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diff --git a/2021/talks/molecular.md b/2021/talks/molecular.md index ecfaec10..ec2317d7 100644 --- a/2021/talks/molecular.md +++ b/2021/talks/molecular.md @@ -8,40 +8,39 @@ # Reproducible molecular graphics with Org-mode Blaine Mooers -Research papers in structural biology should include the code used -to make the images of molecules in the article in the supplemental -materials. Some structural bioinformaticists have started to include +Research papers in structural biology should include the code used to make +the images of molecules in the article in the supplemental materials. +Some structural bioinformaticists have started to include their computer code in the supplemental materials to allow readers to reproduce their analyses. However, authors of papers reporting new -structures have overlooked the inclusion of the code that makes the -images of the molecules in their articles. Nonetheless, this aspect of -reproducible research needs to become the standard practice to improve -the rigor of the science. +molecular structures often overlook the inclusion of the code that makes +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 the code -that makes the images of molecules in the explanatory text. Such a -document allows the reader to reproduce the images in the manuscript. -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. +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. +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 library called orgpymolpysnips for structural -biologists (<https://github.com/MooersLab/orgpymolpysnips>). This -library facilitates the assembly of literate programming documents +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 -molecular graphics program for making images for publication; it has -over 100,000 users, which is a lot of users in the sciences. PyMOL was -used to make many of the striking images of biological molecules on -the cover of Nature and Science. We use the emacs-jupyter package to -send commands from a code block in Org files to PyMOL's Python API. -PyMOL returns the molecular image to the output block below the -code block. Of course, an Emacs user can convert the Org file into a -PDF, convert the code blocks to script files, and submit these for -non-Emacs users. We describe the content of the library and provide -examples of the running PyMOL from Org-mode. We compare using Org, -Jupyter Notebook, Jupyter Lab, and RStudio with PyMOL to do -literate programming in structural biology. +molecular graphics program for creating images for publication; it has +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 +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 +into a script file, and submit these for non-Emacs users. We describe +the content of the library and provide examples of the running PyMOL +from Org-mode documents. # Outline |