Journal club 2.0: share your list of papers

Journal clubs are important moments in everybody's lab life.

A journal club gives you the chance to:
* read some recent publications (we all know that you should read more papers, but you often reschedule this activity for tomorrow! A journal club implies that there are no more excuses)
* learn something new about your research area (or discover a completely new one)
* practice your presentation skills
* share your thoughts with the other members of your lab/department
* (hopefully) find new ideas for your project/for new projects.

The articles that are reviewed in a journal club are usually chosen according to the research objectives and interests of the person who presents, your lab and/or the other participants of the journal club. The list of the articles reviewed at a journal club could be therefore useful to other scientists that work in the same research field or in a related one, but unfortunately it is rarely shared with the scientific community.

I think that sharing this precious list of papers would be a good practice for a “virtuous lab”.

I understood how useful such lists can be by browsing the one shared by a group of scientists at my old institute (http://journalclub.ibis.ulaval.ca/). Thanks to this list I discovered many interesting papers I was not even aware of and it turned out that those papers were useful to develop my current research project.

But is sharing the list of papers reviewed in journal clubs enough? Well, in my opinion it is the first step towards the journal club 2.0, but there is a lot of room for further improvements. Here I share with you some thoughts.

By creating a public library on zotero (https://www.zotero.org/) it is possible to share a list of papers and generate (at the same time) a library of references that is ready to use whenever you write a paper (if you do not use zotero as reference manager, you can still convert the library to another format, I guess).

Further, in zotero you can add notes and tags to each entry. Tags are useful to search specific papers when your library will have hundreds of entries. Notes are even more useful. You really understand a paper when you are capable to summarize it. Use the notes to summarize the paper after you read it, write down ideas, comments and describe why this paper is important (of course be careful of what you share in order to avoid being scooped!).

Another advice is to set as a rule to choose, at least once every five journal clubs an article that is not strictly related to what you are working on. It can be a review, a work you like on another bug/organism, or a paper that you think can help you and the other participants of the journal club broadening your scientific perspective.

Finally, remember to spend 1-2 hours every month to keep you library up-to-date and review the old papers.

That’s it! However, I cannot conclude this post without sharing the list of papers that my lab mates and I reviewed during journal clubs: https://www.zotero.org/groups/1911042/farhatlab_public/items . These papers are mainly useful for scientists that study antibiotic resistance and Mycobacterium tuberculosis.

Journal clubs are much more than annoying moments in which somebody presents a paper you do not even care about. Try to get the best out of them.

Downloading scientific papers from UL

 Recently the policy of the UL library has changed and right now it is not possible to directly download the scientific papers just by clicking on "Full text". 

So, if you want to download, let's say, this paper (http://www.sciencemag.org/content/343/6171/624.full.pdf) you should connect to the web site of the UL library (http://www.bibl.ulaval.ca/services/acces-aux-ressources-electroniques), generate a link, copy it on a new tab, click enter. After that you can finally read your paper. 

I was tired of all these tabs and links! So, today I spent 30 minutes of my life to write a small php page where you provide the URL of your article and you are directly redirected to the paper you want to read (you do not need to generate links, open tabs, etc.). I am aware it is not a big improvement, but I find it cool and can be useful for some people! Here is the address: http://www.bio.ulaval.ca/landrylab/shir/

If you know other (and faster ways) to download the papers, please keep me posted! :)

Here is a screenshot of Shir:

Perl and object oriented programming

When you program and you want to write some code you can reuse, it is always a good practice to use an object oriented approach for your code. Today I realized that I never follow this rule when I program in Perl, because I am not so familiar with the oo synthax for this programming language. So I decided to fill this gap and I wrote a small program to convert a some files containing sequence alignements arranged in a pretty strange format to classic (and readable) fasta files. Here is the result of my experiment (I simplified a lot my script!). I hope someone will find it useful!

 The main script:

#!/usr/bin/perl 

#Perl will search for packages in the current directory
push(@INC,'.'); 

#I load the package Covertcsv

use Convertcsv; 

#I create a new object Convertcsv 

$obj=Convertcsv->new(); 

#I call the method csv2fasta 

$obj->csv2fasta("a.txt","b.fasta");

And the package Convertcsv.pm:

#!/usr/bin/perl 

#this is the package Convertcsv 

package Convertcsv;
use strict; 

#constructor 

sub new{
 my $this={};
 bless $this;
 return $this;
} 

#method 

sub csv2fasta{
 my $this = shift;

 my($file_input,$file_output)=@_;

 #code to convert the files

}

 

After all it is easy to work with objects in Perl too! :)