends to fluid dynamics (ANSYS Fluent, OpenFOAM), cheminformatics (KNIME, ChemAxon), molecular visualization (PyMOL, Chimera), and omics tools and platforms (Galaxy, Bioconductor), providing a comprehensive approach to scientific challenges.

Zifo actively collaborates with open-source communities and vendors to provide valuable feedback, drive enhancements, and ensure seamless tool adoption.

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Comprehensive Clinical Trial Solutions

Zifo programs complex randomization and IP logistics, ensuring smooth site data entry across diverse therapeutic areas, including oncology, neurology, immunology, cardiology, and more. Our expertise extends to medical devices, dental implants, and vaccine studies.

We excel in drug supply management, IRT integrations, and detailed data mapping. With extensive regulatory experience (FDA, PMDA, EMA, HC), including BIMO and ARM/ARS packages, we support global submissions. Our statistical services cover the entire trial lifecycle, from CRF review and protocol development to DSMB/DSUR support and adaptive trial design. We automate summaries, perform QC with SeeWise, and manage deviations. De-identification expertise (Safe Harbor, expert determination) protects participant privacy.

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Automation

Thousands of clinical trials occur across the globe every year, each with its own set of needs and specific data management requirements. Zifo provides risk-based data management, seamlessly integrating with various EDCs (Medidata Rave, Marvin, Viedoc4, and more), including rescue studies and post-go-live amendments. Our real-time safety reporting automates adverse event and protocol deviation reporting, ensuring regulatory compliance (ICH E2B).

With 15 years of SAS expertise, we create SDTM/ADaM datasets and TLGs, leveraging 100+ macros and an automapper tool. Zifo also pioneers R programming and JSON datasets for cutting-edge statistical analysis. We ensure data quality across multiple sources, eliminating duplicates and irrelevant information. Our expertise extends to decentralized trials, offering innovative approaches and solutions for this evolving landscape.

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Artificial Intelligence (AI)

We are enhancing medical writing with generative AI to quickly create standard study report sections, including safety assessments. Our medical coding tools (eXt, mXt) automate processes for accuracy and efficiency, specializing in ATC coding for better drug classification. A cutting-edge bot automates SDTM package and annotated CRF (aCRF) creation, streamlining clinical data management and ensuring compliance. Our team creates high-quality submission packages (CRT, SDRG, ADRG) using in-house tools, ensuring compliance, accuracy, and timely delivery for successful regulatory submissions.

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Change Management and User Adoption

Key components of Zifo’s change management service include assessing the impact of change, engaging stakeholders early, identifying change champions, designing user-friendly training programs, and ensuring proactive communication. This also encompasses user adoption and training, focusing on user-centric design, planning phased rollouts, motivating early adopters, providing comprehensive onboarding support, and using data, such as adoption rates, to refine the approach for maximum success.

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Post Implementation Operations and Governance

Key components of Zifo’s Operations and Governance services include performance monitoring, continuously tracking the performance of implemented systems, platforms, or processes against defined KPIs; user support and issue resolution, providing ongoing technical support to R&D end-users, including troubleshooting and system updates; bug fixes and updates, identifying and resolving post-deployment issues and ensuring software remains current; data quality management, maintaining high standards of data quality, integrity, and accuracy; scaling and expansion, smoothly handling system expansions as R&D projects grow; and governance policies and procedures, establishing clear guidelines for post-implementation system management, including decision-making, issue escalation, and continuous operational monitoring and improvement.

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Integrated Laboratory

Scientists often spend a significant amount of time navigating multiple systems (both hardware and software) to document their research data and derive meaningful insights. Life sciences leadership is increasingly focused on establishing integrated labs—connecting laboratory instruments, software systems, and data management platforms—to reduce this burden. Key components of an integrated lab include equipment integration, connecting instruments like spectrometers, chromatographs, and microscopes to centralized systems for data exchange, and informatics integration, linking lab management systems (e.g., LIMS) with these instruments to streamline data collection, analysis, and reporting.

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Data Management and Migration

Zifo’s Data Management experts can help you assess the complexity of diverse data types, analyze data structures within legacy systems, and address challenges related to data volume and access control. We provide end-to-end support in developing and executing effective data migration and management strategies. Key elements of our solutions include retaining structure data models, centralized data repositories, automated migration, data backup and redundancy, and robust metadata management.

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Scientific Workflow Design and Development

Zifo’s informatics consultants can help with the end-to-end design and development of various workflows. This includes creating predefined templates for different types of experiments, organizational protocols, and regulatory guidelines. Zifo can also configure informatics platforms to automate data entry, capturing data from connected lab instruments, sensors, or external databases, or even scanning barcodes or QR codes for sample tracking.

Furthermore, Zifo can set up review workflows that ensure data is reviewed and validated by the appropriate personnel, whether peer or lab manager. They can also implement alerts and notifications, setting up automatic reminders for key steps or incomplete data. Finally, Zifo can establish workflows that allow for visualization modules to generate insightful graphs and charts for reporting and data analysis.

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Scientific Platform Installation and Upgrades

Zifo’s Informatics experts can help you install or upgrade these platforms to improve productivity, accuracy, and capabilities of research teams, making the tools aligned with the latest technological advancements.

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Business Process Mapping

Key outcomes of Zifo’s BPM exercise include process optimization, identifying inefficiencies, reducing waste, and improving time management. Zifo also identifies repetitive manual tasks suitable for automation to enhance efficiency and streamline operations. Furthermore, the BPM exercise helps onboard new employees by providing clear visual representations of key processes.

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Software and Application Development

We empower scientists to focus on what they do best — analysis and decision-making — by eliminating the need to navigate complex coding or engineering challenges. Our expertise lies in supporting scientific teams handling multimodal data (such as omics, assays, clinical, population studies, consortium, imaging, etc.). Whether it is creating tailored dashboards, deploying agile RShiny applications, or building organization-wide scientific platforms, we deliver intuitive solutions that enable impactful discoveries.

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Data Solutions

Gaining insights from scientific data demands both domain expertise and technical proficiency. Our team bridges the gap by combining deep scientific knowledge with advanced engineering skills to deliver bespoke solutions. Whether it’s mining public datasets for actionable knowledge, building knowledge graphs for specific use cases, or structuring metadata for data lake initiatives or semantic integration, we provide the expertise to support your research and innovation goals, ensuring we follow the FAIR principles (Findable, Accessible, Interoperable, Reusable) and are conscious of data maturity and readiness.

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Scientific Workflows and Omics Pipeline Engineering

Leveraging our bioinformatics engineering and research infrastructure expertise, clients engage with us to build custom omics workflows, transitioning pipelines from legacy systems to Nextflow for enhanced efficiency, and reducing costs by selecting optimal resources. Additionally, we can develop new pipelines and applications within your existing commercial or enterprise systems, ensuring seamless integration and improved performance.

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Analysis and Insight Generation

When companies partner with us, our mission is to transform their diverse data — whether internal or sourced externally (CRO or public datasets) — into actionable insights. Collaborating closely with scientists, we address key research questions and contribute to strategic goals such as target evaluation, indication prioritization and expansion, understanding drug mechanisms of action, pathway analysis, and biomarker identification to enhance patient selection and enrichment.

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