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| -rw-r--r-- | 2021/talks/molecular.md | 10 |
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diff --git a/2021/talks/molecular.md b/2021/talks/molecular.md index ec2317d7..c319114a 100644 --- a/2021/talks/molecular.md +++ b/2021/talks/molecular.md @@ -18,14 +18,14 @@ the images of the molecules reported in their articles. Nonetheless, this aspect of reproducible research needs to become the standard practice to improve the rigor of the science. -In a literate programming document, the author interleaves between blocks -of prose the code that makes the images of molecules. The document allows -the reader to reproduce the images in the manuscript by running the code. +In a literate programming document, the author interleaves blocks +of explanatory prose between code blocks that make the images of molecules. +The document allows the reader to reproduce the images in the manuscript by running the code. The reader can also explore the effect of altering the parameters in the code. Org files are one alternative for making such literate programming documents. -We developed a yasnippet snippet library called orgpymolpysnips for +We developed a **yasnippet** snippet library called **orgpymolpysnips** for structural biologists (<https://github.com/MooersLab/orgpymolpysnips>). This library facilitates the assembly of literate programming documents with molecular images made by PyMOL. PyMOL is the most popular @@ -34,7 +34,7 @@ over 100,000 users, which is a lot of users in molecular biology. PyMOL has been used to make many of the images of biological molecules found on the covers of many Cell, Nature, and Science issues. -We used the `jupyter' language in org-babel to send commands from +We used the **jupyter** language in **org-babel** to send commands from code blocks in Org files to PyMOL's Python API. PyMOL returns the molecular image to the output block below the code block. An Emacs user can convert the Org file into a PDF, `tangle' the code blocks |