Just moved over to Pelican as the machine for the blog generation. As I noted in the last post, it uses Markdown for the posts. I didn’t really want to learn yet another markup language, but it is fairly simple. I think easier than trying to do everything in Org as I have yet to fully embrace Org-Mode again. The advantage of markdown is for simple documents. LaTeX can be somewhat complicated and time-consuming to create a simple document when not that much organization of the document is required. I know LaTeX very well, so creating documents in it is a snap for me, but then translating those documents into something else is not so easy. For instance, my latest manuscript I wrote the draft in LaTeX and it looked beautiful, but then converting it to .doc for submission just murdered it. So why bother creating a beautiful document if you don’t really need to?

For us, I see markdown being of potential benefit for our protocols. I created a Github repository for my medical reference and laboratory reference documents. Creating our protocols in markdown makes it easy to see and track changes in github. We can easily convert the simple markdown documents to pdf for printing. Or any format really. That is the great thing about markdown and Pandoc. Now documents that had previously been maintained as separate entries on the blog with links are going up into the github. This will require translating our protocols into markdown, but that will be simple and we can clean them as we go (first convert the .doc into html then into markdown). The first one that I have up is the microwell staining for multiparameter flow cytometry. I am working on this for the JoVE submission.

The other interesting potential use of markdown is for writing manuscripts. Unless the journal accepts LaTeX formatted manuscripts, which few medical journals do, you have to basically destroy the LaTeX-formatted manuscript to submit it (a heart-wrenching maneuver). For the JoVE article that requires doc format for submission, I started with markdown because it is a very simple and short article and I hate working in LibreOffice (Emacs preferred here). I can very easily convert the markdown document into .odt or .doc to share with collaborators and receive their input on the document. I was concerned about formatting references at first and had seen only lame examples of this online. I then found the Citation Style Language and I can feed pandoc the .csl file for a particular journal and it will format the references correctly from my bibtex library. There are lots of journal styles available at this github link. When placing multiple references back-to-back in the file, you need to separate them with semi-colons like so: [@Master2008;@Jones2010] otherwise, they will not be formatted correctly in text.

On another note, Aim V media and A-549 cells do not get along. Our A-549 alveolar cells do not like to grow in this media. In searching for an exosome/serum free media this one looked like it supported a broad range of cells. They grew very well after replacing the Aim V with R10 for which the FCS had been ultracentrifuged to remove the exosomes.