A ‘new’ job

Thursday, February 1st was the first day of my ‘new’ job. After 130 months of precarious work I am now employed with a permanent and full time position as a Technician for the Bari’s research unit of the Institute for Biomedical Technologies.

Our groups is a Bioinformatics one, and my main duties will remain basically the same: keep servers running, install software, general maintenance and users’ support. What I do hope is to gain new responsibilities and – with them – some decisional power.

Wish me luck!


WoPPER: Web server for Position Related data analysis of gene Expression in Prokaryotes.

Acknowledgments WoPPER

It’s been officially announced the publication of the latest work of my colleagues here at Italy’s National Council of Research Institute for Biomedical Technologies regarding the data analysis of gene expressions in prokaryotes: WoPPER.

Here I am mentioned in the acknowledgements for the server support … for the first time I am thanked publicly for my efforts!

Academicons, a font icon set for academics

Academicons (20160406)

For working reasons I had to work on a project at work were for each researcher I had to link a ‘social’ profile, not on Facebook or other popular – consumer – networks, but for some specialized ones … like ReaserchGate, Google Scholar, Mendeley, etc.. If you’re into academics you know them. Here is Academicons

With a bit of luck I found a GitHub project by James Walsh, a post-doctoral researcher, were he made and collected a series of font icons – 100% compatible with the more famous FontAwesome that solved my need with few lines of code.

password protect your Tomcat powered project

At work we’re in the middle of the development of a new Tomcat powered bioinformatics application, and have reached the stage were you have to show it to some peers but not make it publicly available. I do have an ubuntu 12.04 LTS server, so I took the most out of this Randeep’s post:

password protected directory in Tomcat

Here it is how to do it in few steps:

  1. Add user, password and role in conf/tomcat-users.xml
  2. In the webapps/examples/WEB-INF/web.xml specify role, method and urls.
  3. Restart Tomcat and check the result

solving DESeq2 installation issues

At work a colleague asked me to do a system-wide installation of the R module DESeq2 in one of our internal servers.
The installation procedure is quite straight-forward:


Unfortunately I had some issues on my system, in fact I got:

Warning in fun(libname, pkgname) :
couldn't connect to display "localhost:12.0"
* DONE (maSigPro)

The downloaded source packages are in
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘XML’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘annotate’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘genefilter’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘geneplotter’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘DESeq2’ had non-zero exit status

I then tried to install manually the various dependencies, like XML. Still no luck. After a quick Google search I found that I was missing a couple of -dev packages on my Ubuntu machine, so I installed them:

root@server:~# apt-get install libcurl4-openssl-dev libxml2-dev

… and then re-tried to install DESeq2. This time everything was ok. Problem solved!

But Where Do People Work in This Office?

I could go on and on and on. The pattern keeps repeating.

With everything we know about openplan offices, why are these mega-rich companies knocking themselves out to hire the very best and brightest minds from the world’s best universities, paying them huge salaries, tapping world-class architects to design artisanal office spaces in the most expensive place in the country, and then cramming desks together in noisy bullpens?

Matt Blodgett, But Where Do People Work in This Office? →

On his post Matt asks a question that has always come to my mind when seeing those Big Company workplaces on magazines and specialized blogs.

My desk is usually messy, in a room of four and a lot of times I feel we’re too many, especially when each of us is at work on something different, with different people coming in … in person or via a Skype or phone call.

Google Refine

WOW! This project by Google is extremely interesting and versatile. A colleague of mine has discovered it while studying some solution for a bioinformatics problem he’s facing. This kind of tool will be extremely important for data normalization in biological datasets…

Discover more on the project home page:

Google Refine, a power tool for working with messy data (formerly Freebase Gridworks) →

scientific publications have to make transition to open science

“An inherent principle of publication is that others should be able to replicate and build upon the authors’ published claims. Therefore, a ondition of publication in a Nature journal is that authors are required to make materials, data and associated protocols available to readers promptly on request.”

Nature, Availability of data and materials

OpenSource.com Magazine last June 12nd published an interesting (and promising) article on Nature Methods, one of the most respected scientific publications in the world, shifting with decision to an ‘open science’ model for its articles approval process…