My Biotech Life

Mendeley = paper management + collaboration goodness

Ricardo Vidal — Tue, 01 Jul 2008 03:35:07 +0000

Some months ago, I was looking for software to manage the papers I had been consulting for a large group project I had been working on. At the time, the best (aka cheap or free!) available options where either for Mac or Linux, nothing for Windows.

Mac users have an award winning software application called Papers (not free) that is all the rage or even Yep (free?), the Linux gang have some options like Referencer that did a decent job of organizing and downloading metadata for the files. But Windows users were stuck with… well, expensive software packs like Endnote. Oh, and maybe Zotero that is a Firefox addon.

Well, it seems that this is not an issue anymore, someone has been hard at work and there is now a real option for Windows users (Mac & Linux too (sort of…)), it is called Mendeley.

Mendeley is still in closed beta but it is already packing a punch with some features that make it much more than just a paper manager. In their words:

Mendeley Desktop helps you to manage your research papers as easily as MP3s. When you import your research papers (in text PDF format), Mendeley Desktop will try to automatically extract the metadata (authors, title, journal, etc.), thus giving you a hand in setting up your digital library. In the next versions, we will also introduce Microsoft Word integration, OCR for converting your image PDFs, sharing and collaboration features, and exciting 3D visualizations of your library.

But Mendeley Desktop is just the starting point to get more out of your research papers. In the coming weeks and months, Mendeley Web will begin to provide you with personalized reading recommendations, statistics about your own publications, up-and-coming topics in your academic discipline, a network of fellow researchers, and much more

One of the cool features here is that there is a Desktop and a Web component that leverage the strengths of each platform. It will be interesting to see how the collaborative features in Mendeley Web work.
I’ve just began to use the software today so I can’t really get into any technical issues I may have noticed, but from what I’ve seen so far, it looks great. The user interface is functional and the overall design is also quite pleasant, on both Mendeley Desktop and Web.

The friendly folks at Mendeley have given me access to beta test the application along with 20 no more invites for my readers. If you are interested in being a beta tester, feel free to comment below and I’ll send out invites first come, first served.

I’m sure we’ll be hearing much more about Mendeley in the near future as the features start rolling out. Meanwhile, take a look at this demo (youtube) and let me know what you think about this app.

Post from: My Biotech Life

Riding the open wave…

Ricardo Vidal — Wed, 25 Jun 2008 04:44:23 +0000

It’s now been about 4 months since I arrived in Boston to join the OpenWetWare team. Time seems to fly by when you’re having fun, and it’s been quite a ride so far.

Aside from getting to know the great people responsible for creating OpenWetWare, I have had the opportunity to directly participate in this great project at a core level with the implementation of specific tools like the lab notebook and interact with the great community that makes OWW such an incredible online resource.

I have recently taken on the responsibility of spearheading the OWW Community blog where I’ll be publishing among many things, projects that take place on OWW, tips and tricks that can be used on the wiki, interesting news from the Open Science community and much more.

If you are interested in topics such as experimental biological research, sharing of scientific knowledge, web tools for collaborative research and other similar subjects, I recommend you subscribe to the OWW Community blog. I hope to see you there.

Also, if you happen to be a twitter user, feel free to follow my and/or OpenWetWare’s tweets!

Last but not least, if you aren’t part of the OpenWetWare community yet, what are you waiting for?

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Share science at FriendFeed

Ricardo Vidal — Tue, 17 Jun 2008 02:52:28 +0000

I’ve been using FriendFeed for a while now and it was initially just another spot to share my content flow.
The service allows you to share a ton of information from a large number (40+) websites ranging from Flickr to del.icio.us to twitter.

Recently, the folks at FriendFeed made it possible to create rooms where users could now congregate and drop in links. I think this was a very smart move because it allowed some organization within the enormous flow of content that even a small group of friends generates.

Given these conditions, a small group of life science buddies set up a room called The Life Scientists and it grew quickly to a jam packed 100+ “full” room.

What I find really cool about all this is not just the ability to follow what colleagues and friends are doing online but the comments that they provide. A great example can be seen in the image that follows:

FriendFeed has been growing quite rapidly and by keeping things simple it’s been useful for sharing web content and also maintaining light conversation around specific topics. Let’s hope it keeps that way!

Read more about FriendFeed here and here or catch the latest FriendFeed “Best of” here.

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Synthetic Biology - the journal

Ricardo Vidal — Thu, 05 Jun 2008 04:59:02 +0000

It’s just come to my attention that there will soon be a new scientific journal totally dedicated to this fascinating area of science engineering named accordingly Synthetic Biology.

The new journal will be published by Wiley & Sons and has a respectable editorial board headed by Adam P. Arkin (Berkeley). The board includes well known researchers in this emerging field of bioengineering like Pamela Silver (Harvard), Luis Serrano (EMBL Spain), Ron Weiss (Princeton), Christina Smolke (Caltech) and more.

The new journal is described as follows:

Synthetic Biology as a journal will provide a forum for scientific inquiry in this field. The core will be publishing of Research Articles and Technical Reports that exemplify the cutting edge in both foundations and application for synthetic biology. Perspectives and Reviews will help track the major technical innovations and challenges and the rapid evolution of thought that characterizes this new field and engage the community in discussion of the impact of this science on biology, biotechnology, society, and the economy.

The journal is now accepting research articles, perspectives, reviews and spec sheets. I find the idea of spec sheets in biology, just brilliant (ex: BBa_F2620 Data Sheet pdf).
From some research presentations/articles I’ve already had a chance to look at, the first issue of Synthetic Biology will surely be a success.

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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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