How to get any medical journal into your RSS reader even if they don’t provide an RSS feed


What is RSS?

For the non-initiate, RSS is a very useful protocol that is used all over the web. You can think of it as a way of separating a stream of content from the website where it’s normally viewed. Nearly every blog has an RSS feed, as do news sources, web comics, and even academic journals. Podcasts are like a specialised version of RSS for audio files only.

What makes RSS great is that I can take all the RSS links from all the news sites, blogs, webcomics and journals that I’m interested in and put them together into a single aggregator (I use Feedly). In this way, I don’t have to be constantly checking all these websites to see if there’s new stuff posted.

But what about medical journals that don’t provide RSS?

Unfortunately, there are some medical journals that do not have an RSS feed. For example, the JNCI (the Journal of the National Cancer Institute) does not have one. (If I’m wrong, please put the link in the comments.) So if I want to know what’s been published recently in the JNCI, I have to visit their site, or look on their Twitter. This is annoying, since the whole point of RSS is to have all the content you want to consume (or as much of it as possible) in the same place.

Pubmed allows users to save any search as RSS feeds

Pubmed provides a wonderful and open, standards-compliant service, but almost no one seems to know about it! This is great for people who are actively researching a subject, and also for people who just want to keep up with a particular journal or subject area.

Some of you have probably figured out where I’m going with this by now, but if you haven’t, I’ll spell it out. Let’s continue with the example of JNCI.

How to put new articles from any journal into Feedly

This assumes you already have an account on Feedly, but you can do this with any RSS reader, of course.

  1. Visit Pubmed in your browser
  2. Click “Advanced” under the search field
  3. Under “Builder,” click “All fields” and choose “Journal”
  4. In the text field beside the box where you selected “Journal,” enter the name of the journal you’re interested in (it will autocomplete, if you have done this correctly, you should see something like “Journal of the National Cancer Institute”[Journal] in the uneditable text field at the top)
  5. Click “Search”
  6. Under the search field at the top of the page, click the “Create RSS” link
  7. Choose how far back you want your search to go (I chose 20)
  8. Click the “Create RSS” button
  9. Right-click the orange “XML” button and click “Copy link”
  10. Go to Feedly, and paste the link into the “Search” field at the top right
  11. There should be one result, click “Follow” and choose which collection you want to keep it in

You’re done! Now whenever Pubmed indexes a new entry for that journal, it will appear in your RSS reader!

You can also make RSS feeds for any search you want on Pubmed

Of course, you may not be interested in everything a journal has to say, so you can refine the search to only include “breast cancer” or you can drop the journal identity part of the search entirely. The world is your oyster!


    title = {How to get any medical journal into your RSS reader even if they don’t provide an RSS feed},
    journaltitle = {The Grey Literature},
    author = {Benjamin Gregory Carlisle},
    address = {Montreal, Canada},
    date = 2017-06-15,
    url = {}


Carlisle, Benjamin Gregory. "How to get any medical journal into your RSS reader even if they don’t provide an RSS feed" Web blog post. The Grey Literature. 15 Jun 2017. Web. 23 Jun 2018. <>


Carlisle, Benjamin Gregory. (2017, Jun 15). How to get any medical journal into your RSS reader even if they don’t provide an RSS feed [Web log post]. Retrieved from

Gotcha! This is why piracy happens



This summer, I took a two-week long course on systematic reviews and meta-analytic techniques for which there was some required software, in this case, Stata. As a McGill student, I was encouraged to buy the student version, which was about $50 for “Stata Small.” Not bad. I’ve paid more for textbooks. So I got out my credit card, bought the license, installed it on my computer, and ran the very first example command of the course. I immediately got a string of red letter error text.

The error message was telling me that my license did not allow me enough variables to complete the command. I checked the license, and it said I was allowed 120 variables. I checked the “Variable manager” in Stata, and I had only assigned 11 variables. (I checked the variable limit beforehand in fact, and made sure that none of the data sets that we’d be working with had more than 120 variables. None of them came close to that limit.)

So I emailed Stata technical support. It turns out that the meta-analysis package for Stata creates “hidden variables.” Lots of them, apparently. So many that the software cannot accomplish the most basic commands. Then they tried to up-sell me to “Stata SE.” For $100 more, they said, they would send me a license for Stata that would allow me to run the meta-analysis package—for realsies this time.

I asked for a refund and decided that if I really needed Stata, I would use the copy that’s installed on the lab computers. (Now I’m just using the meta package in R, which does everything Stata does, just with a bit more effort.)

For the record: I am perfectly fine with paying for good software. I am not okay with a one-time purchase turning me into a money-pump. I thought that the “small” student license would work. All their documentation suggested it would. If I had upgraded to “Stata SE,” would that have actually met my needs, or would they have forced me to upgrade again later, after I’d already made Stata a part of my workflow?

It probably would have been okay, but the “gotcha” after the fact soured me on the prospect of sending them more money, and provided all the incentive I need to find a way to not use Stata.


