My Biotech Life

Fold it - Solve puzzles for science

Ricardo Vidal — Sat, 10 May 2008 05:28:40 +0000

Jason from Free Genes pointed me in the direction of this cool project called Fold It that just caught my eye. It’s a game but it’s a game with serious impact.
Based upon a similar concept of grid processing like the protein folding project (folding@home) or the search for ETs (SETI@home), this new approach makes the collective effort of players directly impact the processing.
It’s as if Fold It is an upgraded version of folding@home with the extra special new feature called: human interaction.

The concept is quite simple at the gaming point of view where you try to make the protein fold in the best way possible with points being given for stability through hydrogen bonding, compacting, hydrophobic and hydrophilic positioning of lateral protein chains, etc
The “better” you fold your protein, the more points you achieve.

These conformations are registered by the software and then processed furthermore thus contributing to the overall effort of predicting protein folding and therefore solving puzzles for science!

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Gene Genie: the better late than never personal genomics special edition

Ricardo Vidal — Wed, 16 Apr 2008 06:18:08 +0000

It’s a couple of days off schedule but Gene Genie has arrived. I’d like to thank Berci for the opportunity once again. That said, here goes the juicy genetic content.

NAVIGENICS GETS SOME LINK LOVE
Hsien-Hsien Lei over at Eye on DNA gives us an inside look at Navigenics with an interview with Genetic Counseling Program Director Elissa Levin.

Genetics and Health also had the privilege of interviewing Navigenics with a 7 part (long!) blog post with some great topics.

Looking into Navigenics entrance into the personal genomics market, Thomas Goetz from Epidemix goes local and delivers some inside observations.

THE WOES OF PERSONALIZED GENOMICS
The personalized genomics hype is bringing up the good and the bad. By making genetic testing a spit & pay easy one-click process, the science behind the actual testing becomes somewhat doubted upon by the general public. This may not be the case but it has been seen in the media where words such as “snake oil” have been associated with genetic tests.

Lisa over at DNA Direct Talk gives us a look into this topic with a great post packed with related links.

As we can see, not all companies can be put in the same basket, but there are clues here and there that some of them “haven’t really done their homework“, says Sandra Porter over at Discovering Biology in a Digital World.

THE WHO, WHAT AND WHERE IN PERSONAL GENOMICS
The who, what and where on personalized genomics
Berci from ScienceRoll has done a great job compiling a load of links, videos and quotes regarding personalized genomics that will certainly put you up-to-date.

GENOMICS GOSSIP
And finally, The Gene Sherpa brings us some tabloid style gossip regarding the Navigenics opening cocktail parties. Find the details hiding at the very bottom of a another one of his great posts.

Thanks to all those that submitted links for this edition of Gene Genie. I’m sorry I couldn’t get you all in. Maybe next time :)
The next Gene Genie will be hosted at Gene Expression on the 27th of April.

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Find biotech twitterers @ biotecher

Ricardo Vidal — Tue, 15 Apr 2008 05:07:31 +0000

My buddy Attila over at Pimm came up with a great idea to aggregate biotech related twitter users into one twitter account called biotecher.

I recently posted about twitter packs that were basically a list of science related twitter users (mostly twitterbots for science publications) that you could follow.

However, Attila’s idea is a bit different with all the bio-twitterers being followed by a single twitter account, biotecher. Thus aggregating all the biotech twitter community in one spot.

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Google’s App Engine open to Python enthusiasts

Ricardo Vidal — Tue, 08 Apr 2008 04:23:13 +0000

Google has just announced their new hosted platform called App Engine and it will provide access to it for free (for now…) to the first 10.000 or so users on a first come, first serve basis.

The platform will empower creators of web applications with features very similar to those provided by Amazon’s web service (AWS).

App Engine offers Python runtime which is specially interesting to me since I’m currently getting acquainted to it for a bioinformatics project I’m working on. So, it looks like it has come in good time!

~~Although I haven’t manage to grab an account on Google’s App Engine (yet!), I’m sure they will be distributing access to the platform in a timely fashion.~~ Got my invite!

Meanwhile, I’ll look out for the SDK and documentation.

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NIH wants to hear from you

Ricardo Vidal — Tue, 01 Apr 2008 04:25:22 +0000

Starting today (yesterday?), the NIH is seeking out for some input regarding their Public Access Policy. So, if you have something to say, just drop by the page they’ve set up and leave your comment.

Here are some questions/topics they are interested in hearing about:

1. Do you have recommendations for alternative implementation approaches to those already reflected in the NIH Public Access Policy?

2. In light of the change in law that makes NIH’s public access policy mandatory, do you have recommendations for monitoring and ensuring compliance with the NIH Public Access Policy?

