{"id":22901282,"url":"https://github.com/mooerslab/writinglogtemplate","last_synced_at":"2026-03-02T21:05:28.370Z","repository":{"id":59107918,"uuid":"531157196","full_name":"MooersLab/writingLogTemplate","owner":"MooersLab","description":"Enhanced template in LaTeX for metacognition about writing projects. ","archived":false,"fork":false,"pushed_at":"2024-07-14T13:30:24.000Z","size":974,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2024-09-08T02:42:07.977Z","etag":null,"topics":["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"],"latest_commit_sha":null,"homepage":"https://github.com/MooersLab/writingLogTemplate","language":"TeX","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MooersLab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2022-08-31T16:00:56.000Z","updated_at":"2024-09-03T18:53:28.000Z","dependencies_parsed_at":"2024-03-23T02:27:16.386Z","dependency_job_id":"76575cdc-cf00-4223-ae86-1c1cc78aa522","html_url":"https://github.com/MooersLab/writingLogTemplate","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MooersLab%2FwritingLogTemplate","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MooersLab%2FwritingLogTemplate/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MooersLab%2FwritingLogTemplate/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MooersLab%2FwritingLogTemplate/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MooersLab","download_url":"https://codeload.github.com/MooersLab/writingLogTemplate/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241051954,"owners_count":19900926,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["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"],"created_at":"2024-12-14T01:32:41.666Z","updated_at":"2026-03-02T21:05:28.291Z","avatar_url":"https://github.com/MooersLab.png","language":"TeX","funding_links":[],"categories":[],"sub_categories":[],"readme":"![Version](https://img.shields.io/static/v1?label=writingLogTemplate\u0026message=0.5.8\u0026color=brightcolor)\n[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)\n\n# Writing Tool for Metacognition and Storign Metadata about Research Papers\n\n## Introduction\nThis writing project log contains a diary about a writing project. \nIt also contains the metadata (plans, decisions, correspondence, and progress made) about the writing project, often stored in comments or at the bottom of manuscript documents.\nThese metadata are vulnerable to being accidentally deleted and clutter the main manuscript document.\nThese metadata are very valuable and deserve to be appropriately stored.\nWe think that storing them with the diary about the progress being made on the writing project enhances the use of the diary for metacognition about the writing project.\n\n## Quick start\n\nOpen a new project on Overleaf via uploading the zip file `drag-n-drop-overleafVer058.zip`.\nThe tex file will open and compile. The PDF should appear in a second.\n\n## Slower start\nDownload drag-n-drop-overleafVer058.zip, unzip, and compile the tex file. The minted package is in use. Will compile with `pdflatex -shell-escape`.\n\n\n## Background \n\nThis template document is a thinking tool, NOT a daily writing accountability tool.\nSee the following links for accountability tools:\n\n- [Writing progress by project](https://github.com/MooersLab/writing-progress-2024-25)\n- [Time spent by project](https://github.com/MooersLab/timeSpent)\n- [Writing contract](https://github.com/MooersLab/writingContract)\n- [Writers creed](https://github.com/MooersLab/thewriterslaw) \n\n## Background\nThis document is a tool for narrowing your focus and sustaining momentum on one specific writing project.\nWe know others who have suggested keeping a writing diary, but these diaries are not project-specific.\nKeeping the document specific to one project is essential to narrow one's focus.\n\nBusy academics often have to work on several writing projects in a given week because they do not have the luxury of working on one project at a time.\nThe one project-at-a-time approach has a lower cognition load, but it also gives the subconscious less time to develop ideas in the background of one's mind. \nWorking on several projects in parallel leads to juggling dozens to hundreds of thoughts about several writing projects.\nKeeping all these thoughts across multiple projects in one document leads to a tangled mess that is very laborious and time-consuming to parse.\nThis is why we use one document per writing project; this document is a key part of how we progress on 2-5 writing projects in a given week.\n\nThe writing diaries of others also have little to no support for metadata and metacognition about the writing project.\nWe think an external document for storing metadata about a writing project and thinking about that metadata enhances the focus on the paper's content.