bioinfoblog.it

Today and tomorrow I will be attending a symposium organized here in Barcelona, about bioinformatics analysis of molecular sequences. Many well known bioinformaticians will participate, including Temple Smith (the Smith & Waterman algorithm), Amos Baroch from Expasy and Tim Hubbard from the EBI institute. Check the programme here, or the Streaming Video here.

The organization of this Symposium as been innovative in a “web 2.0 way”, as the participants have been able to interact in advance with the speakers, through a online web forum. For example, we have been able to propose to Tim Hubbard to explain how the concept of reference genome will evolve in the 1000genomes era, and, seeing that he has changed the title of his presentation, it seems that he is going to talk about it.

So, if everything goes well, I will be twitting from there… This is the first time I use twitter during a conference, so be kind with me .

The Scifund initiative has reached its final phase. Now all the projects are publicly visible online on RocketHub.

click on the logo to go to the list of projects uploaded

I am surprised to see how many projects have been presented! The crowd-funding seems to be a good idea to make science, specially in these times of crisis. I will keep it in mind for when I will finish my PhD and start looking for a post-doc. If I won’t find any position soon, it seems to be a good way to obtain funding for a short research project, and survive a bit more .

The blog of the initiative is very interesting. Here are some of my favorite posts so far:

• the story of a successful case of crowdfunding for a research project
• metaphors in science: how to use metaphors to describe complex scientific things to common people. For example, an electrophoresis can be explained as a thin forest that small and big animals have to cross.

And some projects I find interesting:

Continue reading →

The Parque Recerca Biomedica Barcelona (PRBB) is the building where I work. It is a big research center built about 5 years ago, hosting about 2000 scientists working on different fields and of different nationalities.

Here, we organize many different activities related to Programming. For example, we have a Python Programmers Meetup Group which used to meet once per month; or we have a series of Technical seminars about programming related stuff. Plus, we make a short meeting every Tuesday, to discuss about geekish things

To coordinate all these events, I am setting up a wordpress blog. Check it out:

• The PRBB Programmers Corner blog

If you work in the PRBB, you can check this blog to know what is going on, and whether some of the programming related activities may interest you. If you live in Barcelona, you can still check it out, because most of these activities are open to the public. Even if you don’t live in Catalunya, that blog may still be interesting for you, as it is a way to have an ‘inside view’ of what we do here and what tools and programming languages we use. It may also give you some inspiration on the kind of activities that interest a group of bioinformaticians in a big research center, and can be helpful if you want to emulate the initiative .

Today, bitbucket has enabled support for git repositories!! This means that, with a little hack and thanks to the sparkleshare project, we can make a home-made dropbox without limits of disk space.

Bitbucket is a repository hosting service, like github, sourceforge, and many others. The good thing about bitbucket is that there are no limits of space and private repositories. I use it for almost all my personal projects and for backups.

Sparkleshare is a free software designed to automatically syncronize a folder on a remote git repository. In principle, you can choose one or multiple folders in your filesystem, and sparkleshare will automatically syncronize it to a remote repository, such as one on github, bitbucket or another server. Every time you will move or change a file, Sparkleshare will automatically create a commit and push it to the remote server. In short, it is like Dropbox, but it can be used on multiple folders, and you have to find the remote repository to host the files.

So, since bitbucket now enables git repositories, we can use it with sparkleshare. The process is quite simple:

• Get sparkleshare and install it to your computer
• I had difficulties to configure sparkleshare to work directly with bitbucket, so I have created a repo on github first and then changed the url in the config file.
• Create an account on github, upload the SSH key that sparkleshare has created in ~/Sparkleshare, and create a repo there;
• Go to bitbucket, create a private repo, and upload the same SSH key there;
• start sparkleshare, select the ‘github’ option, and tell him to syncronize the folder with your github repository;
• open the folder, and edit the hidden file .git/config; replace the github url with the bitbucket url;
• that’s it; enjoy

Having a limitless home-made dropbox is cool; however, there are many reasons why I don’t recommend you to abuse this system.

First of all, git is slow when handling big files. If you try to syncronize big files such as movies etc (please do not use this for illegal stuff), you will waste a lot of bandwidth, and the syncronization will be very slow.

Second: although there it seems to be not anything against this in bitbucket’s Terms of Use, it is not nice to abuse them. I have opened a bug in Sparkleshare‘s repo and one at bitbucket to see what is the opinion of its authors about this. In any case, I don’t think you want to risk putting all your backup files on bitbucket through this system, and then see that bitbucket removes them because you have abused the Terms of Usage.

Third, and last, there is not really need for this. There are a lot of alternatives that already that provide cloud hosting for your backups. I will list a few:

• dropbox is free and gives you 2 GB, plus 250 MB for each invitation (note: this link is an invitation, if you register through it, you and I will get 250 MB extra).
• Ubuntu One already gives you 5 GB for free, and is great at syncronizing preferences and configurations. Now they have also created a Windows client, so there is no excuse to not use it. I only wish that they will fix the http proxy issue soon.
• Minus.com gives you up to 10 GB of remote file storage, although it doesn’t get syncronized automatically as the other systems (note: this link is an invitation, if you register through it, you and I will get 1 GB extra).