bioinfoblog.it

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:

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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).

#Scifund is an experiment of ‘crowfunding’ for researchers. The idea behind #Scifund is to push scientists toward the world of crowfunding, to teach them how they can propose their research projects on a crowfunding website, and get people to contribute by helping funding them.

So, today #Scifund starts its first iteration. If you have an idea about a research project and you think that you can convince other people to fund it, you have about two weeks to prepare a draft proposal and post it to the #Scifund site. If you need more information, I suggest you to sign to their website and their mailing list.

It is important to note that the funding will not be collected on their website, but on a popular crowfunding website, RocketHub. The scope of #Scifund is not to do the collect the funding there, but to help researchers to prepare their applications to other crowfunding websites. #Scifund will be a web 2.0 website where researchers will compile applications in a online collaborative manner.

Personally, I think that crowfunding is a good idea for research. Of course, they won’t never be able to get the 70 millions dollars needed to test a new antibiotics, or the money needed to support a wet laboratory; but it may be a good resource for bioinformatics. Moreover, even though you are not interested in submitting a research proposal there, their website is a good resource for learning: have a look at their blog, and at all the useful tips they present.

The Ten Simple Rules for Getting Help from Online Scientific Communities paper just came out on the last PLoS Computational Biology issue!

It has been a pleasure and an exciting experience to coordinate the writing of my first Open Collaborative Paper. It has been fun, a different approach toward preparing and publishing an academic paper, and I hope I will be able to promote other similar initiatives in the future.

I am also preparing a blog post where I list some tips and notes about coordinating these type of initiatives. I have learned a lot from this experience, and I would like to share a few thoughts on what can be done to organize them at the best. But let’s see if I will find the time to finish writing it

This paper is dedicated to all the people who enjoy discussing science on Internet. In particular, I would like to give a huge thanks to the people from the Molecularlab Community, and the Biostar Community; and also a huge thanks to Robert Hoffman from WikiGenes for the support.

And if you pass around here in Barcelona in my lab, I will offer you a chocolate candy

Dall’olio GM, Marino J, Schubert M, Keys KL, Stefan MI, Gillespie CS, Poulain P, Shameer K, Sugar R, Invergo BM, Jensen LJ, Bertranpetit J, & Laayouni H (2011). Ten simple rules for getting help from online scientific communities. PLoS computational biology, 7 (9) PMID: 21980280

I wrote a rudimental script to scrape the Uniprot Website and extract some information about a list of Uniprot entries. This may be useful as an example on how to query Uniprot (since I couldn’t find any public API nor library), or to get infos about a list a genes of your interest.

NOTE: the correct way to do this is by the Retrieve Tool from the Uniprot page. The script presented in this post is just an example of how to use the python library Mechanize.

The code is available at bitbucket. Usage is simple: edit the files to enter your email address and the list of IDs you are interested in, and run it as a python script.

Enjoy!

The initiative for the collaborative writing of a candidate ‘Ten Simple Rules’ paper, launched two weeks earlier this month from this blog, has been very successful. So successful that after only two weeks the manuscript is almost ready, in a state where further modifications may be more harmful than useful.

For this reason, we are planning to close the editing phase earlier. The initial deadline was for May 28th; but since it does not make sense to continue working on it, we will probably leave the manuscript editable for a few days more, and then close it.

So, if you want to participate, hurry up! Join the mailing list and add your contribution!

There are some recent news about the initiative of the collaborative article on Post-GWAS analysis launched last December[1]. It seems that a new version of the manuscript has been published on Nature Precedings (link), a few weeks earlier this month.

Well, in the end, with the exception of one figure, they did not include almost anything from what has been contributed in the wiki (I still have to check carefully). They thank the contributers in the acknowledgment section, leaving a link to the wiki page, but saying that these have not been included for reasons of space.

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