To #mendelete or not to #mendelete ?

April 10, 2013 § 5 Comments

My twitter feed is on fire, since the announcement of Elsevier having bought Mendeley, after a few months of rampant rumors. “Elsevier is evil ! They will shut down Mendeley ! Mendeley lost its soul ! We should in no way contribute to Elsevier’s business and benefits”. These are a few of the reactions that quickly followed the announcement. What should I do ? Should I care ?

Elsevier has an awful track record: from fake journals to insane profits on journal bundles, to name a few. Everybody agrees on that, and for sure they realized it and are trying to make up for it, somehow. Now that they own Mendeley, they are going to do all sort of crazy things. Maybe, maybe not, time will tell. Mr Gunn seems confident at this point. Others much less, to say the least.

I have a different take on the current events. I am usually a very pragmatic guy. I used to use Endnote, like everybody else a few years ago when there were no alternatives. Their habit was to update the software every year, although I never found any significant improvement in the update. I remember that sometime the update was WORSE than the previous version, breaking my library. And I had to pay 100$, give or take, to update. Every year, although I quickly gave up on the update. No PDF organization, no way to perform full text search. No sync. Quite rough.

Then Papers came out. And it was awesome. Finally a decent PDF organizer, that quickly improved. Not having the choice of my OS (Win), I had to give up on Papers when I came back from the US. Too bad. A windows version has been developed since, but I already gave up. It’s been bought by Springer since, and I’m not sure Springer is any better than Mendeley.

And then I came across Mendeley. It more or less provides everything I need: easy import (I love the DOI look up), easy organization, full text search, cross plat-form sync. I’ve paid for a data plan for a while to have all my files synced between my laptop and desktop computer (Dropbox is not allowed where I work). Works flawlessly. Excellent to insert bibliography in papers I write. Automatic bibtex file creation when I need to use LaTeX. If only they could provide the abbreviated journal name, that would be perfect. I now trow in it every interesting paper I came across, whether it’s directly related to my interest or not. It is thus becoming my personal, curated papers database. The value I get from this software has very quickly become extremely valuable.

And now it belongs to Elsevier. Well, I try not to submit papers anymore to Elsevier journals (although Acta Materiala is a solid journal in my field), I avoid to review for them. I use Scopus less and less since Google Scholar has become extensive. I get little or no value from Elsevier’s products. But Mendeley is different. As I said, I get a lot of value from it right now, and I don’t mind paying 5$ a month for my data plan, it’s worth it. My files are synced across all on my computers. If the situation turns ugly, I don’t lose anything but the time spent migrating to another platform. So for now, I’ll stick to Mendeley, and see what happens.

Quick data mining of my own library

August 23, 2012 § Leave a comment

Almost back to the lab. It’s been a good summer with the boys, mostly at home. Reading books, papers and blog posts when I had free time. Which does not occur so often with children less than 5 years old, as anyone in the same situation can testify.

A lot of heated discussion are occurring online now about open access and data mining.  While some benefits are straightforward in certain domains such as genetics or chemistry, this is a brand new world to explore. I came across the fascinating comments by Philip Ball on chematica, a network of the transformations that link chemical species. Chemistry is not really my cup of tea, and I don’t have any of the coding abilities, unlike prominent data miners like Peter Murray-Rust. One thing I have, though, is a Mendeley library stuffed with papers (over 1400 as of today). Since my main focus now is on this ice-templating thing, I have a bit more than 350 papers on this topic only.

In addition, I am also fascinated by issues related to presenting data, aka the visual display of quantitative informations , as described by Tufte, among many others. I’ve been playing with Wordle before , it’s all over the internet now. Wordle are beautiful clouds of keywords, where the size of the words relates to their occurrence in a list or a text. You have a good example with the display of keywords in the right column of the blog page.

Today, I did some quick and dirty analysis of my collection of papers. Exporting the Mendeley data to a bib file, I compiled lists of titles of the papers in my library. I used the freely available wordle website. The whole process was really fast, like 15 minutes or so. The first result I got is shown below (clik to enlarge).

