My Biotech Life

Among many other things, I recently read the wide-scope and well disseminated paper by Beroukhim et al (a very very loaded et al!) titled “The landscape of somatic copy-number alteration across human cancers”. An impressive study of 3,131 cancer specimens from 26 histological types of which 158 regions of focal somatic copy-number alterations were found.

I could go into detail about this study but what I wanted to mention here was not necessarily about the potential candidate genes or their possible functional implications. I wanted to mention the awesome web application that was produced along with this study which allows folks like me (read lazy!) to go over their datasets with minimal effort.

The Broad Institute’s Tumorscape is a portal that allows one to browse/search through a database of copy number alterations across multiple cancer types. Basically the findings of the previously mentioned paper.

In my opinion, this is much better than having to go through the raw supplementary data. If I were interested in further pursuing any of the studies performed, I could download the supplementary data, but if I’m just interested in browsing the results of this paper, the Tumorscape makes it far more pleasant.

There is obviously an overhead related to producing this type of portal, however the sheer number of people working on this project and the amount of data produced definitely justified the creation of such a web application.

Sorry if the title of this post was a bit misleading, but hey… it should be awesome, right? :)

About a year ago I wrote a blog post containing my top 10 list of science related apps for the iPhone and iPod Touch. The list is (was?) a personal selection of apps that I had tried at the time and thought others would enjoy. And I’m sure many did, given the feedback I received.

With this in mind, here’s a few more interesting life science related apps that I have recently added to my iPhone and iPod Touch which may be of some interest.

I was amazed that this took so long but Nature.com only recently came out with an iPhone app that is free for download and gives you access to their latest content (Don’t mind the pay-wall :) ) and provides you with an easy way to search and save content.

While using Nature.com’s app, I found Promega’s app (also free) that although needs some design work, it does come packed with great content. Protocols of all type, video media and a simple BioMath calculator which helps with unit conversions.

Another app that’s just recently become available is made by the folks at Invitrogen. Their app called Daily Calcs helps with routine calculations like Molarity calculations, Molecular weight, dilutions, unit conversions and interesting cell culture references. And it’s also free.

If browsing genomes on the go is your thing, then I must recommend you download the GenomePad which basically provides you with UCSC’s Genome Browser on your iPhone. I find it to be a bit difficult to navigate and parse all that data on such a small screen, but it’s great for quick look-ups. Did I mention it’s free?

The last two apps I’ll mention are not so much tools but didactic apps in the sense that they are awesome learning apps. One called Mitosis provides an interactive way to learn about the process of cell division and the other is a science glossary packed with science goodness. Once again, free and free.

As you can see, I’ve only mentioned a hand full of free apps this time as I haven’t had or required to purchase any other science apps. However, if there’s a scientific app out there that you think is worth spreading the word (free or not!), please let me know.

6 months later, this is what I’ve been up to and what is currently going on…

• 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.

There’s been a recurring topic showing up in prominent news outlets that has been getting on my nerves. Well, not really on my nerves but something that I consider to be wrong and was hoping someone would make it stop or at least correct it.

Synthetic biology is great, I really like everything about it. I truly do. I had the privilege of meeting and seeing the work of some of the pioneers in this exciting new approach to genetic engineering last year at MIT.
I must emphasize something about these bioengineers. They are extremely smart, hard working, innovative and, did I say it? smart biological engineers!

So what is it that ticks me off about some of the synthetic biology related articles? It’s not the “Frankenstein” remarks, it’s not the bioterrorism worries and it’s not even the JC Venter veneration!
Nope, it’s the constant comparison between synthetic biology now and computer science in the mid-80’s.

This comparison just brings along a whole truck load of babble that I think is incorrect. Mentioning that synthetic biology makes engineering biology so easy you can do it in your garage as if putting together a new lego set. Stating that people are sequencing their own genomes in their closet as if it were something like baking a cake in your microwave.

These stories are either incomplete or incorrect. You choose. I think that the average reader is going to misinterpret these articles. It’s quite notorious by looking at the comments made on the online news articles.

