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my dusty Mendeley data (with a single button click and a log on), so I started off with a well-populated, if slightly out-of-date, database.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.

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Unconventional Milan

I'm back from the conference on Unconventional Computation and Natural Computation (UCNC) in Milan. Excellent conference, with lots of great presentations, conversations, and food.

My Evernote experience was a success.  I managed to take the notes I wanted, using my Netbook.  Fortunately, the venue being a university, the rooms had suitable benching for resting the Netbook on -- no more bruises where the computer's little feet dig into my legs.  And there were enough power sockets around that I could recharge as necessary.

When there was a particularly useful or interesting figure on a slide, I took a photo of it, and added "[photo]" to my notes at that point.  Then, when I got home, I downloaded the photos, straightened them up, cropped them, adjusted the contrast, and pasted them into Evernote in the right places.  That worked even better than scribbling down a diagram.  But it did mean that I had to remember to sit near the front.

So now I have enough trials to be convinced Evernote is the right approach, for SF conventions, for seminars, and for conferences.  Legible, searchable notes are a boon.

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Unconventional Computation with Evernote

Today I'm off to the conference on Unconventional Computation and Natural Computation (UCNC) in Milan.  I'm running the CoSMoS (Complex Systems Modelling and Simulation) workshop there on the Monday, including giving a talk.  Then it's several days of listening to lots of interesting talks from the "here be dragons" end of computing.  On the Friday, one of my students is giving a couple of talks on his work.

This is the first conference I've been to where I'll be taking notes in Evernote on my Netbook, rather than with a pen in a lab book.  Last year, UCNC was in September, and I didn't start using Evernote until October.  I did use Evernote at the science fiction convention at Easter, where it worked really well, but this is the acid test: using it for the day job!  Like at the con, I've set up a bunch of template notes, one for each session, ready to start taking notes.

I hope there is somewhere to rest the Samsung Netbook so its sharp little feet don't bruise my knees like they did at the con!

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Ctrl-Shift-T

We've gone over to using Google products at work.  For the most part, I like Google Mail.  It has its quirks, but the selling point for me is that, being browser based, mail items have URLs, so I can just paste the relevant URL into my to-do list or Evernote daybook, rather than clutter up my inbox with emails I'm waiting to action or need for meetings.

However, Gmail has a user interface feature I just keep getting wrong.  I consistently click the "Compose" button to move to my contacts, instead of clicking the "Mail" menu, and selecting from there.

I keep clicking "Compose", instead of selecting "Contacts".  Why?

I don't know why I keep doing this (maybe because the first two letters are the same?), but I do.  All the time.  I don't blame myself: I have been well-enough educated in user interface design to believe that if the user consistently makes a mistake like this, the UI is to blame.

This particular mistake is not that serious: I just have to keep binning unwanted empty emails (and muttering imprecations at the interface).  But there's another mistake I keep making, this time with the Chrome browser: I often hit "close tab" instead of "back" when I finish reading a linked page.  And then I've lost that tab's history, in particular, the page I was trying to return to when I closed the tab.

But then the other day, I discovered that all is not lost!  Hit Ctrl-Shift-T, and the tab is automagically resurrected.  Hit it again, and the previously closed tab reappears. And so on. Yes!  A key combination to undo a user interface infelicity.

So why isn't this option in the menu?

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Evernote and the Con

Every year we attend the British National Science Fiction Convention, or “Eastercon”. My first Eastercon was in 1984, and we haven’t missed one since 1996. It’s a great four days, of guest of honor talks, of serious scientific talks, of panels discussing authors and sub-genres, of silly SF-themed quizzes, and of meeting up with friends.

I take notes at cons, partly as a conditioned reflex, and partly because there are interesting ideas, and suggestions of new authors of books, that I want to follow up later. I have put some of my notes up on my website. But the last couple of years, I haven’t had the time (or the inclination) to transcribe the resulting 30–50 pages of notes, so they are languishing on paper only.

