From what I’ve read about her, she was a small framed woman, that worked hard in keeping her brother focused on what he loved, scanning the night sky. Not only did she entertain guests, keep the house, sing and care for her sibling, she also fell in love with the stars as she accompanied her brother on his many nightly scans.

Considering all the chores, the singing lessons and the long nights, she played a big part in her brothers success and even got her name immortalized on an asteroid. Her second name, to be correct. Oh, and a moon crater too.

Update:
I’ve received a few emails regarding this post. I’m sorry if I made it look like all Caroline Herschel did was take care of her brother. I did not mean to pass on that message. I wouldn’t have picked her for Ada Lovelace Day if that were the case.

Considering her difficult upbringing, the fact that she was a woman in an age where only men were taken seriously in science, living with a very talented and demanding brother, I considered her impact and determination toward science to have been quite impressive. Thus my choice.

I could have easily mentioned another more famous and generally known female scientist, but I enjoyed learning about her life and thought it would be interesting to share the fact that there was a great woman doing incredible work in astronomy. Even if she was overshadowed by her brother.

The astronomical and petite Caroline Herschel

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

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]

Synthetic Biology is not your new bicylce

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.

Google Squared and genetics, Wolfram Alpha and engineering

Being interested in all things science, one of the latest uses for Twitter that caught my eye has to do with Open Access repositories.

Tipped by fellow Twitter user Eloy Rodrigues (@cibertecario02), there are currently two open access repositories currently tweeting new deposits. They are Southhampton Univeristy’s ECS repository (@eprintsecs) and Minho University’s RepositoriUM (@repositorium).

I find this to be an interesting way of keeping up with the knowledge flow at universities or departments within universities. I hope to see other OA repositories join Twitter soon.

(HT: Cibertecario02)

Open access repositories one tweet at a time

Well, today something caught my attention regarding two of these terms, namely anaphase and kinetochores. It seems that way back in 1956, a Portuguese researcher by the name of Miguel Mota made a visionary connection between them and published it in “A new hypothesis for the anaphase movement“.

Miguel Mota conceptualized that chromosome movement during anaphase is due to an active role played by kinetochores, minute protein bodies located at the centromeric region where spindle microtubules attach, which he envisioned to act also as “engines” that move chromosomes to the poles.

Mota’s models were only proven supported by more experimental data in 1987 (30 years later!) by Gorbsky and colleagues.

As a tribute to 83 86 year old Miguel Mota’s prescient findings, a symposium entitled: Mechanisms of Chromosome Segregation will take place in Porto, Portugal on the 9th and 10th of March 2009.

There is an impressive list of invited speakers to this tribute event with Gorbsky himself among the list.

I just love learning about this type of stuff. I had no idea that there was this impressive Portuguese researcher named Miguel Mota until today. I wish emphasis was given in school on teaching more about the who’s and the how’s and not only the what’s. Make sense?

A tribute to Portuguese researcher Miguel Mota

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

Take a look, before:

and after:

I also noticed that the new version has a cool network graph feature that allows you to visualize your social network of researchers/friends.

I must confess that I’m not the most active user over at ResearchGATE but feel free to add me to your network!

ResearchGATE with a new look and fancy graphs

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