Archivio per ottobre 2007

“Ten simples rules”…for your research

ottobre 26, 2007

PLoS has published another article of the series “Ten simple rules”. This is a very interesting series with which some researchers (mainly E. Bourne) give useful advices to young researchers willing to improve the quality of their research. Sometimes the hints are very obvious but, we know…”repetita iuvant”. Today is the time of:

Ten Simple Rules for Doing Your Best Research, According to Hamming
Previous papers of this series are listed below:
Ten Simple Rules for a Good Poster Presentation
Ten Simple Rules for Making Good Oral Presentations
Ten Simple Rules for a Successful Collaboration
Ten Simple Rules for Selecting a Postdoctoral Position
Ten Simple Rules for Reviewers
Ten Simple Rules for Getting Grants
Ten Simple Rules for Getting Published

Unified Medical Language System

ottobre 20, 2007

In the last years there has been a huge effort made by the computer scientists toward the transition from machine representable contents to machine understandable concepts. The medical field is probably among the areas in which this transition had the most interesting results (and still has its most promising horizons). The UMLS is a first step in this direction and has been developed in order to facilitate the development of computer systems that behave as if they “understand” the meaning of the language of biomedicine and health. You can find webcasts of this resource supported by NIH at and you can sign-up for the upcoming events at

Should we start to think at virtual physicians for our sons?

Bioconductor 2.1 released

ottobre 10, 2007

Although with some delay, this is the announcement of Bioconductor 2.1 appeared on the web the last October 5. Installation instructions are available at . It is compatible with R 2.6.0 released on 5th Oct 2007.
List of packages available at

Some bugs have been fixed (the Graphviz one included! 🙂 ) and other functionalities have been added!

Link: Bioconductor 2.1
Link: R 2.6.0

Bioinformatics to Systems Biology 2007

ottobre 10, 2007

This is a quite uncommon announcement for a conference. Bizzarro and colleagues, in fact, have announced on that they will organize the conference entitled Bioinformatics to Systems Biology. The happening is going to take place on-line only…amazing, isn’t it? 🙂

Place: On-line
Date: November 16, 2007


– Kasper Lage, Centre for Biological Sequence Analysis, Denmark Technical University. Title: A Human Phenome-Interactome Network of Protein Complexes Implicated in Genetic Disorders
– Anil Jegga, Ph.D., Cincinnati Children’s Research Foundation, United States. Title: Systems Biology Based Integrative Approaches to Identify and Prioritize Novel Disease Candidate Genes
– Manuel Corpas, Ph.D., Spanish National Cancer Research Centre, Madrid, Spain. Title: Quantifying Structural Features Affecting Protein Evolution
– Amar V Singh, Ph.D., University of Louisville, KY, United States. Title: Systems Biology in Understanding Developmental Defects–Efforts and Challenges

This conference is jointly organized by and the ISCB Regional Student Group, Denmark.

Link: Bioinformatics to Systems Biology 2007

PAZAR: yet another transcrition factor DB

ottobre 10, 2007

In this paper Casamar et al describe a novel framework for transcription factor and regulatory sequence annotation: they have named it “PAZAR”.

PAZAR is an open-access and open-source database of transcription factor and regulatory sequence annotation with associated web interface and programming tools for data submission and extraction” [ ].

“myExperiment”: scientific workflows sharing!

ottobre 9, 2007

How many times have you wondered about scientific validiy of an assumption or an experimental design choice? As stated in the homepage of the project:

“myExperiment introduces the concept of a workflow bazaar; a collaborative environment where scientists can safely publish their creations, share them with a wider group and find the workflows of others. Workflows can now be swapped, sorted and searched like photos and videos on the web.

Scientists should be able to swap workflows and publications as easily as citizens can share documents, photos and videos on the Web. myExperiment owes far more to social networking websites such as MySpace and YouTube than to the traditional portals of Grid computing, and is immediately familiar to the new generation of scientists. The myExperiment provides a personalised environment which enables users to share, re-use and repurpose experiments – reducing time-to-experiment.

Well, I think it’s a quite self-explaining descritption of this service. I think it’s worth a chance!

Link: myExperiment

Web Surfers info

ottobre 8, 2007

I would like you to know that, from now on, posting on this blog will continue in english. Ths would be a good way of reminding (and forcing) me to practice english. I beg your pardon for the mistakes I will made…I hope the will tend to zero in a short time!