Thursday, October 25, 2007

Building an e-Science platform with Miscrosoft tools

(via Frank Gibson's Peanutbutter) Hugo Hiden, the technical director of the North-East Regional e-Science Centre (NEReSC) started a new blog where he will explore how to build an e-Science platform based on Microsoft technology. The initial post explains a little bit why he is doing this:
"The reason for this blog is, primarily, to document my experiences with writing a prototype e-Science research platform using Microsoft tools instead of the more traditional approach of fighting with Open Source. This way is easier, supposedly."
and also, what he aims to build:
"The task I have set myself is to recreate, at a basic level, the software being developed by the CARMEN project (http://www.carmen.org.uk). "

Let's see how it goes. Maybe they'll take suggestions later on :).

Sunday, October 21, 2007

Bio::Blogs #16 - call for submissions

The next edition of Bio::Blogs (bioinformatics blog journal) will be hosted at Freelancing science on the 1st of November. If you find anything this month that you think is interesting to add to this addition send an email to bioblogs at gmail. com until the end of the month. Anyone interested in hosting future edition can also send an email to volunteer.

Friday, October 19, 2007

The Fortune Cookie Genome

*in an imaginary future*

Today is the day I get the sequencing results back. It is going be interesting to have finally a glimpse of my very own genome. At the same time I am afraid of the potential disease associations they might find in there. In any case I rather know it with time to do something about it. Thats it ... I exhale and open the main door to the building walking up the desk.

- Hi. I have an appointment with my genetic adviser.
- Oh yes, go up to the 3rd floor, they are expecting you.

I walk up a DNA shaped stairway and walk into the office of one of the attending specialists. He was the one convincing me of how useful it would be to purchase the GenomeSurvey(TM) package.

- I got your email. The results are in ?
- Yes, we have your genome fully sequenced and uploaded into your service of choice. I see you have picked Google Health as your storage provider as part of the package.
- Is there any bad news ? Will I have a serious disease soon ?
- I understand your concern. There is really nothing too serious, but I will come to that in moment. You may login with your Google account here and I can guide you through some of the results.

I login to my health page and I am confronted with the usual simple white-blue Google interface. I noticed the addition of a genome tab and let my adviser tell me more about it.

- As you can see, your genome as been uploaded to your account. It has also been submitted as an John Doe genome to the NCBI personal genomics database. You may select later to make your identity known and/or associate any of your personal history information to it.
- What about the disease associations ?
- Yes. So you can click here on the associations report to have a full listings of the phenotypic associations. You have a very healthy genome, no serious rare diseases. In your case the most important finding is that you have a 2% increased likelihood of developing a heart condition when you are above 60 and a 1% increased likelihood of having Alzeimer's disease after 65.
- That's it ? 2% ? 1 %?
- Well, that is assuming no prior knowledge on your diet and other personal history as established in the large HapMap version 10. From now on you may input into the forms provided in Google Health all your diet and other personal information on a daily basis and as the information accumulates the service will automatically update the probabilities. As your adviser I should tell you that this information can be used by Google to provide you with better targeted advertisement in all other Google products.
- Right ... is this it ? Does the package include anything else ?
- Of course ! As I mentioned to you before you can click here on the prescription tab to get an informal advice on how best to deal with the associations that were found for you. You should always discuss these suggestions with your doctor before doing anything. By company policy I cannot read this information with you, since we are not liable for this. You can read it at home when you get there.
- Well , if there is nothing else I will go.
- Thank you again for choosing our GenomeSurvey(TM) package I am happy to have served you and I hope that you feel more empowered about your own health. Be well.

I go home feeling a bit cheated but obviously happy of having no serious disorder in the horizon. I rush to my home computer to read the prescription that will help me prevent my heart condition and Alzeimers. I click the GoolgeDoctor(TM) button and a clip like avatar jumps around in the screen. A computerized voice reads aloud the text appearing in the screen:

Dear Pedro. You can call me clipy ! I will be your assistant for any of your health needs. In order to decrease the likelihood for the negative phenotypes associated to your genome please consider abiding by the following rules:
- Do a lot of exercise
- Eat a healthy diet
- Find balance in your life

*in an imaginary present*

- Snap out of it, what does your say ?
I look back to the small piece of paper in my hand and read:
- "You must find balance in your life", thats what it says.
- Well, these things are never wrong.

I drop the paper on my dish and finish eating the fortune cookie before leaving the chinese restaurant with my friends.
- You won't believe what I thought of ...

Further reading
The Future of Personal Genomics (21 September 2007 Science)
How much information is there really in personal genomes and how much should patients know ? Extra points for citing a post from Eye on Dna in a Science Policy Forum.
The Science and Business of Genetic Ancestry Testing (10th October 2007 Science)
A discussion surrounding results of genetic ancestry tests and the commercialization of these tests.
Google Says Its Health Platform Is Due In Early 2008 (17 October InformationWeek)
Google is still trying to build a platform to host the health related information. Microsoft already launched a service called HealthVault (read about it from Deepak).
BMC Medical Genomics (17 October BMC blog)
BMC will launch a journal dedicated to Medical Genomics, covering articles on "on functional genomics, genome structure, genome-scale population genetics, epigenomics, proteomics, systems analysis and pharmacogenomics in relation to human health and disease."
Do-it-yourself science (17 October Nature)
This editorial links up several news, opinions and articles in the last issue of Nature to ask the question - How much involvement can patient advocates have in genetics? The most impressive articles is the story of Hugh Rienhoff, a trained geneticist and biotechnology that decided to personally research about his daughter's disease (as in buying a PCR machine etc). (via Keith)
Common sense for our genomes (18 October Nature)
Steven E. Brenner explains the need for a Genome Commons. See discussion at bbgm.

