Friday, September 19, 2008

The DNA Network

The DNA Network

Fwd: MG-RAST User Newsletter No.2 -- MG-RAST paper available // NEW version released // 2nd User Workshop planned [The Tree of Life]

Posted: 19 Sep 2008 06:53 PM CDT

Out sick so email updates will have to do
Got this by email

Subject: MG-RAST User Newsletter No.2 -- MG-RAST paper available // NEW version released // 2nd User Workshop planned

Dear MG-RAST users,

The MG-RAST team has some news we would like to share:

1) MG-RAST manuscript published

The manuscript for MG-RAST has been accepted in BMC Bioinformatics and is available under the following URL:

Please cite:
The metagenomics RAST server F. Meyer, et al
BMC Bioinformatics 2008, 9:386

2) New version of the server software available

After a lot of testing (Thanks again to all beta testers), we have released a new version of our MG-RAST server software. You will notice improvements in nearly all aspects of the MG-RAST platform and user experience.

Here is a  summary of changes and additions:
- added overview page with statistical summary
- ability to download arbitrary subsets of fragments as fasta
- user can change parameters for metabolic reconstruction and phylogenetic reconstruction on the fly
- ditto comparison/heatmaps
- recruitment plot
- metabolic comparison tool using KEGG pathway maps
- updated databases in background (NR no longer from 2006, Silva RNA database included)
- detailed sequence information and alignments
- support for groups and inviting friends to look at data
- much faster user interface
- ability to see/download fragments and see blast alignments
- added Silva rRNA database (from:
- many small detailed fixes

3) MG-RAST workshop planned for winter 2008/2009
In addition to the tutorial at Metagenomics 2008 in San Diego (see: we are inviting participant registration for our second MG-RAST workshop. Please send an email to if you are interested in participating.

-- from the MG-RAST team

Notes from the road: a trip to Corpus Christi and a drama in the airport [Discovering Biology in a Digital World]

Posted: 19 Sep 2008 06:29 PM CDT

Every now and then, people hire me to travel places and give workshops for college instructors and teachers on using bioinformatics. In a couple of weeks, I'll go to Long Branch, NJ. This week, I went to Corpus Christi, Texas and gave two workshops at Del Mar College; one on using Cn3D to understand protein DNA structure, and another on using BLAST to identify the source of unknown DNA sequences.

Del Mar College has a beautiful science facility, with an amazing assortment of fancy high tech equipment. The workshops were fun and I enjoyed seeing the student posters showcasing work on the microbes that populate sea grass.

But, life is getting harder these days for those us who travel by air.

Read the rest of this post... | Read the comments on this post...

FDA Recommends Genetic Test Before Taking HIV/AIDS Drug, Abacavir [DNA Direct Talk]

Posted: 19 Sep 2008 03:41 PM CDT

And speaking of personalized medicine and genetic testing for drug response… The FDA recently recommended that people have genetic testing for HLA-B*5701 before taking the AIDS drug, abacavir (brand-name Ziagen). This test can identify people who carry a genetic marker that is associated with life-threatening hypersensitivity reactions. Right now, abacavir hypersensitivity reaction occurs in around 8% of [...]

Genomes on Rails [ScienceRoll]

Posted: 19 Sep 2008 02:29 PM CDT

Here is a great slideshow I just came across:

And another one Joshua Schwimmer shared with us:


Bridge between physicians and e-patients [ScienceRoll]

Posted: 19 Sep 2008 02:20 PM CDT

Just a quick note about the launch date of, the first medicine 2.0 online service. If everything goes well, it will be launched on the 1st of October.

Until then, if you are interested in a service that aims to help doctors enter the web 2.0 era, sign up for the newsletter or read the FAQ page.


Sergey Brin’s New Blog: 23andMe, Parkinson’s, and LRRK2 [Think Gene]

Posted: 19 Sep 2008 11:57 AM CDT

Sergey Brin’s New Blog: “too” (discuss at Hacker News)

In 2004, my wife, Anne, introduced me to her future cofounders in 23andMe as they were studying the genetics of Parkinson’s Disease. As with my mother’s fear, I was skeptical about the study. I reasoned that if there was much to be learned about Parkinson’s in the genome, there would have to be a high percentage of inherited cases. In fact, I appeared to be right in that this particular study did not bear immediate fruit.

