University of Washington Biology Department (Cabernard Lab)

CRISPR design workflow application

Scientific software development Custom web application Data workflow automation React application development API integration systems

Overview

The Cabernard Lab at the University of Washington is a biology research group focused on cellular and genetic mechanisms, led by a tenured faculty principal investigator.

We built a CRISPR design application that streamlined their genome editing workflow by unifying multiple biological data sources into a single guided interface. The application itself became the subject of a peer-reviewed publication.

Published paper: https://academic.oup.com/g3journal/article/16/1/jkaf251/8294580

The challenge

  • Manual genome editing workflow across multiple data sources
  • Repetitive, rule-based decision process for CRISPR target selection
  • Time-consuming visual gene identification and validation
  • Fragmented use of external biology databases and APIs
  • High cognitive load during experimental design

What we built

We built a full-stack application that unifies genomic data sources and guides researchers through CRISPR target selection.

Data and genome processing system

  • Integration with FlyBase genomic database
  • Aggregation of multiple biological data sources
  • Automated retrieval of genome regions and annotations
  • Structured normalization of genomic datasets

Application layer

  • React-based interactive genome exploration interface
  • Node.js backend for data orchestration
  • Multi-step guided CRISPR design workflow
  • Dynamic highlighting of relevant genomic regions
  • Query-based genome lookup and filtering

Integrations

  • FlyBase API
  • External genomic data sources
  • AWS EC2 deployment environment
  • MariaDB for structured biological data storage

Key complexity

  • Translating complex biological workflows into deterministic software logic
  • Handling domain-specific genomic data structures
  • Mapping abstract research methodology into user interface flows
  • Ensuring accuracy and traceability of biological data transformations

Results

  • CRISPR design workflow fully digitized and streamlined for the research team
  • Application became the subject of a peer-reviewed publication
  • Co-authorship on published scientific paper
  • Significant reduction in manual genome selection and validation effort
  • Improved accessibility and usability of genomic data within the lab