New Bioinformaticist, waiting for orders! :)

08 Jun
Published by dalloliogm




general open research


My name is Giovanni and I'm a student fo bioinformatics, from Italy.

I'm interested in contributing to the synaptic leap. I've noticed that this website isn't seeing too much activity lately, and I'm sorry for that, but I do believe that the idea of a Scientific Community inspired by the OpenSource one is very good.

I have skills in massive data analysis (ehi, remember I'm still a student ;) ) and in mining web-resources (finding articles, databases, and organizing them) and I can program in python or in perl.
I'm also very interested in the use of communication in Science, so what does it means, I believe that communication is a very important thing and that technologies liki wikis and blogs and other web 2.0 stuffs are a great opportunity for the science of the next years.

How can I help the synaptic leap?
I was reading the projects pages from the various communities... the problem is, that all the projects are too big to be carried alone: I would like to contribute during my free time, and I can't follow all the advances of all the projects easily, so, it would be better if somebody gives me some kind some kind of analysis to do and Iwill carry it.



marcius's picture

Hi Giovanni,

It is nice to see people so active in using Web2.0 tools for Bioinformatics. Ginger Tylor and I (Marc A. Marti-Renom) have been discussing for long time ( to implement a "flickr" type of front end for biological data. Unfortunately, I have had no time for implementing such thing.
Maybe you would like to get involved on that? Would you be willing to use some of your "free" time to develop such project?
Where are you now, in Barcelona or Bologna?
Looking forward to hearing from you.
All the best!


I'm back in Barcelona right now! I was in Bologna past week, but now I will remain here for some months.

Ok you're saying about a 'Flickr'-like system for sharing data: this is very interesting but do you already know
It's a project to make a platform in the style of mySpace (which I don't known at all), for the scientist to have a space in which share opinions and data about their experiments.
They're working on this since a while and the project come from the same team which has made taverna and the scufl language, a program / language that can be used to describe an experiment's workflow.


marcius's picture


No. I did not know about myExperiment but I did know about Taverna. However, what I am thinking about is slightly different. If one thinks about Flickr and what makes it very successful is the fact that it allows people to organize their pictures as well as show theworld"how good they are"! Then the end user gets automatic credit for it. Now, if we provide the researchers out there tools for organizing anddisseminatingtheir scientific data, I believe we will have a good chance of doing something interesting. The point here is to find a model that is useful for the researcher and at the same time incentivates(somehow) its use.

The model should have.

- A way of storing and organizing biological data (ENTRIES), which could be genes, proteins, structures, chemicals, literature, blogs, web pages, etc...The flickr equivalent would be pictures, cameras, etc...

- A way of AUTOMATICALLY relate all those entries (homology searches, literature searches, database integration etc...).

- A way of MANUALLY relate entries (bookmarklets).

- A way of visualizing in a simple representation ALL that is known about a particular entry.

- A way of annotating a particular entriesand show the rest of the users WHO (give credit) did the annotation.

- A way of sharing each user's world to the rest and motivate communication between themwith one-click.

- A way of visualizing the relationship between entries between users.

- etc...

In other words, the end-user goes therebecausehe/she wants to have a place fororganizinghis/her biological data as well as a nice place to visualize and annotate his/her findings. Of course, we will ask the user to ONLY worry about his/her little world. Then the rest (if enough users sign) will get into place because we will start seeing a supra-organization of the data given user-centric organization.

We can talk more over the phone if you wish. Mail me at marciusmr .at. gmail .dot. com (however, we shall keep this discussion also on-line at the Synaptic Leap for others to know.



jcbradley's picture

I was very happy to see your post! We certainly do need collaborators to run docking studies and the manipulation of SMILES strings. I've put up a few items on our ToDo list and you can brief yourself on the UsefulChem project from links on that page:

We started with the synthesis of anti-malarials but with the recent interest of Dan Zaharevitz from the National Cancer Institute, we are also testing them as anti-tumor agents.