Sean's Research

Hello, Org

Nov
27

This is a test blog post for writing wordpress blog items using org-mode. I’m hoping this will let me populate my blog in a more seamless manner than editing it via the WordPress web interface.

Introduction

When Ι started this blog, I got an account with an ISP and installed WordPress using some kind of automatic template. The good thing about this is that I could start a blog without knowing what I was doing. The unfortunate part about it is that when I need to configure the blog, I have no idea whatsoever about how things are set up. Also, I would need to log in to the WordPress site and use their editor to build the pages.

But what I really want to do is use org-mode directly to upload posts to my blog. As I do most of my work documentation it would be awesome to convert some of that to my web site. Fortunately some awesome person has already done the work to make this possible. It’s called Org2Blog, created by Puneeth Chaganti, and currently maintained by Grant Rettke. It’s an org-mode package that allows you to edit posts using org-mode markup and extensions. You can edit and upload the post without leaving emacs, which is great!

The remainder of this post contains some fairly useless examples of this packages capabilities.

Examples

Figure 1 is an example of html import for images. One of the nice things about org-mode is you can specify different output parameters for images in pdf and html export formats. This can be handy for making things work in HTML.

avatar image

Here is an equation, in case you ever need to know the solution to a quadratic equation:

\[ x = -b \pm \frac{\sqrt{b^2-4 a c}}{2a} \]

  • Here are some points
    • \(\LaTeX\) is great to put inline into your blog, like \(\sum_{i=0}^n i^2 = \frac{(n^2+n)(2n+1)}{6}\)
    • Centered equations use two dollar signs, as opposed to inline equations like that above, which use only one

    \[\sum_{i=0}^n i^2 = \frac{(n^2+n)(2n+1)}{6}\]

I have not yet done much to see what can be done with org-mode and wordpress. There are several things I don’t know how to do. For example, to center the image above I had to set margins, and if I were to caption it, the caption would be left aligned. I also don’t know how to number equations. References would be the next interesting thing to try hruschka2010two. Well, it seems that citations from a bibtex file will export to WordPress, but the citation style, based on the key, does not seem to change (ie I can’t get numbered or superscript citations). Nonetheless, I’m declaring the export sufficiently capable to be useful for most blog posting purposes.

Bibliography

  • [hruschka2010two] Hruschka, O’Byrne & Kleine, Two-component Doppler-shift fluorescence velocimetry applied to a generic planetary entry probe model, Experiments in Fluids, 48(6), 1109-1120 (2010).

Research notes

May
26

One of the problems I have been engaged with for many years now is the idea of how to keep a consistent record of my research that I can come back to years later and pick up where I left off.

Having thought a lot about this, I have some important criteria for such a record.  Lab notes must be

  1. Future-proof (not dependent on proprietary software);
  2. Based fundamentally on ASCII text;
  3. Flexible enough to cope with a variety of experiment structures (one-off experiments, repetitive experiments, numerical experiments etc);
  4. Easy to input and maintain;
  5. Able to time-stamp the state of an experiment at the time it was performed;
  6. Able to incorporate the source code used to analyse the data;
  7. Able to facilitate collaboration with my group members and external colleagues;
  8. Easy to transform into outputs like papers and presentations;

I have tried many different notetaking systems to achieve this, including commercial systems like LabArchives, Microsoft OneNote, Microsoft SharePoint, My own TikiWiki webpage, Zim desktop wiki, Tiddlywiki and others I have forgotten, but none of them could give me what I need according to the above 8 points.  I believe I now have a system that works the way I need it to for lab notes, though I know it is not for everyone: emacs org-mode.  I hope to write up a little more about org-mode in the future, and why I think it’s a great way to produce consistently high-quality, self-documenting research outputs.