Author Archives: Alison

A perfect day in eastern paradise

Cross-posted from Kayak Yak.

ParcdelaRiviere_07Sept09_2_400v

Perfect days don’t just happen in the West Coast Paddling Paradise – sometimes they happen here in the east. Today’s forecast was for calm until the afternoon, then 10-15 knot SW winds, and a high of 25 C, and that is exactly what I got on today’s trip to Parc de la Rivière-des-Mille-Îles (actually my fourth). Despite a technical hitch involving my Opus (Metro) card and a missed train, I was at Cartier station in plenty of time to catch the 0829 #73 bus and discovered to my pleasure that the #73 was no longer on diversion prior to the Parc, the resurfacing on pont Marius Defresne (the right-most bridge on the map) having migrated south of the intersection with boulevard Ste-Rose . I alighted at the Parc gates, was just about first up to the counter to rent a kayak de mer, and paid attention to the paddle (feathered), the seat (snugly fitting with solid back support) and the footrests (adjusted to my height), all of which I’d neglected to check the last time I was out (last Monday). I let myself drift off the dock while I made sure I found the panorama settings on the Olympus waterproof – I’d decided that traveling with two point and shoot digitals and one film camera was maybe a little excessive. Then I headed north-east out of the entrance of the lagoon, around the tip of Île Gagnon on water that was so glassy the kayak just slip-slid along, every so often twitching with a fillup of river-current. The skin of the water was alive with tiny water-beetles, like tossed handfuls of blue-black seed-beads.

Mirrored clouds above the bridge of the autoroute de Laurentides, QuebecPausing frequently to take photographs, I moseyed up in the direction of the wetlands area I’d discovered in my first trip back in July. At the time I set out, the sun was filtered by a thin film of cirrostratus, with denser streaks of cirrocumulus; it looked like the weather was changing, but by the time I reached the wetlands, the cirrostratus had cleared and the sun was alternating bright sunshine with the shadow of small cumuli, and in the four and a half hours I was out, the clouds – small cumuli and cirus – gathered and dispersed several times, none of the clouds dense or substantial enough to more than dim the sunlight. The wind, as forecast, did not pick up until close to noon, at which point I was paddling south against the current on the west side of Île de Mai, the long island running north-south at the left of the map.

I’ve been out four times now, twice in July, once at the end of August, and today. The water-level has appreciably dropped, such that the flooded stand of silver maples I got to paddle through in July (nourishing the resident flies in the process) were quite dry and aloof to the water now, and the hairpin between Île des Jiufs (how I read it on the map) and Île aux Fraises (both north-west of Île Gagnon) was because I got all the way through and found the channel blocked by a ridge of toothy boulders and the branches and debris they had strained out. A large culvert beneath the peninsula that carries the autoroute des Laurentides (the second river-spanning bridge) was also impassible due to a snag. I had more scrapes and grounded out my paddle more often today; on the up-side, a summer’s growth had brought the weeds very close to the surface, though they were too thick with algae and mud for me to recognize more than ribbon-shape or branching brush-shape. And as I paddled down to the south of Île Lacroix (just east of the marshlands) on my return I was able to look down and see schools of tiddlers scattering at the vibrations of my passage.

I’d meant to go into the marshlands, as I did in July, but there was a great blue heron fishing in the shallows just beside the one barely navigable channel – I’d made it a little way up that channel on my last outing, but between the water level sinking and the summer’s growth of reeds and weed, it was only a little way. So I stood off and watched the heron prowl along the edge of the reeds. There is something catlike about them, with the stillness, the hunkering low, the pounce – and the little ruffled insouciant shiver as they collect themselves after a failed strike. There were ducks aplenty, mainly mallards, browsing in pairs and more often than not standing tails to heaven in the still waters. I caught sight of a single kingfisher, a flash of white against the trees, and later on saw two flying between islands, squabbling all the way – are they territorial birds?

