Friday, 30 August 2013

what do these have in common?

Searching for “systematic data collection” on Amazon yields:


Wednesday, 28 August 2013

the nights are pulling in

Yet it seems like only yesterday that sunset was around 9:30pm

sunset, 7:45pm

Monday, 26 August 2013


I’ve read and enjoyed some of Joel Spolsky’s Joel on Software posts, in dead tree format.  So the other day, I was link surfing, followed a link to his site, and ended up reading How Trello is Different, a mere 18 months after it was originally posted.

I was taken with the sentence: “The great horizontal killer applications are actually just fancy data structures.” Trello is a “team coordination system” that is a fancy data structure comprising a “list of lists”. (Actually, it is a list of lists (boards) of lists of lists (cards) of lists of lists (checklists); or tree, as we say in the trade.)

The point is that any killer app can be used for multiple different purposes, mostly not thought of by the original developer: Excel, for example, isn't just a calculator, it’s used for almost anything that needs tables.

So Trello is good for any task that needs lists of lists – including to do lists. I hadn’t consciously been looking for a to do list manager, as I was happily using Toodledo. Toodledo is great for to do lists, but I was finding that maybe I wanted something with a little more structure: not just a single to do list, but ... a list of lists! The pro version of Toodledo has more capabilities, but that requires a subscription. So, finding Trello felt like serendipity, and I decided to give it a try (it’s free, and web-based, like so many things nowadays; there is a pro version, but it looks well beyond my needs).

And it’s really great. I now have (a list of) seven boards, the major list category: think project, or similar large slice of life. I have one for teaching in general, one for a specific module I’m teaching, one for research, one for tracking my research students, one for travel and events, one for miscellaneous to do items, and one for template lists.

Each board has several lists: categories of tasks or items in that board. So my specific module teaching board has a list for lectures, for practicals, for seminars, for the web site, and for the assessment.

These lists are just called lists. They are lists of cards. Each card is a task or other specific unit of work. So my practicals list has a card for the preparation I need to do for each individual practical, and a further card for things I need to do for all the practicals. Lists, and cards within lists, can be dragged around to reorder things how you want.

It doesn’t stop there. There’s loads of data that can be associated with a card. Flip the card over, and there’s a free text field, a due date, coloured tags, a list of activities (things that have happened with the card), a list of checklists, and more. Each checklist is itself a list of check items. And that’s as far down as the lists go, I think.

For the group working part, multiple people can be members of a board, can be assigned different cards, and so on.

I’ve been using Trello for a few weeks now, and it fits in very smoothly to my workflow. There’s an “all cards” view that you can use to show cards with a due date, in date order, so I can easily see what’s urgent.

I liked it enough to want to use it permanently. But there was one issue: backup. The data is stored on the Trello server. If I lost my to do list, I would be in deep trouble. I went to the help page, searched on “backup”, and found:
To export your data, simply open a card or open the sidebar Menu, then click the ‘Share, Print, and Export’ button, and you’ll find export options. Currently, we allow export to JSON, which is a format that lends itself well to Trello’s specific data storage model.
Yes, but if Trello disppears, how will that help me? (I have no reason to believe Trello will disappear. But, I'm paranoid about backups.) I clicked the export button, and was delivered a .json file. I decided to see how easy it would be to extract my to do life from the file. I wrote a little Python and CSS, and converted the relevant bits of the file to HTML:

The CSS just formats to HTML to look like the original Trello board. It looks a bit different, because I added the info from the back of the card to the front in this backup display.

So that’s okay, then. I can recover the data, provided I remember to backup the boards. But that’s a bit boring, having to backup seven boards individually. Boring backups are no good: they tend to get skipped. So I went back to the site to see if there was a command to backup all the boards in one go. No, but there is an API; I’d seen that originally, but forgotten about it.

The API lets you get and set your data remotely. So I modified my Python script to read from URLs rather than JSON files, and voila, backup of the entire set of boards with a single click.

So now I’m happy, and will go over to Trello. And I’m not even scratching its surface yet: I haven’t made any use of the multi-person aspects so far. I may think about doing that on a new project that’s about to start up.

Friday, 23 August 2013

Thursday, 22 August 2013

Lockhart's Lament

I can't remember the route by which I arrived at this. But it's glorious. Not so much a "Lament" as a scream of anguish. To all who enjoy mathematics, despite their schools.
So we’re supposed to just set off on some free-form mathematical excursion, and the students will learn whatever they happen to learn?
Precisely. Problems will lead to other problems, technique will be developed as it becomes necessary, and new topics will arise naturally. And if some issue never happens to come up in thirteen years of schooling, how interesting or important could it be?
A bit of background here.