Well, as you can expect, being interested in porous ceramic materials templated by ice crystals, these keywords are obviously dominating the wordle. In the upper right you can find “zirconia”, reminiscent of my PhD on the low temperature degradation of zirconia containing ceramics. This was in the pre-Mendeley years, I don’t have many papers left on this topic.

Things get more interesting if I restrict the analysis to the titles of the papers related to ice-templating. I got about 340 of them. I’ve followed really closely the ceramic domain, and much less the polymer field. Polymers are thus largely under-represented in the following analysis, although ice-templated polymers came first.

The first obvious observation is the absolute domination of “freeze”, “casting”, “porous” and “ceramics”. They are almost in every tile. So if you want to be original, don’t come up with a paper entitled “freeze casting of porous ceramics”. The other dominant keywords are “structure” and “properties”, which is a pretty good image of the current approach to the phenomenon. Freeze whatever you have and look at the structure and properties. Not groundbreaking, most of the time. But the underlying mechanisms are so complex that very few people are willing to tackle them. “Tissue” and “scaffolds” are pretty strong too, and tissue engineering have indeed been one of the main focus so far in terms of potential applications. “Ice” is less prominent than “freeze”, and reflects how people are currently describing the process, “freeze-casting” instead of “ice templating”. I am not a big fan of “freeze-casting”, since it was originally used to describe the processing of dense materials. Although pretty much everyone is doing porous materials, “freeze-casting” still dominates. “Ice-templating” exclude all solvents other than water, so it’s not perfect either.

I also did the same analysis compiling all the abstracts. This is much closer to mining the full text of the papers. The output is much more balanced.

“Pore”, “porous”, “structure” and “freeze” still dominates, but the relative occurrences of other keywords is much more balanced. Since people tend to report almost exclusively positive results, we got a lot of “increased”, “high”, “new”, “novel”, “potential” “significantly” and “significant”, better represented than “low” and “decreased”. “Defects” is noticeably absent, although it remains a major issue of the process. “Control” is missing from the wordle (well, not really missing, but it’s really tiny), a fair representation of the majority of the papers, where people exert no control whatsoever. Freeze and see.
“Properties” is relatively large, although people are almost exclusively looking at mechanical properties (hence the presence of “MPa”). People became interested only very recently in other properties, such as conductivity or piezoelectricity.

Regarding materials, “silica” and “alumina” are the only ones found here. A lot of room for testing other materials, and therefore other properties. “Water” and “camphene” are of similar size, as people are equally interested in both solvents.

Missing keywords are equally interesting. “Colloids” is hardly visible, although everyone is dealing with colloidal suspensions. Ceramists are usually talking about slurries instead of colloidal suspensions, which is why we get “slurry” and “slurries” instead. Maybe. I still believe we have a lot to learn if we look at the colloid science papers.

“Interface” is the other elephant in the room. The control of the process largely depends on controlling the interface, and is something that people have largely ignored so far.

Without digging too much into the details, this quick and simple analysis is very informative about the current state of the art. Having followed very closely the domain for the past 5 or 6 years, the keyword clouds obtained here are very representative of the current state of the art. I’d love to extend this analysis to the full text of the papers, although I will need different tools to do it. Maybe I should get an access to the Mendeley API. They are responding to over 100 millons calls to their database each month, they can surely afford a few more. In the meantime, I’ll try to apply the same analysis to a different domains, using Google Scholar or Scopus and Mendeley. More later if I’m successfull.

Funny coincidence, this month’s issue of Nature Materials was released today while I was playing around with this analysis. Check out the front cover

Find and follow public author profiles

February 1, 2012 § Leave a comment

Another addition to Google Scholar, if you like tracking papers from specific academics. I am using RSS feeds based on Scopus for this. The big difference is that people do not have to be registered to have a profile in Scopus. Profile number need to grow before this new feature can be useful.


Zotero 3.0 release

February 1, 2012 § Leave a comment

An important update. Most notably, it is now a standalone application. The reference manager war is running and that’s a good thing for us. Also a new word processor integration that looks very similar to that of Mendeley or Papers. I am not planning to switch, though, if it ain’t broken, don’t fix it ! I am happy with Mendeley so far.