As a customer of 23andMe, I have always been excited about the product. I have found what pieces of DNA I share with various relatives. I checked whether other Brins were related. I explored my various gene journals — learning, for instance, that I have one copy of the fast twitch muscle fiber. I also looked over the health related entries and found that my genetic risk for most diseases is modestly lower than average but for a few diseases it is modestly higher.

Why do you care about kinetic imaging? [Reportergene]

Posted: 19 Sep 2008 11:12 AM CDT

A new optical imaging device has been released from Caliper, the IVIS Kinetic. Compared to older imaging workstations this new product allows acquisition of biological events within milliseconds by fluorescence or bioluminescence imaging both in sleeping or conscious animals. That machine, exploiting a highly sensitive EMCCD camera, will be mainly suited for monitoring real-time functional events like perfusion dynamics and pharmacokinetis, or rapid events like calcium transients or immunological reactions. I'm in doubt whether this one will be a significant advantage toward reportergenomics maturity. Speaking about in vivo reporter gene imaging, both luciferase and GFP family suffer from low sensitivity due to:
  1. relatively low light-emission - this explains why there is low time-resolution (you need to integrate signals over minutes, no hope to have a millisecond resolution);
  2. scattering and absorption by tissues - this explains why there is low space-resolution (you get a planar image and no satisfactory 3D solutions have been made so far).

Probably these limitations less influence imaging of bright chemical probes (not reporter-genes) explaining some marketing decisions from Caliper. Or maybe, really this is a revolutionary machine with surprising performances even for reporter imaging. Let it be.

LRRK2, NYT, Trust and Sergey! [The Gene Sherpa: Personalized Medicine and You]

Posted: 19 Sep 2008 07:28 AM CDT

What I find interesting is how a SNP finding and a blogger can set the press a fire.....especially when the blogger is a junior member of the billionaire's club. In this case I am speaking of...

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Revisiting Chernobyl [Sciencebase Science Blog]

Posted: 19 Sep 2008 07:00 AM CDT

chernobyl-nuclear-power-plantChernobyl. The very name strikes fear into the hearts of those who hate everything about the nuclear industry. It conjures up images of an archaic, burning industrial site spewing out lethal fumes, of farm animals dying of radiation poisoning in their thousands and contaminated meat, of ecosystems devastated, and of people with radiation sickness and for those spared the acutely fatal toxicity, the prospect of cancers to come and perhaps generations of mutations. But…

Korean researchers argue that while the 1986 accident at the Chernobyl nuclear power plant, Ukraine, was the worst catastrophe involving radiation to humans, but has led to an unfortunate and unwarranted degree of radio-anxiety. It is not radiation that is the health issue, but this anxiety.

Chong-Soon Kim of the Korea Institute of Radiological and Medical Sciences and colleagues say that despite warnings of pent up health problems from Greenpeace and the World Health Organisation (WHO), “there is no convincing evidence that the incidence of leukaemia or solid cancers have increased in the exposed populations.” They add that the apparent evidence of decreased fertility and increased hereditary effects has not been observed in the general population despite claims to the contrary.

According to the WHO, some 4000 people - emergency workers and residents - died or could die in the future because of Chernobyl. Greenpeace insists that this figure is almost 100,000 across the globe. Kim and colleagues point out first that although the incidence of thyroid cancer has increased in the Chernobyl area, it is actually regions less contaminated by radiation where the greatest incidence has been reported.

“In this case we have to be cautious on the point that the results came from extrapolation using insufficient individual doses, and so far
from cancer
have not been
reported as predicted
so far deaths from cancer have not been reported as predicted,” say Kim and colleagues.

The radiation exposure level is the most important factor to estimate the cancer risk due to the Chernobyl accident. There are three types of exposed people. First, the exposure of recovery operation workers ranged up to about 500 millisieverts for a short period after the accident, with an average of about 100 mSv. In the case of evacuees, the average dose estimate of Ukrainian evacuees is 17 mSv (range 0.1-380 mSv), and the estimate for the Belarusian evacuees is 31 mSv, with a maximum of about 300 mSv. The average effective dose estimate of the general population in contaminated areas from 1986 to 2005 (some 5 million people) is 10-20 mSv.