A few years ago, I bought a number of pieces of classical music through the iTunes Store. I shopped around, compared different performances, and found recordings that I really liked. This was back when the iTunes store had DRM on their music.

I’ve recently switched to Linux, and now much of the music that I legally bought and paid for can’t be read by my computer. Apple does have a solution for me, of course! For about $25, I can subscribe to a service of theirs that will allow me to download a DRM-free version of the music that I already paid for.

This is why I won’t even consider buying television programmes through the iTunes Store: It’s not that I think that I will want to re-watch the shows over and over and I’m afraid of DRM screwing that up for me. It’s because I’ve had some nasty surprises from iTunes in the past, and I can borrow the DVD’s from the Public Library for free.

For the record: I do not mind paying for digital content. But I won’t send you money if I think there’s a “gotcha” coming after the fact.

I’m really trying my best

People who produce good software or music should be compensated for their work. I don’t mind pulling out my wallet to help make that happen. But I don’t want to feel like I’m being tricked, especially if I’m actually making an effort in good faith to actually pay for something.

Since DRM is almost always fairly easily circumvented, it only punishes those who pay for digital content. And this is why I’m sympathetic to those who pirate software, music, TV shows, etc.


    title = {Gotcha! This is why piracy happens},
    journaltitle = {The Grey Literature},
    author = {Benjamin Gregory Carlisle},
    address = {Montreal, Canada},
    date = 2015-05-22,
    url = {}


Carlisle, Benjamin Gregory. "Gotcha! This is why piracy happens" Web blog post. The Grey Literature. 22 May 2015. Web. 23 Jun 2018. <>


Carlisle, Benjamin Gregory. (2015, May 22). Gotcha! This is why piracy happens [Web log post]. Retrieved from

So I started learning Lojban .ui


This Friday past, I started learning Lojban. For the non-initiate, Lojban is a constructed language based on predicate logic that is syntactically unambiguous. I’d known about it for years, probably hearing about it first on CBC, maybe 10 years ago. It’s the sort of thing that shows up in Dinosaur Comics or in XKCD periodically. Up until this weekend, the existence of Lojban had mostly been one of those “cocktail party facts,” but then I finally took the plunge. After 1 weekend of working on it, I’m about 35% of the way through Lojban for Beginners, having downloaded it to my Kobo for reference during the car ride to Stratford.

It’s often billed as being an ideal language for fields like law, science or philosophy, due to its unambiguous and culturally neutral nature. So I set out to find out certain specialised terms from my field, bioethics, and it turns out that they mostly don’t exist yet. This, of course, offers some exciting opportunities for a grad student. :)

I’ve convinced a few people in Montréal to learn Lojban with me, and even found a Montrealer who speaks Lojban on a #lojban IRC channel. (Yes, IRC still exists!) We may “ckafi pinxe kansa,” as they say in Lojban, apparently.

If you too want to get in on the ground floor of Lojban Montréal, let me know!


    title = {So I started learning Lojban .ui},
    journaltitle = {The Grey Literature},
    author = {Benjamin Gregory Carlisle},
    address = {Montreal, Canada},
    date = 2014-09-22,
    url = {}


Carlisle, Benjamin Gregory. "So I started learning Lojban .ui" Web blog post. The Grey Literature. 22 Sep 2014. Web. 23 Jun 2018. <>


Carlisle, Benjamin Gregory. (2014, Sep 22). So I started learning Lojban .ui [Web log post]. Retrieved from

Why I dumped Gmail


Reason one: I need my email to work, whether I follow the rules on Google Plus or not

Google has linked so many different products with so many different sets of rules to the same account that I feel like I can’t possibly know when I am breaking some of its terms of use. And I’m not even talking about specifically malicious activity, like using software to scrape information from a Google app or a DDoS attack. I mean something as basic as using a pseudonym on Google Plus, or a teenager revealing that she lied about her age when signing-up for her Gmail account. (These are both things that have brought about the deletion of a Google account, including Gmail.)

For starters, I think it is a dangerous and insensitive policy to require all users to use their real names on the Internet, but putting that aside, I don’t want to risk having all my emails deleted and being unable to contact anyone because of some Murph / Benjamin confusion on Google Plus.

Reason two: it’s actually not okay for Google to read my email

Google never made it a secret that they read everyone’s email. Do you remember when you first started seeing the targeted ads in your Gmail? I bet you called a friend over to look. “Look at this,” you said, “we were just talking about getting sushi tonight, and now there’s an ad for Montréal Sushi in my mailbox! That’s so creepy,” you said.

And then you both laughed. Maybe you made a joke about 1984. Over time, you got comfortable with the fact that Google wasn’t even hiding the fact that they read your mail. Or maybe you never really made the connexion between the ads and the content of your email. Maybe you thought, “I have nothing to hide,” and shrugged it off, or did some mental calculation that the convenience of your Gmail was worth the invasion of privacy.

I guess over time I changed my mind about being okay with it.