Author Wordle !

November 4, 2011 § Leave a comment

A new SciVerse application. Not sure how useful that is, but it looks really cool, at least. Here is mine.

Mendeley/PLoS Binary Battle results out

November 2, 2011 § Leave a comment

Some interesting stuff. Check it out here and there. My favorites are Vyzkumap and PLoS Impact explorer. Two more parts to come.

ScienceDirect iPad app quick review

November 2, 2011 § Leave a comment

I just discovered that ScienceDirect, aka Elsevier, released an iPad app. I was really curious to see what they came up with. Short version: I am extremely disappointed. This is a half-baked effort at best. Long version: read below.

The confusion starts from the beginning. On the App Store, you have the choice between a free and a paid ($2.99) version. It took me a while to find the differences between both. The description on the iPad app store does not really help. With the screenshots, I noticed that on the paid version you can also browse by journals. $2.99 for this ? They got to be kidding. Looking around on the science direct website, I finally found the differences. The benefits of paying are :

  • Browsing journal by Journal Name; by Subject Area or in Favourites
  • Setting up Alerts
  • Downloading PDF (iPhone Only)
I wasn’t too far off. The only benefit is the PDF download option, which curiously is only available on the iPhone ??? It’s a hundred times more convenient to read the PDF on the iPad, and yet you can only do it on the iPhone. Curious choice.
Anyway, I downloaded the free version to test it.
The start page is minimalist, with large icons providing access to the main functions: search and saved articles (and journals on the paid version). There is also a similarly huge icon for the information section, which is basically the “about” section. Which at best you will use once. Why would anyone want to have a permanent and quick access to this ? Curious choice, again.
More interesting is the “new on ScienceDirect” below, which you can customize with saved searches.
The search function is ok. Kind off. You can only filter by journal or authors. Why not other choices, like those offered on the website ?
The worst part is when you start reading paper. Some bugs make figures appear multiple times, three times, actually. So does the corresponding legend.
The font size is pretty darn small, and you cannot adjust it. You got to have some pretty good eyes. This is particularly annoying when you browse the table of contents and want to tap the section you want to reach. It’s easy too miss your target with such a small font size. The references section is equally poor and useless. No link to the papers or a search function to find them if they are not on ScienceDirect. Moving to the Figures and Table section, things are wrong again. No numbering of the figures (???). You cannot zoom on the figures, which would be the most basic convenience I can think about. On the abstract section, there is not link to email the corresponding author.
What else ? You would think that they tool care of syncing the app data (e.g searches) with your profile on ScienceDirect ? Well, no such luck:
Q: Can I view articles saved on SciVerse ScienceDirect mobile app through my desktop computer?
A: For now it’s not possible to coordinate your saved articles between the SciVerse ScienceDirect mobile app and from the Internet. This means that articles and searches you’ve saved in the mobile app will not be stored in account but you can email saved article records to yourself.
“email saved article records to yourself” ? Wow, this is the 21st century, guys ! I emailed the customer support a few months ago, when I was having trouble to sign in the iPhone version of Scopus, (to their benefits: they solved the issue quickly) and asked them if they were planning to offer the sync between the website and the app. Nope. They are built on different engines, so it’s wrong from the beginning. ”A tough cookie”, as they told me. The took the same path with the ScienceDirect app, apparently.
One thing they got right, though: the login authentication. It recognized properly my user account from the website, through which I have an institutional access to ScienceDirect.
To sum up, I can see no reason to use it now. All the basic functions are poorly executed or absent, and the absence of a proper sync with the website is really annoying. Some bugs are inexcusable (this is version 1.2.1 already), like the multiple appearance of figures. You would think that coming from such a large publisher (with lots of money, over 1.5 billion of profit), they would develop the app as a proper service to their customer (us). Yet, they claim in their annual report
Good progress on launching new content sets and innovative tools
For sure they were not thinking about their iOS app, right ? In the meantime, it’s more comfortable to use the ScienceDirect website on Safari. Try again. Removed from my iPad.

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