From 016134bf4531b687188c9515dc2cc064da722f4b Mon Sep 17 00:00:00 2001 From: Blaine Mooers Date: Tue, 26 Oct 2021 05:54:10 -0500 Subject: Extensive edits of the abstract. --- 2021/talks/molecular.md | 55 ++++++++++++++++++++++++------------------------- 1 file changed, 27 insertions(+), 28 deletions(-) (limited to '2021/talks/molecular.md') 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 (). This -library facilitates the assembly of literate programming documents +We developed a yasnippet snippet library called orgpymolpysnips for +structural biologists (). +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 -- cgit v1.2.3 From d87baf350f1ed4384ecb4b71151460f0a800de05 Mon Sep 17 00:00:00 2001 From: Blaine Mooers Date: Sat, 30 Oct 2021 07:50:07 -0500 Subject: Minor formatting edits. --- 2021/talks/molecular.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) (limited to '2021/talks/molecular.md') 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 (). 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 -- cgit v1.2.3