Torfinn Nome » Biotech

Galaxy (interactive and reproducible genomics)

Torfinn Nome — Wed, 29 Oct 2008 08:50:25 +0000

Russel Smithies (of AgResearch) suggested using Galaxy assisting in setting up a local GBrowse service (fetching UCSC Btau4 data, converting to a format compatible with GBrowse) at work (CIGENE, Centre for Integrative Genetics).

Galaxy is a web application that deserves attention! Fetching data, sorting data, combining data sets, alignments, manipulations, fetching other data resulting from manipulations, statistics, ++. All with a very-very nice, simplistic interface.

“It is designed to help two communities that often have difficulty communicating:
- Experimental biologists: “I really have no time to program but I want to do whole-genome analyses to find targets for experimental validation”.
- Computational biologists: “I develop algorithms but have no time to develop interfaces”.

There are also a number of screencasts available.

Example of usage:
“Suppose you want to find top hundred protein-coding exons in human genome with the highest density of single nucleotide polymorphisms (SNPs). Answering this question is not trivial. To do so one needs to compare all human exons to all human SNPs. To put this into perspective the current version of human genome (hg18) includes 357,517 known exons and 12,351,941 SNPs.”
Elegantly solved, using Galaxy, in this screencast.

Galaxy also lets you create workflows (screencast).

I’m very impressed, and I’m already planning a local Galaxy server integrating our local data sources and tools.

Now, all that’s needed is to teach people how to use Galaxy. Hm. And I probably have to look for a new job…

Le Fin

Torfinn Nome — Sun, 22 Jun 2008 12:05:53 +0000

I actually did it. I defended my thesis last week. Believe it or not. I certainly do not. At least not yet. A summary of the thesis can be seen in the above picture (courtesy of Wordle).

Now what?

Insufficiencies

Torfinn Nome — Thu, 31 Jan 2008 23:17:29 +0000

Lately, being part of an academic environment, I have increasingly been aware of the insufficencies we face as human beings. Not that I don’t gape in astonishment of what is being achieved in both medical and technology related research advancements these days. But we have the potential to achieve so much more. And I feel, more than a little, annoyed by the way we seem to deliberatly waste resources on obviously counter productive projects. Productive projects that eventually would make, pardon the cliché, our lives better. Pouring billions of dollars into military operations is obviously an easy way to make friends with people running the military industry. But it’s not much affecting the way we deal with treating cancer, enhancing ways of expoiting alternative energy sources, speeding up the making of a space elevator, or understanding the complex ways of gene transcription interactions. And I do believe those extra billions could make an impact. However, thankfully, we are making progress nonetheless. And the progress is gaining speed in a way only J.B.S. Haldane and H.G. Wells could dream of (while Ray Kurzweil knew all along…). But it’s not enough. Professors and other scholars, with life long knowledge and experience, do retire. And even tho they are able to share their valuable knowledge through their companions and peers before leaving academy, much is lost. I want humanity to be able to pass on this knowledge in a new way. I want us to be able to share everything. Knowledge. Experience. Not in writings. Not in teachings. The process is too slow. But in a way numerous scifi story writers have been telling us for years. My new boss, Stig W. Omholt (director of Centre for Integrative Genetics), showed me not long ago an article in New Scientist. About researches involved in technologies “extending human capabilities“. We don’t have time waiting for evolution to make human brains inter-connect, sharing intelligence, knowledge and experience, vastly improving our scientific progress. We need to understand the way the human brain store information, and its nearly endless creativity. And be able to reproduce it. Thankfully, The Singularity Is Near. And it will change everything.

If You Can’t Smile And Say Yes

Torfinn Nome — Fri, 08 Dec 2006 19:18:41 +0000

Our lab environment is polluted by not only cancer inducing chemicals like ethidium bromide and the neurotoxic polyacrylamide. Even more disturbing is the frequent usuage of the radio. Or, to be more precise, the lack of a radio station that does not suck. Here in Norway we have a couple of commercial nation wide channels in addition to some channels provided by the public broadcasting institution. I can’t stand commercial channels, with the non stoppable annoying advertisements. But, even worse: The channels we listen to (we switch a lot) have one thing in common that annoys me the most. The repetition rate of some of the music. I mean, I don’t want to listen to the same tune 9 times during just a few hours.

Anyway.

Lately I have started wearing my trusty old DAP, which luckily carries an endless number of hours of music. After a few weeks I have come to the conclusion that I prefer some kind of jazz inspired music while doing lab work. Even tho my favourite band this week has been Gotan Project, which is a fusion of tango and electronica.