After the wetlands, I wanted to circumnavigate Île de Mai, the recommended way this time. The second trip I made in July, I looped out on the west side of the island and nearly did not make it, hitting what I suspect was an underwater bar within sight of the end. It was also the day after severe thunderstorms, when the water was murky brown and running fast, and there were downed and split trees all along the channel. I came to a standstill, paddling full-force, and had given up and was drifting downstream when in a fit of cussedness I decided to try the other side, crossed over, and succeeded in paddling through the stall, though literally gaining an inch at a time at one point. I was consoled that a two-person canoe whom I passed on my downstream drift, wound up doing exactly the same. It wasn’t until I got back that I looked at the Parc guide and saw that the marked route went up the east side and came down the west. So this time I did it the easy way. No stalls, though some churning water off Île aux Moutons (the small island north east of Île de Mai, and definite current, then wind. A small culvert underneath that promontory was open this time, and I paddled against the wind and the current up to the open waters, where the powerboats were churning in circles. Those coming through the channel kept their speed down, with one exception, a white powerboat that came crashing past Île de Moutons as I was starting up the channel, steering between a pair of kayaks. The buzzed kayakers coped all right, but a couple of others in the vicinity were visibly uneasy being bounced around in the reflected waves.

Waterplants in bloom, Parc de la Rivière-des-Mille-ÎlesHaving made it to the tip of Île de Mai, I got to ride down with the wind and current, and when I hit the point I’d hung up before, I got a brisk kick from behind, much easier going north than south. I needed a pit-stop, so I turned back to Île Chabon, which was marked on the map as having latrines, and, since there was no helpful signposting, walked three quarters of the way round the island before finding the sign and the hutch in the wood (with toilet paper, too). On the sunny side of Île Chabon, the turtles were out once again, warming themselves on fallen logs and rocks; I still don’t know what kind they are, not having been allowed close enough. Then I headed down through the weed-clogged channel south of Île Lacroix, tiddler-spotting and being buzzed by dragonflies, large black and smaller bright blue. Ducked under the bridge to Île Locas, avoiding fishing-lines slung from the bridge, and under the long autoroute de Laurentides bridge. Decided that I was not going to make it back within the four hour mark and I might as well be hanged for a sheep, etc, so detoured across to try and navigate the channel between Île de Juifs and Île aux Fraises, and found it blocked, so I then doubled back around the western tip of Île Gagnon, under a bridge into the lagoon, and found it milling with boats as the holiday monday afternoon canoists and kayakers and peddle-boaters all turned out. Lingered in the Interpretation Centre until my (hourly) bus was due, puzzling out the descriptions of the river milieu in French and writing down names of plants to look up. Aside from the water-lilies, one of the water-weeds was flowering, small dense pink flowers on conical stalks, forming mats along the edges of the reeds, downstream from the islands, and even at shallow points in the middle of channels.

More photographs to follow in my Flickr collection. For now, I must acknowledge the imminence of Tuesday.

A few of my favourite tools: DokuWiki and MAMP

From the first time I met one, I took to wikis for information gathering like a bluebottle fly to an old fish-head, partly because of their non-linear nature, and partly, since they were web-based, I could style and lay them out to suit myself. With a wiki, I can start collection information at any point and with the most rudimentary framework, grow and restructure at will, design my own menus, and create multiple cross-links between entries. My present wiki engines of choice are DokuWiki and Tiddlywiki. DokuWiki was originally designed for documentation in small companies, which makes it ideal for my present challenge of keeping up with my learning on four different stats packages (R, SAS, STATA and WinBUGS). I keep programming notes, reusable code snippets, a personal Rosetta stone of command-equivalents, and lists of links and references in the form of a DokuWiki run on a MAMP server (see below) on my MacBook.

Familiarity breeds comfort, but DokuWiki’s advantages are that I have found it straightforward to install and configure (particularly now that the user access controls are provided through a web interface), it is FOSS and platform independent, the developer is actively maintaining it, there is an active user community, the mark-up syntax is easy to work with and readable in the raw, and it does not require a database but writes everything to flat-files and folders. The latter, for me, is a key point: at my scale of operations, flat-files are just fine, and they have the major advantage that they are program- and platform-independent. There’s no database to get corrupted (been there, done that). There’s no vendor lock-in. If I ever want to migrate, I probably won’t be alone and someone will have written a tool; even if they haven’t, flat-files, meet Perl; I know you know each other .

For comparisons of wiki software, see the relevant page on wikipedia and WikiMatrix. A sampling of reviews: From Open Source Magazine (Badger, 2007), and Linux.com (Popov, 2008). Implementations I’ve noticed around the web are DokuWiki’s own wiki and the Zotero documentation.

