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authorBlaine Mooers <bmooers1@gmail.com>2021-10-30 07:50:07 -0500
committerBlaine Mooers <bmooers1@gmail.com>2021-10-30 07:50:07 -0500
commitd87baf350f1ed4384ecb4b71151460f0a800de05 (patch)
tree212a584de941519aa433499cb3130edb082e5021
parent5dd6c5e970c21ff4a5c792f3e31d7a85e85bd936 (diff)
downloademacsconf-wiki-d87baf350f1ed4384ecb4b71151460f0a800de05.tar.xz
emacsconf-wiki-d87baf350f1ed4384ecb4b71151460f0a800de05.zip
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diff --git a/2021/talks/molecular.md b/2021/talks/molecular.md
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@@ -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