Press "Enter" to skip to content

Tag: software

On Elsevier buying Mendeley

[Update: Steve Dennis, a developer for Mendeley, posted a comment explaining a bit more about the data collection and privacy concerns some users have with Mendeley Desktop. It adds some pros and cons about the process outlined here.]

Two days ago (2013-04-08) Elsevier (the academic publishing company that is the subject of some controversy) bought Mendeley (the reference manager and a tool often mentioned when discussing 'open' research). The Mendeley Blog does a quick Q&A covering what changes will take place (they take the position that this will be better for everyone), while the folks over at The Chronicle examine the sale with a slightly more critical lens. Some accounts I follow on Twitter began using the hashtag #mendelete, taking an even more critical stance on the sale. (Someone has even made a guide to exporting data from and then deleting one's Mendeley account - useful, even if just for the exporting data portion.)

While it remains to be seen what changes will, in fact, take place, the simple fact remains that Mendeley is not open source and remains controlled by a company that does not have my (and your) best interests in mind. The most important thing for Elsevier is making money, and, for now, keeping Mendeley operating serves this goal. However, my work is too important to rely on a tool that somebody else controls. (I did a pretty thorough post on my views about this after the discontinuation of Google Reader.)

Now, Mendeley advertises itself as both a reference manager (think iTunes for PDFs) and a social network. This social network aspect has generated a lot of data, and many researchers seem to find it useful. Consequently, Mendeley has integrated their web services and their desktop client so that a single account is required to use both. Yes, an account is required to use the desktop software that would work perfectly well without an online account. Sure, it is enhanced by internet connectivity, but an internet connection is not required to organize my documents.

The login window that appears when Mendeley first launches.
When Mendeley first launches, there is no option to skip logging in.

But, an account is not really required. With a teeny bit of work, the Mendeley desktop software can be configured to work without a Mendeley account. This solution comes from the Mendeley support website, and is used to help people launch Mendeley when there are issues with the software and/or accounts. It is a 'feature' for support, but is certainly not something they advertise. The trick is to add --setting General_FirstRun:false (with two dashes, an underscore, and a colon) as an argument to the program when it launches. I'm doing this on Windows, but as Mendeley is cross-platform, it should ostensibly work on OS X and Linux, too. (Let me know in the comments if it does or doesn't work.)

To add this argument, right click the shortcut for Mendeley (e.g. the one on your desktop) and select properties. Then, add it to the box labeled "Target" outside of the quotation marks. Check out the image below.

Mendeley Desktop Properties window with the Target field circled
Notice the argument is outside the quotation mark and uses two dashes (-- not -).

After clicking Apply, you may need to grant Administrator approval for the changes to be saved, depending on your UAC settings. Adding this to the launcher skips the initial window that asks for your account information allowing you to use the offline features of Mendeley in peace. (You can add an account later by choosing "Tools" followed by "Options".)

Now, this option works with at least Mendeley Desktop 1.8.4, but there are no guarantees about 1.8.5 retaining this same feature. (Though there are many uses for this ability in a support context and removing it would be silly.) I feel somewhat assuaged knowing that I can use Mendeley on my computer whenever, wherever. Moreover, if I ever need to install Mendeley and their servers are unavailable, I can still use it.

I'm not Men-deleting my account. Not yet, at least. I'm still holding out hope that the program will be made open-source, assuaging even more of my concerns. There may still yet be hope according to something I saw from William Gunn, Mendeley's Head of Academic Outreach:

A conversation on Twitter between @TheDougW, @mrgunn, and @MendeleySupport.
Apparently open sourcing Mendeley is still being talked about.

So, open source is still being talked about, and the API is remaining open. These are promising signs. For the meantime, at least, I'm going to check out using Zotero in addition to Mendeley. I've been hearing some good things about Zotero, and it never hurts to have options. As the saying goes, "Two is one, one is none."


On Google Reader and Software as a Service

Eating from the tree of the knowledge of good and evil

Photo of a rendition of the tree by YashiWong
Copyright YashiWong CC 3.0 BY-SA (from Wikimedia Commons)

The year is 2013, and computers are faster and more ubiquitous. All aspects of education - and life - are being revolutionized. With the increases in computing power and bandwidth and decreases in cost and size, computers are becoming increasingly reliant upon servers, software-as-a-service, and "The Cloud" (a buzzword I use with mild disdain). This trend requires that we trust the companies and organizations providing the services to us to A) continue to provide the functionality for as long as we, the consumers, need it and to B) take adequate steps to protect our privacy and the security of our information.