\nWe have found that the more time we spend on metacognition about the writing project outside of the manuscript, the more effective our time is when working inside that manuscript because our efforts are more focused and directed.\nWe have been struck by the diversity and extent of metacognitive activities associated with a specific writing project.\nThe writing log is a place for documenting these vital activities.\nThis record is a valuable resource for documenting decisions made about the current paper and for stimulating ideas for new manuscripts.\n\nThis enhanced writing log is also a tool that eases re-engagement in an interrupted writing project.\nIt is like a master thinking document or a second brain for a writing project.\nIt is a safe storage site for your thoughts about a writing project that could otherwise clutter your mind and get in the way of your next generative writing session for a particular project.\n\nThis writing log is for research papers.\nThe contents of our writing log for a grant application, book, platform talk, lecture, and seminar would be similar in nature but differ slightly in content.\nWe have not developed writing logs for these particular kinds of writing projects yet.\nWe plan to do so when time permits.\nIn the meantime, you can use this writing log as a template to develop writing logs for these other writing projects.\n\nWe do most of our writing in LaTeX.\nThe most advanced version of this writing log document is being developed in LaTeX.\nAt the moment, it is undergoing a spurt in development as we add new features.\nWe will update the other formats listed below when it reaches the next stable state.\nIf you are anxious to use the latest version in a different format, you can convert it to other formats using pandoc.\nYou may have to do some subsequent editing because pandoc is not perfect.\n\n\n- [Writing log template in Org-mode](https://github.com/MooersLab/writingLogTemplateInOrg) a superset of markdown for Emacs. Org can be used in VS Code, too. The org files will be rendered to HTML on GitHub like md files.\n- [Writing log template in reStructuredText](https://github.com/MooersLab/writing-log-rst) reStructuredText is used by programmers for documentation.\n- [Writing log template in Markdown](https://github.com/MooersLab/writing-log-md) Markdown variant. Read and rendered to PDF by most good text editors.\n- [Writing log template in ODT](https://github.com/MooersLab/writing-log-odt) ODT can be read by Open Office, LibreOffice, and MS Word.\n- [Writing log template in DOCX for MS Word](https://github.com/MooersLab/writing-log-docx) MS Word variant. This is the least suitable format for this task.\n- Planned: a version for typist.\n\nThe LaTeX version will have the most features.\nThe `logXXXhiddenCommentsVer0.5.8.tex` file is easy to edit in a free account on [Overleaf](https://www.overleaf.com/).\nYou can view it in the rich text format if you cannot tolerate LaTeX.\nOverleaf is accessible to anyone with access to the World Wide Web.\nAs a result, this format best follows the FAIR principles because not everyone has access to MS Word.\n\nWhen using LaTeX, use this writing log in parallel to the main writing project document to track your progress and record your plans.\nThis template can be used in any text editor that supports LaTeX, including online servers like Overleaf.\nOther compatible text editors include Visual Studio Code, Vim, NeoVim, Emacs, TextMate, Sublime Text, etc.\nVisit [here](https://mooerslab.github.io/pymolsnips/#editors) for an informal review and install instructions for 18 leading text editors.\n\nIf you start the name of the writing log with the word `log,` this will make navigating to the current file easier when using a terminal supported by tab completion.\nI use `log` followed by the project number and name in the Camel or Pascal case.\nThis helps distinguish the log file from the `main*.tex` file that contains the manuscript.\n\nOn Overleaf, we store the writing log with the manuscript in the same project.\nWe have no trouble jumping between the manuscript and the writing log.\nWe keep both under version control in the same project.\nHowever, we can see the case for storing the writing log separately in a local subdirectory and then editing it in a text editor while continuing to edit the main manuscript in Overleaf in the browser.\nIn this approach, you may avoid committing conflicts by storing these two documents in different git repositories.\n\n\n\n## Features\n\n- Protocol for planning a manuscript.\n- A table of contents that is automatically generated and hyperlinked.\n- An automatically generated index that is hyperlinked.\n- Support for generating a references cited section from a Bibtex library.