The impact of Chernobyl on mental health and the future of nuclear as a viable renewable energy industry with public support, is perhaps the most serious problem. Among residents of the region and the emergency workers major psychological problems, such as depression, anxiety, and post-traumatic stress disorder are common. Anxiety levels are reported to be twice as high as in controls, the researchers say.

“Health effects, including cancer deaths, due to the Chernobyl accident have not reached the serious situation that was predicted,” the researchers say. There is, of course, some uncertainty in these figures although solid cancers usually form over a fifteen year period, rather than twenty years.

Young Woo Jin, Meeseon Jeong, Kieun Moon, Kwang Hee Yang, Byung Il Lee, Hun Baek, Sang Gu Lee, Chong Soon Kim (2008). Health effects 20 years after the Chernobyl accident International Journal of Low Radiation, 5 (3) DOI: 10.1504/IJLR.2008.020255

Revisiting Chernobyl

Around the Blogs [Bitesize Bio]

Posted: 19 Sep 2008 05:30 AM CDT

It’s Friday again, so what do you say we hit the feed reader and see what’s goin’ on Around the Blogs…

We Are Science
There is no “Science.” There is no “Academia.” These things do not exist as coherent entities, any more than “The Market” does.

Linkage and the Antibiotic Resistance Problem
New data show that antibiotic resistance genes travel together, at least in E. coli isolated from farms.

Science Writers Need Science History
…science writers need to recall some history. [...] In other words, scientists already knew fifty years ago that some segments of DNA that did not encode proteins were useful.
[But be sure to check out SciPhu's counterpoint for this specific instance.]

Altruism in Bacteria? Allowing Yourself to Die for the Good of the Species
A recent study by Ackermann, et al in last month’s Nature, shows a form of altruistic behavior being practiced by Salmonella typhimurium.

Marketing Science in the Public Square
Just this week, the Washington Post's Monday science "page" was reduced to a 1/2-page feature article, plus a 1/2-page ad. This science feature article will appear only every second week.

David Goldstein on the failures of genome-wide association studies
In the New York Times yesterday, Nick Wade profiles highly-regarded geneticist David Goldstein of Duke University, who provides the most sober assessment I have yet seen in the mainstream press about the outcomes of the genome-wide association study frenzy:

The Evolution of Assholes [Bayblab]

Posted: 19 Sep 2008 05:29 AM CDT

No, I don't mean Denis Leary. In an article in Nature [Nature News summary], two scientists from the University of Hawaii try to tackle the burning question of the origin of the anus.
Today, two evolutionary biologists have published genetic evidence in Nature that they claim refutes the leading theory of anal evolution. Their work suggests that the anus may have evolved multiple times in many different organisms, and they propose that, in some lineages, the anus may have formed through a fusion of the gut with the reproductive organs.
Current theory holds that in early organisms with one hole (a mouth used for both eating and excretion - imagine the aftertaste!) the mouth eventually separated into two orifices, one of which gradually to migrated to the opposite end (anus next to the mouth? - imagine the smell!).

The new study examined developmental gene expression patterns in worms. They found that in both worms with one 'hole' and those with both a mouth and an anus, the same genes were involved in forming the mouth. However anus-forming genes were different, contrary to what would be expected if the anus branched off from the mouth. Similar 'backside' genes were also expressed at the posterior of the no-asshole worm - one of them in the reproductive tract. This led to the suggestion that rather than branching from the mouth, the reproductive organs may have evolved first and then joined with the gut - think cloaca.

Why do we need a separate class for programming in bioinformatics? [Mailund on the Internet]

Posted: 19 Sep 2008 05:19 AM CDT

In a previous post I asked “Why are we teaching an introductory programming class for bioinformatics, where there is already an introductory programming class in the Dept. of Computer Science?”  Below, I’ll try to answer that question.

A different approach to programming

The short answer is that the approach to programming is very different between computer science students and (real) science students. Computer science students consider programming something worth learning in itself, whereas other students often consider it a necessary evil they have to learn in order to work with the material they are really interested in.

This is perfectly understandable. If your interest is in biology, then it is the biological questions that you are interested in.  Statistics and programming is necessary for analysing your data — more and more so as the types and the quantity of data changes — but your main interest is not the statistics or the programming; it is the biology.