On 1 April 2004, Google launched Gmail, a webmail service that offered the unheard of storage capacity of 1 GB. It was originally an invite-only service, and I was an early adopter (sometime in June 2004). I began to use Gmail almost exclusively, and this marked the beginning of my reliance on software as a service. Having been around computers since my early childhood, I understood the dangers of relying on third parties to provide tools that I use, and I experimented with running my own servers (for mail, web, and IRC). Despite my beliefs about the dangers of software as a service, I became lazy and complacent. My vigilance waned.

Canary in the coalmine

In May 2009, Google announced Wave, a service that was hoped to revolutionize the way people communicated and collaborated online. Briefly, the core idea was that standard email and chat systems rely on old Web 1.0 paradigms and that with the ubiquity of high-speed internet and computing that these paradigms could be challenged. As with Gmail, I was an early adopter of Wave. It turned out, however, that everyone that used Wave was an early adopter (in that there wasn't a deluge of people that began to use it after us).

Original Google Wave logo
Google Wave logo

In August 2010, Google announced that Wave was being discontinued, and by April 2012 the system was officially offline. While I hadn't used Wave in any substantial capacity (mostly using it for brainstorming and collaborating on small projects for school), I saw the potential in Wave and saw its place in my life. I was on a trajectory for slowly but steadily increasing my use and reliance upon Google's incarnation of Wave.

Apache Wave logo
Apache Wave logo

Wave perished but did not die. The core technologies live on in two forms: the rebirth of Google Docs (and later Google Drive) and Apache Wave. The former is another cloud service that resembles parts of Google Wave. The latter is the true successor to Google Wave with the goal of continuing work on the software and protocol with the eventual goal of making it so that there can be private Wave servers that are able to communicate with each other (e.g. I could run my own Wave server on my terms but still derive the benefits of a community of users - similar to how the Diaspora project is approaching social networking).

Spring cleaning

Google is famous for many reasons, among them a spirit of innovation and a willingness to try new ideas (e.g. Wave). Not all of them are as successful as they would like, and to ostensibly keep their focus on core products strong, began discontinuing products and services that were not widely used or had been superseded by other technologies. The first round of spring cleaning was in 2011, and it has occurred several times, the most recent being in March 2013. In this latest round, they announced the demise of Google Reader, a web-based RSS reader.

The discontinuation notice displayed on Google Reader. "Google Reader will not be available after July 1, 2013"
The discontinuation notice displayed on Google Reader.

The writing has been on the wall. In 2011, the community features were removed from Reader coinciding with Google's expansion into other social networking ventures (i.e. Buzz and Plus). I didn't use the social features much, so I didn't much care. ("First they came...") With the total discontinuation of Google Reader (due to a declining user base), a product I use daily, I am starting to see the naivete in my reliance on Google's services. Many have argued for the value of Google Reader, and many have argued that it was past its time. Petitions were started (this petition has over 125,000 signatures at the time of posting - one of them mine), and competitors offered seamless transitions. It seems today that Google will continue with the discontinuation despite the outcry.

This has two key consequences. First, one must always anticipate that software as a service will be discontinued in time, even by colossal companies like Google. When someone else controls the systems, you don't. Period. Secondly, niche groups may suffer more than others. In the end, when Google Reader dies I'll find an alternative. I may use Google's services less in the future, but being an American I have a plethora of options. For many Iranians, Google Reader is the only reasonable option. Google Reader is accessible as with an encrypted connection. The easiest way to block Google Reader for the Iranian censors would be to block the entirety of Google - a move that incited outrage when exactly this happened in September 2012. While Iran is very crafty at censoring the internet, Google Reader remains one option for accessing censored parts of the web for Iranians. (Of course, Iran is preparing a halal domestic internet that will result in blocking all western sites - including Google - so this may be a moot point.)

The state of affairs

I'm glad that Google broke my trust with Google Reader. It shattered the illusion I had about their benevolence and will force me to confront my reliance upon an organization that does not have my best interests in mind. Google exists to make a profit, not for the betterment of Doug-kind. As I type this, I have five different Google websites as pinned tabs in Google Chrome. I use an Android phone. My email is through Google. My phone number is controlled by Google. Google's seamless integration across services is wonderful, and I can't imagine it any other way.

Or, I couldn't until last week. Henceforth, every piece of technology I use will need an exit strategy. I always have had a vague notion of the alternatives for various programs and websites that I use, but vague notions are simply not good enough. An explicit exit strategy is required.

There is, of course, a spectrum of reliance. On one end is software as a service. Gmail, Google Reader, Microsoft Office 365, EA's Always-on DRM used in games such as Diablo III and SimCity 5, and countless other pieces of software and websites are entirely reliant upon both the internet and a company maintaining the servers on the other end of the line to operate. If this is no longer in their best (financial) interest, then the software or service will cease to work. Using software as a service may make sense at times, provided the limitations are understood.

