Standardizing Oligo Synthesis Workflows with Dotmatics

Overview

Excelra helped a leading biotechnology company streamline their oligonucleotide therapeutics workflow by implementing standardized protocols in Dotmatics. The solution improved efficiency, reduced manual data entry, and ensured reproducibility across multiple projects. By integrating fair data principles in pharma and leveraging advanced scientific application services, the client achieved consistent data capture, seamless analytics, and scalable workflows that support accelerated drug discovery and decision-making.

Our client

Our client is a leading biotechnology company specializing in nucleic acid therapeutics in the United States. Focused on advancing innovative RNA- and DNA-based drug development, they aim to accelerate research efficiency while maintaining high standards of data integrity and FAIR data compliance. Their operations span multiple research projects requiring scalable, reproducible, and standardized workflows for oligonucleotide therapeutics, making them an ideal partner for implementing advanced scientific application services and bioinformatics-enabled solutions.

Client’s challenge

The client’s oligonucleotide synthesis workflows were fragmented and relied heavily on manual processes for data capture and protocol execution. Scientists were spending significant time on manual data entry, increasing the risk of transcription errors and slowing decision-making. The lack of standardized processes also created inconsistencies across teams, limiting reproducibility and compliance with fair data principles in pharma.

Client’s goals

The client aimed to develop and configure standardized protocols for oligonucleotide therapeutics synthesis in Dotmatics, with the objective of improving efficiency, ensuring data integrity, and enabling reproducible results across multiple research projects.

Consequences of the Problem
If left unresolved, these issues would continue to delay drug discovery timelines, reduce operational efficiency, and limit the ability to reuse and analyze data effectively — ultimately increasing R&D costs and slowing progress toward critical go/no-go decisions in data-driven drug discovery.

Our approach

We collaborated closely with the client through a structured, multi-phase approach to ensure the solution aligned with their scientific and technical requirements, leveraging scientific application services best practices.

Discovery & wireframe

• Conducted a project kick-off and reviewed existing documentation to understand current workflows.
• Facilitated functional and technical workshops with stakeholders for detailed requirements gathering.
• Created a wireframe as prototypes, technical architecture, Design documents and ERD

Design & development

• Built data source tables and views, designed forms with field logic, buttons, checkboxes, and attachments, and converted them into canvases.
• Configured protocols, assigned canvases, and set up processing scripts, using SQL column lookups and column alterations for configuration.
• Cover End-to-end Dotmatics workflows, siRNA synthesis—from registration and QC to UV analysis, MS purity normalization, and duplex creation. Protocols are segmented for both small- and large-scale synthesis
• Developed procedures, triggers, and Python scripts to automate workflows, ensuring accurate and consistent data capture across workflows.
• Ensured that all workflows were compatible with bioinformatics solutions to support downstream analytics and reproducibility.

Testing

• Identified test environments and prepared sample assay datasets.
• Validated configurations ensured correct data flow across components, and simulated assay execution end-to-end through protocols.
• Verified that all data was stored accurately in source tables and views.

UAT

• Conducted UAT fully in the test environment with business users.
• Collected feedback, resolved defects, and obtained formal sign-off prior to production deployment.

Manual migration & Go-Live

• Performed manual migration of validated configurations and reference data from test to production environment.
• Followed a controlled migration checklist to ensure environment parity.
• Conducted final smoke testing in production before enabling workflows for live use.

Post-Go-Live hypercare

• Supported users during the initial production usage period.
• Provided issue resolution, knowledge transfer, and transition to steady-state operations.
• Training Videos: Step-by-step walkthroughs to onboard users quickly and ensure smooth adoption of the workflows.
• User Manuals: Comprehensive documentation covering protocol usage, data entry guidelines, and troubleshooting tips.

Our solution

Our implementation successfully standardized the client’s oligo synthesis workflows within Dotmatics, creating a seamless, reproducible process from protocol setup to data capture and enabling alignment with fair data principles in pharma.

Key Results achieved

1. Improved efficiency: Scientists reduced manual data entry significantly, allowing them to focus on analysis and decision-making.
2. Reproducibility & data integrity: Standardized metadata capture ensured consistent experiment documentation, enabling reproducibility across teams and projects.
3. FAIR Data compliance: Configured workflows ensured data was findable, accessible, interoperable, and reusable, making it easier to support downstream analytics, bioinformatics solutions, and collaboration in data-driven drug discovery.

Ongoing benefits

• Faster go/no-go decisions in drug discovery programs.
• Greater confidence in experimental results due to standardized workflows.
• A scalable solution that can be extended to future assays and protocols, including additional oligonucleotide therapeutics pipelines.
• Integrated with platforms for digitalization in drug discovery.

Workflows