Mortarboard

Seamlessly tying together data exploration and analysis, technical blogging, and academic paper writing.

The vision:

Write about your ideas, hypotheses, and experimental setup with syntax that stays out of your way with Markdown
Put executable code in code blocks to load your data and analyze it
Display generated plots and tables inline
Output to PDF in the correct format of your target academic publication to see how the final paper will look as you go
Output to HTML in a technical blog style for easier sharing
Automatically make the tables and plots interactive so collaborators and strangers can manipulate and play with your data in new ways.

Technology

Pandoc: generate HTML or Latex from Markdown (or a slew of other markup languages)
- extensible so we can build filters specifically for common use cases
R's knitr package: actually execute R code blocks and display generated plots inline!
Plotly: take ggplot plots and automatically make them interactive, letting you drill into the data

Currently Latex/PDF generation is working pretty well.
- Still trying to work out kinks in Pandoc/Knitr's mechanisms for references and labels
- Would like to add \autoref functionality, seems like Pandoc has some efforts in the works but nothing ready
HTML generation currently poor because we're generating PDFs for plots and not converting them
- use Plotly when generating HTML to fix this problem