Bioinformatics students are probably somewhere in between computer science students and biology/medicine students.  If you do not enjoy working with computers, bioinformatics is not the topic for you.  If you do not care about the biological questions but only the algorithm design, software engineering, etc. you are better of in computer science than bioinformatics.

Anyway, in the class I will teach next term, about 60 of the students are not bioinformatics students nor computer science students.  They are studying medicine and just need some basic programming to be able to solve bioinformatics tasks in their “real” work.

Showing then “neat tricks” or clever design patterns is not the way to go.

One size doesn’t fit all

The kind of programming you need to learn depends a lot on what you want to do with your programs. If you are doing number crunching, you want to worry about numerical algorithms and such. If you are building real-time systems, time constraints and response time is everything.  If you are building large software systems with millions of lines of code, the key thing is proper software engineering.

In Aarhus, we teach the computer science students to be a mix of “classical” computer scientists and software engineers / software designers.  We have a lot of classes that are pure theoretical computer science — everything is done on blackboards and implementing anything is frowned upon — and we have a lot of classes concerning software architecture and such.

There isn’t really a market for pure theoretical computer science outside of academia here, so most of our students end up in jobs where designing and implementing large software systems is the main focus.  The introductory programming class reflects this.  There is the necessary basic programming, such as learning the control structures and a bit about data structures, and on top of that it is design patterns and the type system and such.  The programming language is Java, probably because it is popular, statically typed and OO.

This is fine for computer science students.  It is just their first programming class, and they will specialise in other classes.

I don’t think it is the right choice if it is the only programming class you take, and you want to use the programming for bioinformatics.

It isn’t the right choice for the physics or chemistry students that really should worry more about numerical algorithms (which is not covered in this class) and would probably be better off with a Matlab tutorial and some numerical analysis.

But physics and chemistry students are not my concern and not my problem…

Scripting and programming

Ignoring spreadsheets — which might be the most important tool for many analyses — I would guess that 90%+ of the programming tasks a bioinformatician needs to solve are what I would call “script programming”.

You write a program to automate a work-flow.  You need to parse simple text files to extract relevant information.  You combine programs in pipelines with small converter programs in between them, to translate the output format of one program into the input format of the next.

There is very little focus on this in the computer science programming class.  There it is all about “proper” programming: designing the right class hierarchies, combining the right data structures, choosing the right algorithms for the task at hand… Worrying about IO is only a necessary evil, and one that is mostly ignored, and I doubt that there is any communication with other programs.

In scripting, the right data structure and the right algorithm is rarely much of a problem.  If your scripts are much too slow, you worry about it, but more often than not, you are happy if they can do what they do in reasonable time.  It is not worth the effort to speed them up.

The right structuring of the code isn’t that much of an issue either.  Of course the code should be readable when you return to it after a few weeks or months, but you never worry about the grand design, since the program is pretty small anyway.

Sure, there are some applications where you need all the canons from computer science, but it is pretty rare in day to day life.  If you need it, take a class at that time, or just give a computer scientist a Mars bar and a Pizza to do it for you.

Learning it, just in case, is most likely just wasting your time.

The programming tasks in bioinformatics simply do not align with the skills taught in the introductory programming class in the Department of Computer Science, and that is why we need our own.

As for what goes into it, that is a topic for another day…

That’s it, no more Linux on my desktop [Mailund on the Internet]

Posted: 19 Sep 2008 03:21 AM CDT

Maybe it’s just me, but I am getting more and more frustrated with Linux as a desktop computer. There is always some small problem that you have to struggle with, and I am getting fed up with it.

I’m sitting in a train right now. There is a wireless network here, so I can be on the Net while I’m travelling. All good and well, except that connecting to it through my Ubuntu machine is a major struggle.

Well, in itself it doesn’t sound like a lot: I have to open a dialog to find the network and then connect. For some reason I have to be root do do this, but okay, it doesn’t take that long to type in the password. I have to open just the right dialog to connect, of course, because if I just click the icon in my menubar I am politely told that the wireless interface does not exist. If I go through the Network item in the menu, that doesn’t seem to bother the computer and I can connect there.

