Stem Cell Informatics
We are a small, focussed research group providing software development and bioinformatics facilites to the Stem Cell Engineering group. We also support he bespoke stem cell engineering team, which does not rely on LIMS systems so much owing of the nature of their work.
What do we produce?
The most visible aspect of our work is the public reporting available to everyone in LIMS2
There you can see a summary of clones targeted in our human and mouse stem cell experiments. Clicking on the linked numbers takes you to drill-down reports for more information including alignments, trace files and a host of other relevant data.
We provide 3-tier webapp support, using the Model-View-Controller design pattern exclusively for functional separation. The system is backended by a PostgreSQL relational database. LIMS2 tracks clones using a directed acyclic graph, which is stored in the database and access through the model layer of our webapp.
Quality control is managed by the web application and by supporting scripts, which us the parallele processing capabilities of the linux farm available at the Sanger Institute.
WGE – CRISPR database for genome editing
We provide tools for oligo order generation, sanger sequencing submission and review, CRISPR damage analysis and integration of standard tickecting systems for production narrative.
Dr David Parry-Smith
Senior Scientific Manager
Dr Parry-Smith leads the Stem Cell Informatics Team. His role is to interact with scientists at all levels, understand and gather requirements for developing and maintaining informatics systems supporting Stem Cell Engineering. He is a biophysicist software developer interested in bioinformatics of genome editing using CRISPR/Cas9 (see WGE), algorithms for tracking lab processes and sequence pattern recognition.