\n- Section for lists required for most manuscripts like keywords, alternate titles, and potential reviewers.\n- Includes inventories of the private and public data locations.\n- A checklist to monitor manuscript completion.\n- A timeline with milestones. A plan without deadlines is just a wish list.\n- A list of questions to ask during assessments of the project's current state.\n- Generation of a list of barriers to project completion.\n- A pre-writing protocol to warm up for the day's generative writing.\n- A writing log section for recording notes on each day's accomplishments.\n- A section for the next action item to ease starting the next day.\n- A section for to-dos.\n- A section for future project ideas, related tangents, and rabbit holes.\n- Plot of wordcount by writing session to track your progress.\n- A section for protocols, guidelines, and checklists.\n\n## Instructions\n\nInstructions for using the writing log are found in the annotations in the template.\nYou can use [logXXXXhiddenCommentsVer0.5.8.tex](https://github.com/MooersLab/writingLogTemplate/blob/main/logXXXhiddenCommentsVer0.5.8.tex), which hides the comments in commented-out lines to spare you the trouble of deleting them while retaining them for future reference.\nReplace XXXX with the project number or number-name.\n\nVersion 0.5 of the writing log was divided into five sections: \n\n- Project initiation\n- Project management and assessment\n- Daily entries\n- Future additions and tangents\n- Guidelines, checklists, protocols, and helpful tips\n\nThe subsections of these five sections are shown below.\n\n## Project initiation\n\n- Rationale\n- Elevator pitch\n- Audience\n- Target journals\n- Related projects\n- Research program mind map\n- Potential Introduction\n- Potential Results\n + Potential figures\n + Potential tables\n- Potential Discussion points\n- Published discussion points\n- Results and Discussion mind map\n- Potential titles\n- Potential keywords\n- Potential abstract\n- Abbreviations\n- Acronyms\n- Required plasmids\n- Required cells\n- Required lab supplies\n- Required software\n- Required safety training\n- Potential collaborators\n- Potential competitors\n- Potential reviewers\n- Draft cover letter\n- Inventory of data on hand and where is located\n- List of associated GitHub repositories\n- List of relevant blog posts\n- List of relevant videos\n- List of relevant literature to search and read\n- List of relevant collections of papers in literature management software (e.g., collections in research rabbit)\n- List of relevant RSS feeds\n- Acknowledgments\n- Funding sources\n- Project summary for grant report.\n- Project summary for annual report.\n- List of plans (likely stored elsewhere).\n  + Timeline to do the required experiments to test the hypothesis. \n  + User proposals for national laboratory resources.\n  + User proposals for HPC resources.\n  + Gather the appropriate information from the literature.\n  + Related current grant(s) and specific aim(s)\n  + Funding sources and account information (e.g., chart field spreads).\n  + Recruit collaborators.\n  + Recruit lab members to do the work.\n  + Career development plans for each lab member, including you.\n  + Biosafety.\n  + Authentication of key biological and chemical resources.\n  + Statistical sampling and power analysis.\n  + data analysis.\n  + Data management (backups, archives).\n  + Data sharing.\n  + The NIH PEDP.\n\n## Plan for timely completion of this project\n\n  - A checklist for the completion of the manuscript.\n  - A timeline with milestones.\n  - Snapshots of the project's current state.\n  - Current list of barriers to project completion.\n\n\n## Protocol for pre-writing exercises\n\n\n## Daily entries\n\n- Daily Protocol.\n- Daily Log.\n- Next action.\n- To be done.\n- Timeline or Benchmarks.\n- Word Count.\n- Update writing progress notebook.\n- Update personal knowledge base.\n\n\n\n## Future additions and tangents\n\n- New branches on the above mind map for this project and research program.\n- Mind map for the research program (the big picture that includes related manuscripts, talks, posters, funded grants, grant applications). This is a super metacognition tool.\n- Ideas to consider adding to the manuscript.\n  + Introduction\n  + Results\n  + Discussion\n- Graphical abstract\n- To be done someday\n- Spin-off writing projects\n  + manuscripts\n  + grant applications\n  + books\n  + talks\n  + posters\n\n\n## Guidelines, checklists, protocols, helpful hints\n \n- Tips for using Overleaf\n- Protocol for running Grammarly in Overleaf\n- Guidelines for debugging the annotated bibliography\n- Graphical Abstract\n- Guidelines for benchmarks\n- Guidelines for using the Writing Progress Notebook\n- Guidelines for using a personal knowledge base\n- Guideline for writing a cover letter.\n- Guideline for responding to reviewers.\n\n## Backmatter\n- bibliography\n- index\n- glossary\n\n## Sorting of lists\n\nSome of the above lists must be sorted, and duplicates must be removed when augmented with new items.\nMost text editors will support the sorting of lines.\nSome text editors support the removal of duplicates in a list.\nMost text editors ignore blank lines.\n\nThe function below for Emacs combines the above 3 functionalities into the keyboard shortcut `Control-c s`.\nThe keys linked by a dash are pressed down in unison.\n\n```elisp\n(defun clean-sort-list-in-region (beg end)\n  \"Clean and sort the lines in the selected region.\n   Removes duplicate lines, blank lines, and sorts alphabetically.\"\n  (interactive \"r\")\n  (let ((lines (split-string (buffer-substring-no-properties beg end) \"\\n\" t))\n        (cleaned-lines nil))\n    ;; Remove duplicates and blank lines\n    (dolist (line lines)\n      (when (and (not (string-blank-p line))\n                 (not (member line cleaned-lines)))\n        (push line cleaned-lines)))\n    ;; Sort alphabetically\n    (setq cleaned-lines (sort cleaned-lines #'string\u003c))\n    ;; Replace the region with the cleaned and sorted lines\n    (delete-region beg end)\n    (insert (mapconcat #'identity cleaned-lines \"\\n\"))))\n(global-set-key (kbd \"C-c s\") 'clean-sort-list-in-region)\n```\n\nThis function removes the blank lines in a selected region, and it removes the duplicated lines. \nThen this function sorts the remaining lines in alphabetical order.\nTo select the list by creating a region, move the cursor to the first line, enter `Control-space` (or `C-space` in Emacs shorthand), and use the down arrow to select the list.\nEnter `Control-c s` (i.e., C-c s) to apply the function to the list.\nThis function is useful for updating keywords and other lists in the writing log.\n\n\n## Usage on Overleaf\n\n- Upload the files into your current writing project.\n- Open the writing log file to edit and compile it on the fly.\n- Compile times are lightning fast.\n- You can configure Overleaf to use its default, Vim, or Emacs key bindings.\n\n\n## Usage in Emacs\n\nEmacs has the `latex-mode` built into the main distribution.\nYou can install the `AUCTeX` package on top of it.\nCompile times are several seconds on a 2018 MacBook Pro with 32 GB of RAM.\n\n- `git clone https://github.com/MooersLab/writingLogTemplate` into your current writing project folder.\n- Start Emacs, perhaps using the [latex-emacs](https://github.com/MooersLab/latex-emacs) profile.\n- Load the writingLogTemplate.tex file into Emacs via the pull-down menu or the keybinding `C-x C-f`. \n- Essential keybindings for editing this file include (note that most of these operations are available via the pull-down menus):\n  + `C-g` to abort the current command.\n  + `C-x C-c` to quit Emacs\n  + `C-x C-s` to save the current document.\n  + `C-x C-w` to write the current document to a new file name.\n  + `C-x u` to undo the last change.\n  + `M-UP` or `M-DOWN` to shift lines up and down. UP and Down are the arrow keys.\n  + `C-c =` to create a navigable table of contents at the top of the `tex` file.\n  + `C-c C-a` to export to pdflatex, bibtex, make index, and open the resulting PDF in the default PDF viewer.\n\nFor more keybindings, see the README.md file of the repository for the [latex-emacs](https://github.com/MooersLab/latex-emacs) profile.\n\n## Bash helper functions\n\nFunction for creating a writing log template for a new writing project.\nThe most recent template has been copied to `current.tex`.\nEdit the file paths to customize to your situation.\n\n```bash\nfunction logtex {\necho \"Create writing log template for a journal article in LaTeX.\"\nif [ $# -lt 1 ]; then\n  echo 1\u003e\u00262 \"$0: not enough arguments\"\n  echo \"Usage1: logtex projectIndexNumber\"\n  return 2\nelif [ $# -gt 1 ]; then\n  echo 1\u003e\u00262 \"$0: too many arguments\"\n  echo \"Usage1: logtex projectIndexNumber\"\n  return 2\nfi\nprojectID=\"$1\"\nmkdir abib$1\ncp ~/6112MooersLabGitHubLabRepos/writingLogTemplate/current.tex log$1.tex\ncp ~/6112MooersLabGitHubLabRepos/writingLogTemplate/wordcount.tex .\n}\n\nfunction texlog {\necho \"Create writing log template for a journal article in LaTeX.\"\nif [ $# -lt 1 ]; then\n  echo 1\u003e\u00262 \"$0: not enough arguments\"\n  echo \"Usage1: logtex projectIndexNumber\"\n  return 2\nelif [ $# -gt 1 ]; then\n  echo 1\u003e\u00262 \"$0: too many arguments\"\n  echo \"Usage1: logtex projectIndexNumber\"\n  return 2\nfi\nprojectID=\"$1\"\nmkdir abib$1\ncp ~/6112MooersLabGitHubLabRepos/writingLogTemplate/current.tex log$1.tex\ncp ~/6112MooersLabGitHubLabRepos/writingLogTemplate/wordcount.tex .