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!

Tomcat 7, munin and Ubuntu 14.04

Lately I had to reconfigure an Ubuntu 14.04 server.
Dealing with Tomcat 7 I’ve encountered those two situations:

Enable larger file uploads via Tomcat manager

I had a ~180 war file to deploy. Ubuntu’s Tomcat setting put a limit at 50MB. This has been solved using the tips in this post by skotfred. Unfortunately I haven’t found a more orthodox way of achieving this other than modify the /usr/share/tomcat7-admin/manager/WEB-INF/web.xml in the values max-file-size and max-request-size.

Enable Tomcat monitoring in Munin

Here I’ve followed the tips over this Serverfault discussions.
Adding a [tomcat_ *] was the key.

Who is afraid of Peer Review?

John Bohannon
A spoof paper concocted by Science reveals little or no scrutiny at many open-access journals.

On 4 July, good news arrived in the inbox of Ocorrafoo Cobange, a biologist at the Wassee Institute of Medicine in Asmara. It was the official letter of acceptance for a paper he had submitted 2 months earlier to the Journal of Natural Pharmaceuticals, describing the anticancer properties of a chemical that Cobange had extracted from a lichen.

In fact, it should have been promptly rejected. Any reviewer with more than a high-school knowledge of chemistry and the ability to understand a basic data plot should have spotted the paper’s short-comings immediately. Its experiments are so hopelessly flawed that the results are meaningless.

I know because I wrote the paper. Ocorrafoo Cobange does not exist, nor does the Wassee Institute of Medicine. Over the past 10 months, I have submitted 304 versions of the wonder drug paper to open-access journals. More than half of the journals accepted the paper, failing to notice its fatal flaws. Beyond that headline result, the data from this sting operation reveal the contours of an emerging Wild West in academic publishing.

Read more on this scary news on Science magazine →.

one more year at ITB, Bari – CNR

Technical Collaborator …

Aug. 1st I’ve started (yet again) a 12 months collaboration contract with Bari’s section of the C.N.R.’s Institute for Biomedical Technologies for the “Identification, classification and configuration of a bioinformatics infrastructure for the RNA-Seq noncoding RNAs data functional analysis” within the LIBI project.

http://www.seqahead.it/cost-bari-2013

COST-workshop-Bari-2013-20130222

Friday I gave you the URL of the most recent website I’ve realized for my AllBio assignment here at ITB, Bari. The “NGS and non-coding RNA data analysis Workshop” that will be held here in Bari (Italy) in April.

After a slow start, updates and details will be more frequent in the next weeks, so be sure to follow the News section of the website to be kept up-2-date.