Software East

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Agile Development in a DNA Sequencing application - with Andy Brown

Event Details

Agile Development in a DNA Sequencing application - with Andy Brown

Time: November 18, 2010 from 6:30pm to 8:15pm
Location: Red Gate Software (Cambridge)
Street: Newnham House, Cambridge Business Park
City/Town: Cambridge
Website or Map:…
Phone: +44 (0)1223 323326
Event Type: talk, networking
Organized By: Mark Dalgarno
Latest Activity: Nov 19, 2010

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Event Description

18:30 - 19:00 Networking and light buffet
19:00 - 19:45 Talk
19:45 - 20:15 Networking

Register by adding your name to the event guest list. Attendance free.


Since investing in new sequencing technologies, the amount of raw data being produced is around 5Tb a day. We then use provided applications to convert to DNA sequence, and then more bespoke or open source applications to convert to different file formats, compare sequences against known references, and run QC analysis.

This presentation shows how we completely redesigned the pipeline to make it more flexible and extensible, using agile methodologies, new software technologies and Test Driven Development, including examples of a change to the provided applications meant needing more in-house functionality, and how we are coping with the introduction of an in-house replacement for some of the provided apps.

Andy Brown has been a software developer at the Wellcome Trust Sanger Institute for 3 years. Before this he was a DNA sequencer and a Chemistry Teacher. His specialisms are Perl and Web Technologies, and insisting my boss reads more about Agile. Outside of work, he enjoys SciFi and Vampire games, Photography and dressing up as a Dame in the local AmDram group.

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Comment by Andy Brown on November 19, 2010 at 8:16
Thanks Mark for inviting me to speak, and to everyone who came along for a very interesting discussion afterwards.

I've uploaded the slides to slideshare:

Looking forward to seeing everyone in January.
Comment by Mark Dalgarno on November 18, 2010 at 22:15
Thanks to Andy Brown for speaking tonight and to participants for 30 minutes of questions and discussion.

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