And no, this isn’t because I have some huge terrible secret, or because I’m a criminal or anything like that. I just don’t want to send the message that I’m okay with this sort of invasion of privacy anymore. Google’s unspoken challenge to anyone who questions their targeted ads scheme has always been, This the price you pay for a free service like Gmail. If you don’t like it, you can leave.

This is me saying, I don’t like it. I’m leaving.

Reason three: Gmail isn’t even that good anymore

When I signed up for Gmail, there were three things that set it apart:

  1. Tag and archive emails—forget folders!
  2. 10 gigabytes of space—never delete an email again!
  3. Web-based interface—access it from anywhere!

I’ll deal with each of these in turn.

1. Tagging was fun, but it only really works in the Gmail web interface, or in an app specifically designed for use with Gmail. Unfortunately, Gmail just doesn’t play nicely with other email apps, like the one in Mac OS X, or Mail on the iPhone or the BlackBerry. You could make it work through IMAP, having it tell your mail client that each tag was a folder, but it was always a bit screwy, and I never figured out how to put something in two tags through a 3rd-party app or mobile device.

The value of being able to organise emails by simultaneously having them in two categories is outweighed by the fact that I couldn’t access this functionality except through the browser.

2. The amount of space that Gmail provides for emails is not very much these days. I have a website (you may have guessed) and it comes with unlimited disc space for web hosting and emails. 10 gigabytes is just not that big a deal anymore.

3. I can do this with my self-hosted email as well, and I don’t have to suffer through an interface change (“upgrade”) just because Google says so.

So what’s the alternative?

Full disclosure: I haven’t shut down my Google account. I’m forwarding my Gmail to my self-hosted email account, so people who had my old Gmail account can still contact me there for the foreseeable future. I am also still using a number of other Google products, like the Calendar and Google Plus, but my life would not go down in flames quite so quickly if those stopped working as compared to a loss of email access.

Basically, I am moving as many “mission critical” aspects of my life away from Google as I can, to keep my technological eggs in a few more baskets. Email, for example, will be handled by my web host, of which I make backups on a regular basis.

I’m not trying to go cold-turkey on Google. I’m just not going to pretend to be as comfortable as I used to be as a guest on Google’s servers.

Update (2013 Nov 18)

I switched back to the Thunderbird email client a couple weeks ago. It supports tagging and archiving, just like Gmail.

Update (2018)

I switched to Protonmail!


    title = {Why I dumped Gmail},
    journaltitle = {The Grey Literature},
    author = {Benjamin Gregory Carlisle},
    address = {Montreal, Canada},
    date = 2013-09-27,
    url = {}


Carlisle, Benjamin Gregory. "Why I dumped Gmail" Web blog post. The Grey Literature. 27 Sep 2013. Web. 23 Jun 2018. <>


Carlisle, Benjamin Gregory. (2013, Sep 27). Why I dumped Gmail [Web log post]. Retrieved from

A review of and rationale for Bitmessage


Bitmessage address

Bitmessage address

There is a little bit of crypto-anarchist in all of us, and bowing to that spirit, I’ve been checking out Bitmessage, the peer-to-peer encrypted messaging protocol, which I commend to you as a fun experiment. It is not ready for mass-consumption (yet), but it shows a lot of promise. If you would like to test for yourself whether or not the software is actually impervious to the NSA’s prying eyes, download the software with a friend (Mac, PC) and send each other messages whose content would normally get you on the “do not fly” list, then book a flight and go to the airport. Say goodbye to your loved ones before you leave—there is limited internet access for inmates at Guantanamo Bay.

“I have no need to use Bitmessage because I have nothing to hide”

You might be asking yourself why anyone would even be interested in using Bitmessage. After all, if you are not emailing about child pornography or drug trafficking, you have nothing to worry about, right? I can think of 4 reasons why I might want to switch as many of my communications to Bitmessage as possible. I will outline them below, and then go into some of the more interesting aspects of the protocol that I’ve been thinking about.

1. You’re probably guilty of something.

The laws of Canada, the United States and pretty much every modern nation state are at the moment, so convoluted, contradictory and difficult to understand and follow, that it is likely that every single person alive today has already done enough to warrant time in jail, whether they realise it or not.

Affluent straight white males without mental health issues don’t notice this because it is not good politics to arrest them very much. But it doesn’t take much of an excuse for the police to take a homeless guy away, or to declare that a black guy was acting suspiciously and treat him accordingly. This might not bother you if you are, in fact, an affluent straight white male without mental health issues, until you realise that:

2. Sometimes messages that are perfectly acceptable in their proper context, can be very damning when quoted out of context.

I don’t know from first-hand experience, but I’m betting that the NSA/CSIS/whoever’s getting my email doesn’t have a human carefully reading through every single email and flagging the ones that are explicitly related to terrorism. I bet they’re searching for key words and phrases. And if you happen to have the wrong sorts of phrases in your emails, combined with the wrong sorts of Google searches, etc., you might find that the government might decide to scrutinise what you’re doing, and this is a problem because of reason 1, outlined above.