On the other end of the spectrum is software that one develops personally, entirely from scratch (and on hardware that one has built from scratch). This is almost certainly not feasible in a pure form. Developing an entire computer system - hardware and software - from scratch is a pipe dream, and would preclude the rest of one's activities for several lifetimes. (As Carl Sagan said, "If you wish to make an apple pie from scratch, you must first invent the universe.")

I perceive a spectrum of control over one's computing, from most to least control (not exhaustive, with appropriate nuance and gradation):

  1. Inventing the entirety of the hardware and software that one uses
  2. Using strictly open source software and open hardware (Richard Stallman does this)
  3. Using strictly open source software on readily available - but closed - hardware (gNewSense is one Linux distro that is 100% Free Software)
  4. Using software and hardware that is run entirely from computer systems under one's control (i.e. no reliance on any computers - even on the internet - that one does not have absolute authority over)
  5. Using software and and hardware that one can make backups of and install without an internet connection (i.e. now allowing reliance on the internet for some functions, though not mission-critical - using an Android phone as a computer might fall into this category as one doesn't necessarily need to use it as a phone)
  6. Using software that requires an internet connection to a fixed set of servers not under one's control (e.g. activation servers needed for things like Microsoft Windows and Office)
  7. Using software that requires a constant internet connection to use, even software that could otherwise operate without the internet (e.g. single-player video games that require a constant internet connection)
  8. Using some software that is hosted entirely remotely (i.e. true software as a service)
  9. Using entirely software as a service (i.e. computing 100% in The Cloud)
  10. Using entirely software as a service on borrowed, proprietary hardware (e.g. a leased or borrowed computing platform that interfaces entirely with the internet with no local software or storage)

Right now, 1, 2, 9, and 10 are unreasonable for many people and organizations. Most people will be in the 3-8 range, depending on their specific needs (both for capabilities and finances). Right now, with my reliance upon Google's Gmail, Voice, Calendar, etc., I think I fall into the 8 range. I'd like to be able to get down to the 5 range for all possible things (recognizing that I will still rely on the vague concept of 'The Internet' to exist and facilitate things such as email and other network services). Even if I don't operate at level 5 and continue to operate at level 8, I want to have a technology exit strategy that will allow me to rapidly and without much loss of functionality and simplicity transition to level 5. This involves identifying alternative ways of doing whatever computing is necessary and understanding ways of transitioning one's data into them. (e.g. Google Takeout is a service - out of the benevolence of Google - that allows one to export one's data from Google's services and this could be used to transition data, but alternate strategies should also be found.)

Identifying alternatives and their limitations is no small task. I don't expect that I will achieve this overnight, but I hope that I will be able to find offline, open-source alternatives for (nearly) everything I use. If not, I will accept the limitation and plan accordingly. Some things may rely in principle upon running my own servers (e.g. hosting this website and email servers from my own computers). This may be practically unreasonable, but is technically possible. (Of course, I still need to rely on external DNS servers for the domain name to resolve...)

Moving forward

If Microsoft stops developing software, I can continue to use Windows 7 and Microsoft Office on my laptop indefinitely. I'm okay with having physical copies of software that is functional today, even if it is no longer developed and irrelevant in the future. (I could still install Word Perfect on DOS and use it to its full potential. Not practical, but could be useful in some nightmare scenario.) In the near future I'll do my best to identify where I rely on other companies and services and what alternatives exist. When I do, I'll post them. For now though, I just need to internalize the fact that The Cloud will not always be there, and that reliance upon it is a recipe for disaster. This may seem obvious, but it really hits home when services that one uses cease to be. (This is like backing up data. Go backup your data! Don't wait to lose it all!)

1 Comment

On a return to blogging after a hiatus

With the winter holiday I returned to my lazy, non-blogging habits. A New Year's resolution did little to change the situation. I suppose one just jumps in, though. I'll try to keep up with things more this semester. Really.

Plans for this semester

I'm currently taking a seminar on statistics education and an introductory course on qualitative methods. While the former is clearly my area of interest, the latter is proving to be more enjoyable than I had anticipated. One of the books for the course is Crotty's The Foundations of Social Research: Meaning and Perspective in the Research Process which is a bit more abstract than I was expecting, focusing on epistemologies and theoretical perspectives. It is a refreshing change, and I'm currently working my way through Feyerabend's Against Method after having my views on post-positivism challenged. (They seemed to be most aligned with Popper before this academic year.) Other plans include a trip to San Diego for LOCUS-related things and In-N-Out Burger, insha'Allah.