Thursday, October 11, 2007

JournalFire


A new science related service called JournalFire has started. It was apparently created by a group of graduate students that are "frustrated with the current system of scientific discourse and publication". According to the initial blog post this service "provides a centralized location for you to share, discuss, and evaluate published journal articles. You, the scientists, are put in charge of determining what studies are significant and noteworthy."

I did not have a chance to test it since it is in private beta but I have asked for an account. It looks like anyone with an .edu account should be able to access it already. It sounds promising but has many of these services a lot depends on the capacity to attract a sufficiently large group of people to sustain interesting discussions. I will update the post if I get an account to test the service.
(I wonder if the people from OpenWetWare have anything to do with this)

Monday, October 01, 2007

Bio::Blogs #15

Welcome to the 15th edition of the bioinformatics blog journal Bio::Blogs.

I complained a while ago that there was very little expansion of the bioinformatics blogging community but at least in the last couple of months it looks like this is changing. Although not necessary started last month here are three blogs that I only recently noticed: At the end of the day from Stephen Spiro (Spiro lab homepage), Paradoxus and Saaien Tist from Jan Aerts.

Not only are there more blogs there are many more examples of bloggers posting original ideas and research. Most people agree that being open about research should foster collaboration but so far few people have really tried to do it. It is inspiring to read trough these examples and trying to imagine how we might be doing science in the next couple of years.
This month was also marked by the many conference reports that we had available to read and by the experiments of taking real life conferences into Second Life.

Keeping this short and to the point this edition of Bio::Blogs focuses on these conference reports and on the ongoing experiments of using blogs to post about original research. I hope this nudges more people to go ahead and give blogging and open science a try.

Conference Reports

Neil Saunders was at the ComBio2007 conference and posted his notes about it in a four part series (1,2,3,4).

Allyson from Systems Biology & Bioinformatics provided a very extensive coverage of Integrative Bioinformatics 2007. Read all about it in chronological order from parts 1 to 10 (1,2,3,4,5,6,7,8,9,10).

From my blog here are two blog posts on the FEBS workshop - "The Biology of Modular Protein Domains" (1,2). This was not really about bioinformatics but I hope it will be interesting from the perspective of what data is coming that requires good integration strategies.

I'll jump know from real life to virtual talks. Those creative people at Nature keep testing out the potential of the web to improve interchange of knowledge. They kicked-off a seminar series of digital talks in the Second Nature island withind Second Life. The first talk by Philipp Holliger, entitled "New polymerases for old DNA" was about the engineering of new polymerases to amplify ancient DNA. Joanna Scott (working at Nature) has a very nice report on the talk in her blog.

Continuing on with virtual talks, in the past month there were another 3 sessions of the series SciFoo Lives On, organized by Jean-Claude Bradley and hosted also in Second Nature. JC Bradley covered the sessions on his blog: Sept 4 - Definitions in Open Science,Sept 10 - Communicating Science with Video, Sept 24 - Open Notebook Science Case Studies. Additional coverage by other bloggers can be found via the wiki page.

Blog articles

What are some of the most frustrating bottlenecks in bioinformatics research ? Where do we really spend most of our time ? Given that we work with digitized information it should in principle be mostly about the ideas. Thinking about interesting questions, crossing information and interpreting the results. At least for me this is typically not the case. What usually takes time is gathering all the necessary information in a way that can be analyzed. Three blog posts this month discuss this problem. Hari Jayaram and Neil Saunders posted about the problems they faced when attempting to do conceptually simple tasks. In response Deepak wrote a thoughtful post on how science databases should focus also on making the information easily accessible via appropriate APIs.

From online discussions to great examples of open science we start off with Jeremiah Faith's post were he describes an idea to determine the effect of sequence level mutations on transcription, translation, and noise.

Michael Barton from Bioinformatics Zen created a new blog dedicated to posting about his research on gene expression in yeast. Jump over there to read the many blog posts that he has already there, to provide feedback and maybe find common ground for collaborations.

Also this month, RPM from Evolgen re-started his attempt to publish original research on the blog. He is trying to study the evolution of a duplicated gene in Drosophila. There are two posts covering the introduction to the problem (part 1, part 2).

The last post highlighted in this month's edition is from Benjamin M Good. He has been working on a tool called Entity Describer to add semantic controlled vocabularies to Connotea and he has posted the manuscript they will try to publish on his blog and in Nature Precedings (10101/npre.2007.945.2).

This is it for this month. As usual, if anyone is interesting in serving as editor for any future edition, tell me by email.

ICSB 2007

I am attending the eighth International Conference on Systems Biology (ICSB 2007) in Long Beach. I typically prefer smaller conferences but this one is probably the best one to get an overview of the recent progress in systems biology. As expected the program has a broad scope and unlike last year's meeting there are no parallel sessions so I will have a chance to ear more from others fields. Any other bloggers attending ?