3. Just because you know that what you’re doing is fine doesn’t mean that someone else won’t punish you for it.

For example, I am a homosexual. This is fine. My family/friends/co-workers think it’s fine. I’ve never been physically attacked or had anything like that happen to me because of it. However, if I were planning on going to Russia as a tourist during the Olympics, I would be rightly afraid, and not because I’m doing anything even slightly wrong.

4. Solidarity with the less privileged is a generous gesture.

Let’s imagine that you are an affluent straight white male who has very vanilla sexual tastes and no mental health issues, whose email correspondence is so clear that it could never be misconstrued badly, and against all odds, you know for certain that nothing you have done is now, or ever will be illegal. You still might want to switch to something like Bitmessage, just out of solidarity with the rest of us who aren’t so privileged. After all, if we have to constantly switch between regular email and Bitmessage, we’ll eventually mess up.

Now that you’re all on-board the Bitmessage train, let’s settle down and look at what it is and what it does differently.

What I find interesting about the Bitmessage protocol itself

Bitmessage is still in a beta-version, so it does not allow rich text formatting, attachments (although in principle, it could) or any sort of filtering, searching tagging or sorting of your messages once they’re in your inbox. It’s more of a proof-of-principle release, than anything that’s designed for actual communication.

Unfortunately, it’s not pretty.

The big selling point of Bitmessage is that all messages are encrypted, and the protocol makes it difficult even to discern the sender / receiver of a message. Beyond that, it has some interesting properties that could be exploited, the most interesting of which I will explain here:

The address of the sender of a bitmessage can’t be faked

Something you may not have known about regular email: There is nothing preventing anyone from sending an email from any address she chooses. Any person could send an email from your email address to any other email address, without needing to get access to the sender’s email account. That’s why you sometimes see extra information next to the sender’s name in Gmail. It’s kind of like regular mail. You can write anyone’s name you like in the top-left corner of an envelope and have it delivered.

Have you ever wondered why, whenever you sign up for something online, you have to put in your username / password, then it sends you an email, and then you click a link in the email, which sends you back to the site you came from? It’s a weird and awkward system, and it’s not even very secure, but we’ve been doing it for so long that we’ve forgotten just how weird it is.

If a website required a bitmessage address for sign-up instead of an email address, the sign-up process could be streamlined or changed in a number of ways: It could be as simple as, “Fill out the Captcha to reveal a bitmessage address. Send a blank bitmessage to the address to sign up. Your bitmessage address is your username. You will receive a password in reply to the message you sent.” There you go. That might be what sign-ups look like, once web servers start installing a bitmessage client.

Just by building a protocol such that sender addresses can’t be faked, we can finally eliminate the cost of constantly writing software to confirm the identity of a user.

Proof of work: the end of spam?

If you’ve tried sending a bitmessage, one thing you might have noticed is that it needs to do a “proof of work” before the network will accept a message for sending. It takes about a minute on my year-old MacBook Air to do, but the bigger the message is, the more difficult the proof of work becomes.

This isn’t much of a burden, if you’re sending messages only as fast as you can type them, but it becomes a huge drain on computer resources and electricity if you’re trying to send thousands of spam messages. This in itself may make spam uneconomical. Also, having an incentive to keep emails short and to keep attachments to a minimum is a good thing.

There are some legit cases in which you may want to send out a message to a large number of recipients. Some people actually do want to receive updates on projects they’re interested in, for example. Bitmessage allows “broadcasting” for this. Users subscribe to a bitmessage address, and anyone who has the address receives messages broadcast to it, which requires only one proof of work.

Addresses are not human-readable

A bitmessage address doesn’t look like an email address or a Twitter handle. In fact, you can’t really pick an address in the same way you did for pretty much every other web service you ever signed up for. Addresses are generated either randomly or deterministically from a user-chosen passphrase.

This is an example of a bitmessage address:


These addresses are not meant to be read and transcribed by humans. To be honest, relying on humans to remember and reliably communicate specific exact strings of characters never worked really well. (E.g. “Was that a one or a lower-case L in your email?” or “Did you mean the numeral ‘6’ or the letters ‘S-I-X’?”)

Even better, it means that we can finally move past “vanity” email addresses. You don’t have to deal with addresses like [email protected] and you don’t have to try to think up a dignified user name when signing up for a Gmail to use for applying for jobs when your real name is already taken. We can give up on human-readable addresses and let QR codes and the copy / paste commands take over.

Addresses are “disposable” by design

You can make as many addresses as you like, and by virtue of the fact that they are disposable, you can use one per project / contact / context, and keep track of how other users get your contact info. For example, you might be a member of a message board for Russian political dissidents. You could post a bitmessage address there, and mark in your bitmessage client where you posted it and when, and if you ever received a message on that address, you’d know that ultimately, that’s where the guy got it from. You could trade another address with your family, use another just for a particular school project, or print a QR code for another one on a poster for your indy-music band, etc.

Deterministically generated addresses are an interesting property of the bitmessage protocol as well. Be sure to use a very good passphrase if you want to generate them in this way, otherwise you run the risk of an “address collision,” where you and another person have generated the same address. If this happens, you will receive each other’s messages.