Recently at work, I’ve moved from paper to a computer-based daybook, based on Evernote. It started as an experiment, to see if it would work, but within a month I had abandoned paper note taking completely, and am exclusively Evernote-based. So I decided to trial Evernote at this year’s Eastercon, too. Here’s how it went.

Before the con

Gone are the days of waiting to get the Con programme guide on arrival at the con hotel. Nowadays it is up online in advance. So the day before we were due to drive to Bradford (these cons are in such exotic locations) I sat down with the online programme guide, and decided which items I would attend, from the four parallel sessions. First I created a new Evernote notebook for SF cons. Then I made a new note for each chosen item, adjusted its “creation time” to that of the item itself, and copied in the item title, location, and abstract. This had the helpful side-effect of giving me a schedule I could easily consult on my phone when I wanted to know where I was supposed to be next, and a reminder of what it was about.

At the con

I used the same Samsung N145 Plus Netbook for note-taking that I use at work. This has a 10" screen, and a nice keyboard that accommodates my just-about-4-fingered, semi-touch typing skills (although the Caps Lock is a bit too easy to hit accidentally).

ouch!

It weights in at 1.2 kg, which is fine for toting around between talks, but after a couple of days of it resting on my lap as I took notes, I became uncomfortably aware of its two sharp little feet at the back. It also runs quite hot. However, the battery is nicely long lasting: the Friday and Monday were less than full days, and I got by with a single charge; the Saturday and Sunday, being longer, required a recharge. One day that involved leaving it charging in the hotel room over dinner; the other day I found an unoccupied power socket in the programme room, and sat by it for that item.

It was all very straightforward to use: arrive at the item, sit down, open netbook, type in my password, click on the item’s note, and start typing. The keyboard is quiet, and so (hopefully!) the sound didn’t disturb anyone around me. And this set-up has one great advantage over manual note-taking. In the main programme hall, tech switches the lights off during items (I assume this is to aid with recording said items). This makes it rather difficult to take hand-written notes. But with the netbook, I just closed it up slightly (to around a 90 degree angle), which directed enough light from the screen to illuminate the keyboard sufficiently. Another advantage: no writer’s cramp. A further advantage: the notes synchronise to the cloud, so I didn’t have to make backups during the con.

After the con

Back home, I synched Evernote on my desktop machine, and started tidying up the notes, correcting spelling mistakes, removing irrelevant and incomprehensible bits, and tracking down interesting references and linking to them. This took about half a day (partly because I was spending time reading up about some of the interesting stuff I’d found). Once I was happy with the notes, I made a new note to act as an contents list for the entire event, comprising a bullet list of links to each of the item notes. That was very easy to do using Evernote’s “Copy Note Link” function. I sorted the list into earliest first order (rather than the latest first order I usually use), selected all the notes, then exported them as a single HTML file. I edited that file with Notepad++ (my current HTML editor of choice) to add in some preliminary material, and modify some of the formatting provided by Evernote. Hey presto, my con report web page! Everything from “Programme highlights” onward is output from Evernote. All in well less than a day.

What I’ll do differently next time

This was definitely a great success. However, next time I will add a little more markup to my note templates, to tag the title, panellists, and summary parts. This will let me use Notepad++’s regular expression-based search and replace more easily to modify Evernote’s formatting to my specific requirements. And that’s it, essentially.

What I’d like Evernote to do differently

Evernote is great, and the more I use it, the more I like it. But it’s not perfect, and the more I use it, the more the imperfections bug me. The main niggles from the con use:

