Cellular Informatics

Pipeline Solutions

Cellular Informatics (CI) develops custom laboratory information systems (LIMS) and computational research tools (WGE) for high-throughput laboratory analysis of human stem cell experiments. We are a team of software developers and data scientists working on a variety of challenging tasks collaborating with and supporting our lab-based colleagues, as well as our colleagues in the rest of Informatics and Digital Solutions.

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.

Tracking Software

Our software development is mainly done in Modern Perl, with significant portions of JavaScript. Our current LIMS systems is LIMS2, which is a successor to the HTGT (High-Throughput Gene Targeting) informatics system, which supports only the tracking of mouse clones and is now a legacy system. In LIMS2, we track clones from both mouse and human species. Most of the tracking in LIMS2 is related to human clones.

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

This valued research tools is described in detail on our WGE tool page. This tool is implemented in Perl, JavaScript and C++.

Other tools

We provide tools for oligo order generation, sanger sequencing submission and review, CRISPR damage analysis and integration of standard tickecting systems for production narrative.