This could be a bug or a feature, depending on how you look at it. I can imagine that a government agency or a company might want to have a copy of all their employees’ communications—one that can’t be deleted in the case of a scandal. You could write a little application for use on company computers that generates addresses, and when it does so, it informs the user, as well as a “listening computer,” which uses an agreed-upon set of passphrases to deterministically generate the same addresses. In this way, a government agency or a department within a company wouldn’t have the option of deleting old emails that would reflect poorly on them, unless they go and delete them on the “listening computer.”

Emails were never really reliable, anyway

Do you remember when Gmail went down for a few hours a couple years ago? I really didn’t know what to do. I was in shock. I went outside, wandered around and reconsidered the priorities in my life.

Gmail, like all email servers, has a single central physical location. This means that if power goes out, or a meteorite strikes, or if climate change floods that location, you no longer have your normal means of communication. It doesn’t happen much, but it could. Bitmessage is a distributed peer-to-peer network, so it doesn’t have the same sorts of vulnerabilities.

Even outside of catastrophes, email is a bit unreliable. Sometimes emails legitimately go missing. Again, not often—it’s usually a user error or a misfiled message. But the fact is, you can’t tell if someone has received a message you sent them, or if the message disappeared into the ether. Automatic spam filters are also common culprits for the loss of email messages.

Bitmessage sends receipts for messages, indicating that the receiver’s client has downloaded the message from the network, but not that she has read it.

Have you tried Bitmessage yet?

Let me know if you do download it and give it a try. Hit me up and we can send secret messages to each other!


    title = {A review of and rationale for Bitmessage},
    journaltitle = {The Grey Literature},
    author = {Benjamin Gregory Carlisle},
    address = {Montreal, Canada},
    date = 2013-08-13,
    url = {}


Carlisle, Benjamin Gregory. "A review of and rationale for Bitmessage" Web blog post. The Grey Literature. 13 Aug 2013. Web. 23 Jun 2018. <>


Carlisle, Benjamin Gregory. (2013, Aug 13). A review of and rationale for Bitmessage [Web log post]. Retrieved from

How to automatically back up WordPress or ownCloud using cron jobs


Recently I set up WordPress for my research group in the Medical Ethics Unit. We will be blogging our journal clubs, posting links to our publications and upcoming events. In related news, my research group has been using DropBox to coordinate papers in progress, sharing of raw data, citations, and all manner of other information. This was working pretty well, but we have been bumping up against the upper limit of our capacity on DropBox for a while, so I installed ownCloud on the web host we got for the research group blog. I’m pretty happy with how nice it is to use and administer.

Of course one of our concerns is making sure that we don’t lose any data in the case of the failure of our web host. This is unlikely, but it does happen, and we don’t want to run into a situation where we try to log in to our cloud-based file storage / sharing service and find that months’ worth of research is gone forever.

For a few weeks, the following was more-or-less my workflow for making backups:

  1. Log in to phpMyAdmin
  2. Make a dump file of the WP database (choose database > Export > Save as file … )
  3. Make a dump file of the ownCloud database
  4. Save to computer and label with appropriate date
  5. Log in to web server using FTP
  6. Copy contents of WP’s /wp-content/ to a date-labelled folder on my computer
  7. Copy contents of ownCloud’s /data/ to a date-labelled folder on my computer

This worked pretty well, except that it was a pain for me to have to do this every day, and I know that if I ever forgot to do it, that would be when something terrible happened. Fortunately for me, my boss mentioned that he had an old but still serviceable iMac sitting in his office that he wanted to put to some good purpose.

I decided to make a fully automatic setup that would make backups of our remotely hosted data and save it locally without any input on my part, so I can just forget about it. I made it with cron jobs.

Server side cron jobs

First, I set up some cron jobs on the server side. The first one waits until midnight every day, then dumps all the MySQL databases into a gzipped file on my web host, then zips up the WordPress /wp-content/ and ownCloud /data/ folders and puts them in the backup folder as well. The second server-side cron job empties the backup folder every day at 23h00.

  • 0 0 * * * PREFIX=`date +%y-%m-%d`; mysqldump -u USERNAME -h HOSTNAME -pPASSWORD –all-databases | gzip > /path/to/backup/folder/${PREFIX}-DBNAME-db.sql.gz; zip -r /path/to/backup/folder/${PREFIX} /path/to/wordpress/wp-content/; zip -r /path/to/backup/folder/${PREFIX} /path/to/owncloud/data/;
  • 0 23 * * * rm -r /path/to/backup/folder/*

A few notes for someone trying to copy this set-up

  • Your web host might be in a different time zone, so you might need to keep that in mind when coordinating cron jobs on your web host with ones on a local machine.
  • My web host provided a cron job editor that automatically escapes special characters like %, but you might have to add back-slashes to make yours work if you’re manually editing with crontab -e.
  • You might want to put a .htaccess file in your backup directory with the following in it: “Options -Indexes” (remove the quotes of course). This stops other people from going to your backup directory in a browser and helping themselves to your files. You could also name your backup directory with a random hash of letters and numbers if you wanted to make it difficult for people to steal your backed-up data.

