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

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

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