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

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

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

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

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

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

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

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

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: