Projects in Awesome Lists by MooersLab
A curated list of projects in awesome lists by MooersLab .
https://github.com/mooerslab/pymolshortcuts
The repository pymolschortucts contains the a collection of shortcuts that are loaded on startup of PyMOL. These shortcuts enable websearches from within PyMOL as well as many other convienent functions that make work in PyMOL more productive..
agile-programming agile-pymol aliases biomolecular-artwork efficient-programming ergonomic-keyword-use figure-making image-making molecular-artwork molecular-graphics pdb pml protein-structure-analysis pymol pymol-plugin pymol-python scripting shortcuts startup-script structural-bioinformatics
Last synced: 16 Mar 2026
https://github.com/mooerslab/pymolsnips
Pymolsnips is a library of PyMOL scripting language code fragments for several popular text editors.
atom autocompletion code-fragments cudatext gedit molecular-artwork pml pymol pymol-code-fragments pymol-macro-language pymol-snippet-library pymol-snippets snippet-library snippets st3 sublime-text-3 tab-triggers text-editors textmate vsc
Last synced: 13 May 2025
https://github.com/mooerslab/jupyterlabpymolpysnips
Python snippets for PyMOL to be run in Jupyterlab via the jupyterlab-snippets-multimenus extension.
biomolecular dna-structure grayscale jupyter jupyter-notebook jupyterlab ligand literate-programming mmcif moleclar-graphics molecular molecular-representation notebook pdb protein-structure python ribbon-diagram rna-structure snippets
Last synced: 08 May 2025
https://github.com/mooerslab/latex-emacs
Emacs version 29 profile for use with LaTeX in academic writing.
academic-writing auctex emacs emacs-profile ghosttext latex latex-emacs org-agenda org-mode org-roam
Last synced: 08 May 2025
https://github.com/mooerslab/easypymol
Script to facilitate the making of horizontal scripts
ambient-occulsion biomolecular-structures black-and-white-cartoons coordinate-covalent-bonds horizontal-scripts metal-coordination molecular-artwork molecular-graphics molecular-structures molecular-visuallization pml protein-structure pymol pymol-macro-language rna-structure roundview scripting startup-aliases structural-bioinformatics tutorial-videos
Last synced: 08 May 2025
https://github.com/mooerslab/curve-fitting-software
A collection of links to free and proprietary curve fitting software.
curve-fitting data-fitting data-plotting data-visuallization graphical-data-analysis numerical-analysis reproducible-research scientific-communication scientific-computing
Last synced: 10 Feb 2026
https://github.com/mooerslab/snippet-org-mode
Blaine's yasnippet snippets for org-mode.
Last synced: 15 Mar 2026
https://github.com/mooerslab/orgpymolpysnips
Supports the use of PyMOL in literate programming in org-mode, which is best run in Emacs.
emacs emacs-jupyter literate-programming mmcif molecular-graphics org-babel org-mode pdb protein pymol
Last synced: 08 May 2025
https://github.com/mooerslab/writinglogtemplateinorg
Template for writing.log in org-mode
accountability daily-log hypothesis-centered-writing hypothesis-driven-research master-document personal-productivity planning-document planning-tool project-management science-writing scientific-writing second-brain self-monitoring stress-management time-management voice-commands workflows writing-accountability writing-productivity writing-project-management
Last synced: 08 Jan 2026
https://github.com/mooerslab/colabpymolpysnips
Library of PyMOL Python snippets for Google Colab.
biomolecular-structure ca-trace code-fragments code-snippets colab colab-notebook drug-molecules grayscale ligand-binding-sites literate-programming molecular molecular-graphics molecular-surface notebook protein protein-structure pymol python ribbon-diagrams
Last synced: 04 Oct 2025
https://github.com/mooerslab/configorg
Package.el dependent config.org file for Emacs
configuration emacs literate-programming org-mode
Last synced: 06 Oct 2025
https://github.com/mooerslab/writing-progress-2024-25
Track words written and time spent on writing projects in 2024 and 2025.