So it is a little work but nothing to complain too much about, I guess. The problem is just that network is a bit unstable, so I loose connection to it for short periods every so often. Then I have to do it all again. Forget about keeping the dialogue open. For some reason it automatically closes if you leave it alone more than a few seconds. I suppose it is to be friendly.

I have spent more time trying to connect to the network now than I have spent time using the network.

Anyway, so now I rebooted into my Windows partition. Here, I am informed of the presence of the network, I connect, and whenever the network is dropped, I just right-click on the network icon in the taskbar and repair the connection.

It “just works”.

Of course, there isn’t much else that I enjoy about Windows. I find Outlook an exercise in frustration, and the lack of virtual desktops / “spaces” makes the desktop a mess, but I think my problems with this is simply that I am not as used to Windows as I am to Linux.

I’ve gotten used to Mac OS X since I bought an iMac for the office, so now I’ve decided to buy a Mac laptop as well. Maybe a Mac Air, just for the coolness factor.

For computations, Linux will probably still be my choice in the future. A Linux cluster is the right choice for number crunching. But as a desktop computer, I just can’t be bothered with it any more.

Too bad, since the eye candy on Linux is getting really cool. Better even than the Mac. Eye candy just isn’t enough, though, if it means you have to struggle with drivers and shit whenever you want to do the simplest little thing…

The realities of personal genomics bite Google founder Sergey Brin []

Posted: 19 Sep 2008 01:36 AM CDT

Sergey Brin (Googles uber-billionaire founder) has discovered via 23andme that he carries some very strongly predisposing alleles for Parkinsons. He makes this annnouncement this on , and there is a about it. Sergey carries G2019S of (leucine repeat-rich kinase 2).

Read more and join the community...

Great Galloping Gerbils! [Omics! Omics!]

Posted: 18 Sep 2008 08:50 PM CDT

An item on CNN mentioned that satellite technology will be employed to monitor the endangered California Kangaroo Rat. This reminded me of a Nature paper this summer I meant to mention, because the image blew me away (plus it's the first time I've seen Google Earth used as a source for a scientific paper!).

The paper is about models of disease spread (these gerbils are reservoirs for plague), but the thing which jumped out was the Google Earth image; the two images above are from around the same region of Kazakhstan. The gerbils clear vegetation from around their burrows, and these burrows are in huge complexes. The more zoomed in image above is several kilometers wide and yet is packed with gerbil burrows. If you have Google Earth and look around 44.766991 76.449699 you can zoom way out and still see the gerbil complexes. I saw some huge prairie dog towns out west when I was a boy, but nothing on this scale!

How many animals leave traces which can be seen from 30+Km up (the image quality is uneven for this region of the world in Google Earth -- clearly shots are merged from different seasons and resolutions, but 30Km is a conservative estimate)? Human activity obviously. When I think of animal-built structures I generally jump to beaver dams or termite mounds, but they aren't nearly this extensive.

Personalized Therapeutics at IU [PredictER Blog]

Posted: 18 Sep 2008 08:47 PM CDT

In August 2008, the Indiana University Department of Medicine's Division of Clinical Pharmacology began a new series of compelling seminars that may be of great interest to those involved in predictive health research ethics. The Personalized Therapeutics Seminar series commenced on August 5th with a presentation on the FDA's Sentinel System for Post-market Drug Safety Surveillance given by Barbara Evans, J.D., Ph.D. from the Health Law and Policy Institute at the University of Houston Law Center. Additional speakers this fall, all from the Indiana University School of Medicine, have included Dr. Noah Hahn presenting on the Indiana University Cancer Biomarker Study, Dr. David Haas addressing PREGMED and the search for individualized pharmacotherapy in pregnancy, Dr. Zeruesenay speaking about emerging in vivo phenotyping methods and Dr. Tatiana Foroud addressing the results of whole genome association studies and how they may change our approach to medicine. The next seminar, entitled Personalized Therapeutics in Breast Cancer: A Model for Translating Pharmacogenomics, will be presented Dr. David Flockhart, Chief of the Division of Clinical Pharmacology, on September 9th. All seminars in this series are held on Tuesdays from 12:00pm – 1:00pm, in room W7120 on the 7th floor of the Wishard Myers Building.

For a complete schedule, please see: [link edited 9-18-09]

Amy Lewis Gilbert

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