Tag Archives: notes

website to jekyll

While my research diary has stalled out because I haven’t been researching (other than some administrative tasks like collecting and organizing article PDFs, and typing notes into Mendeley), I have made some progress on updating my website.

Specifically, I have switched over to using Jekyll, which is software that converts markdown/HTML and SASS/CSS to static web pages. Why do I want to do it? Because I want to have a consistent header and footer (navigation and that blurb at the bottom of every page) across the whole site, but don’t want to manually edit every single file every time I update one of those, or update the site structure/design. I also didn’t want to use PHP because then all my files will be .php and on top of it, it feels messier. I like static HTML a lot.

I’m just writing down my notes here for others who might want to use it too. I’ve only found tutorials that talk about how to publish your site to GitHub Pages. Obviously, I have my own hosting. I also already had a full static site coded in HTML and CSS, so I didn’t want to start all over again with markdown. (Markdown is just a different markup language from HTML; from what I can tell, you can’t get nearly the flexibility or semantic markup into your markup documents that you can with HTML, so I’m sticking with the latter.) I wondered: all these tutorials show you how to do it from scratch, but will it be difficult to convert an existing HTML/CSS site into a Jekyll-powered site?

The answer is: no. It’s really really easy. Just copy and paste from your old site into some broken-up files in the Jekyll directory, serve, and go.

I recommend following the beginning of this tutorial by Tania Rascia. This will help you get Jekyll installed and set up.

Then, if you want a website — not a blog — what you want to do is just start making “index.html”, “about.html”, folders with more .html files (or .md if you prefer), etc., in your Jekyll folder. These will all be generated as regular .html pages in the _site directory when you start the server, and will be updated as long as the server is running. It’ll all be structured how you set it up in the Jekyll folder. For my site, that means I have folders like “projects” and “guides” in addition to top-level pages (such as “index.html”).

Finally, start your server and generate all those static pages. Put your CSS file wherever the head element wants it to be on your web server. (I have to use its full URL, starting with http://, because I have multiple folders and if I just put “mollydesjardin.css” the non-top-level files will not know where to find it.) Then upload all the files from _site into your server and voilà, you have your static website.

I do not “get” Git enough yet to follow some more complicated instructions I found for automatically pushing my site to my hosting. What I’m doing, and is probably the simplest but just a little cumbersome solution, is to just manually SFTP those files to my web server as I modify them. Obviously, I do not have to upload and overwrite every file every time; I just select the ones I created or modified from the _site directory and upload those.

Hope this is helpful for someone starting out with Jekyll, converting an existing HTML/CSS site.

arsenal of research: organizing citations, PDFs, notes, brainstorming, and drafts

Post title courtesy of the tyrannical Brian Vivier.

Although I post about the content of my research quite a bit (when I do post), I thought I’d take a step back and talk about the research process today. I’m going to write about a very specific aspect: the ways in which the computer helps me organize and engage in my research.

Obviously, there are things like databases and library catalogs, which are a topic for another day. Many people I talk to don’t know the first thing about WorldCat, so it needs to be addressed! But let’s pretend I already have my sources. Now what do I do?

When I read, I’m very traditional. I take notes with pen and paper when I have a book or a photocopied source. In fact, I used to print out PDFs too, and highlight and write in the margins. Well, that turned out to be a terrible idea. Your highlights and margin notes are not very accessible when you’re coming back to the document later to brainstorm, outline, or write.

My lesson learned – learned after many difficult situations – was to take notes like I’m never going to see the source again. My advisor recommended I do this with primary sources, but if you take long notes that involve mostly direct quotes from the sources, there’s no need to buy the book or really even check it out again. There’s no need to keep binders and binders of printed-out PDFs. So that’s the kind of note-taking I do with pen and paper, first.

The next step is to get them into the computer, because I want them to be 1) stored somewhere safe (I do daily external HD backups, plus sync, more later on that), and 2) searchable, and also 3) copy and paste-able. But where to keep them? How to organize?

I have gone through several pieces of software trying to figure this out, and I’ve settled on Mendeley. I first used Scrivener even for note-taking, which is a great program, but bad for citation management. I then tried Zotero, but that turned out to be bad for PDF management. What I really wanted was a good database that would save my citations, any PDFs I happened to have (I’m currently digitizing all of my sources from my dissertation so they don’t get lost or damaged, and so I can free up my filing cabinet for other things), and ideally let me take notes and even annotate or highlight the PDFs.

Well, despite Mendeley being owned by the devil (Elsevier), it’s free and it actually does everything I need with only a few minor nitpicks, and does it in a way that makes me supremely happy. (My nitpicks are no nested bulleted lists in the notes, and no shortcut keys for bold/italics in the notes.) If you have a PDF attached to your citation and it has OCR, Mendeley’s search function will search not only your citations, notes, and annotations, but also inside the PDFs. It can be overkill at times, but it’s pretty amazing.

So step two of my research organization process is the painstaking, mindless, thankless task of typing my pen-and-paper notes into Mendeley under the appropriate citation. It’s boring but worth it. As I mentioned above, it searches all my notes, and I can copy and paste them into Scrivener, which I will address next. As I type my notes, at the very least I copy and paste them into brainstorming documents as appropriate (usually full quotes), and if I’m up to it, I do some free-writing to brainstorm how the source informs my topic and what I could write about related to it. This usually brings up new ideas I didn’t know I had.

What happens after I get all the notes typed in, PDFs organized and annotated if I have them? I next move over to Scrivener. I’ve been using it for over five years, for both research and creative writing, and can’t sing its praises enough. It’s a word processor that creates a database for your project, where you can store your reference materials, brainstorming ideas, notes, and draft. And more, if you can think of other areas you need to record notes in. Unlike old Scrivener (when I first started using it), you can now add footnotes and comments that port straight to MS Word when you compile your document for it, making the transition to final draft in Word very easy. (Sadly, publishers seem to prefer things that are not Scrivener databases when reviewing.) The typical things I store are the draft itself (of course), a research diary of brainstorming that I update periodically, brainstorming specifically about sources and particular concepts or points, and also under the “Notes” section the comments and suggestions and draft corrections I receive from others. So I keep my full writing process, except for mind mapping/concept mapping (another post), all in one place. It’s amazing.

I’m extremely happy with these two pieces of software; my only complaint is that neither of them does all of what I want, and I have to use two different things complementarily. Well, the situation is still significantly better than several years ago, when I used Mendeley Alpha and it deleted my entire library of citations multiple times. Yikes. Now its syncing works perfectly and I haven’t had a library failure yet. (Fingers crossed).

Next posts will include mind mapping software, how I take notes, how to effectively find and import source citations, and how I deal with multiple languages in my citations.

more room for annotations

Poking around on the Kindai Digital Library, as I am wont to do, I came across yet another book that leaves ample room for reader annotations without providing any of its own (where they would usually appear). This is a page from 華胥国物語 : 履軒中井先生遺稿:

For comparison, here is a page from Murasaki Shikibu nikki (1892) that does have annotations in that spot:

As you can see, too, there’s quite a difference between working with the first edition of a mid-Meiji book (my photo, immediately above), a microfilm version (not pictured), and a scanned and PDFed version of the microfilm version (the first image in this post). Thankful as I am for the Kindai Digital Library, its source material could be a lot better. (Post forthcoming on their new efforts to digitize and what a difference it makes. I’d like to point out that that photo was taken with Instagram on my iPhone, not some kind of high quality camera, and is yet still higher quality and more readable than most of what is on KDL.)