Software

Software written and hosted by the McCarthy Group

Presented today at ASHG 2018 in San Diego, Chipendium is a web application for determining the identity of your microarray platform from a list of genotype variants ids.

It is common for genotyping datasets to lose record of the exact chip platform used, especially where there are numerous versions of each chip. Chipendium will detect the chip platform of your data. You can then strand align your dataset using Will Rayner’s strand website.

Upload your Illumina chip metadata and Chipendium will interrogate our catalogue to suggest the most likely chips platforms. Currently our catalogue contains over 166 chips (Oct 2018) and is regularly kept up to date.

Implementation

Chipendium is a collabaration between two McCarthy group members. The server-side logic (STAASIS) was developed by Will Rayner in Perl as part of his work into strand alignment. The middleware and webapp were written by Neil Robertson in Java/Javascript/HTML.

Find out more about Chipendium here.

Toppar, by Dr Thorhildur Juliusdottir, is a database-driven interactive association result browser written in JavaScript and HTML. It uses the Flot library for plotting, zooming and panning and DataTables for listing the data.

Toppar has now been published in Bioinformatics, please find the paper online here: https://doi.org/10.1093/bioinformatics/btx840

Data integration and visualization help geneticists make sense of large amounts of data. To help facilitate interpretation of genetic association data we developed Toppar, a customizable visualization tool that stores results from association studies and enables browsing over multiple results, by combining features from existing tools and linking to appropriate external databases.

The McCarthy Group deployment of the Toppar web application can be found here.

We have developed ScatterShot, a web application for generating cluster plot images for chip genotyping experiments. This initial deployment has been customised for the UK Biobank dataset.

Our aim has been to produce a centralised web application so that the end user can simply access clusterplot images without the nuisance of accessing, downloading, storing, handling and configuring the underlying data itself; which in the case of UK Biobank is significant!

Find out more about ScatterShot for UK Biobank here

I am a software developer and data analyst for the McCarthy Group at the Wellcome Centre for Human Genetics and OCDEM.

My personal webpage at Wellcome can be found here

A detail from the McCarthy Group’s OWL LIMS. OWL interfaces with an FluidX XTR 96 rack scanner over TCP/IP; the scan is initiatiated by OWL, the samples tubes are scanned and results are returned. The database is then interrogated and the technician is presented with a display summarizing the changes that have been made to the rack. The technician has the choice of cancelling or committing the rack scan.

The display is designed to give intuitive visual feedback to the user about the physical state of the rack. The featured image at the top of the page is a logic defying test case to showcase all possible states. Actual use cases will typically be much more like the image below in which a single new tube has been added to an existing rack.

Rack scan display from OWL

The single yellow circle is surrounded by a darker outer circle; this indicates an previously empty well into which a new, unallocated tube has been placed. The remaining 95 tubes were previously present and are unchanged.

In the image below we have a more complex use case involving tube shuffles, allocations and no reads. This rack scan should not be committed, the rack should be cleaned and scanned again.

Rack scan display from OWL

Four of the wells (in orange) have not been read, so the rack will need to be rescanned. Three of these wells contained existing tubes. Six of the wells are coloured in blue, which indicates that these tubes have been shuffled within the rack. Nine new tubes have been allocated to the rack, all into previously empty wells.

Images are rendered in browser with SVG using the Snap.svg Javascript library.

I am a software developer and data analyst for the McCarthy Group at the Wellcome Centre for Human Genetics and OCDEM.

My personal webpage at Wellcome can be found here