Bettina’s Bioconductor Package

A landmark for the lab with our first ever BioConductor package now available.  SimBindProfiles allows comparisons of ChIP-array binding profiles to identify differential binding in different datasets, while there are tools to this with ChIP-seq data there was little or nothing usable for array based analysis.  Bettina put it together with some help from Enrico and Robert Stojnic to facilitate our work on Dichaete and SoxN binding but it is broadly applicable to any ChIP-array datasets.

I think this is a fabulous piece of work – well done Bettina!

Dichaete Paper Out

Jelena’s Dichaete genomics paper is now out in BMC Genomics.  Great job troops.

The new grad students

A very warm welcome to Alex Chen and Josh Maher, who have just joined the lab as grad students.  Alex will be working on the Hox specificity project and Alex will be extending the Joy of Sox into other insect species.

Hope you have fun guys!

Cool!

Alfonso Martinez-Arias has disseminated a copy of the spoof journal Cool (get it here) that has been pinned to my office wall for well over 20 years. I keep it to remind me what science is actually about (and Cool is not!). Alfonso uses it to illustrate some of the things enraging him about the current state of research – his blog is worth a read.

Engineering HEGs paper out

David and Sang’s work with our Colleagues at Fred Hutchinson & Pregenen in Seattle, engineering homing endonucleases to recognise new target sequences, is now available from PLoS ONE. Great job everyone.

Well Done Max

Many congratulations to our PartII project student Max Fitz-James on winning the Thoday Prize for the best Genetics student this year.  Good luck with your impending PhD in Edinburgh Max.

Papers on Mendeley

Papers (& full library) now on Mendeley.  Profile at http://www.mendeley.com/profiles/steve-russell/

Max does some DNAse-seq

We done to Sarah’s PartII project student Max Fitz-James, he generated some pilot DNAse-seq data from melanogaster and yakuba embryos. Around 12 million mapped reads from the IonTorrent generated ~ 1.5 billion bases of sequence. Not so bad for an 8-week project.

Music Library

The addition of mbv finally tips the iTunes library over the 30,000 tracks barrier – my obsessive music collecting (definite sad old man syndrome) has accumulated 92 days worth of music at an average rate 0f 2 tracks a day since I bought my first record in 1975 (Pink Floyd – A Nice Pair). Estimated cost in excess of £20 grand, estimated value – priceless.

January Music

I have been tardy in updating the SysBio centre iTunes library, consequently there is about 5 days of new music that’s just been added.  I’m liking The Lost Tapes, a series of CAN tracks from 68-77, and well worth a listen.  This spurred me to get digital copies of my old vinyl so plenty more CAN.  Other stuff includes Errors, Eat Lights Become Lights, Gnod, Godspeed You! Black Emperor, Neil Young & the Horse (Psychedelic Pill – excellent), Richard Hawley (standing at the ski’s Edge – very good), PAWS (a young Glasgow band on FatCat records) Psychedelic Horseshit, Odonis Odonis, Crocodiles, King Creosote, Scott Walker & loads more.  Your sure to find something worth listing to!