Quite immediately the silly and equally far-fetched comments/answers started coming in. Some would do such things as walk into volcanoes, leap from buildings/planes and perform other generally mortal activities. However, others took a more cautious route by stating that they would not tell anyone for fear of scientific probing or media exposure. The answers said quite a bit about each commenter’s personalities, to say the least.

However, what I found most interesting were the follow-up questions to the original question. Some quite entertaining and others rather important, given the hypothetical situation.

• “If I jumped from a building, would I get injured at all? If so, would I recover from my injuries or remain injured for eternity?”
• “Although immortal, can I feel pain?”
• “How did I discover that I could not die?”
• “Do I grow old despite not dying?”

My inquisitive nature finds the questions to the original question far more enticing than the immediate comments made without further interrogation. They [the following questions] open up far more hypothetical answers to the original question. The necessity of specifics to provide a correct and conclusive answer to a question is so ingrained in my thought process that it sometimes leads an answer to be delayed until all scenarios are covered. Rambling a bit more, the answers to the various questions asked after the original question would further define my answer and therefore lead to a more specific hypothetical answer.

In short, if you had to answer the question above, would you answer as is or attempt to find out more about the hypothetical situation before answering?

I guess the easiest (and probably lamest) answer is “It depends.”

The questions to the hypothetical question

• I finished my thesis, I presented my thesis, I concluded my Master’s degree. Good grade, Happy dance.
• I took my (32!!) driving lessons, I passed the written tests, however I did not conclude my driving exam (more on this, later).
• We made a decision, a difficult decision. Time will tell.
• We celebrated our 1 year wedding anniversary. Champagne for all!
• We moved to Canada. First Toronto for a while, now Kingston.
• I switched to Mac. My 6 year old laptop may rest in peace.
• I’m now a Ph.D. student in Squire Lab at Queen’s University.

There were some good (great!) and bad (really bad!) moments since last August, but no need to go further into detail here.

OK, done that, let’s get back to semi-regular blog posts of awesome science stuff.

It’s been a while…

If you don’t know what Mendeley is, here’s a quick and short answer:

Mendeley is free social software for managing and sharing research papers. It is also a Web 2.0 site for discovering research trends and connecting to like-minded academics

I’m excited to be the first to join Mendeley as Community Liaison and I hope my contributions may help engage the academic community to get involved and actively participate in Mendeley’s roadmap decisions.

Also, I’ve set up a disclaimer so that things don’t get misinterpreted down the road.

Community Liaison @ Mendeley

2008
So last year I planned to do the following:

Conclude my Master’s

Unfortunately I haven’t been able to do this due to a number of reasons but I should finish up within the next couple of months. Thesis writing is painfully slow…

Learn a new programming language (or master the one I know…)

I managed to start coding in Python. Although I’m still at a novice level.

Travel to at least 3 different countries

This was a bit of a stretch but I did travel quite a lot in 2008. I moved to Boston, MA, USA in February for a 6 month internship at MIT. I visited family (twice) in Toronto, Canada. Flew to Palo Alto, California for BioBarCamp unconference. Relaxed in the sun and sand of Tunisia.
Took off and landed in various cities, namely Buffulo, Chicago, San Francisco, London, Toronto, Lisbon, Tunis. So I think that resolution was well taken care of.

Read anywhere between 6 and 12 books

2008 was probably the year that I read the most. But not the most books. Since I don’t consider bits and pieces of technical books, scientific papers and online text to be “books”.
However, I did manage to read a few in my spare time:

• Genome by Matt Ridley: Each chapter focusing on a specific gene and the story related to it’s discovery or understanding.
• The Know-It-All by A. J. Jacobs: One odd fellow’s adventure reading the whole Encyclopedia Britannica, from A to Z.
• 21: Bringing Down the House by Ben Mezrich: I was interning at MIT, and even had the opportunity to see a talk by the folks this book was based upon. So it was a must-read (or not).
• The God Delusion by Richard Dawkins: Good read but took me a while to get through it. Kept putting it aside to read lighter things.
• A Matematica das Coisas by Nuno Crato: Short book focused on how math can be found in everyday activities and some mathematical background about them. (In Portuguese)
• Update: Getting Real by 37signals: I assume everyone has read this. Quick and interesting read.

