After that big storm last month, we still have no telephone and therefore no Internet access at home.
I’m amused to see that it is the latter which has become more troublesome than the former, cell phones making up for some of the inconvenience.
I stayed home this morning in anticipation of technicians from my service provider coming by, who needed to see with their own eyes that the lines are still lying on the sidewalk before registering a report with France Telecom.
In the end, their coming by was not as illogical or as much of a waste of my time as I had initially thought, as there was some sort of patched-up cabling – literally, with masking tape – that enabled my neighbors to have access to these services and not us, and that will be sorted out (to our benefit, not to their detriment).
Meanwhile, I spent the morning only with my computer. We had a good heart-to-heart. I am trying to learn how to use CisGenome software, subject of an article in Nature Biotechnology, and more generally trying to imbibe the sorts of approaches that one could use to analyze the kind of sequence data – 179,308,044 basepairs – in which I am currently swimming. (Drink it, rather than drown in it.)
There is only a certain amount I could do offline (my online lab notenook musings here but you can’t get them to wrap and it’s pretty unreadable anyhow), given that I have not installed a genome browser on my laptop. Also, it’s fun to just browse. I think I understood some things that I hope I don’t forget meanwhile.
And one online thing I like to do, when I think of it, is to let last.fm sample what music I play and suggest other things later that I might enjoy listening to, along the same lines. Useful social software.
Off to examine some peaks and valleys and try not to get distracted by any more philosophical discussions for the time being.
I don’t even know what a genome browser is, but it sounds like something I need to learn. Or can people who deal only with coding regions, like me, get by with online sites like EBI and NCBI?
Don’t talk to me about phone engineers. I waited in 8 hours on Saturday for one that didn’t show despite repeated assurances. Another two hours wait yesterday but at least this time someone did appear and seemed to fix the problem, though we now have another problem. Sigh.
@Jenny – I think ENSEMBL at EBI is one the leading genome browsers. The UCSC genome browser is the other one people mention.
@Jenny – I don’t even know what a genome browser is
They do come in a range of different forms. One variant is also known as ‘speed dating’…
Hi Frank – yes, I use ENSEMBL, but it’s not a programme you install on your computer. It sounded as if Heather was doing something more high-tech.
Stephen, that’s a terrible pun!
No, it’s pretty low-tech; I believe you can upload the UCSC browser and any tracks you like onto an offline computer. Then you “build” it. But I am not sure I really want/need to do that – the human genome sequence data alone that I needed for CisGenome, without the annotations I like to access, is something around 4 Gb. I should probably make use of the NN collaborations group finally, eh? but I do like to puzzle these things out. Less efficient use of time, but then I understand better.
By the way, Visigene and the in silico PCR tester are pretty awesome and useful little features for day-to-day work.
@Jenny – true!
But it wasn’t entirely unscientific…
@Frank – much sympathy from someone who’s been there three times now, awaiting RdV #4…
@Stephen – it was clever, I’ll give you that. Still doesn’t make me want to sniff even my husband’s shirts, though.
Wintle’s guide to Genome Browsers 101:
ENSEMBL – fussy, and the interface is ugly
UCSC – good, but the interface is ugly
NCBI – godawful, and the interface is unusable
I use UCSC almost exclusively, unless (shameless plug) I’m looking at copy-number variants, in which case I use the (DA-DA DA DAAAAAAAAAAA!!!) Database of Genomic Variants.
Ooo, and Heather – I was at a colleague’s office in Montreal recently, and he showed me something their bioinformatics folks had whipped up the night before. He brought up the UCSC browser, which then did some kind of hand-shaking with their own system, and Voilà! it displayed his region, with custom tracks showing their own data and linking through to FISH images from our facility (not dynamically, but resident in his own data store). It was very cool – the backbone of all the public genome browser tracks with his own custom tracks of private data superimposed.
Maybe this is easy/old hat, but I was impressed. Very handy. I’m pretty sure it was using UCSC’s browser though, not downloading it all and building it locally (which would be a bit painful I think).
I think I need some bioinformatics folks, too. Yes, custom tracks is pretty cool; I can do that much. Well, I could. Round two with CisGenome, since I didn’t take notes when I sludged through round 1, is not only reinventing the wheel but not getting it to rotate quite as far. Grr. And still no Internet at home, when I would have been doing the kind of putzing about that will enable me to make progress; there is too much distraction in lab, and the cells are growing too well. That’s the only reason I would want to compile the browser locally, and now I’ve seen that I need to refresh any rudiments of Linux, I’m quite discouraged from the whole venture and think I will just do this during working hours in the end.
I wanted to look at your link, but could not get the server to wake up. Time difference, perhaps?
you should go to your GP.
Linux is really good Richard: you should try it.
Wilson! Would you like to come compile the offline UCSC browser on my currently (ouch) Vista-running laptop? (Meaning, you’ll have to repartition my disk.) I do have a Linux partition on the computer at home, but if I invite you over, some people might interpret that badly.
Dear Heather
If you were to invite me to give a seminar I am sure we could come to an arrangement. I would like to see Paris at least once.
Seeing Paris will happen if you want it to, sooner or later. However, I’m currently in Toulouse and very impatient… (but will make use of local colleagues, never fear).
Heather – our servers were down for some maintenance or other recently – give it a try now if you like. Recurring problems, email me. Once in a while a domain will get blocked if it’s been shoveling spam at us (like all of Brazil for a while recently, which caused a certain graduate student no end of grief, and me no end of emails, for a while).
No recurring problems, and interesting tools. I’ve passed on the links, incidentally.