Igor Pro.

Igor Pro 

Multi platform, scriptable and easy to use in conjunction with matlab.
Quality graphs, and bombproof stability in osx and even under windows(tested windows 7, 64 bit).

 In depth review and and comparison(origin lab, qtiplot and scidavis and others) coming.

 Wish you all nice holidays.

Papers 2.

Papers 2.0 (edit 30-11-2011, papers version
(image from arstechnica.com)

First of all i'm not going to do an in-depth review of this piece of software, i will just point to an amazingly good review on arstechnica (REVIEW).

Papers2 is mac-only. Not a big of a deal but i like software to be multi-platform. And it's not free but a free trial is offered and big student discount is available (and that's fantastic, every sowftware house should do big discounts for students.)

What i'm going to do is to point out pros and cons in the every day usage.
First: the interface is gorgeous, I mean really gorgeous. It's a mac perfect UI, very easy to work with and very pleasant.
The color coding feature is just an immense point in favor of this software (in my present thesis I have to deal with copper and silver, copper is red silver is grey: super east to find immediately the article I'm searching for).
All of those nice features comes with a cost though, papers 2 is not as fast as mendely for instance.
It's not overly heavy or plainly sluggish it's just not lighting fast wich is a drawback.

Every thing works as pointed out in the aforementioned review. Bur I've found two major drawbacks.
First: bibtex. If you use  M.S. World ( and you shouldn't) you don't care about bibtex but if you are using latex then papers2 requires to export every time your library there isn't a sync to bibtex feature.

Second: THE CLOUD. Papers livfe is a nice touch but it's too much social (think sharing with colleagues) and not enough cloud. There isn't the option to access your papers from another desktop's browser.

If you can live with this two drawbacks, and you have a mac, then papers2 is just a joy to use.

edit 30-11-2011 h 3:22 GMT,  papers2 has been updated to 2.1 they report a massive speed improvement. My evaluation period has ended though so i can't report on that !!

First up: Mendeley

First up:


I'm starting with this program because i'm currently using it on a daily basis for my thesis.

focus on Mendeley.

In the first screenshot you can see how the interface looks like on a mac, on windows is quite the same just blue colored instead of graphite: clean and intuitive.

The interface is tabbed: the first tab will always be the "my library" tab the others tab will be show pdfs in mendeley's embedded viewer.

Let's concentrate on the "my library" tab: on the left we have a split pane, in the lower part you can select some predefined filters(i.e. authors, tags and so on), in the upper part you are presented with three sections.
  • My library: quite self explanatory you can add folders but no smart folders, favorites and so on
  • Groups tab: quite a sexy feature i will explain that later
  • Trash: every deleted document will be there, you can restore them later or empty trash forever
The search bar in the upper right corner will let you perform deep searches even inside your pdf, keywords tags author and so on.
Focus on mendeley groups feature.

 If you share papers with your team groups is a key feature.
 You can create public or private groups to share papers with: all you have to do to share them is drag and drop from your library.
You and your team will then have a shared library, if you place a note in a shared paper it will show who wrote  it and when, with is perfect for a collaboration environment.
You can also select in the group setting if you want to sync only the references or the pdfs.

Papers in the cloud.

Mendeley free account gives you 500 MB of free shared web space  for your groups' papers, but also a 500 MB for your personal account.
You can also access you mendeley database either from your iPhone, mobile device or web browser  no additional costs involved.


Mendeley can also export and sync to bib latex but it will make a mess if you export/sync all of your library and collection into one bib file. (mess means  duplicate and such.)
I myself prefer to sync each collection to his own .bib file, much more clean and organized.
Right-clicking a reference in your library gives you the option to copy the latex citation key, very handy at times.

Mendeley it's able to import most of the common reference software bibliography formats, you can clip references from major scientific portals (e.g, web of science, science direct, scopus .. )
Lastly you can import papers from your disks, and compare them with google scholar to finish up all the reference details.

Though it has all of these great features it has of course its drawbacks.

 I'll start with minor and maybe personal gripes. 
It has no color coding, while it may seems a bit ridicule at times color coding can save you a whole lot of time.
Embedded pdf reader can be glitchy at times, especially with the highlighter tool.
Lastly sync process is non "automagic" and sometimes it just hangs up.
Web clipper is not polished enough.
Pdf can be matched only with google-scholar; even tough g.scholar is great a better option would be the possibility to choose from more services. 
No smart folders, they can be very useful.

All in all Mendeley is my favorite reference manager program for its multi platform and free nature.

Comparison of reference management software.

Such an hard and complicated topic is up next.
 We are still in a transition between paper and paperless workflow.
Yet it's safe to say that most of us have do deal mostly with .pdf files.
So how do you organize, search and share them?
I've seen a lot of people still going the old school folder-tree way. I must say that after all it's not the worst way ever, provided you lose an insane amount of time creating manually every folder with the right name,date,journal etcetc. Not really a good way of doing things in 2011 in my opinion.
Do you share papers (NOTE:people you share papers with must have legal access to those papers anyway) sending them by mail, printing or what?
I find all of those still time costuming, and after all not that reliable. 
Luckily for me and for all of us a plethora of reference management software have been developed.

After an year of trial and error I'm going to share a real word comparison between some of these software.
   (for a complete overview head to Comparison_of_reference_management_software wikipedia from here i will take some information too.)

The contenders:
  1.  mendeley 
  2. endnote
  3. zotero
  4. bibdesk
  5. quiqqa
  6. papers2
Now it's time for you to think about your workflow: fast internet access, sharing with colleagues, multi platform, free(both as free beer and free speech ).

The battle will begin in the next post. Stay tuned 

Hello world

From today I will explain my student experiences in research projects.
 The focus of this blog is mainly to explore how 2.0 technologies can interact with research both from students' and from teachers\researchers' point of view.