accountability career-management excel getting-things-done google-sheets libre-office open-office project-management scientific-writing self-motivation time-management time-power writing-project-management
Last synced: 16 Mar 2026
https://github.com/mooerslab/berlinemacsaugust2022
*Document preparation with LATEX in Emacs*
academic-writing books-in-latex emacs journal-articles-in-latex latex latex-profile-for-emacs lecture-slides lecture-slides-in-latex letters-in-latex posters-in-latex uses-of-latex-in-academic-science writing-log
Last synced: 08 May 2025
https://github.com/mooerslab/thewriterslaw
The Writer's Creed
writers-creed writers-law writing-habits writing-productivity
Last synced: 26 Feb 2026
https://github.com/mooerslab/colabopensourcepymolpysnips
Code snippets for colab-notebooks running open-source PyMOL
google-colab literate-programming molecular-graphics open-source-pymol pymol
Last synced: 16 Sep 2025
https://github.com/mooerslab/mooerslab
Landing page for MooersLab repository
cctbx colab crystallographic-computing emacs jupyter literate-programming neovim pymol saxs scientific-writing speech-to-text supercomputing time-management vim voice-computing writing writing-aids writing-tools
Last synced: 07 Jul 2025
https://github.com/mooerslab/emacs30ubuntu22
Protocol to install emacs30 on ubuntu 22.04 LTS with tree-sitter support.
combobulate compile emacs profile tree-sitter ubuntu
Last synced: 06 Jul 2025
https://github.com/mooerslab/annotatedbibliography
Annotated bibliography template in LaTeX for specific writing projects
Last synced: 08 May 2025
https://github.com/MooersLab/thewriterslaw
The Writer's Creed
writers-creed writers-law writing-habits writing-productivity
Last synced: 04 Sep 2025
https://github.com/mooerslab/manuscriptinlatex
Template for the first submission of a manuscript
first-submission latex-template manuscript
Last synced: 08 May 2025
https://github.com/mooerslab/writing-time-spent-heatmap
Hours spent writing journal articles per day as a GitHub style heatmap
academic-writing automated-self-regulation calmap calplot heatmap matplotlib science-writing self-regulation time-management-tools workflow writing writing-accountability writing-habit-tool writing-project-management
Last synced: 15 Apr 2025
https://github.com/mooerslab/emacsatx4may2022
Brief introduction to functional programming in Emacs Lisp
elisp emacs functional-programming
Last synced: 08 Jan 2026
https://github.com/mooerslab/writing-log-md
Writing log template in markdown
accountability daily-log hypothesis-centered-writing hypothesis-driven-research master-document personal-productivity planning-document planning-tool project-management scientific-writing second-brain self-monitoring self-regulation stress-management time-management voice-commands writing-accountability writing-productivity writing-project-management
Last synced: 08 Jan 2026
https://github.com/mooerslab/manuscriptinorg
Manuscript in org-mode
emacs first-submission ghosttext latex manuscript-template org-mode org-to-latex overleaf pdf research-paper-in-org science-writing
Last synced: 07 Oct 2025
https://github.com/mooerslab/cctbxsnips-sublimetext3
snippets for CCTBX formatted for use with Sublime Text 3
cctbx cctbx-snippets cctbx-snips code-snippets code-snippets-python colab colab-notebook crystallographic-computing crystallography ghosttext jupyter jupyter-notebook python snippets sublime-text sublime-text-3 websocket
Last synced: 07 Oct 2025
https://github.com/mooerslab/pymolwallhangings
Protocol for making large scale images to be framed or for background images of posters.
large-scale-image molecular-graphics poster-sized-image pymol wall-hanging
Last synced: 19 Mar 2026
https://github.com/mooerslab/org-mode-voice-in
Org-mode related voice commands for the browser-based Voice In.
Last synced: 19 Mar 2026
https://github.com/MooersLab/emacs30ubuntu22
Protocol to install emacs30 on ubuntu 22.04 LTS with tree-sitter support.
combobulate compile emacs profile tree-sitter ubuntu
Last synced: 11 Mar 2025
https://github.com/mooerslab/modular-annotated-bibliography-bibtex-latex
A template for an enhanced annotated bibliography with many features
annotated-bibliography annote-field-free bibliographic-entries bibtex code-reuse illustrated-bibliography information-retrieval knowledge-management latex literature-review modularity reference-management research-documentation research-methodology
Last synced: 08 Jan 2026
https://github.com/mooerslab/voice-in-basics-quiz
Interactive quiz written in Python3 about the basic commands for the dictation plugin Voice In for Google Chrome.
interactive-quiz jupyter-notebook spaced-repetition-learning
Last synced: 22 Jan 2026
https://github.com/mooerslab/diary2024inlatex
A diary or logbook with one tex file per day in LaTeX. Includes auto generated table of contents, index, and bibliography.
complex-latex-book-document diary electronic-notebook electronic-scientific-notebook full-featured-nonfiction-book-template-in-latex latex-technical-book-template technical-book-template
Last synced: 19 Mar 2026
https://github.com/mooerslab/oscer-supercomputer-tutorial
Beginner’s Guide to Doing Science on the OU Supercomputer
Last synced: 19 Mar 2026
https://github.com/mooerslab/manuscriptintypst
Template for first submission of manuscript.
scientific-writing template-journal-article-first-submission typst
Last synced: 30 Jan 2026
https://github.com/mooerslab/dsd4xtals
Crystal improvement with Definitive Screening Designs (DSDs)
Last synced: 19 Mar 2026
https://github.com/mooerslab/talon-contractions
TalonScript file of expansions for common contractions in English
Last synced: 19 Mar 2026
https://github.com/mooerslab/cctbxsnips-ultisnips
cctbx-snips for the ultisnips package for Vim and NeoVim
cctbx-snips colab colab-notebooks jupyter neovim python snippets ultisnips vim
Last synced: 05 Apr 2026
https://github.com/mooerslab/time-blocks
PDF of Form for daily schedule as time blocks.
daily-planning daily-schedule daily-scheduling efficiency-analysis efficiency-tool getting-things-done gtd personal-productivity project-management time-blocking time-blocks time-management to-be-done to-be-dones work-life-balance
Last synced: 19 Mar 2026
https://github.com/mooerslab/tmux-rocks
tmux cheet sheet
enhanced-terminal-workflow panes-inside-terminal tmux-cheat-sheet
Last synced: 01 Apr 2025
https://github.com/mooerslab/gantt-chart-py
Gantt chart for planning projects, manuscripts, grant proposals, and so on.
academic-writing gantt-chart matplotlib multiple-writing-projects python python-script time-management-tools writing writing-project-management
Last synced: 26 Feb 2026
https://github.com/mooerslab/writinglogtemplate
Enhanced template in LaTeX for metacognition about writing projects.
automated-index automated-table-of-contents current-state-snapshots electronic-writing-notebook emacs knowledge-management latex latex-template metacognition-about-writing overleaf project-specific-diary time-management voice-commands word-count-plot writing-accountability writing-diary writing-log writing-progress-tracking writing-tool
Last synced: 02 Mar 2026
https://github.com/mooerslab/voice-in-plus-contractions
Expand English contractions automatically when using Voice In Plus for dictation.
Last synced: 13 May 2025
https://github.com/mooerslab/markdown-chat-to-org-mode
Convert downloaded chats from markdown to org
basb bash chats-from-chatbot-sessions denote ekg emacs file-conversion-with-pandoc information-retrieval knowledge-management markdown-to-org-mode org-roam personal-knowledge-management pkm zettelkasten zk
Last synced: 04 May 2026
https://github.com/mooerslab/pymolshortcuts4rna
An extended version of pymolshortcuts for working with RNA structures.
Last synced: 01 Apr 2025
https://github.com/mooerslab/pymolrc
Blaine's pymolrc file, the configuration file for the molecular graphics program.
molecular molecular-graphics pymol pymolrc
Last synced: 19 Mar 2026
https://github.com/mooerslab/writing-project-gantt-chart-py
Gantt chart for writing project
academic-writing accountability benchmarks gantt-charts matplotlib named-tuple progess-tracking python scientific-writing timelines writing-project-log writing-project-management
Last synced: 14 Feb 2026
https://github.com/mooerslab/qemacs
Quizzes about Emacs to aid learning the key-bindings
emacs-lisp emacs-quizzes emacs-self-study
Last synced: 19 Mar 2026
https://github.com/mooerslab/latextips
Tips for greater productivity with LaTeX
beamer latex overleaf posters productivity slideshows
Last synced: 10 Jun 2025
https://github.com/mooerslab/writing-log-odt
writing-log-odt: Writing Log for Open Office
accountability daily-log hypothesis-centered-writing hypothesis-driven-research master-document personal-productivity planning-document planning-tool project-management science-writing scientific-writing second-brain self-monitoring self-regulation stress-management time-management voice-commands writing-accountability writing-productivity writing-project-management
Last synced: 15 Jan 2026
https://github.com/mooerslab/posterinlatex
Template for making compact poster in LaTeX
latex-template poster-template
Last synced: 30 Jul 2025
https://github.com/MooersLab/writingLogTemplate
Enhanced template in LaTeX for metacognition about writing projects.
automated-index automated-table-of-contents current-state-snapshots electronic-writing-notebook emacs knowledge-management latex latex-template metacognition-about-writing overleaf project-specific-diary time-management voice-commands word-count-plot writing-accountability writing-diary writing-log writing-progress-tracking writing-tool
Last synced: 04 Sep 2025
https://github.com/mooerslab/cctbxsnips-neosnippets
CCTBX snippets for neosnippets package for Vim and NeoVim
cctbx-snips code-snippets colab colab-notebooks ghosttext jupyter jupyter-notebook neosnippets python snippets
Last synced: 28 Apr 2026
https://github.com/mooerslab/writing-log-docx
Template for writing log in in format for MS Word
accountability checklists-for-manuscripts daily-log focus hypothesis-centered-writing master-document planning-tool science-writing scientific-writing second-brain self-regulation thinking-tool time-management writing-diary writing-productivity
Last synced: 19 Mar 2026
https://github.com/mooerslab/emacs30venturatreesitterconfig
Configuration file for Emacs 30.0.5 with tree-sitter and combobulate for macOS
academic-productivity academic-research academic-writing combobulate concrete-syntax-trees emacs structured-editing time-management tree-sitter
Last synced: 29 Jan 2026
https://github.com/mooerslab/mooerslab-functions-el
Home-made functions in Emacs Lisp
collection-of-helper-functions elisp emacs-lisp
Last synced: 30 Jan 2026
https://github.com/mooerslab/bareboneslatex
This is a bare bones LaTeX template document.
latex latex-bare-bones latex-bibitems latex-document latex-template
Last synced: 07 Feb 2026
https://github.com/mooerslab/scientific-writing-books-voice-in
Books about scientific writing as voice-in plus commands
Last synced: 19 Mar 2026
https://github.com/mooerslab/snippet-pymol-mode
yasnippet snippets for pymol-mode
Last synced: 19 Mar 2026
https://github.com/mooerslab/moleculargraphicslinks
Molecular Graphics links for the molecular graphics and structure analysis short course at OUHSC that ran from 2010 to 2019
Last synced: 12 Feb 2026
https://github.com/mooerslab/annotated-bibliography-org
Template for making annotated bibliography in org-mode
emacs knowledge-management manuscript-preparation note-taking org-mode
Last synced: 28 Feb 2026
https://github.com/mooerslab/bash-whisper-transcription
Bash function to ease the transcription of audio files with OpenAI's whisper.
asr audio audio-file-trancription audio-messages automate-the-boring-stuff automatic-speech-recognition automation bash bash-function beginner-friendly speech-to-text stt whisper
Last synced: 15 Feb 2026
https://github.com/mooerslab/dsw-2024-org-mode-init
Emacs init.el configuration file for org-mode demo at November 22 meeting of Oklahoma Data Science Workshop
config-for-org-mode-gnu-emacs emacs-for-writing emacs-for-wrting-sceince gnu-emacs-init-file org-mode-for-writing-science writing-science-in-org-mode
Last synced: 19 Mar 2026
https://github.com/mooerslab/acronymstex2yaml
Python script to convert acronyms.tex into acronym.yml for use with R's acronymsdown package.
Last synced: 19 Mar 2026
https://github.com/mooerslab/modular-annotated-bibliography-typst
modular, illustrated, and enhanced annotated bibliography in typst
annotation-reuse biblatex bibliography information-retrieval knowledge-management modularity reserarch-tools typst-template
Last synced: 19 Mar 2026
https://github.com/mooerslab/writinglogintypst
Template in typst for writing log for scientific journal article
template typst writing-log-for-journal-article writing-project-management
Last synced: 19 Mar 2026
https://github.com/mooerslab/biological-crystallography-voice-in
Voice commands about biological crystallography for the speech recognition software Voice In
Last synced: 19 Mar 2026
https://github.com/mooerslab/emacs-simple-init-org
A simple approach to the configuration of Emacs via a org file that is easy to navigate.
Last synced: 19 Mar 2026
https://github.com/mooerslab/aca2021
Slides show presentation on August 3, 2021 at the American Crystallographic Association annual meeting.
Last synced: 11 Jan 2026
https://github.com/mooerslab/colabcctbxsnips
CCTBX code fragment library in colab snippet notebook.
cctbx cctbx-snippets colab-notebook crystallographic-computing literate-programming python3
Last synced: 15 May 2026
https://github.com/mooerslab/qclj
Quizzes about Clojure syntax and other features.
