As this is my first post about R, statistics and Bioconductor, I won’t go over the various things I believe should change within the R/Bioconductor community. I’d rather just take this opportunity to show my appreciation for such a cool and powerful tool, or should I say, set of tools.

From simple statistics to amazingly complex visualizations, I’ve slowly grown to fall in love with R. Well, I love and hate R. But I’ll keep things positive for now.

Where my biggest interest falls is in the interface between data and art. Visualizing data in interesting and new ways that allow us to extract new or better understanding from said information. This is what I hope I’m moving towards as I spend many and long hours coding R and attempting to find patterns in my scores of biological data.

Another side effect from spending so much time sifting through data sets is seeing data everywhere. It’s as if everything can be re-analyzed or further processed to produce new and interesting results.

Simple things like waiting at the bus stop lead me to think that it would be interesting to see how efficient the buses are or if their routes could be improved. Looking at the seating in the cafeteria makes me consider the many possible optimizations in table/chair positioning, etc.

I know that this is not necessarily due to R or data but rather more interest in mathematics and statistics. However, the fact that I live and breathe R, statistics and data sets has been making the cogs move…

Diving into R and swimming in data

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? :)

Supplementary data should be awesome like this

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.

More life science apps for iPhone and iPod Touch

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.

Using the (Google) Wave to surf the streams

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?

Mendeley gets a face lift

So, what does it do? Compounds is a stoichiometry “grams-to-moles” calculator and works like a charm:

1. Add compounds to the beaker.
2. Rotate iPhone to enter the formula.
3. Type in the formula for each compound using the Period Table as a keyboard.
4. Enter the coefficients (or ratios).
5. Shake! to solve.
6. Adjust the amount in grams of any compound and see the results immediately.

I’ve had the privilege of giving it a test run and I must say it’s pretty cool. The “shake to solve” feature is great!

Keep in mind that it’s not a Periodic Table app, it just presents the periodic table as an easier way to type in your compounds. Nice touch, if I must say so.

It’s not yet available for download at the App Store so I can’t provide a direct link, but be sure to find the link here when it does become available.

Compounds brings chemistry to your iPhone or iPod Touch

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

A while back I found Mendeley and have been using it for my thesis research. Zotero still has space in my daily motion but it’s for non-PDF related tasks, but I digress.

I’ll be writing more about my experience with Mendeley and all the cool new features they have recently been pumping out or their London offices.

Meanwhile, I got the chance to interview Victor Henning, one of the three Mendeley co-founders and here’s the outcome:

When and how did the idea to create Mendeley come about?

A few years ago, Jan and I were meditating high up in the Himalayan mountains, and on the seventh hour of the seventh day we heard a voice telling us to create Mendeley. True story. But since no one believes it, here’s what we usually tell people:

Soon after Jan and I had started our Ph.D.s in 2004, we realized that finding relevant literature was quite difficult if you were working in a field of research that you didn’t know too well. So we had the idea for a 3D visualization tool which would automatically group papers into related cluster, then map out relationships between academic disciplines and theories.

However, we soon realized that, first of all, we would need data for this. That’s where we got the idea for developing software which could extract metadata, keywords and cited references from your collection of research papers automatically, then create this 3D visualization for you – that was in 2005. That’s when our focus shifted to bibliography and reference management, with a social twist.
Interestingly, our first alpha and beta versions of Mendeley (which were released in early 2008) still contained the 3D visualization tool, but we took it out for the public beta release because it was too slow and clumsy – but we’re planning to sneak it back in again at some point.

So, over time, the idea evolved to what it is now: A combination of desktop software and social network for managing and sharing academic papers, with research statistics, recommendation engines, and an open, semantic research paper database coming down the road.

Why Mendeley? Where did the name come from? Were there other potencial names before settling on Mendeley?

When we started developing the desktop software, our working title was “Literacula” because we imagined how it would sink its teeth into literature and automatically suck the metadata out of it. Besides, the cheesy “B-movie monster” sound of the name made us giggle. Unfortunately, no one else liked it, let alone knew how to pronounce it.