1. Undo. It doesn’t always work properly. Most of the time, it’s absolutely fine, doing what you’d expect. But every so often, it doesn’t restore to the exact previous state. A typical problem: paste in something with a format, realise you meant “Paste as plain text”, undo – but it doesn’t (always) reset to the previous format.
2. Bullet list indent,outdent commands. These don’t always work properly. Again. most of the time, everything is fine: use tab or the icon to indent, use Shift-tab or the icon to outdent. But if you copy a bullet list, this can get messed up, and on indenting/outdenting, the bullets disappear. This is a big deal for me, as I am an inveterate user of nested bullet lists.
3. Spelling mistakes. As you type, spelling mistakes are highlighted with the usual red wiggly line. However, when you move away from a note and come back, notes no longer highlight the spelling mistakes. This made the “tidying up” process harder. SF notes have a lot of weird words in them, and it’s easier to scan and ignore the red wiggles than step through the list using the manual spell-checker.
4. Daylight savings time. This one is bizarre, and very annoying. As is often the case, Daylight Savings Time (here the move from Greenwich Mean Time to British “Summer” Time) kicks in over the Easter weekend (hey, let’s steal an hour from your holiday weekend!) On Sunday morning, I noticed that all the “created” times on my Sun/Mon notes were out by an hour: Evernote had changed them! It had decided that, when I created a note during GMT, even though I created the note for a time when BST would be in force, it needed to update it. Mutter, mutter. Later, when looking back at my previous notes (all my previous notes), I discovered that their creation times had also changed by an hour! That is, Evernote is currently displaying the creation times of all my notes, no matter when created, in BST. I can think of no circumstance when this would be the desired behaviour. This is definitely a bug. I suspect Evernote is treating daylight savings time as a different time zone, and “correcting” for the change (which is often not what is wanted in that case, either).

However, despite these grumps, I’ll be continuing to use Evernote. The more I use it, the ever more useful it becomes, because the more material I have in it, have linked from it, and can access really easily.

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Evernote as a laboratory daybook

I started using Evernote three weeks ago.  I've been trialling it as my "daybook" at work, where I keep my notes of all meetings, projects, and any work-related items.  It's been very successful, so now I've switched over to it in entirety, and retired my hardbound logbooks.

One of my Evernote "notebooks" is my daybook.  For each day I keep a single note that's the "miscellaneous" stuff, plus a separate note for each scheduled event (lecture, practical, seminar, student supervision, project meeting, committee meeting, whatever).  I put a little thumbnail picture -- of the person, or something iconic for the meeting, in the note, which then shows up in the snippets window.  I've also made a set of "day" icons for the single "miscellaneous" note, that show the day, date, year, and week of term/vacation.  These thumbnails allow me to scan the snippets and usually find the correct note rapidly, without needing a search.

the end of last week

At the beginning of each day I add new notes for the meetings from my diary, and edit the "create time" to be the start time of the meeting.

I use templates for each of my semi-regular meetings.  When it's the day of the meeting, I copy the note from the template notebook, where it already has the right date and time.  When I know the time of the next occurrence (known in advance for regular meetings, sometimes agreed in the meeting, sometimes not agreed until after the meeting), I edit the template accordingly.  This means my template notebook also acts as a mini calendar of future appointments.  I found this useful within the first couple of weeks. I had forgotten to set the time of my next meeting with a student; still with the date of our previous meeting, their template was noticeably languishing at the bottom of the list, reminding me to do something about it.

At the beginning of a meeting, I select the relevant note, and can start typing straight away.  Also, I can "search" for the name of the meeting, and then the snippet window shows just these.  So I can quickly go back to an earlier meeting (eg, to look up what we agreed to do for this meeting).

Each meeting note has three sections:

• pre-meeting notes: preparation for to the meeting (for a committee meeting this might be reports on any actions I've discharged; for a seminar it will be the speaker's abstract, etc; I also add links to relevant documents)
• meeting notes: I have a 7" Netbook with a useable keyboard -- I've found I can type notes fast enough if it's on a table, or perched on my lap (although this is a bit uncomfortable on some chairs)
• post-meeting notes: for example, any clarifications or further information I've looked up after a talk -- I find it useful to clip a few sentences from a relevant website to help illuminate some point a speaker has made

Rather than keep big pdfs in Evernote, I keep them in my Dropbox, and just put a link in the note.  Also, I can link to specific gmail conversations, for example, the one containing the agenda and minutes of the meeting.  This is a great aid to going paperless.