No doubt that synthetic biology makes engineering biology easier but it’s not something you’ll be doing in your garage/kitchen/bedroom closet. At least not legally, or with much success. Besides, the people that seem to be championing such efforts are mostly graduate students in fields related to biological sciences, not your regular Make magazine reader or science buff.

I’m not against the DIYBio movement. I just don’t think it should be synonymous with “garage synthetic biology”, because it’s not. They have a ton of really interesting projects that I believe would make more sense to put effort into.

So yeah, let’s not get ahead of ourselves.

In summary: Synthetic biology is great awesome! But unlike Obama, it’s not your new bicylce.

[Photo: Alexander van Dijk]

While many are going on about how Wolfram|Alpha, Google Squared and also Bing compare one to another, I took the opportunity to give Google’s latest lab release a go with some topics I’m interested in, namely genetics.

GOOGLE SQUARED AND GENETICS
Search terms: DNA sequence

Search terms: Genomes

Search terms: Genetic Diseases

Search terms: Genes

WOLFRAM|ALPHA AND ENGINEERING
And now, let me just put in my quick 2 eurocents (roughly 2.84 US cents) regarding Wolfram|Alpha.
I’ve found it to be a really valuable tool with any work that requires looking up tabulated data and proceeding with any type of calculations upon such data.

Wolfram|Alpha would have been such a time saver while I was working on my biotech industries project. Loads of engineering calculations and data to look up that would have been made so much easier. No need to skim through Perry’s handbook, through process engineering and transport phenomena books looking for figures, graphs and constants. Wolfram|Alpha would have made most of it a simple search.

In summary, Wolfram|Alpha is, in my opinion, a really large and structured Almanac with a super scientific calculator mashed-up into it and therefore a very useful reference tool. However, it’s pretty poor when it comes to anything outside it’s “comfort zone”, like life sciences. I’ll have more to say about this in a future post.

Just when you think you’re getting the hang of things… Google shows you how it should be done.

Like most of my geek/nerdy friends, I have a system that I use share, organize and discover new and interesting things online. I subscribe to a (large!) number of rss feeds, have an account at most of the major social networks, participate in the microblogging world via twitter and tumblr, and just to keep track of most of it all, FriendFeed comes to the rescue to aggregate most of my and my friends streams of content.

Well, this all sounds pretty overwhelming but it’s not. I mean, it is. I can’t read everything that runs across those pipes, but it’s rather easy to manage, to filter and to “save for later”.

Said that, today at Google’s I/O conference, a fancy little thing called Google Wave was presented.

What is Google Wave?

Google Wave is a new model for communication and collaboration on the web

What is a Wave?

A wave is equal parts conversation and document. People can communicate and work together with richly formatted text, photos, videos, maps, and more.

A wave is shared. Any participant can reply anywhere in the message, edit the content and add participants at any point in the process. Then playback lets anyone rewind the wave to see who said what and when.

A wave is live. With live transmission as you type, participants on a wave can have faster conversations, see edits and interact with extensions in real-time.

Although I don’t think that Google Wave will be a substitute for all the services and networks I use online, I am pretty sure that it will become an amazing hub for collaboration, participation and in some way redefine how most of us will communicate online. Just like previous Google products have.

FriendFeed rooms (or whatever they are called nowadays), Twitter and other online networks with real-time activity will have some serious alternatives, unless they too join the wave.

As a biological engineer, the use of Google Wave for scientific discussion, collaboration and dissemination is really important to me. I hope to see science related waves pop up and get developed before the software/service becomes available mainstream. Martin Fenner at Nature Network hopes that Google Wave doesn’t forget the scientists. I hope so too.

Earlier today, the Mendeley website was not available for a few minutes while it was “updating…”. Shortly after, the site reopened with a complete new look. A very light and bright site with more information than the previous version.

Being part of the Mendeley team, I knew that a redesign was underway but had not had the opportunity to see the finished “product”.

The logo has changed slightly, it’s jumped out of the square and now is a more horizontal logo, giving more visibility to the name.

The new version has a nice section called How it works that shows some of the key features in Mendeley and basically how to use them.

Although I’m obviously biased, I must say I like the new look. What do you think about the redesign?