So after going through a whole bunch of other bad ideas, we thought that derivations of scientists’ names might be a good thing: There was Dmitri Ivanovich Mendeleyev (alternatively spelled Mendeleev), who developed the periodic table of elements, and Gregor Mendel, who is often called the “father of modern genetics”. We liked the analogies to our vision: Just as Gregor Mendel studied the inheritance of traits in plants, Mendeley will enable you to trace how ideas and academic theories evolve and cross-pollinate each other. Dmitri Mendeleyev formed the periodic table based on the properties of known elements, then used this data to predict the properties of elements yet to be discovered – and Mendeley will help you discover new literature based on the known elements in your library.

This was the short version – if you want to read the full story behind our naming choice (including the list of bad ideas we had!), you can find it on our blog, here.

Was the success of Papers, the award winning Apple software application, an added reason/motivation to develop Mendeley?

Neither Jan nor I are Mac users, so we hadn’t heard of Papers until sometime in 2007. At that point, we were already working on Mendeley almost full-time. I believe the first version of Papers was released in 2006, right? But yes, the good reviews for Papers were an added motivation once we discovered it. We also met Mek (its main developer) a couple of times last year – he’s a really nice guy.

How has the general uptake been? Have the reviews been positive?

The reception and the reviews have been very positive so far. I think yours was probably one of the first! Of course, many reviews have pointed out that it’s still beta software, so there have been a couple of bugs and stability issues, but by now we have a pretty stable version that researchers around the world use productively. For example, Dartmouth College’s library recently named us the “Best Bet for PDF Management”, and many researchers tell us they’ve replaced EndNote with Mendeley.

Your software seems to aim at being both Desktop and web-based. Although the desktop version has seen further progress, is the web-based version planned to be as fully functional? And where does social networking fit in?

Yes, the plan is to offer the same functionality on the web that we offer on the desktop – that is managing, tagging and sharing your papers, automatic metadata and reference extraction, full-text search, a PDF viewer and annotation tool, and more. You’ll see many of these features on the web in the coming weeks and months.

The social networking aspect of Mendeley has been and will be centered around the research paper libraries of our users. First of all, you need to be contacts with another user on the Mendeley network in order to share research papers. We’ll also enable users to make their library public (entirely or parts of it), so that users can discover other researchers with similar interests. Based on the papers in their library, we’ll also match researchers with similar interests to each other – provided they have opted in to that, to preserve privacy. I did my Ph.D. on the role of emotions in decision making, and I would have liked to meet other Ph.D. students researching the same topic – on Mendeley, they’d be recommended to me automatically.

Also, when you have a profile on the Mendeley network, you will soon get personalized research statistics about your own publications. Say you’ve published a few papers and you’d like to know who’s reading them: Mendeley will give you a breakdown of your audience by academic discipline, geographic region, research interests, academic position etc. Again, to preserve privacy, it won’t let you identify your readers individually, unless they’ve chosen to make their library (and thus the papers they’re reading) public.

And it’s also FREE, which is obviously very attractive for the typical grad student. Are there already specific plans on how you will monitize your services?

The voice in the Himalayan mountains left us specific instructions about that. In any case, whatever is free will always stay free! We won’t charge for any of the things which are available now. Later this year, we will add additional premium features which will be available for a very reasonable monthly fee – e.g. less restrictions on sharing papers, more upload space, customized access to research statistics, or additional group management and collaboration tools. We’ve also had requests from private sector R&D departments for an in-house version of the Mendeley sharing server.

Further down the road, we’ll also look into advertising on the website. Also, we’ve had some interest from academic publishers about using Mendeley as a distribution system – very much like an “iTunes for research papers”.

Mendeley’s current chairman is Stefan Glaenzer, which previously held the same position at the ubiquitous Last.fm. How has his experience helped with the project’s development? How was he brought aboard?

Jan and I know Stefan since 2003. He was a guest lecturer in Entrepreneurship at our university, the WHU Koblenz. Together with two of our professors, he published a book with case studies about start-ups, to which Jan and I contributed a case.

So when we had the idea for Mendeley, he was the first person we tried to get on board as a business angel. That was in the summer of 2007 – Last.fm had just been sold to CBS, so it was great timing for us as Stefan was looking for a new challenge. He holds a Ph.D., too, so he knows the problems that researchers are facing on a daily basis.
Moreover, there were many conceptual similarities between Last.fm and Mendeley’s vision, so we managed to snag him as a co-founder! Before Last.fm, he had founded Germany’s first auction website (before eBay) and one of Europe’s biggest blogging platforms, so his experience with pretty much anything has been invaluable. Where to focus at which stage of the start-up process, how to hire the right team, how get further funding – he’s been helpful in all of these areas. He was also the one who introduced us to Skype’s founding engineers, who are now our investors as well. Combined, they obviously know a lot about building large-scale client-server-applications, and how to make them user-friendly, fast and safe.