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Monday, 19 August 2013

The Ballad of Russell and Julie

This is even better if you are of a certain age, and remember the Victoria Wood original.

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Academia risks research future

What are we doing to ensure that the software supporting our research projects is up to scratch?

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Sunday, 18 August 2013

suddenly, apples! thousands of them!

The earlier predicted apple glut is well on its way, having been helped by sunshine and rain:

the young apple tree: crunchy Coxes

the old apple tree: tasty cookers


goldfish brain

For the last eleven years and more, I’ve been driving between home near Cambridge, and work in York, nearly every week. I know the 350 mile round trip rather well by now. Despite this, I’ve taken to having the SatNav on during the journey. That’s because there can often be delays due to accidents, or road closures due to roadworks, and a little advance warning can let me choose a route more useful than the suggested diversion.

Last week, the inevitable happened. I was tootling up the A1 to York, when the SatNav advised me: “Road closed at J36 due to roadworks. Calculate alternative route?” Yes.

Whirr, whirr, whirr. “Confirm new route?” The map is very small, but I could see this new route at least approximated the M18 diversion I had already intended to take. So, yes, let’s take that one.

Pause. “Road closed at <somewhere I’d never heard of> due to roadworks. Calculate alternative route?” Okay, that’s a nuisance, so yes, calculate new route.

Whirr, whirr, whirr. “Confirm new route?” The map is very small, but I could see this new route looked close to the original A1 route.  But, hey.  Yes, confirm new route.

Pause. “Road closed at J36 due to roadworks. Calculate alternative route?”  Aargh! it had put me back on the original closed route.  I could guess what would happen next, but I tried it anyhow.  Yes, calculate alternative route.

Whirr, whirr, whirr. “Confirm new route?” Back on the M18 diversion. Yes, confirm. Pause. “Road closed at <somewhere I’d never heard of until a few minutes ago> due to roadworks. Calculate alternative route?”

Clearly the system has a diversion buffer of size one.  I decided to take the M18 diversion. Once I was on that bit of road, the system the quite happily found me a diversion around the diversion.

(left) intended route, but the A1 was closed around Doncaster; (mid) SatNav suggested alternative, but then found to be closed somewhere south of Selby; (right) final SatNav suggested route, once commited to the M18 east of Doncaster

very #FirstWorldProblems

Saturday, 17 August 2013

Beethoven and Theramins

Beethoven's Ode to Joy, played on 167 theremins housed inside matryoshka dolls.  Yes, really.

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Monday, 12 August 2013

Elite next gen

Amazing!  I remember when Elite was state of the art.

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Saturday, 10 August 2013

39 explosions for the price of one

I used to think Gerry Anderson's multiple explosion shots in Thunderbirds, etc, were implausible.  Not any more!

(via BoingBoing)

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Friday, 9 August 2013

science v scientism

I thought this blog post about science versus humanities was interesting. Sometimes I forget how not everyone is into interdisciplinarity!
Scientism is the idea that only science is the proper mode of human thought, and in particular, a blinkered, narrow notion that every human advance is the product of scientific, rational, empirical thinking. Much as I love science, and am personally a committed practitioner who also has a hard time shaking myself out of this path (I find scientific thinking very natural), I’ve got enough breadth in my education and current experience to recognize that there are other ways of progressing. Notice that I don’t use the phrase “ways of knowing” here — I have a rigorous enough expectation of what knowledge represents to reject other claims of knowledge outside of the empirical collection of information.

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Wednesday, 7 August 2013

gigantic mix-up

For all you inveterate Amazon customers -- beware of clicking the wrong button!

SEATTLE (The Borowitz Report)—Jeff Bezos, the founder of, told reporters today that his reported purchase of the Washington Post was a “gigantic mix-up,” explaining that he had clicked on the newspaper by mistake. 
“I guess I was just kind of browsing through their website and not paying close attention to what I was doing,” he said. “No way did I intend to buy anything.”

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Sunday, 4 August 2013

clearly typecast

Peter Capaldi as John Frobisher
Peter Capaldi has just been announced as the twelfth Doctor.  Given he played Caecilius in the 2008 episode The Fires of Pompeii, and John Frobisher in Torchwood season 3, he's clearly no stranger to the Who universe.

His IMDB entry shows a less obvious connection:

But to me he will always be The Angel Islington.

a new piling system

I write academic papers, and read a lot of other papers. What with hard copy scattered through filing cabinets, and soft copies on a wide variety of websites, it can be hard to keep track of what I’ve read, made notes on, made BiBTeX citation data, and referenced.