Local cron job

Then on the local machine, the old iMac, I set up the following cron job. It downloads the files and saves them to a folder on an external hard disc every day at 6h00.

  • 0 6 * * * PREFIX=`date +%y-%m-%d`; curl${PREFIX}-DBNAME-db.sql.gz > /Volumes/External HD/Back-ups/${PREFIX}-DBNAME-db.sql.gz; curl${PREFIX} > /Volumes/External HD/Back-ups/${PREFIX}; curl${PREFIX} > /Volumes/External HD/Back-ups/${PREFIX};

If you were super-paranoid about losing data, you could install this on multiple local machines, or you change the timing so that the cron jobs run twice a day, or as often as you liked, really. As long as they’re always turned on, connected to the internet and they have access to the folder where the backups will go, they should work fine.


This isn’t a super-secure way to back up your files, but then we’re more worried about losing data accidentally than having it stolen maliciously. I don’t think the world of medical ethics is cut-throat enough that our academic rivals would stoop to stealing our data in an effort to scoop our papers before we can publish them. That said, I’m not about to give away the exact URL where our backups are stored, either.

The practical upshot of all this is that now we have at least three copies of any file we’re working on. There’s one on the computer being used to edit the document, there’s one stored remotely on our web host, and there’s a copy of all our files backed up once a day on the old iMac at the Medical Ethics Unit.


    title = {How to automatically back up WordPress or ownCloud using cron jobs},
    journaltitle = {The Grey Literature},
    author = {Benjamin Gregory Carlisle},
    address = {Montreal, Canada},
    date = 2013-05-20,
    url = {}


Carlisle, Benjamin Gregory. "How to automatically back up WordPress or ownCloud using cron jobs" Web blog post. The Grey Literature. 20 May 2013. Web. 23 Jun 2018. <>


Carlisle, Benjamin Gregory. (2013, May 20). How to automatically back up WordPress or ownCloud using cron jobs [Web log post]. Retrieved from

Conventional computing vs the corporate cloud vs the “personal” cloud


Everyone loves cloud computing. Users love it, tech blogs love it, and tech companies are all trying their hand at it—even ones who have no concept of how to provide a half-decent web service. And yes, I’m talking about Apple’s iTools. I mean, dot-Mac. Oh sorry, it’s called iCloud now. Whatever it’s called, it’s still terrible.

More interesting to me than the corporate offerings of cloud-based services (and in some cases withdrawals of those offerings, e.g. Google Reader) is all the new open-source cloud-based software available for anyone to install on their own web host of choice. To clarify, I’m talking about pieces of software that are more like WordPress than Microsoft Word—this is software that you install on a web server, and that you access through a browser, not software that you install on your own home computer. I will refer to this type of software as “personal” cloud software.

Here are a few examples of different categories of software, and rough equivalents for conventional computing, corporate cloud offerings and “personal” cloud alternatives. This is not meant to be a comprehensive list of such services, just a list of examples. Also, the examples given here aren’t meant to be endorsements of the services either.

Conventional computing Corporate cloud “Personal” cloud
Document editors Microsoft Word
Google Docs
Microsoft Web Office
OX Documents?
WordPress (sort of?)
Email Outlook
Yahoo Mail
Squirrelmail, etc.
Note-keeping Any text editor, really Evernote
Google Keep
Photos iPhoto
G+ / FB
File storage Hard disc Dropbox
Google Drive
Music iTunes / iPod Your favourite music streaming service
RSS reader Newsfire, etc. Google Reader (hahaha)
Bitcoin wallets Wallet on hard disc May not exist?

Usually the debate is framed as being between conventional computing and corporate cloud computing. Sometimes a very nuanced look into these different services will compare different corporate cloud-based services, but rarely does anyone compare the pros and cons of conventional vs corporate cloud vs “personal” cloud services. So, as far I see them, the following are the major issues to consider. Depending on your own level of technical expertise, your priorities, budget and the level of importance that you assign to a particular task that you wish to perform, you may weight these differently. For simplicity, I assigned each category a value of +1 (this is good), -1 (this is bad) or 0 (this isn’t very good or very bad).

Conventional computing Corporate cloud “Personal” cloud
Who has access to your files? Only you (+1) You, corporation, NSA (-1) You, web host (0)
Who owns the software? You own a licence (0) Corporation (-1) Often open source (+1)
When do you pay? Only once—when you buy the software (0) Never (+1) Every month (-1)
Can a company mine your data for advertising info? No (+1) Yes (-1) No (+1)
Are there advertisements? No (+1) Often, yes (-1) No (+1)
Accidentally losing files? Very possible (-1) Unlikely (+1) Unlikely (+1)
Rolling back to previous versions? Only if you make backups (0) Often yes (+1) Often yes (+1)
Open source software? Sometimes (0) No (-1) Almost always (+1)
Level of technical expertise required to install software? Medium (0) Low (+1) High (-1)
Can the whole service be “Google Reader-ed”? No, but development of your app might be cancelled (0) Yes (-1) No (+1)
Whose computer must be working for you to access your files, etc.? Only yours (+1) The corporation’s (-1) Your web host’s (-1)
Can you collaborate with other users? Not really (unless you count “track changes”) (-1) Yes (+1) Yes (+1)
Accessing / syncing content across multiple devices No (-1) Yes (+1) Yes (+1)
Security depends on whom? You (+1) Corporation (-1) You + web host + software developer (-1)
Is your work available when the internet goes down? Yes (+1) No (-1) No (-1)

