Nettab2011 – Network Tools and Applications in Biology, 12-14 ottobre 2011, Pavia – Nettab 2011

Ritorna come ogni anno l’importantissima conferenza internazionale Nettab –Network Tools and Applications in Biology, organizzata dal professor Paolo Romano dell’Ist di Genova. Quest’anno si terra’ a Pavia in Lombardia, il 12, 13, 14 ottobre 2011.

Ecco l’annuncio di sottomissione dei contributi.

NETTAB 2011 on
“Clinical Bioinformatics”
October 12-14, 2011
Collegio Ghislieri, Pavia, Italy

NETTAB 2011 is the eleventh in a series of international workshops on Network Tools and Applications in Biology.
These workshops are aimed at presenting and discussing emerging ICT technologies whose adoption in support of biology could be of particular interest.

This year, NETTAB is focused on Clinical Bioinformatics and it is aimed at presenting the methods, tools and infrastructures that are nowadays available.
It will also show some of the most interesting applications in this field.

Invited Speakers
Yves A. Lussier, Institute for Translational Medicine, University of Chicago, USA
Thomas Illig, Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
Jan-Eric Litton, Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
Isacc S. Kohane, Harvard Medical School, Boston, USA

Tutorials given by:
Carlo Combi, Department of Computer Science, University of Verona, Verona, Italy
Pierre Zweigenbaum, LIMSI – CNRS, Orsay, France
Marco Masseroli (to be confirmed), Dipartimento di Elettronica e Informazione, Politecnico di Milano, Milan, Italy
Amnon Shabo, IBM REserach Lab, Haifa, Israel

Call for Papers
Submitted contributions should address one or more of the following topics:
– Methods and Technologies:
Data warehouse – Natural Language Processing – Data Mining – Ontologies, Interoperability, Standardisation – Search Computing – Decision Support
– Tools:
ICT architectures to support – Clinical research – BioBanks – Software for next generation sequencing – Data management and storage
– Applications:
Risk assessment – Diagnosis – Therapy planning- Drug Design

Type of contributions: Oral communications – Posters – Software demoes
Contributions length:
– oral communications: between 3 and 5 pages
– posters and demoes: no more than 3 pages

· July 15, 2011: Oral communications submission
· September 5, 2011: Posters and demoes submission

Submit your contribution through the EasyChair system at

All contributions submitted to NETTAB 2011 will be invited to a restricted Call for full research papers to be published in a Supplement of BMC Bioinformatics.

You can register to the NETTAB 2011 workshop by using the form at
Early registration ends within September 30, 2011.

Visit the website

Contact the organization by sending an email message to nettab(AT)

Interviste(3): Pierre Lindenbaum dell’Universita’ di Nantes

Pubblichiamo oggi un nuovo articolo per la sezione “interviste” inaugurata qualche tempo fa. Oggi intervistiamo Pierre Lindenbaum, postdoc in genetica presso l’Universita’ di Nantes (Francia) e curatore del blog Yokofakun.

Who are you and where you work at?

I’m Pierre Lindenbaum. I got my PHD in virology in 2000 (I studied theprotein-protein interactions between the rotavirus and the host cell). During my PhD , I needed a program to quickly find the best subcloning strategies using a set of restriction enzymes. I wrote the program in ‘C’ ( and, as I had much fun in doing this, I decided to move my career to bioinformatics.
I now work as a postdoctoral researcher in UMR915/Nantes ( )

Which subjects do you study and research?

We”re working on the genetics of the cardiomyopathies. Using next-generation sequencing,  we’re trying to find what are the common genes involved in a cardiac disease.

Briefly describe your career

1996-2000: PhD at National Institute for Agronomic Research. protein-proteininteractions between the Rotavirus and the host cell
2000-2002: PostDoc at National Center of Genotyping (CNG ). Iwrote a program to find the best strategies for genotyping using mass-spectrometry.
2002-2008: Worked as a Bioinformatician at Integragen ( ). I wrote the programs/databases dedicated to our business.
2008-2009: I worked at the CEPH ( on a biological database based on the key/value datastore berkeleydb.
2010- : post doc in Nantes

What is it like in your university?

I’m working in a new building close to the “Hotel-Dieu hospital”
( ) and facing the “Loire” ( )
We’re also close to a heliport, so it often smells the gazoline.

What is it like in your research lab?

There is a really good atmosphereand people are nice. We counted 14 king ‘s cakes in January for celebrating the epiphany.  😛
There a large number of phd students as well as some physicians: so we’re closeto the patients and their problems.
Some views of my desk & my lab here:

What is it like in your country?

Right now, it’s raining.

Are you plannin’ and go elsewhere to work in the future?

Ask my wife, she decides all 😛

How did it come to your mind to open a bioinformatics blog?

I was in a very bad mood.
The day I started my blog, I told people about but they did notcare. Furthermore I was asked something like “Can you blast the Genome vs itself to see if there is something interesting ? Can we have the result tomorrow in a nice Excel spreadsheet”.  So I started my blog to tell the world about the things I like.

Which are the most important functionalities of it?

It’s my notebook. I can use it to see how I solved a problem some months ago. It also reflects my skills an my interests.

Which advantages did you get durin’ your career for havin’ it?

Thanks to my blog I got an invitation to scifoo2007 ( ) and two invitations to attend the BioHackathons in Japan

D’you think bioinformatics blog are too few around?

At least for French bioinformaticians, I can say they are rare. Why ? I don’t know.

D’you think bioinformaticians should get more in contact thru the web?

Not necessarily, if people come to work with their usual professional network. In my case, I had some nice experiences with FriendFeed
–  After a discussion about RDF
( , I got an invitation to be one of the authors of a chapter  of “Beautiful Data”

– Andrew Su (  asked for a bioinformatician to help
him with the GeneWiki effort ( ). At the end, I was the second author of an article published in an issue of Nucleic Acids Research.

Which bioinformatics organizations are you a member?


Do you visit and want to signal some other bioinformatics blog or website? is currently one of my favorite destination because some of the questions asked  here can be very challenging, fun  and it gives an overview of the other’s problems.
For the blogs, you will find the usual suspects at:



Ringraziamo Pierre per la sua disponibilita’!