Roger Pettett › Comments

Unfortunately, I don't think there was any video :( - Deepak Singh

You can always add an audio track in your abundant spare time ;-) - Neil Saunders

<funny> - Graham Steel

I recognise a lot of those slides! :) - Roger Pettett from twhirl

and, i might add, many of those sequencing figures were from ~18 months ago - Roger Pettett from twhirl

:-) yep but the big ones I only know "offline", so not sure I can put them on a slide - Deepak Singh

I look forward to pictures of the long silken moustache. - Bill Hooker

congrats for your new job - Pierre Lindenbaum

Congrats - I spent 6 1/2 years at the EBI, and it was one of the most rewarding work experiences I've had. By the way, it's not just the Red Lion that's there - you can also go to the Red Lion. Or the Red Lion. Yes, the 3 closest pubs are all called the Red Lion :) As for norman-no-mates, just go to Burns Night run by the sports & social club in Jan - that'll sort you out. Lots of perks, but right in the middle of lots of countryside (not even a post office!) - that's EBI for you :) Have fun! - Allyson Lister

Congratulations, we should meet up for a pint - Frank

@Bill I'm working on the moustache, I may be some time though @Pierre thanks @Ally cheers (lets go the the Red Lion next time you're here) @Frank I'm all ready and primed for beer - Duncan Hull

you do realise will will hold you to the moustache. I knew you could not go to long withough copious amounts of hair in and around your head :) - Frank

I'm sure you'll enjoy it - I spent ten years at Sanger in various groups - on the whole it's a pleasant, talented community to be a part of - Roger Pettett from twhirl

Good luck. I have to ask though, which bit of Manchester am I missing which is cheap? :P - Michael Barton

@Michael prices are all relative of course, I'm thinking mostly of the cost of renting and the cost of buying a house, both of which are considerably better value for money in Manchester than Cambridge IMHO. Food, beer and other essentials probably aren't that different pricewise. - Duncan Hull

@Frank will a comedy fake 'tache do or does it have to be a real one? Facial hair is not my strong point :-) - Duncan Hull

Congratulations on the new job, dullhunk. I'll maybe stop by and visit you the next time I'm there - we have collaborators on the Hinxton campus I come down on the train (or drive) every now and then. And I do have on my long-term agenda to at some stage work at @EBI/Sanger, for the experience as Allyson said. - 'Mummi' Thorisson

@Mummi thanks, you're welcome to come and drop by... - Duncan Hull

It is a different culture, there's good stuff about cambridge. come and say hi at some point Helen - Helen Parkinson from email

@Helen oh yes, I'll come by and pester you :-) - Duncan Hull

Slighty late but good luck on you new endeavours @dullhunk. WRT el silken moustache, if you kept your locks after they were chopped off, you would be able to produce one hell of a false moustache and just in time for http://uk.movember.com/ ;-) - Graham Steel

@Graham great idea, I'll just have to grow one instead. Are you participating in movember? - Duncan Hull

Duncan, I wish you a great start in Hinxton. - Martin Fenner

@Duncan, I've been off this week so as usual, no shaving. As such, and since my 'tash growing prowess is not brill, tempted to miss that bit out b4 I go back to work on Monday. - Graham Steel

I keep having this feeling that a DAS server solution based on rails should be very simple to use. But has not been implemented yet afaik. - Jan Aerts

Maybe it's overkill. All I want to do is view (a lot of) short read data on a genome browser. Is there an easier way? I've spent all day trying to get ProServer or LDas running on Intrepid. Failed miserably. Have MyDas, but now have to implement the AnnotationDataSource class to parse the short read files and it's been a while since I've done anything in Java. - Cass Johnston

I don't know much the DAS protocol but (i may be wrong) it just returns a simple XML for a given segment/assembly. Why do you need a complicated library for this ? Why not using a custom simple PHP|Servlet|... ? - Pierre Lindenbaum

have you tried using UCSC and their BED file format? http://genome.ucsc.edu/FAQ... I'm interested to hear what solution you settle on... - Andrew Su

I usually go with Gbrowse for this kind of thing. If you think a local server is overkill, Andrew's idea is good: mung your data into a form that you can upload somewhere else (such as UCSC). - Neil Saunders

The files are really too big to upload to UCSC, hence the das. how much of a battle is gbrowse to setup? - Cass Johnston

and also, with gbrowse, how easy is it to integrate other sources of annotation (eg ensembl transcripts or similar) - Cass Johnston

please drop me a note with the issues you had using the proserver+intrepid combination. I've not tried that combination but I can take a look for you - Roger Pettett from twhirl

hmm, that was this morning. Memory a bit hazy. tests failed with something about sourceadaptor, but I can't remember exactly what. Sorry, I should have taken notes, but it was supposed to be a quick solution to show some biologists the data. I'll go back and have another go at it when I've got a bit more time and let you know how it goes. - Cass Johnston

you might also try jbrowse... http://www.jbrowse.org/ - Andrew Su

jbrowse looks quite good actually. If I hadn't spent all bloody day trying to install stuff, I'd try it. Next time maybe ;) - Cass Johnston

I asked yesterday about DAS+RDF at BioDas.org. The answser is here: http://www.biodas.org/wiki... "Short answer: No, but there's definitely interest in this sort of thing." - Pierre Lindenbaum

Gbrowse + Wig files is pretty efficient. Easy? Depends on how you are at installing Perl modules. http://gmod.org/wiki... - Jason Stajich

I've been using Gbrowse2 (from CVS) a lot in recent weeks; few if any issues and a bunch of great features (including ajax panel refresh). - Neil Saunders

@Jason (or anyone else who knows) Am I right in thinking that if I'm using a MySQL backend, wig files don't make any difference cos you need to convert them to gff to load them into the DB? - Cass Johnston

Also, it was quite easy to install and get running. Thanks for the suggestion! - Cass Johnston

I think there are 2 components with wigfiles: a GFF3 file which goes into your database as normal and a binary .wig file which lives in a directory specified by your config file. See http://gmod.org/wiki.... - Neil Saunders

The docs for wiggle2gff3.pl suggest that it should be used if you have too many features to load into GBrowse, and they define too many as "thousands". I have about 13 million. Does anyone know if it's going to be ok on that kind of scale? Will it break if I split the original wig file into multiple files and generate separate binary wig & gff files for each one? - Cass Johnston