Entries by Neil Robertson

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ScatterShot for UK Biobank Beta Deployment

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 […]

Scanning a rack of 2D barcoded tubes with OWL

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 […]

Gotcha! AWK field separators

Some UNIX tools, such as CUT, by default expect tabular files to be separated by single TABS. But not AWK! Given a tabular file (awk_test.txt) with the structure: A<TAB>B<TAB>C<TAB>D<TAB>E A<SPACE>B<SPACE>C<SPACE>D<SPACE>E A<TAB><TAB>B<TAB><TAB>C<TAB><TAB>D<TAB><TAB>E A<SPACE><SPACE>B<SPACE><SPACE>C<SPACE><SPACE>D<SPACE><SPACE>E If you run an AWK command to count the number of fields: awk ‘{print NF}’ awk_test.txt Each of these lines has 5 fields! […]