If you aren’t scared off by MySQL databases or PHP, the “level of technical expertise” row might be scored differently, or if you doubt your own ability to keep your files secure, you might think that your work’s security depending on Google is a good thing. Haggling over the pros and cons aside, it’s a kind of an interesting result of this exercise that unless you’re really scared of losing work, or unless multi-user collaboration is very important to you, you might be better off avoiding cloud services entirely.

Another interesting result: if it comes down to a choice between a corporate cloud service and a “personal” cloud service, it looks like the “personal” cloud is the way to go—it beats the corporate cloud on every category except price and ease of installation. (And also possibly security.)

Edit (2013 Apr 6): I have added a row for “accessing content across multiple devices.” (Thanks Morty!)

Edit (2013 June 15): In light of recent revelations regarding the NSA’s surveillance, I have added them to the row for “Who has access to your files?”


    title = {Conventional computing vs the corporate cloud vs the “personal” cloud},
    journaltitle = {The Grey Literature},
    author = {Benjamin Gregory Carlisle},
    address = {Montreal, Canada},
    date = 2013-04-5,
    url = {}


Carlisle, Benjamin Gregory. "Conventional computing vs the corporate cloud vs the “personal” cloud" Web blog post. The Grey Literature. 05 Apr 2013. Web. 23 Jun 2018. <>


Carlisle, Benjamin Gregory. (2013, Apr 05). Conventional computing vs the corporate cloud vs the “personal” cloud [Web log post]. Retrieved from

The Kübler-Ross stages of grief and an open-source solution to the death of Google Reader


Over the past week, I was actually in the middle of writing a blog post about how I sometimes toy with the idea of switching to Ubuntu, just so that my technological life is not entirely beholden to any particular company’s corporate whims. I didn’t quite finish that post before Google very famously killed off its well-loved news aggregator, Google Reader. Most users of Google Reader are going through the classic Kübler-Ross stages of grief:

  1. We all experienced the initial shock and denial. (“What? There is no way they’re shutting Google Reader down.”)
  2. Anger followed.
  3. Then the bargaining.
  4. Next people will get sad about it. They probably won’t blog sad things about Google Reader, though, out of fear of looking pathetic.
  5. As far as acceptance goes, lots of people are now trying to profit from this, by selling their own alternatives to Google Reader. Digg has decided to make building a new aggregator a priority. Users are largely scrambling to find another reader.

My solution to the Google Reader problem

I used to use Newsfire before I switched to Google Reader, but in the time that has elapsed since then, they started charging $5 for it. That’s not a lot, but then I was getting Google Reader for free, so I kept looking. Besides, Newsfire is a newsreader that’s all stored locally on my computer, and my ideal solution would be cloud-based.

I looked around at the currently-available web offerings, and I couldn’t find any that were very appealing. I nearly despaired myself, when I found an open-source web-based solution.

This won’t work for everyone, but it will work for anyone who already has access to a web server with the following capabilities:

  • Apache
  • MySQL
  • PHP
  • Cron jobs

I installed a copy of the open-source RSS reader, selfoss on my web server, and I have been using it instead of Google Reader. I’m pretty happy with it. I’ve had to make a few changes already, but it seems like a good solution to the problem. Here are the advantages, as I see it:

  • Web-based, so it will work on all my devices
  • It’s hosted on my own server, so it will work as long as I keep paying my hosting bill
  • The software won’t be “updated” (read: altered arbitrarily) unless I want it to be
  • No one will decide later that there needs to be ads on my news reader

Good luck in finding a solution to your Google Reader problem!


    title = {The Kübler-Ross stages of grief and an open-source solution to the death of Google Reader},
    journaltitle = {The Grey Literature},
    author = {Benjamin Gregory Carlisle},
    address = {Montreal, Canada},
    date = 2013-03-14,
    url = {}


Carlisle, Benjamin Gregory. "The Kübler-Ross stages of grief and an open-source solution to the death of Google Reader" Web blog post. The Grey Literature. 14 Mar 2013. Web. 23 Jun 2018. <>


Carlisle, Benjamin Gregory. (2013, Mar 14). The Kübler-Ross stages of grief and an open-source solution to the death of Google Reader [Web log post]. Retrieved from

Montréal Métro iPhone app


Logo for Montréal Métro Exits

Logo for Montréal Métro Exits

On and off for the last little bit, I’ve been working on a little bit of a side-project: Something for when I don’t want to think about research ethics anymore. I was inspired to do this by something I heard on CBC a while back. A guy in London, UK made an iPhone app that would tell you which car to exit so that you would be closest to the exit on the subway.

