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

• 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…

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

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

Although it’s not a science social network, I recently came across a new site called Lappiz which presents the tagline “Learning has evolved“.

From the official about page, Lappiz is:

“… a collaborative web tool that allows students, especially those in higher education, to share academic content between them. Its purpose is purely educational, providing students universal access to all kinds of documents that might be interesting in a particular area of study.”

Rui Marinho, co-founder of Seegno, the Portuguese company that created Lappiz, was kind enough to answer a couple of my questions:

You’re a biomedical engineering student, right? How did you get involved into creating Lappiz?
I am currently attending the 4th year of the Integrated Masters in Biomedical Engineering, at University of Minho, Braga, Portugal. I have chosen to specialize my studies in the Medical Informatics branch, one of the four available in this Masters.

Lappiz was developed at Seegno, a startup based in Braga, Portugal, which I co-founded with Jorge Pereira and Tiago Ribeiro. My involvement on the idea that made Lappiz what it is today started within my academic life at University of Minho, where the concept was firstly tested. It then became our pet project at Seegno and followed a partnership with Innovation Point – with which we had already cooperated in developing the Gasmappers application.

How did the name Lappiz come about? What does it mean?
Nowadays, a meaningful name and a valid international domain are a difficult pair to get together. Specifically, working on this service as a brand is a demanding effort. We had several brainstorming sessions to come up with a simple and somewhat meaningful name.

We wanted something that could vaguely relate to being a student. In Portuguese, Lappiz is pronounced “lapis”, which means “pencil” in English. It is also vaguely recognized in the english language through “Lapiz Lazuli”. Since Lappiz is all about the academic life where the process of handwriting and taking notes is common, we found it to be an appellative name, while still being able to have a qualified international domain.

Did the idea to create Lappiz come out of necessity or was there a niche you noticed that needed to be filled?
In a way, it came out of necessity, since none of the existing systems at the time actually matched what we had in mind. The idea of Lappiz was born in University of Minho, where the concept was initially tested on a more restricted set.

Some of us, at Seegno, while students at University of Minho, ran a first test between students of Informatics Engineering and, later, Biomedical Engineering. We then approached Innovation Point to see if they were interested in participating on the further development of this idea. After founding Seegno, the partnership came to life in order to launch Lappiz on a global scale.

There are (a lot!) of social networks out there, what makes Lappiz stand aside from the pack?
Most social networks have a high relevance and penetration on a global level, but they are generalist in nature, as they focus on bringing in large quantities of people. Lappiz targets a more specific audience, with a purpose in mind that goes beyond simple socializing,befriending strangers and putting yourself out to the world. It has an associated concept that responds to a concrete need, namely in terms of presenting each participant as a valid source of academic information.

Although Lappiz has some features found in other social networks, it is particularly focused on sharing information resources like study notes, exercises, trials, exams, practical works, reports and thesis. There are several features available for this very purpose, and many more are planned. Dynamic organization, personal activity follow-up, feedback, peer review procedures, resource management, bulk uploading and tag assignment are some of the distinctive functionalities of Lappiz. Also, in the near future we plan to expand the platform and its functionalities in very significant ways.

Facebook integration is also a key feature of Lappiz, and as a member, you have immediate access to Lappiz, without the need to register, bringing with you your personal friends’ network. After this step, you can then enjoy an academic trip without the rigidity of the institutional platforms. Discussing topics or asking questions to the community are now simple and intuitive processes. In a way, our focus on integrating with other platforms is a statement on our intent not to compete with other social platforms, and rather be a complement to a specific population – students and ex-students – which is already typically a user of those platforms.

From a quick first glance, Lappiz seems to provide some of the functionalities that social networks like Epernicus already provide, how do you think your site differs?
There are many social networks available worldwide, and many more are emerging. Our approach, since the initial prototypes, was to position Lappiz as a tool to explore the overlaying of students and their learning interests and not as competitors to world-wide social platforms. This is one of the reasons why we have such a deep integration between Lappiz and Facebook.

Unlike Epernicus, Lappiz’s social tools work as a complement to the fundamental collaboration effort for a better academic success, and not as a professional network constructor.

Lappiz is available in English and Portuguese. Being from Portugal, knowing the Portuguese education system and the average Portuguese students, what do you think the uptake will be?
The idea of having both languages demonstrates our effort to captivate the attention of both foreign and Portuguese students, including those in programs like Erasmus. We have an ambitious plan that aims to register 10.000 Portuguese students in the first few months, and 100.000 students until the end of the year, between Portuguese and foreign students. We believe Lappiz will become a reference in the academic area.

These estimates are a result of the number of students that enter higher education institutions in Portugal and foreign countries. In Portugal, about 70.000 new students join these institutions every year, contributing to a universe calculated to be of around 300.000 students. Abroad, every year more than 4 million new students also enter higher education institutions.

One of Lappiz’s goals is to “simplify students’ lives”. What particular tools does Lappiz provide to do so?
We have built several tools that simplify students’ lives. For instance, they may keep track of the activity in their university, course or subject, in order to be always alert of new resources, replies to questions they made, new discussions and so on.

As you are aware of, academic studies often rely on numerous digital documents. Students using Lappiz are likely to submit these files to share with their colleagues, additionally including work of their own. We have implemented a bulk uploading tool which allows students to submit several simultaneous files in a painless way, with built-in features like tagging, which will facilitate future searches.
It is also important to distinctly identify the best content available. As Lappiz grows, it is expected that the available resources increase largely. By integrating feedback and peer review procedures, we are allowing students to identify the most interesting, informative, important and helpful resources.

Lappiz’s also has a simple filtering system which allows users to select criteria such as Most Recent or Popular entries, and it is also possible to filter it by type of content, such as resources, questions or discussions. For instance, one can choose to see what are the most popular resources on a university or the most recent questions on a subject.

Have you had support, financial or other, from your University or any other institute to create Lappiz?
Lappiz is the result of a partnership between Seegno and Innovation Point. We haven’t had any support, financially or other, from University of Minho or any other institute.

Is there a defined business model already set up for Lappiz? Publicity, premium features, etc?
The current business model predicts an advertisement-based support. We are confident that in the near future we will be able to provide services of added-value that are useful and interesting for Lappiz’s community. On the other hand, we do not want to fill the platform with intrusive elements just for the sake of generating revenue. We expect to deliver highly targeted advertisements and services.
Online business models are complex and we are still studying this matter. However, Lappiz will remain a free platform for the purpose it was built for, independently of the revenue model applied in the future.

Is there anything else you’d like to let my readers and/or Lappiz users know?
I want to thank everyone for their effort on testing Lappiz since its early stage and to all the people who have submitted feedback about it. I would also like to let your readers know that Seegno focus in exploring innovative ideas and in the development of Information Solutions, meeting the higher standards in technical quality, simplicity, aesthetics, robustness and user experience. As an open company, we are interested in new ideas and in bringing projects to life – you may reach us at any time – we would love to hear from you!

Interview with Rui Marinho from Lappiz

Based upon the DNA Network logo I created about 2 years ago, here are 4 color variations of the same wallpaper for anyone to use on their iPhone or iPod Touch.

I’ve updated the science logo and icons page but here’s the direct download link just in case.

DNA themed iPhone & iPod Touch wallpapers