One last question: Since all three founders of Mendeley studied in Germany, how come are you based in London, UK?

What did Rick say again in Casablanca? “We came for the water”. We just love rain, that’s why we’re here. Also, our third co-founder, Paul, was already working on London as a freelance web developer; Stefan was already here because of Last.fm; we wanted to be an English-language company because science is mostly English-language, too; and there are great universities in front of our doorstep – Imperial College, King’s College, UCL, LSE, Oxford, Cambridge, just to name a few. And apart from the weather, London is a nice place to live. Just consider this: We rented our first office from Monty Python’s Michael Palin and met him at work almost every day.

Interview with Victor Henning from Mendeley

What was supposed to be a quick app search turned out to be a long study-break looking for life science related apps.

I’ve installed quite a few apps and here’s my top 10 list:

10. Lab Timer: This app may only come useful to those doing work at the bench. It’s what the name says, it’s a lab timer. Allows for 4 separate timers with descriptions. Simple, intuitive and above all useful. [@ iTunes]

9. Measures – Unit Converter: A great help when working with odd units like the English system. Hah! [@ iTunes]

8. Primer Jot: A very simple way to keep your primers and oligos in order. Although I haven’t used a PCR in quite a while, I’m sure this can be useful for those that run PCRs regularly. [@ iTunes]

7. The Chemical Touch: This is probably the best of the Periodic Table apps I got a chance to use. Very intuitive and it also comes with a extra functionality that includes all the amino acids with detailed info, including chemical structure. [@ iTunes]

6. Evernote for iPhone: This award winning piece of software has been improving since day one and they keep outdoing themselves with new features. The free app allows you to synchronize anything from notes, photos, snippets and now even files! Great app for taking notes that you can later check on your computer, or vice-versa. [@ iTunes]

5. Solutions: This awesome app comes from the guys that are responsible for the award winning Apple software, Papers. If you have trouble with your solubility calculations or just don’t want to keep running numbers through your calculator, this is definitely worth every penny. (My short review of Solutions)

4. Molecules: This free app lets you glimpse at molecules in 3D. Allowing you to rotate them and zoom in to see their structure. Great stuff! [@ iTunes]

3. iCut DNA: Restriction enzymes are the scissors that allow us to engineer our very own source code, DNA, and there are plenty of them. This app comes in handy, allowing quick access to the restriction enzyme database (REBASE) and detailed info on each restriction enzyme. [@ iTunes]

2. PubSearchPlus: For a few bucks more than the non-Plus version, you get full-text access to PubMed search. Everyone knows how useful this can be. [@ iTunes]

1. Papers or Mendeley for the iPhone or iPod Touch. I’m quite sure that neither of these great applications are available for iPhone/iPod Touch yet, but when they do become available, I’m also sure they will be right at the top of my list. Nothing like having your papers at the tips of your fingers.
Until then, Air Sharing [@ iTunes] or Dropbox (webapp) will have to do.

Honorable mention: Although not a native iphone app, I must refer you to the Biocourseware web apps for iPhone and iPod Touch. A bunch of tools ranging from Bio/Chem Dictionaries to Genetic decoders. A great resource.

I’m sure there are many more life science related apps that I’m not aware of. Do you recommend any that may not be on this list? I’d like to hear about other useful apps.

*** UPDATE*** 20/Jan/2009
Great news!! It looks like the folks at Mekentosj.com are beta testing Papers for iPhone/iPod Touch! I’ll do my best to share impressions as soon as I get a chance to use it. I wonder if Mendeley is in the process of making an app too? Anyone know?

*** UPDATE *** 20/Jul/2010
It looks like there is will be a Mendeley app for your iPhone, iPodTouch and iPad coming out very soon!

Top 10 life science related apps for the iPhone and iPod Touch

The guys that brought you Papers, the award winning software to organize your papers, have now come out with this cool Mac app for the iPhone or iPod touch that allows you to easily perform the calculations for preparation of chemical solutions. The software’s name is as original as Papers‘ – it’s called Solutions.

Yet another reason for me to get an iPod touch. If you already have one, you can find the app @ iTunes, here.

Solutions brings chemistry to your iPhone or iPod touch