I thought that this was a great idea. I would certainly use an application like that! Turns out someone already did it for Montréal, but they did a crappy job of it. The data set is incomplete, and the interface leaves much to be desired. Also, this other app tells you nothing about which car to board in order to transfer. In fact, the other app told you only which métro car to exit in order to be near the exit, not which métro car to enter, which seemed to undermine the point of the app. You need to know which car to board before you get on the train. (You can’t just infer one from the other, though, since in some cases the train approaches from the right side of the platform and in some cases it approaches from the left.)

I decided to write an app that would be really simple from the user’s perspective—just choose two stations, and the app tells you which car to get into at your departure station, and then which car to get into at your transfer station(s) (if applicable). I thought it would be a good exercise, just as practice for some other ideas for iPhone apps that I’ve had.

So, a couple weeks ago, I donned my lab coat, grabbed a clip board and went to every métro station in Montréal and wrote down where all the exits were. I also collected information regarding transfers. Writing the app wasn’t so hard, although submitting it to the iTunes store was a bit of a headache. That said, it was approved on my first try, and it took less than a week. (Thanks, Apple!)

It was getting Apple to process my tax forms that was the longest part of the development process.

The app was approved on Friday the 18th, and Apple processed my Canadian tax info last Tuesday. I had to fill out some US tax forms (just indicating that I wasn’t a US citizen) and then today they finally started selling my app on the iTunes store.

Tell your friends! Seriously. Every month I get roughly 300 visits to my blog from people in the Montréal area. If I could get a few of you guys to post this to your Facebook, I’d be raking it in. :)

Now that I’ve sort of figured out how to write and submit an app for the iPhone, I’ve got my sights set on bigger cities where this sort of app hasn’t been written before. (Yes, there are still some. Not many!) Also, I have a few ideas for other, better iPhone apps that I think could be a lot of fun. I’m not about to start posting my ideas on the internet though: That’s a great way to have someone else make my app before I do. :P


    title = {Montréal Métro iPhone app},
    journaltitle = {The Grey Literature},
    author = {Benjamin Gregory Carlisle},
    address = {Montreal, Canada},
    date = 2011-03-31,
    url = {}


Carlisle, Benjamin Gregory. "Montréal Métro iPhone app" Web blog post. The Grey Literature. 31 Mar 2011. Web. 23 Jun 2018. <>


Carlisle, Benjamin Gregory. (2011, Mar 31). Montréal Métro iPhone app [Web log post]. Retrieved from

Comment spam in WordPress


Something that shocked me when I first started blogging was the existence of “comment spam.” I had no idea that spam existed outside the world of emails. But then, every day there’s roughly 50 comments for my blog that aren’t real comments from real people.

They have different levels of sophistication, too. The simplest ones are just extensive lists of URLs for places to buy drugs online. Those are easy to pick out.

However, the majority of them look, at first glance, like an actual comment. They don’t have any links in the body of the comment, and many of them just have (usually) flattering but unspecific comment.

For example:

Essentially, the article is actual the sweetest on this noteworthy issue. I consent with your consequences and will eagerly look forward to your next updates. With your authorization allow me to grab your feed to be up to speed with future articles. Thank you a million and please keep up the fabulous activity.

This is an actual comment spam that is pretty typical of a lot of spams that I receive. And of course, there would be a link to some site that they would put in the “website” field, so that they can get some links from my blog to theirs. (Being linked to gives one a higher spot in Google search results, and of course just makes it more likely that someone will click the link in error, which is why there’s so much spam of this type.)

Then, there are also comment spams that are just weird or ungrammatical:

I not to mention my guys were found to be looking at the good hints located on your web blog and so immediately got a horrible feeling I had not expressed respect to the web site owner for those secrets. My young boys appeared to be totally stimulated to see all of them and now have certainly been using these things. Thanks for truly being really thoughtful and for making a decision on this kind of important guides millions of individuals are really desirous to understand about. My honest apologies for not saying thanks to you sooner.

My temptation is to remove the back-links, but keep the vague and flattering comments and respond to them all as if I actually believed that these spammers found my website helpful in such a nonspecific way.

Here’s an interesting and somewhat related question:

Recently, I went to my (actual, physical) mailbox in my apartment, and found an unsolicited print advertisement had been delivered there. I took it out, and remarked to my friend that I had only received spam. At that point, we both wondered whether something can be spam if it is in print, or if that appellation is suited only for emails? Can I get spam by post?


    title = {Comment spam in WordPress},
    journaltitle = {The Grey Literature},
    author = {Benjamin Gregory Carlisle},
    address = {Montreal, Canada},
    date = 2011-02-22,
    url = {}


Carlisle, Benjamin Gregory. "Comment spam in WordPress" Web blog post. The Grey Literature. 22 Feb 2011. Web. 23 Jun 2018. <>


Carlisle, Benjamin Gregory. (2011, Feb 22). Comment spam in WordPress [Web log post]. Retrieved from


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