Move into my own place

Technically it’s not my place. It’s our place. I got married in October (!!!) and we moved into a nice little apartment. Check!

Switch to Ubuntu or OS X

I wasn’t in a position to spend much on a new laptop, so I kept with my 5 year old ASUS laptop and gave Ubuntu a try (dual boot) and used it everyday for roughly 4 months. I ended up moving back to WinXP because it was just too buggy. So, I guess when I get a MBP this year, I’ll finally switch to Mac OS.

Get my driver’s license

Didn’t get my license just yet. However I’m beginning lessons soonish!

Get more (any!) exercise

I’m proud to say that being in Boston made me pick up a good habit. Running. I was the type that wouldn’t even run to catch a bus, but soon after the snow melted I began running around the Charles and it’s been great ever since. Over a year, I went from no running to being able to run 10km!

2009
So, based on last year’s resolutions, for 2009, this is the list of things I’d like to get done:

• Finally finish my Master’s
• Start driving (as soon as I get my driver’s license!)
• Visit at least 3 different countries/cities I’ve never been to.
• Try again to read at least 6 or more books.
• Get into a PhD program related to stem cells, synthetic biology, immunology or any combination of the three.
• Attend a workshop or course in any of the following: Matlab, R, Processing.
• Move abroad. Order of preference: USA, Canada, UK, Germany.
• Purchase a MBP!

So that’s it for now, let’s hope I can achieve these goals and that everything goes smoothly!

In 2009 I plan to:

The MIT kid, possibly a computer science graduate, was going on about how all his friends were coders working at Cisco earning 33 bucks an hour. Some where at Google, got paid less but had better perks.

The BU guy followed by saying something along the lines: “Wow, 33 an hour! I should have gone into computer sciences…”. To what the MIT kid replied “Nah, everybody is into bio these days… That’s where the money is!”.

Shortly after, the MIT kid said “Anyways, I hate bio!”. The BU guy concurred with a simple “Me too”.

Everybody is into bio these days…

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 their reference management 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.

Mendeley = paper management + collaboration goodness

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.

From Blog to Boston

I’m on my way…

This year I plan to:

• Conclude my Master’s
• Learn a new programming language (or master the one I know…)
• Travel to at least 3 different countries
• Read anywhere between 6 and 12 books
• Move into my own place
• Switch to Ubuntu or OS X
• Get my driver’s license
• Get more (any!) exercise

Listed in random order.

Note: I have some other personal goals but they need not be listed here ;)

In 2008 I plan to:

Over the last 12 months so much has happened that I’m still dumbfound at the amount of people I’ve made contact with, the number of doors that have opened and the progress I’ve made academically…

2007 was the year of the DNA Network, a community of Biotech, Genetics, DNA and Health related blogs founded by Hsien-Hsien Lei from Eye on DNA and myself. It’s been growing at a healthy pace (40 blogs so far!) and the members joining us have contributed with fantastic content and knowledge in their areas of expertise.

Working as a part-time freelancer, I got involved in a bunch of great projects with some very interesting and talented people (some are now members of the DNA Network!) and produced a few logos, some small websites and helped out wherever I could.

Two examples of science related logos produced this year that received quite some feedback where the DNA Network and the Gene Genie logos (see below).

Academically I achieved close to all of the milestones I had set to hit. I completed a truck load of classes and got the oh-so-complex biological industry group project handed in on time.

The end of this year was specially different since I moved out my apartment near campus and came back home (700km away!). I’m just a couple exams and a 6 month internship away from concluding my degree (finally!)

Obviously there was much more to this year. A lot of emailing, chatting, Skyping, networking in general and above all, learning from it all.

Some of the events that took place this year opened doors to many new and fantastic things that will certainly take place in 2008.
I can only wish that everything goes as well as last year and that all those that I’ve made contact with achieve everything they aspire for.

2007 was great but I can bet that 2008 is gonna be a beauty!

2007 – There she goes…