\n}\n\n```\n\n\n\n\n## Related projects of possible interest\n\n- [Writing log template in Org-mode](https://github.com/MooersLab/writingLogTemplateInOrg)\n- [Writing log template in reStructuredText](https://github.com/MooersLab/writing-log-rst) reStructuredText is used by programmers for documentation.\n- [Writing log template in Markdown](https://github.com/MooersLab/writing-log-md) Markdown variant. Read and rendered to PDF by most good text editors.\n- [Writing log template in ODT](https://github.com/MooersLab/writing-log-odt) ODT can be read by Open Office, LibreOffice, and MS Word.\n- [Writing log template in DOCX for MS Word](https://github.com/MooersLab/writing-log-docx) MS Word variant. This is probably the least suitable format for this task.\n- [Voice computing-related repos](https://github.com/MooersLab#voice-computing)\n- [LaTeX manuscript template](https://github.com/MooersLab/manuscriptInLaTeX/edit/main/README.md)\n- [Org-mode manuscript template](https://github.com/MooersLab/manuscriptInOrg/edit/main/README.md)\n- [Slideshow template in LaTeX](https://github.com/MooersLab/slideshowTemplateLaTeX)\n- [Annotated bibliography Template in LaTeX](https://github.com/MooersLab/annotatedBibliography)\n- [Diary for 2024 in LaTeX](https://github.com/MooersLab/diary2024inLaTeX)- [latex-emacs profile](https://github.com/MooersLab/latex-emacs)\n- [default Emacs profile](https://github.com/MooersLab/configorg)\n- [snippets for latex-mode in Emacs](https://github.com/MooersLab/snippet-latex-mode)\n- [Quizzes about Emacs to improve recall of keybindings](https://github.com/MooersLab/qemacs)\n- [Slides from talk about GhostText, Data Science Workshop, July 2022](https://github.com/MooersLab/DSW22ghosttext)\n- [Video link to talk about GhostText, Data Science Workshop, July 2022](https://mediasite.ouhsc.edu/Mediasite/Channel/python/watch/4da0872f028c4255ae12935655e911321d)\n- [Slideshow about using LaTeX in Emacs, Berlin Emacs Meetup, 31 August 2022](https://github.com/MooersLab/BerlinEmacsAugust2022)\n- [The writer's crede](https://github.com/MooersLab/thewriterslaw)\n\n\n## Version History\n\n|Version           | Changes                                                                                          | Date                     |\n|:---------------- |:-------------------------------------------------------------------------------------------------|:-----------------------|\n| Version 0.3      | First posted.                                                                                   | 2024 January 22 |\n| Version 0.4.0    | Added subsections on data and code inventories.                       | 2024 April 5         |\n| Version 0.4.1    | Added subsections on lists of videos and blogs.                          | 2024 April 7         |\n| Version 0.4.2    | Added version with hidden comments.                                         | 2024 May 17       |\n| Version 0.4.2    | Edited the README.md for improving readabiity.                        | 2024 May 30       |\n| Version 0.5.0    | Added subsubsection for mindmap.                                             | 2024 June 11       |\n| Version 0.5.1    | Added subsubsection for GitHub repos.                                       | 2024 June 12      |\n| Version 0.5.2    | Added subsubsection for Plans.                                                   | 2024 June 12       |\n| Version 0.5.3    | Expanded lists to include nuts and bolts.                                     | 2024 June 15       |\n| Version 0.5.4    | Added subsection on rewriting protocol.                                       | 2024 June 18      |\n| Version 0.5.5    | Added section on planning for project completion.                       | 2024 June 19      |\n| Version 0.5.5    | Added six paragraphs to README.md explaining advanced features.        | 2024 June 20    |\n| Version 0.5.6    | Added the writer's creed.                                                              | 2024 June 24      |\n| Version 0.5.6    | Minor typos fixed in the README.md.                                         | 2024 June 25      |\n| Version 0.5.7    | Inserted list of plans.                                                                     | 2024 July 14       |\n| Version 0.5.8    | Added header with short author list, running title, date printed, and 1 of N page numbers.  Added glossary. Moved to zip file. | 2024 October 25       |\n\n## Sources of Funding\n\n- NIH: R01 CA242845\n- NIH: R01 AI088011\n- NIH: P30 CA225520 (PI: R. Mannel)\n- NIH P20GM103640 and P30GM145423 (PI: A. West)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmooerslab%2Fwritinglogtemplate","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmooerslab%2Fwritinglogtemplate","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmooerslab%2Fwritinglogtemplate/lists"}