Tag: opensource

GeoFestival powering the E-luminatefestival website


So in two weeks (working like maniacs) we managed to create and set up a pretty cool system to provide a platform for festivals which have different events that spawns in multiple places at different time.

Right now the platform powers the first happening of the E-LuminateFestival. It is built using Django, no, not this Django, this Django, it uses Leaflet for the map integration, using the geographical data from OpenStreetMap. It’s mobile friendly with the use of Bootstrap and some help from us as well.

The events can be submitted only by participants who are approved by the administrator of the site. The code is available under GPL, but if you want us to set it up and tailor it for your event, just give us a shout.

Creating a new twitter bootstrap theme for jekyll

Yoda On OpenSource

Yoda is wise. And green, as well (ok, maybe not relevant but he is green!)

Now that I’ve finished my Ph.D. at the EBI, it was time to set up a personal page where people could find easily some of my contacts info to have a quick way to contact me. The decision was to use the good old github pages with a cname for hosting, and I’ve written how I’ve done it in this post.

Although a quick html page was a good compromise, I felt It was a bit too short and quick, not giving an enough informative picture. Moreover, I wanted the ability to create several pages to describe projects and other stuff which maybe will come up. Being already on github pages, I’ve decided to use jekyll. Jekyll is a text processor, which converts markup into HTML, having the ability to create a blog if same convention are followed. I love text processors, ’cause it means I can write stuff using an editor and focusing on the content. Then, at later stage, magic happens and the contents looks also good and very well formatted. Same other examples of this process are LaTeX, which is amazing to write scientific publications, and Sphinx, which it’s awesome for documentation (especially Python programs). Easier is the markup language, easier it will conquer the world. for example Markdown is awesome ’cause it feels like writing using decent default (or at least, default that resonate with me.) Ok, stop wandering around and let’s get back on track.

Getting started using Jekyll is quite complicated, because jekyll does not come with any preloaded site or anything, therefore you have to create everything. However, jekyllbootstrap is up to the rescue. Jekyllbootstrap, created by Jade Dominguez, is a series of preloaded template and clever series of addons to jekyll, including themes and external service to handle comments, which it makes possible to decrease the time to start to close to zero!

Jekyllbootstrap gets shipped with the classic (yeah, it’s a classic nowadays) twitter bootstrap, which is a pretty cool frontend helper. Twitter bootstrap version 2.0 has seen a major improvement versus the 1.4 version, where responsive behaviour has been added to the frontend framework. Responsive behaviour is the ability to perform well on any kind of device, using some clever resizing tricks, where the web page changes format and font to adapt to an android or iphone screen, to a tablet, to a laptop screen or to a massive desktop video. All this comes for free, just using bootstrap, therefore it’s very handy to use it. You know, it’s 2012 and mobile should be treated as first web citizen.

I was already thinking to bring the 1.4 theme to 2.0, when I’ve actually found that Geoffrey Dagley had already taken care of it, creating a new repo for it.

So I’ve just installed and I had the theme set up. All was looking good, when I’ve actually find out that there was a problem with the tagline. The tagline was not computed from the metadata, but it was left there as placeholder. Therefore, being a good opensource citizen, I’ve forked the repo,  fixed the problem,  and opened a Pull Request to put it back to the original.

Then, given the fact Thoms Park created bootswatch, I’ve picked cyborg, one of the available theme, which is using the same twitter bootstrap markup, but it has different colors and font, and I’ve created a new theme for jekyll, in its own repo.

So after all this I’ve set up my new website in a bunch of days, corrected and sent a pull request to fix a problem on one of the theme, created a new theme based on bootstrap and bootswatch.

The commodity of jekyll is amazing, ’cause I can create a new file using the nice rake shorthand:

rake post title="a decent title for a new post"

which sets up the file for me and I have only to open it up in gedit and write it!

How does it look like? Check it out!

Michele's web new graphic

P.S.: If Gedit doesn’t recognise Markdown, it’s due to some crazy mime-type problem. Check out this tweet for help:
[tweet https://twitter.com/mattions/status/209684943981379586]

Opensource philosophy to science?

Lately there has been a clear movement to move science towards a more open way to make research.

I’m not talking about Open Acess Publishing, which is still important, but to the real art and sweat to do science.

Science has always been very collaborative, however the dimension of this collaborative effort has always been restricted to a small group. This is not the case when general problems seems to be tackle.

For example, when the problem is the definition of a standard, like NeuroML or SBML, the development of it is a community driven project, where the community works as a whole to achieve a standard which is backed by the biggest number of people interested, so can be easily adopted.

The beneficial impact of standard is not the topic of this post, and for the sake of brevity I just want to point out that a well-coded model in a well-recognised standard gives the possibility to share the work of a modeller (in this instance) and make the model be re-used by other people.

On the same line OpenWetWare wanted to share the protocols used in the lab as soon they were established, and actually even before that as ‘Work in progress’.

The ability of a scientist to be a part of a community is not taken in account at all, due to the Publish or Perish system which is right now up and running. This model does not encourage collaboration, and actually create groups of people which are competing on the same topic to scoop each other. This is a broken system.

It’s so broken that some people even decide to leave academia, and that is only one of the cases. A lot of letters are also available in Nature and this article from the Economist got quite famous as well.

Therefore I watched with a lot of interest the new way proposed by Dall’Olio  which consist in collaborative editing of papers.

So far, if I didn’t miss any, at least two papers with this approach have been written, which is very interesting and shed a bright light for the future.

Still the number of places available in academia and the way the recruitment is organized uses the current model, which does not fit the market, and it’s prone to discard talented people very easily. There should be at least a live debate on how to fix this problem, and move science to a super collaborative discipline.

Happier scientists and better science sounds good to me.

Diaspora in the wild

Today Diaspora is releasing its code. In short diaspora is a social network which takes the privacy of the users really seriously, given the possibility to control the information, the hosting and the way is delivered.

On top of that, contents created with Diapsora remains with the user and it’s not property of Diaspora.

The software is in still alpha mode, however I really like the idea and the vision of the developers.

As already noted several time, digital personal identity is something which should be taken more seriously and people should be more aware what that means, how to use it  and what they can do with that.

This is a moving target field, where things change rather quickly, so the dust is not yet set to understand what are the big innovations taking place.

I hope diaspora will make it big, and I hope it would be one of the gateway to make the net-citizen aware that their digital personal identity is important and should be protected.