Nearly two years ago I had a go at using Mendeley, designed to help with this very task. But for some reason, it never gelled for me, and I gave up using it. Then, when I became an Evernote convert, I fiddled about with using it to store data on the papers: author, title, etc, notes, BibTeX, and links to the papers themselves. But it was clunky work-flow, requiring a lot of hand-effort. Only the note keeping part of it worked well.

Then a colleague raved about Paperpile on his G+ stream. I had a look. It has a similar concept to Mendeley and other such systems, keeping references, supporting tags, good searching, associated notes, and citation output in multiple formats (although I only care about BibTeX). Instead of being a stand-alone application, however, it’s Chrome-based, and uses your Google Drive as a repository to store your papers. It’s currently in Beta, and I thought I’d give it a try. I emailed off for an account, and about a week later I got one.

The first thing I did was import my dusty Mendeley data (with a single button click and a log on), so I started off with a well-populated, if slightly out-of-date, database. I decided to trial it on the paper I had just started writing.

I defined a tag for the new paper. As I was writing, each time I included a reference in the text, I checked if that reference was already in my Paperpile database; if not, I added it. (Since there is usually a fair amount of overlap between bibliographies of papers in a similar domain, this should get faster as the db gets more populated.) Then I tagged it with the paper’s tag, and any other relevant tags.

My current Paperpile db, with 321 entries

To generate the BibTeX, all I needed to do was select the tag, which selected all the references, and then export the whole BibTeX file in one go.

The real benefit showed up when I got comments back on a draft of the paper. One was about a short quotation I had included, and I needed to find the quotation in its original context in order to address the comment. Click the Paperpile tab in Chrome. Type the author’s name into the search box; the paper’s details appear. Click the “view PDF” button. Voila! The paper is on my screen! I can’t think of a faster way to achieve that, without using telepathy.

You can upload in various ways, including PubMed, arXiv, doi, navigating to a website, or just giving it a PDF.  When you upload a PDF directly, the system searches the web to find the right data to populated the various fields. It gets this mostly right, but there have been a couple of odd peculiarities. Still, the system is in Beta. I reported the couple of weird results, and got very fast and helpful responses from the team. (I like Beta testing. I can whinge about software, and feel virtuous about doing so!)

One thing I particularly like is that the uploaded PDFs are stored in my Google Drive in a very sensible way. The files have obvious names: <Author> <Year> - <Title>.pdf. So if Paperpile were to disappear for any reason, I still have all my PDFs in a very usable form. (I’m not expecting it to disappear; I’m just paranoid: I have my Google Drive synched to my hard drive at home, in case Google disappears!)

I haven’t used all the facilities, in particular, I haven’t exploited the Google Docs integration. The Paperpile team report that some people are using it to write their papers collaboratively in Google Docs. That looks potentially useful, but I don’t use this plain format: I write my papers in LaTeX/BibTeX, using TeXnicCenter.

One part of the system I probably won’t use that much is the notes field. It’s perfectly fine, but I like to keep more substantial notes, with formatting, sketches, figures, and the like. So I’ll continue using my Evernote “papers” notebook, but now just for the notes, not the entire paper and other detials. For a paper with notes, I add a link from the Paperile entry to the relevant Evernote note, using the URL field which gives a clickable link (and I add an Evernote tag, to make it clear to me that there is a note). Similarly, I have a lot of already existing book reviews on my website. So when I include a book that I own, I add a link to the review on my site.

In fact, I think that having a variety of tools that each does their own thing well, with links between the relevant parts, works better than trying to shoehorn all capability into every application. So in Evernote, for example, for a meeting note, I don’t copy the agenda from the email notification, I just store a link to it. Evernote Webclipper allows you to clip the whole email into Evernote, but that just seems to cause unnecessary duplication. It’s good practice to keep only one copy of data (except for backups, of course!), otherwise there is the potential for copies to get out of synch. When that agenda is inevitably later updated, and a new copy emailed out, I don’t have to do anything: provided it is sent out with the same subject line, the Gmail link pulls up the entire conversation, and I can select the most recent agenda. (One day, the agenda setters may start using Google Docs, and so everyone will always have the most up to date version – provided they haven't clipped it into Evernote!) With all these web-based tools, the URL can link everything together.

In summary: first impressions of Paperpile are very favourable. I’ve successfully and productively used it for writing a paper, and it being web/Google based means it’s available at work, at home, and elsewhere, without me having to do anything special. I’ll report on progress if and when it gets more deeply integrated into my web-life.

Thursday, 1 August 2013