As for the platform, I’ve used the built-in OSX server in the past, but turning on the OSX server involved opening ports that I didn’t necessarily want open, even if I had been confident in my editing of .htaccess. So when I found out about WAMP, I went looking for a Mac version. MAMP, which is intended as a development server with Apache, PHP, MySQL, and Perl. Download and installation of MAMP were straightforward with the help of an on-line tutorial and instructions, and from there it was a matter of setting up and configuring DokuWiki according to the instructions, with a little help from the equivalent instructions for WordPress – blogging software is a possible alternative to a wiki for keeping notes, if they are more linear.

Mes noveaux vélos

Cross-posted from The Bicycle Diaries.

I promised the gang a report from Montréal on the subject of Bixi, the new public bicycle system, which I joined just in time for Anticipation, the 2009 World SF Convention, and here it is. No pictures – keep forgetting to go out and snap some bikes at their stands. But my effort may be redundant.

I signed up and paid my initial subscription on-line while still in Victoria – $28 for a month, which covers any number of 30 minute trips (as long as they’re at least 5 minutes apart) during the month. Any number, not one per day. When I arrived back from Victoria, helmet in holdall, my package was waiting, including a shiny red plastic key with an identifying number and embedded chip-that-tells-all, and a small foldout map indicating stations and coverage and bicycle routes. The only complaint I have about the latter is it doesn’t show the direction of these bicycle routes. I had to log in to the website to activate the key, and on Wednesday August 5, I was ready for my maiden voyage, down to the Convention Centre to help set up.

So, out to the stand nearest where I lived, put the key into the slot by the bicycle. Yes! Green light. Tug at bike. Nothing happens. Tug a little harder at bike. Nothing happens. Try another bike. Oops, red light. Back to original bike, insert key, get green light. Tug firmly, bike releases. Magnetized holder.

OK, I haz bike. It’s a solid, sit-up-and-beg design, dull silver finish, broad black plastic handlebars. Cradle with a bungee cord in front to function as a carrier. Helmet on, adjust seat, hop on, wobble into bike lane. Haven’t done this for a while. After a couple of blocks I discover initially a second and then a third gear, accessed by twisting a ring medial to the right handlebar. By then the wobble has evened out considerably, and I’m picking up speed in the bike lane heading down St Urbain, dodging the cracks, the manhole covers and the potholes.

That first run was straight down St Urbain to the Convention Centre, the only hazard some construction that narrowed the street down uncomfortably. I missed having a handlebar mirror – my neck ain’t made of rubber no more. It took 13 minutes, according to my trip record on Bixi Space. There was a stand with vacant spaces just outside the Convention Centre, so I cruised to a stop, lifted the bike into place, pushed, green light went on, all done.

Getting home proved to be more of a challenge, since by the time I left the Convention Centre, my straight route through the centre was blocked off due to a street festival. I worked my way east and west and eventually found myself going up Saint-Laurent with all the diverted night traffic, jousting with a bus and dodging parallel-parkers. Trip home, 29 minutes, one shy of the 30 minute free limit. Based on that experience, the next home trip I did, I caught the metro past the centre of town, and then picked up a bike.

The longest trip I’ve done so far was a 33 minute run to the limits of the service at Jean-Talon. For that I will have incurred a $1.50 fare. That was the first bike I reported as having problems, having discovered after I started out that not only was one of the brake levers broken in half, but the gears were slipping – I suspect a previous rider had tried to force 10 gears out of 3. Every time I hit a bump, it would spontaneously drop a gear. Mind you, that was to be preferred to the Millennium Sparrow’s (my 1980 Nishiki, aka the Spuggie) trick of gearing up in cold weather, particularly on hills. Reporting in consisted simply of pushing a button on the station. The only other problem I’ve encountered is a bike that refused to check in at the first 2 stands I tried, but I requested an extension on my time, went round the block and it checked in fine. It would be an advantage to have a cellphone for such occasions, and it would be best to make allowances in timing for not getting the bike into the first station.

The one-way deal is wonderful. It frees me up to, for instance, bike in daylight and take the Metro back late at night (the bike is, however, equipped with reflectors and a flashing head-light), or bike to the market with empty bags and take the Metro back with 5 lbs of tomatoes and 3 lbs each of apples and pears (I go a little crazy in the market). I get the impression the bikes are well used: I see quite a number of them during commuting hours along the main cycling thoroughfares, pedalled by people in business suits, and I see them by ones and twos in the side streets off hours, pedalled by tourists. The same rack, completely full in the morning, will be completely empty in the early evening. There are iPhone apps for tracking availability.

Bixi announced recently that it will be moving into London and to Boston, and I see they are doing a trial run in Ottawa-Gatineau. Hmm, I wonder if my key would work …?