I use Evernote on my netbook for taking meeting notes, and on my main machine for making notes while I'm working at my desk.  A couple of times I've closed the netbook, sat at my desk, and started updating the meeting note, only to discover I haven't given it time to synchronise.  I now manually synchronise before I close the netbook.  However, I haven't lost anything, since Evernote keeps both versions, and puts them in a "conflicting changes" notebook.

One issue I have is with the automatic choice of image to use as the thumbnail in the snippet view. It automatically chooses "the image with the largest smallest dimension" (btw, it took me essentially no time at all to find that link, as I'd clipped it into Evernote when I was looking for it originally).  That's almost always the wrong choice for me: I want a thumbnail icon, such as a small photo of the person involved, which nearly always has the smallest largest dimension.  Since I often take whiteboard photos to accompany technical meeting notes, I can end up with a bunch of identical-looking whiteboard thumbnails!  I would much prefer being able to override the default.

But apart from that v minor niggle (and the printing issue noted below), I'm finding this almost perfect as a daybook.

Caveat: if you need to keep a formal logbook, with date stamps and signatures, you will need to find a way to print out your notes -- which is easy for a single note, but non-trivial as a batch exercise.

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my magpie habits finally virtualised

I'm in love ... with Evernote.

I first heard of apps to organise clippings, etc, several years ago, from Steven Johnson talking about DEVONthink in one of his books.  It sounded great, as I kept a paper commonplace book, and had an overflowing scrapbook, and wanted something more systematic to keep all those notes and thoughts and cuttings.  However, DEVONthink is Mac-only, so I started keeping an eye open for something else.

During my intermittent reviews of applications over the next few years, I came across Evernote, which seemed to be another alternative that people really liked.  But it too was Mac-only.  So I kept looking, experimenting with the odd app now and then, but nothing really seemed what I wanted.

Last week, I was having yet another look around.  This time, I was after something to keep an electronic laboratory day book, as my Word document version is too clumsy.  There didn't seem to be anything specific, and I was wondering whether to use a new blog, but in my web trawl, I again came across Evernote.  I noticed that now there is a Windows version, and an Android smart phone version.  I looked closer.  It seemed ideal for a clippings container.  I decided to give it a try, as a commonplace book at least.

I downloaded it to my home machine last Saturday, and experimented with it for a while.  I installed the Web Clipper app into Chrome, and started surfing/clipping.  I downloaded it to my phone, and played around some more.  It's got great searching capabilities, and a nice interface.  I particularly like the way the bullet lists work -- tab to indent, and return to outdent again -- very natural for note taking (where I am an inveterate bulleter).

my desktop version: snippet list on the left, detailed notes on the right

On Sunday, once I had a feel for what it could do, I decided I would also experiment with using it as a lab book. I planned to use one note per meeting/seminar/lecture, plus a "day note" for all the other bits and bobs that need recording on a given day.

Back at work, I downloaded Evernote to my work desktop and my netbook.  There I used it all last week, taking electronic notes in meetings, and during seminars.  It was really smooth.  For example, for one meeting I made a note that contained: what I'd done in preparation for the meeting; my notes typed in during the meeting; what I did to discharge the actions after -- all in one place.

Then I found the excellent blog of Jamie Todd Rubin, Evernote's "Paperless Lifestyle" Ambassador.  This opened my eyes to many other ways of using Evernote -- not just as a commonplace book and a lab book, but for other notes, projects, and whatever, and for automating various parts of the process.  I now have seven notebooks on the go, and more in mind.  (Although I probably won't go completely paperless.  But I am thinking of getting a faster scanner.)

I am seriously considering upgrading to the premium version, to get more monthly upload allowance, and some other nice perks.

Now all I need is for someone to port Penulimate to Android -- so I can scribble diagrams as well as textual notes in meetings.

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