Tag Archives: Information management

A few of my favourite tools: Tiddlywiki

This started as part of my earlier post on DokuWiki and MAMP, and then grew to demand a separate entry. Tiddlywiki, a demonstration of über-Javascripting, goes places other wikis cannot. It is a completely self-contained, platform- and server-independent wiki, capable of being run from any rewritable media and on any system that supports a modern browser. Everything, script, entries and plug-ins, is included within a single .html file; installation consists of downloading the empty file, setting a couple of options (name and saving), and starting to edit.

Why? Because I as I said before, I like wikis, I work cross-platform, and I find I work best by separating out my projects. So, one Tiddlywiki per project. To date I have run Tiddlywikis on all three major operating systems, though using Firefox by preference as a browser.

A series of articles by Mark Gibbs at Network World (Jan – Feb 2009) covers the basics. Some of his readers express reservations about the quality of the documentation, but it occurs to me that that in part may be because much of the documentation appears in Tiddlywiki form (see, for example, tiddlywiki.com). A potential user coming to it without previous experience may need a few moments to decipher the conventions of the interface (in a traditional tiddlywiki, look to the right hand menu for actions and lists of previous entries), as well as come to terms with the jargon (although, in 2009, “tiddler” cannot seem any more whimsical than “tweet”).  Tiddlywiki for the rest of us provides a more conventional presentation of the basics, and tiddlywiki.org‘s documentation is built on a MediaWiki engine. Admittedly there are aspects, like the styling, that are intricate beyond simple documentation. I have reached the point that I can tinker with other peoples’ styles, but have not progressed beyond that; fortunately, there are a couple of styles I quite like.

My uses are admittedly rather bland: keeping ongoing research notes on emerging treatments in a disease area, keeping bibliographies, keeping a off-line, but still portable list of resources for my medical/regulatory writing activity, keeping a concordance for a loose series of short stories. Other people are much more adventurous, using tiddlywikis for home, education and commercial websites, presentations, weblogs, course notes, course materials, bibliographies, and developing and presenting scholarly papers – see the Tiddlyspot gallery, and Tiddlywiki in Action. As tiddlywiki is open source, developers have produced a number of variants, including a popular one one that incorporates the tasks-projects-place structure of Dave Allen’s Getting Things Done (GTD) strategy, complete with checkable to-do lists; I’ve flirted with this, but have always returned to Backpack.

My own collection of Tiddlywiki Resources page is here, on Backpack. I started it after I spent far too long hunting around for a site that contained a plug-in I knew I’d seen in passing and wanted to include. My page on Tiddlyspot (a service for hosting Tiddlywikis online, worth an entry in itself), on the German Imperial Navy, shows a number of my favourite modifications, including restyling to the Blueberry template (from Tiddlythemes) and the addition of a tag cloud.

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.

Programs worth extolling: DoubleTake, Skim, PDFLab

DoubleTake. A recent MacWorld article (Software Treats, August 2007) put me onto the excellent DoubleTake, a shareware program that enables the stitching together of multi-shot panorama photographs. I’ve accumulated quite a number of these over the years, but never had the patience for manual assembly. DoubleTake takes away most of the grief: It is extremely easy to use, with direct drag and drop from the Finder or iPhoto (or who knows else), live previews of changes in scale, orientation and exposure (among others – but no independent colour adjustments that I can see), and the ability to save into a number of formats. Its matching is remarkably accurate in most instances, and if it misjudges, then all you have to do is drag the added photograph into rough alignment and let the software refine. I’ve now put together 2 – 7 photograph panoramas, most in well under fifteen minutes. I’m putting them on a separate page, in the form of iframes to allow for scrolling of the wider pans.

Skim. Courtesy of MacResearch, I discovered Skim, which satisfied a yearning for something that would let me annotate PDFs on screen in the same way Adobe Acrobat does (which I don’t have on Mac). The program is freeware, and under active development (having reached v 0.6.1). It has replaced Preview as my default PDF reader.

PDFLab. I take full advantage of the ‘Print to PDF’ functionality in OS X to reduce the amount of paper I print out. Periodically I would go in search of a means of assembling multiple PDFs into one file, encounter intimidating strings of command-line instructions which would induce me to back away slowly, and resolve that I could live with numbering them sequentially and sticking them in one folder until I had the hour I would need to work out and document the methods described. MacWorld to the rescue again, by introducing me to PDFLab. Again, it really is as simple as dragging and dropping, or clicking add, setting files in order, hitting the appropriate button, and typing in a filename. I’m sure it’s invoking all the command-line magic, but it certainly didn’t take me an hour to produce my first PDF!