Last synced: 19 Mar 2026
https://github.com/mooerslab/aca2022
Slideshow to talk in August 2022 at 72nd Annual Meeting of the American Crystallographic Association
aca cloud-computing colab-notebook emacs ghosttext literate-programming molecular-graphics pdb-database protein-structure pymol python sublime-text vim vsc
Last synced: 07 May 2026
https://github.com/mooerslab/taggedpymolpysnips
PyMOL Python Script Writing with Code Templates in Jupyter notebooks with JupyterLab using the Elyra extension
elyra jupyter-notebook jupyterlab literate-programming pymol tagged-snippets
Last synced: 29 Oct 2025
https://github.com/mooerslab/bib2item3
bib2item3 converts a bib file into a txt file with bibitems.
bibitems bibtex citation-management citations latex latex-template reference reference-manage reference-management
Last synced: 08 May 2025
https://github.com/mooerslab/software-development-voice-in
Software development jargon voice snippets for Voice-In Plus
Last synced: 19 Mar 2026
https://github.com/mooerslab/jupyter-voice-in
voice-triggered snippets for use in Jupyter notebooks with Voice In Plus
coding-assistance interactive-computing jupyter-lab jupyter-notebook software-engineering text-replacements voice-computing
Last synced: 01 Apr 2025
https://github.com/mooerslab/setup-grant-application
Script for creating common subfolders for a large grant application (e.g. NIH, NSF, DOD).
Last synced: 01 Apr 2025
https://github.com/mooerslab/writingprogess2023
Workbook for tracking minutes spent and words written per day per writing project.
word-count-html writing-productivity writing-tool
Last synced: 19 Mar 2026
https://github.com/mooerslab/voice-computing-with-python-in-jupyter-notebooks
Slides to talk at PyTexas 2024
accessibility interactive-computing jupyter-notebooks markdown mathjax pytexas-2024 speech-to-code speech-to-text voice-computing
Last synced: 18 May 2026
https://github.com/mooerslab/talon-voice-quizzes
Quizzes to support recall of Talon Voice commands.
Last synced: 14 Jul 2025
https://github.com/mooerslab/jupyter-st3-pymolpysnips
PyMOL Python snippet library to edit live Jupyter notebook cells with Sublime Text 3 using GhostText
Last synced: 19 Mar 2026
https://github.com/mooerslab/setup-manuscript
Script for creating common subfolders in a folder for a manuscript. Also writes a AAAreadme.md file with a description of the role of the subfolders.
Last synced: 02 Aug 2025
https://github.com/MooersLab/mooerslab-functions-el
Home-made functions in Emacs Lisp
Last synced: 12 Aug 2025
https://github.com/mooerslab/count-lines-of-code
Python and bash functions for counting lines of code
coding count-lines-of-code loc productivity
Last synced: 14 Jul 2025
https://github.com/mooerslab/multiplefiletransfer
Transfer multiple files by scp without repeated manual password entry
Last synced: 26 Jan 2026
https://github.com/mooerslab/chatbot-reformat-my-transcript
Prompts to reformat text from audio file transcription or direct speech-to-text.
Last synced: 05 Jan 2026
https://github.com/mooerslab/tmux-bashed
Bash function to automate the setting up of tmux sessions, windows, and panes.
automation bash-scripting daily-setup tmux workflow
Last synced: 01 Apr 2025
https://github.com/mooerslab/slideshowtemplatelatex
Template for making slideshows in LaTeX
beamer code-listings equations import-figures latex slideshow table template-slideshow
Last synced: 01 Apr 2025
https://github.com/mooerslab/aimless-summary-table-extraction
X-ray diffraction data processing: extract summary table in aimless log file
agile-biomolecular-crystallography agile-crystallographic-data-processing agile-diffraction-image-data-processing aimless-summary aimless-summary-table autoxds-post-processing bash-function crystallographic-computing x-ray-diffraction-data-processing
Last synced: 01 Apr 2025
https://github.com/mooerslab/smallanglescatteringwebpage
Small angle scattering webpage.
Last synced: 08 Jan 2026
https://github.com/mooerslab/ouhs-voice-in
Voice-In dictation commands for jargon associated with the University of Oklahoma Heath Sciences
Last synced: 19 Mar 2026
https://github.com/mooerslab/timespent
Electronic workbook for tracking effort by project
googlesheets monthly-reports project-management time-management time-tracking
Last synced: 01 Apr 2025
https://github.com/mooerslab/taggedcctbxsnipsplus
CCTBX snippets that can be retrieved in Jupyter via tags. A second copy of the code is included in a block comment. The tab stops are marked with dollar signs and placeholder values are inside curly braces. These mark sites to be considered for editing.
Last synced: 19 Mar 2026
https://github.com/mooerslab/jupyterlabpymolpysnipsplus
jupyterlabpymolpysnipsplus
Last synced: 01 Apr 2025