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

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

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

The new repository government-supported site for hosting multiple repositories which is currently indexing over 13091 documents from 10 repositories has been announced as a project funded by the Knowledge Society Agency (UMIC) and will be technically maintained by the National Scientific Computations Foundation (FCCN).

This looks like a cool project and I sincerely hope it gathers some momentum and becomes a useful resource.

The 10 repositories that are currently contributing to this main centralized repository are mainly university DSpace-based repositories or similar.
My university happens to show up on the list but is listed as contributing 0 documents. Yes, zero. Maybe it’s new.

This [zero docs] isn’t really a surprise since I had been considering submitting a proposal to set up a Dspace-based repository at my university earlier this year along with a buddy of mine. However, higher priority things took it’s place in my to-do list, like my thesis work.

Anyhow, I must congratulate everyone involved in this project and wish the best of luck. Maybe my thesis will be a part of this once it’s finally complete!

RCAAP – The Portuguese Scientific Open Access Repository

I sit here at my desk in an apartment in Cambridge, MA, thinking how all this has come to be…

In the early Summer of 2006, after years of just commenting on the blogs of others, I decided to start my own: My Biotech Life. It started off with the typical corny posts written just to fill up the homepage but soon gained some outreach (I think!!)

Soon after, I was establishing contact with very people whose blogs I’d previously commented on. One of those people I maintained contact with is Hsien-Hsien Lei from Eye on DNA (previously blogging at another genetics related site).

At some point, after swapping some ideas via email, we decided to create an aggregator of blogs related to genetics, genomics and DNA, currently known as the DNA Network.

The network grew (and is still growing!) slowly but steadily with new members joining from all over the globe. From Hungary to New York, our members include doctors, scientists, students and more.

My contact with the members of the network opened way to a fruitful relationship, both educational and professional. With my (amateur) graphic design skills I was able to help a few members and friends which would later pay back double fold with an opportunity of a life time.

Hsien Hsien Lei, who has been incredibly helpful and friendly since day one, had put me in contact with a great guy named Jason Bobe. Yes, the Jason Bobe from The Personal Genome.

Well, by some cosmic circumstances, Jason Bobe hooked me up for an interview with the very kind folks at OpenWetWare who happened to be looking for someone with my profile and to make an already long story shorter, I am now working at OWW at MIT in none other than Drew Endy’s lab.

Therefore, I must say that starting my blog in the summer of 2006 was definitely a marking moment that sparked a chain reaction of events that led me to where I am now.

Thanks guys and above all, thanks Bá for your support and patience.

From Blog to Boston

I’m on my way…

Over the last 12 months so much has happened that I’m still dumbfound at the amount of people I’ve made contact with, the number of doors that have opened and the progress I’ve made academically…

2007 was the year of the DNA Network, a community of Biotech, Genetics, DNA and Health related blogs founded by Hsien-Hsien Lei from Eye on DNA and myself. It’s been growing at a healthy pace (40 blogs so far!) and the members joining us have contributed with fantastic content and knowledge in their areas of expertise.

Working as a part-time freelancer, I got involved in a bunch of great projects with some very interesting and talented people (some are now members of the DNA Network!) and produced a few logos, some small websites and helped out wherever I could.

Two examples of science related logos produced this year that received quite some feedback where the DNA Network and the Gene Genie logos (see below).

Academically I achieved close to all of the milestones I had set to hit. I completed a truck load of classes and got the oh-so-complex biological industry group project handed in on time.

The end of this year was specially different since I moved out my apartment near campus and came back home (700km away!). I’m just a couple exams and a 6 month internship away from concluding my degree (finally!)

Obviously there was much more to this year. A lot of emailing, chatting, Skyping, networking in general and above all, learning from it all.

Some of the events that took place this year opened doors to many new and fantastic things that will certainly take place in 2008.
I can only wish that everything goes as well as last year and that all those that I’ve made contact with achieve everything they aspire for.

2007 was great but I can bet that 2008 is gonna be a beauty!

2007 – There she goes…

The project title is “Production of Potassium Cephalosporin-C” and it was a hell of a ride. It’s a nice 300 pages worth of engineering and another 500 pages of annexes to follow along.

And to top off that nice heap of dead trees, we have our industrial process all laid out and programmed in the engineering software we used.

Mission accomplished!

It seems that three fellows, Ron Milo, Paul Jorgensen and Mike Springer from the Systems Biology department at Harvard, decided to start compiling data related to the numbers in biological research and came up with what they call BioNumbers, a database of useful biological numbers. Brilliant!

At the moment, the data is available via a Google Spreadsheet document which doesn’t really provide proper navigation but I suspect that there are plans to change this as the database grows. There are already some ideas in the pipeline:

• The comparative tables builder: you will be able to choose your properties and and organisms of interest and get a table comparing the values. We hope this will make comparative studies much easier, and will lead to new insights into quantitative design principles. Blanks will denote where we need more data.
• The comperaVisulaizer: a graphical interface that will visualize values for different organisms and different properties that share the same units. Kind of like the scale of lengths showing the progression from molecules to galaxies.

This project is open to anyone that would like to participate. If you happen to know about a useful biological number that isn’t yet in the database, feel free to contribute by sending in your info using the following format.

For more information, please visit BioNumbers at OWW.

BioNumbers – the database of useful biological numbers

“In the “old days”, you would devote yourself to the study of a single system – a process, an organism or even a gene. You’d publish 20-30 papers entitled “Gene A in organism B encodes protein X involved with process Y” and eventually, be in the running for tenure. Bioinformatics means that we don’t have to work that way anymore. I can look at archaea one day, humans the next. I can apply whatever computational methods I see fit and am able to learn to any dataset that takes my fancy. In short, I don’t fit well into academia at all :)”

Quote of the Day – Neil Saunders