(Yup, Nat King Cole works pretty darn good for me.)

Living amongst Barley, Trees and Bees.

Torfinn Nome — Sun, 25 Jun 2006 12:53:42 +0000

The confocal microscopy wasnt’ the blast I was hoping for. Not because 3D visualization using laser and fluourescence isn’t fun and impressive. But, mostly me having high hopes: Looking at living mammal cells. Manipulated proteins with different stains, interacting, colourful images… Oh well. Instead, we watched a dull image of some cells involved in the breaking loose of the leaves of the flower Poinsettia. There are times I really dislike studying at an agricultural university, one of them being now. :)

BIO300 – Mikroskopiteknikker

Torfinn Nome — Wed, 14 Jun 2006 14:36:32 +0000

I’m attending a 3 week long course teaching different microscopy techniques. We are 8 people. Yesterday, I fell hopelessly in love. With their brand new scanning electron microscopy! I was kind of suspecting this to happen, having wanted to work on a SEM for along time, but I was really blown away. I definetly need to integrate it in my thesis. I have a hunch the confocal microscopy might not be too disappointing either…

Using intense lobbying (I believe), two … collegues (Lasse and Marthe) of mine got me a job at the Norwegian Institute of Public Health, all July and most of August. Thanks!

Substitute for Love!

Torfinn Nome — Sun, 05 Mar 2006 21:00:57 +0000

Initiating a new transformation process this Friday, I spent most of the weekend in the lab. Mostly … waiting. This evening, at 19:30, looking at the result (after restriction enzyme cutting): The transformation was successfull! Nothing to write home about, really… But. After a week of feeling crappy. Lacking results. Nothing going the way you want them to. Finally looking at a successfull result materialising in front of your eyes somehow makes it all worth while, and then some!

Functional food – and beyond!

Torfinn Nome — Mon, 27 Feb 2006 15:31:37 +0000

You have probably heard the phrase functional food. In Norway, the government have quite strict rules of what modifications are allowed to food and beverage. I don’t know the details, but so far I’ve only seen orange juice with artificially added calcium, milk with vitamin D, yoghurt with the probiotic Lactobacillus rhamnosus GG (LGG), etc.

One of my colleagues in the protein engineering lab, our resident super star (as in music), Lasse Fredriksen, is taking this a step further. His master thesis will aim towards finding a way to use one of these lactobacillus bacteria as vaccine carriers to our intestines, where our immune system will create antibodies, hopefully giving us immune resistance to the specified disease. And all you ladies out there, the vaccine he will try to incorporate is against the HPV type 16! (Associcated with cervical cancer.) Interesting stuff. I’m sure the future will bring loads of these specialised functional modifications. Maybe even directly linked against your own, personal, genome.

Oh, and btw, check out his band: Sanguine

…or lack of.

Torfinn Nome — Mon, 27 Feb 2006 15:04:47 +0000

That is, lack of successfull transformation. I got my colonies on the LB agar, and was happy, everything going on as planned. But, darn, something wasn’t right. Using restriction enzymes to cut the new plasmids, checking if my genes actually had been incorporated, showed … nothing. I’ve spent the last days trying to find out what went wrong. My PCR products seems all right. The plasmid we’re using for transformation has a “suicide” gene which gets transcribed if there is no successful gene incorporation, inhibiting growth. But, I got my colonies, the bacteria did grow. I even tried several different restriction enzymes, and restriction buffers, just to be sure. But, nothing, nada, my gene is not there. Weirdness. I will probably end up doing the transformation from scratch. Albeit I really want to know what went wrong…

Transformation

Torfinn Nome — Mon, 13 Feb 2006 18:02:10 +0000

I’ve learned a lot these first weeks. And the feeling of being totally lost is gradually fading. Still, talking about green fingers, my head definitely feels green sometimes… Anway. I got the primers. I did PCR. I did gel electrophoresis, isolating the genes I multiplied. Today I started the transformation progress, using the Zero Blunt TOPO technology. Tomorrow I will know if my first GMO (Gene Modified Organism) experiment was successfull or not. And later this week I will know if I actually managed to insert the correct sequence into the E. coli or not. Looking forward to checking out the agar plates tomorrow! My other life: Weekend; at our cabin in Valdres. The weather was absolutely perfect. Blue sky, no wind, -5 celcius. I spent the days enjoying cross country skiing, reading a norwegian classic horror book (“Døde menn går i land”), and listening to the Olympics on the radio.