Informatics

Paul Fisher

Current Status• Work done on Trichuris muris

– Joanne Pennock and Scott Levison– PubMed : 20687192 – gene expression analysis using workflows (re-use)– QTL paper under review (re-use)

• Atopic Dermatitis – results being looked at by PhD student

• Epilepsy/BPP data published online (at myExperiment)– open access for everyone to download….no restrictions imposed– Twitter sent to various people – please re-tweet if you see it !!!– No paper to be published on results– Nature Proceedings opinion to be written on Open Data and publishing

papers… notably that the process is slow to new discovery– As a result of Josh Summers talk and achievements on sharing– Hope is to speed up community awareness and discoveries

• Scope for a re-use paper for Bioinformatics from Trichuris work

Local outreach• FLS want to collaborate

– Josh Knowles based in CS– William Rowe based in FLS– Doug Kell has an interest in this too

• Ideas on closed-loop optimisation / Genetic Algorithms

• Lots of components of genetic algorithms based on a few modules– “The interesting thing about genetic algorithms is they are modular in

structure, so by coding a few different modules up in taverna we can create lots and lots of different flavours of algorithms.“

• Visualisation of data using external tools – link to Taverna as plug-ins

• Need some assistance with use cases and Taverna integration

Personal opinionsIntegrate command line tools for Next Generation Sequencing

– Find competition– Identify tools– Identify use cases

• Apply to use cases/samples– from Mario at TGAC

• Kickstarter projects - http://www.kickstarter.com/– Short term funding for carrying out sampling and sequencing– Sequence endangered amphibians…..could pair with Manchester museum (

http://goo.gl/PlOUL - crossbreeding frogs)– Run through Taverna – Get some biology results – novel drug targets from poisonous frogs, improve

evolutionary trees, novel proteins, increase understanding of biology in general– Extend to all amphibians or endangered species – complementary to

biobanks !!– Why Not ?

Anyway……

Alignment

• ????

• How much data can I push through Taverna, and can I break it ?

• Biology outreach – people in the labs are willing to use Taverna-derived results– Epilepsy, Trichuris, Colitis, Dermatitis– Just need to talk to them and get their data !!