Dealing with Protected/Secured PDFs

Occasionally I'll come across a PDF that is Protected/Secured (it says 'SECURED' in the title bar of Adobe Reader) which are rather annoying to deal with. I've been using Mendeley to organize the articles/books I've read, and I copy the abstract into the software so that it can be searched. Alas, one journal whose articles I often read secure every single PDF so that copying cannot be done. Really frustrating.

Thankfully, this "secured" state is not encrypted or password protected. From what I gather, the state is determined by setting a bit in the file to disable certain features and Adobe, upon finding this information, respects the file's instructions. Not all software respects the file's instructions, and those that don't allow copying without issue. Two such readers are Evince (part of GNOME) and Okular (part of KDE). Both are open source, and both at least have options for disabling the DRM on the files. They are also both available on Windows (as well as many other platforms and are exceedingly common on Linux); if you're just looking for a quick download on Windows, Evince might be better. Either way, problem solved.

Leave a Comment

Even more minor updates

A few more quick updates to stay on the Monday/Thursday update schedule. I'll try to get some actual content up next week, but it might end up being placeholder comics.

I went through and updated all the media links from the website reorganisation by hand. There was probably an easier way, but I wanted to get it done.

Mendeley has been working well for organizing PDFs. I'm getting close to deciding to start relying on it. (I still want to try out some more features, though.)

The projects I'm working on for my REM courses are slowly coming along, as is updating the artwork for my advisor's grant. The DokuWiki I set up as a research logbook is working well. A little clunkier than I'd hoped (particularly with regard to tables), but I'm getting the hang of it. I've found a couple of useful plugins, and there are quite a few promising ones out there. I'll likely do a post about my research process in a few months as I settle in to a productive routine.

Lastly, this seems as good a time as any to mention a statistics comic that might be of interest. On 23 July 1994, Dilbert was about the median. It is a pretty decent comic that I've used before in teaching. However, I'm not able to post it here. I've secured permission either implicitly or explicitly to post all the comics on here, but Universal Uclick, the company that syndicates Dilbert, charges $50 to license the comic for use on a blog. This seems pretty reasonable I suppose, but I make nothing off this website and can't justify the expense. I would link to the comic, but Universal Uclick has a linking policy with which I have a philosophical disagreement. It isn't too difficult to find, though, and it is a good comic for teaching.

Also,  Happy Thanksgiving.

Leave a Comment

A few quick updates

I don't have anything exciting to post today, but I do want to keep up with my Monday/Thursday update cycle which dictates that something be posted today. So, here it goes:

Current Projects

  • I'm currently just doing some minor work for my advisor's grant
  • I'm working on a simulation study for class (quasi-experimental design)
  • I'm working on a proposal for a simulation study for a class (item response theory)
  • All of the other little side projects I'm always doing

Website Updates

  • I had originally install WordPress into my website's root folder. I finally got around to reorganizing the public_html folder this weekend.
    • I followed the instructions here and it worked pretty seamlessly. I was pleased
    • I also created made the path public_html/ and was able to make things work pretty easily by changing subdomain options in cPanel.
    • (Edit: I see some dead links and images now because wp-content is now at wordpress/wp-content. I'll update those later tonight.)
  • I installed DokuWiki at as private research logbook (works in progress, notes, etc.). It seems to work pretty well so far. I went with this over something like MediaWiki because the idea of plain text files storing the content was appealing (as opposed to a not-easily-read-by-humans database such as MySQL).

Other Quick Thoughts

  • I'm installing Cygwin with the hopes of being able to use curlftpfs+rsync to automatically backup my websites (I'm currently just periodically logging in via ftp and copying files over). We'll see how this goes. (Inspired by this thread on StackOverflow.)
  • I really dislike how Cygwin doesn't have broad-but-not-every-package groups of packages to add. I keep having to re-launch the setup.exe and add things in that I overlooked because of my inexperience. Only way to learn I guess.
  • Wikis are awesome. DokuWiki seems to work well for this goal (particularly because I might want to use it for collaborations in the foreseeable future), but for a single-user, offline Wiki I've had success with TiddlyWiki. I don't use it much now, but that's more for a lack of time to do the projects I was using it for and less to do with the software (which was quite good).
  • I'm trying to use Mendeley Desktop to organize my references. So far it is promising, but I'm not sold yet. (Not thrilled that it isn't open source and that one needs an (albeit free) account to use it.)
  • I judged a middle school science fair. It was... almost what I expected. Not many students seemed to understand variability or sampling error (about what I thought), but three of the 20 or so projects I looked at were really phenomenal. I'd love to keep doing this judging if I have time.
  • I've got some larger posts in the works, and enough comic posts in a scratch file to keep me going for a while, but I prefer to do comics no more often than every-other-post. But still, whatever it takes to keep the Monday/Thursday update cycle going.
Leave a Comment