3. In addition to the information already posted at http://publicaccess.nih.gov/communications.htm, what additional information, training or communications related to the NIH Public Access Policy would be helpful to you?

Visit the site and leave a comment.

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I Have The Results of My Genetic Genealogy Test, Now What?

Ricardo Vidal — Wed, 12 Mar 2008 04:21:53 +0000

So you’ve signed up at one of those fancy new genome sites, sent your spit in and have now received the information from your DNA testing. Now, a couple questions start popping up. What’s the next step? What does all this information mean?

Fellow DNA Blogger, Blaine Bettinger, has taken the time (and plenty of it, so it seems!) to write a FREE downloadable eBook titled “I Have The Results of My Genetic Genealogy Test, Now What?” that focuses on genetic genealogy. It’s a 28 page booklet that is easy to read and goes over some important topics throughout 4 chapters.

Chapter 1: What Is (And Isn’t) Genetic Genealogy?
Chapter 2: How Do I Interpret My Y-DNA Results?
Chapter 3: How Do I Interpret My mtDNA Results?
Chapter 4: Monitoring the Field of Genetic Genealogy

If you’re interested in knowing more about genetic genealogy, take these two simple steps. First, download the FREE eBook (PDF) and read it carefully and if that’s not enough to quench your thirst, visit Blaine’s blog, The Genetic Genealogist.

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Genome Projector - zoomable user interface for molecular biology

Ricardo Vidal — Wed, 12 Mar 2008 03:51:19 +0000

I ran across this interesting tool today called Genome Projector. It’s a creative application that uses the Google Maps API to render visual genomic maps with a load of detailed information.

Using the zooming capabilities of the Google Maps API, you can zoom around the large images and even search for pinpoint positions as if looking for a street address.

With 320 bacteria genomes at your disposal, you can explore each one of them via 4 different maps: Circular Genome, Genome, Pathway and DNAwalk.

I recommend giving it a try, even if just to see how the Google API was implemented.

[HT: digitalbio]

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From Blog to Boston

Ricardo Vidal — Mon, 03 Mar 2008 06:40:05 +0000

The turn of events that lead me to travel, from sunny Portugal across the Atlantic to chilly New England, is intricate and is also proof that if you stick your mind to things and work hard, you can go the extra mile. In my case, 3200 miles!

I sit here at my desk in an apartment in Cambridge, MA, thinking how all this has come to be…

In the early Summer of 2006, after years of just commenting on the blogs of others, I decided to start my own: My Biotech Life. It started off with the typical corny posts written just to fill up the homepage but soon gained some outreach (I think!!)

Soon after, I was establishing contact with very people whose blogs I’d previously commented on. One of those people I maintained contact with is Hsien-Hsien Lei from Eye on DNA (previously blogging at another genetics related site).

At some point, after swapping some ideas via email, we decided to create an aggregator of blogs related to genetics, genomics and DNA, currently known as the DNA Network.

The network grew (and is still growing!) slowly but steadily with new members joining from all over the globe. From Hungary to New York, our members include doctors, scientists, students and more.

My contact with the members of the network opened way to a fruitful relationship, both educational and professional. With my (amateur) graphic design skills I was able to help a few members and friends which would later pay back double fold with an opportunity of a life time.

Hsien Hsien Lei, who has been incredibly helpful and friendly since day one, had put me in contact with a great guy named Jason Bobe. Yes, the Jason Bobe from The Personal Genome.

Well, by some cosmic circumstances, Jason Bobe hooked me up for an interview with the very kind folks at OpenWetWare who happened to be looking for someone with my profile and to make an already long story shorter, I am now working at OWW at MIT in none other than Drew Endy’s lab.

Therefore, I must say that starting my blog in the summer of 2006 was definitely a marking moment that sparked a chain reaction of events that led me to where I am now.

Thanks guys and above all, thanks Bá for your support and patience.

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I’m on my way…

Ricardo Vidal — Thu, 21 Feb 2008 13:00:47 +0000

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Semantic Science Commons makes FasterCures top list

Ricardo Vidal — Tue, 29 Jan 2008 01:05:48 +0000

Great news from the hard working folks at Science Commons. They’ve just made it into the FasterCures list of top 10 to watch 2008!

FasterCures is a nonprofit organization dedicated to “saving lives by saving time”.

Their contributions to making scientific information accessible via the openness that is characteristic of SC but also via the use of semantic web technology, is making a strong contribution to scientific research.

And if you happen to be wondering what semantic web is… here’s a snippet from the SC blog.

In the simplest terms, it’s a way to mark research data so computers can help us make sense of it. The driving concept is that collaboration in science needs to make a shift from human-mediated to computer-mediated, from single-database access to data integration, from reading papers by people to reading papers with machines, and so on.

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