A few of my favourite tools: Zotero

Zotero, developed under the aegis of George Mason University’s Center for History and New Media (CHNM), is a Firefox plug-in for reference management. It offers an emerging cross-platform FOSS alternative to the mature and widely-used proprietary bibliographic software Endnote and Reference Manager. Zotero has been reviewed in the Journal of the Medical Library Association (Thomas E. Vanhecke, 2008), Inside Higher Ed (Scott McLemee, 2007), and the New York Times (Olivia Judson, 2008) – and many others (Google search).

The screenshot on the left shows the layout of the Zotero interface, which can be toggled on and off from a button on the lower right hand corner of the browser window. By default, it expands to fill half the browser screen, although it can be expanded to fill the full screen. The left pane contains the list of collections (folders and subfolders) within the library, and the tag filter search box. The middle pane contains the contents of the selected library, listed by creator, title, and journal abbreviation. The right hand panel contains the bibliographic information and notes for a single, selected entry. Control buttons and search-box are across the top of the Zotero pane. Very important: the icon to add bibliographic entries is in the address bar, at the top of the browser window. From an interface point of view, I’d quite like more user-control over positioning and panel layout. It’s not the ideal setup for a small widescreen computer, unusuable for any length of time on the 7” eeePC (taking things to an admitted extreme), and cramped on a 12-13” laptop – although I admit I probably wouldn’t have noticed before getting spoiled by 19-20” screens. But the ability to reshuffle and close windows would be a luxury.

Zotero maintains a SQLite database of citation information that can be scraped from a large number of database and journal sites.To date, I have mainly used it to collect results from literature and web searches; both single articles and indexed lists (eg, the results of Google Scholar searches) can be added via a single click of a small icon in the address bar. The filters for core sites such as PubMed, Highwire Press, PubMed Central, Google Scholar, WorldCat and JSTOR have all performed well in my hands, as have those for journals such as NEJM, Blood, Lancet and a number of others, with the caveat that in such a complex ecosystem, things will get updated, and do get broken – but tend to be fixed promptly.

Web pages can be collected as links or saved as screenshots, though I’m so familiar with print to PDF on a Mac that if I want to keep an article that only exist as a web-page I tend to print it to a PDF and then bring it into Zotero. PDFs can be imported in a number of ways, including dragging and dropping from the desktop into the window, and automatically, if linked without access restriction from a cited article. A recent update has given Zotero the ability to retrieve PDF metadata from Google Scholar, and complete indexing is possible using free third-party plugins. I tend to import abstracts from PubMed first, to be able to bring in the MeSH headings as tags – saves much tagging and ensures a consistent vocabulary for search. I can add additional tags if need be. Then if there is a free PDF of the article available, I re-import from the publisher’s site, drag the PDF from that entry to the entry from PubMed, and delete the duplicate.

The addition of PDFs carries the caveat that the database can grow very quickly. I’ve not done a thesis or book-sized project in it yet, but I have done article-sized projects, not to mention adding to ever-growing accumulations of materials of interest. Within libraries, materials can be tagged and files in folders and subfolders. It is possible to keep multiple databases, ie, one per project or subject, accessing them through preferences. At present, only one database can be accessed at a time, and Firefox must be relaunched to switch databases. An alternative approach is to keep separate Firefox profiles, and switch between those. I’ve actually done both, but I’m not the only person who thinks easier access to multiple libraries is a good idea.

For the creation of bibliographies, Zotero has plug-ins available to work with (certain versions) of Word and OpenOffice. Bibliographies can also be manually generated by right-clicking on selected entries in the middle pane of the database.

Recently, with Zotero 2.0 beta, the developers added the ability to  synchronize Zotero libraries across multiple computers (via a Zotero.org account), and the ability to share libraries between members of groups, and make them publicly visible. Here is the group for “All Things Zotero“. Having registered at Zotero.org, I effortlessly synced one of my libraries between my Mac running FF 3.5, and my eeePC running FF 3.05 – simply a matter of entering details in the preferences pane in both computers and clicking the green sync icon.

In pushing into new areas, and in taking advantage of developments in Firefox, the developers have sacrificed some backward compatibility: Zotero 2.0 is not compatible with Firefox versions before 3.0, and I notice when I upgraded I was warned that it was, as far as my databases are concerned, one way. I hope that stabilizes, at least to some extent – my older G4 PowerBook (2005), for instance, cannot be upgraded to Firefox 3.