{"id":22901261,"url":"https://github.com/mooerslab/manuscriptinorg","last_synced_at":"2025-10-07T13:09:39.700Z","repository":{"id":165234149,"uuid":"534671785","full_name":"MooersLab/manuscriptInOrg","owner":"MooersLab","description":"Manuscript in org-mode","archived":false,"fork":false,"pushed_at":"2025-08-22T12:26:36.000Z","size":1856,"stargazers_count":3,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-08-22T14:40:51.314Z","etag":null,"topics":["emacs","first-submission","ghosttext","latex","manuscript-template","org-mode","org-to-latex","overleaf","pdf","research-paper-in-org","science-writing"],"latest_commit_sha":null,"homepage":"","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,"zenodo":null}},"created_at":"2022-09-09T14:15:35.000Z","updated_at":"2025-08-22T12:26:40.000Z","dependencies_parsed_at":"2025-05-08T01:46:19.800Z","dependency_job_id":"0f222b94-e82c-41eb-a223-d85e7c408028","html_url":"https://github.com/MooersLab/manuscriptInOrg","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/MooersLab/manuscriptInOrg","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MooersLab%2FmanuscriptInOrg","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MooersLab%2FmanuscriptInOrg/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MooersLab%2FmanuscriptInOrg/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MooersLab%2FmanuscriptInOrg/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MooersLab","download_url":"https://codeload.github.com/MooersLab/manuscriptInOrg/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MooersLab%2FmanuscriptInOrg/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":278779186,"owners_count":26044304,"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","status":"online","status_checked_at":"2025-10-07T02:00:06.786Z","response_time":59,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":["emacs","first-submission","ghosttext","latex","manuscript-template","org-mode","org-to-latex","overleaf","pdf","research-paper-in-org","science-writing"],"created_at":"2024-12-14T01:32:34.513Z","updated_at":"2025-10-07T13:09:39.667Z","avatar_url":"https://github.com/MooersLab.png","language":"TeX","funding_links":[],"categories":[],"sub_categories":[],"readme":"![Version](https://img.shields.io/static/v1?label=manuscriptInOrg\u0026message=0.7.2\u0026color=brightcolor)\n[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)\n\n\n# Manuscript template in org-mode for the first submission \n\n## Background\nThe first submission of a research paper for peer review can be in a generic format as a PDF.\nThe advantage of a plain generic template is that it can be submitted to many different journals.\n\nThis is an org-mode variant of the main.tex file in the MooersLab/manuscriptInLaTeX [repo](https://github.com/MooersLab/manuscriptInLaTeX).\nThis template is for people who prefer to write research papers in org-mode because they do a lot of their other work in org-mode and do not want to switch to working in LaTeX.\nThey would rather spend all day in org-mode; it is that fun to use.\nOrg supports easy shuffling and other manipulations of document subtrees, very easy table generation, and literate programming.\nYou can also integrate manuscript writing with time management via org-agenda and knowledge management via org-roam more efficiently by staying in org-mode. \nThese features are beyond what is readily possible in LaTeX without using extra packages.\n\nIf you are already a strong LaTeX user, there is plenty of tweaking of the preamble of this template that you can do to add your favorite packages and settings.\nOrg-mode recognizes many LaTeX commands directly.\nLaTeX code can also be utilized inside of code blocks that can be evaluated on the fly.\nSee the [org-mode manual](https://orgmode.org/manual/).\n\n```elisp\n#+name: hello-world\n#+BEGIN_SRC latex\n\\LaTeX code\n#+END_SRC\n```\n\n\n\n## Sample title page\n\n![Screenshot 2024-08-18 at 6 40 00 AM](https://github.com/user-attachments/assets/fbc7cbb8-4711-427b-864d-569178196adb)\n\n## Sample second page\n\n![Screenshot 2024-10-11 at 1 14 19 PM](https://github.com/user-attachments/assets/126466ab-05cb-4150-af5a-fc33f16c9a3c)\n\n\n\n## Default Features\n\n- Line numbers.\n- Block paragraphs. Reset the indent on the line `\\setlength{\\parindent}{0pt} ` if you want indented first sentences.\n- No numbering of the sections. This is suppressed in an org-mode setting in the header (i.e., num:\\nil). Remove this setting to apply section numbering.\n- Blank lines between paragraphs. This is set by the line `\\usepackage{parskip}` in the preamble.\n- Narrow margins to conserve paper in drafts. Edit the line `\\usepackage[letterpaper, total={6.75in, 9in}]{geometry}` to change the margin width.\n- Single-spaced abstract.\n- Double-spaced main text.\n- Wrapping of sentences written one per line for sane version control.\n- Helvetica font.\n- Page numbers in the upper right-hand corner.\n- No page number on the first page.\n- The LaTeX preamble is in a drawer so you do not have to look at it when working in Emacs.\n- Comments are now in GUIDANCE drawers that can be closed with `Shift-TAB` in org-mode to reduce clutter. The contents of these drawers are not printed on export to PDF. You may want to delete them after duplicating the template.\n- Running title eases handling printed versions when traveling with several manuscripts that are being edited in parallel. The left side has the first and last author. The center has a running title (you set this in the preamble). The right side has a page number in 1/N format. \n\n## Installation\n\n1. Git clone the repo `git clone https://github.com/MooersLab/manuscriptInOrg.git`.\n2. Copy main.org to your project folder.\n3. Load `main.org` file in Emacs via the File pulldown menu or `C-x C-f`.\n4. Edit the file to customize to your manuscript.\n5. Edit the paths to your `global.bib` file and your image files.\n6. Enter `C-c C-e l o` to compile and open the resulting PDF in your default PDF viewer.\n\nCompiling takes several seconds on a 2018 MacBook Pro with 32 GB of RAM. \nOrg-mode is built into recent versions of Emacs. \nThe main.org file will be compiled into the final PDF without any configuration.\nTry `emacs -Q main.org` and then enter `C-c C-e l o`. \nThe PDF will open in your default PDF viewer.\n\n\n## Assumptions\n\n1. LaTeX is installed with all of the required style files. However, my installation was missing the **break cities.sty** file. I installed this with the `sudo port install texlive-bibtex-extra` command.\n2. You will use the LaTeX cite command and let LaTeX handle the generation of the literature cited section. This package *citar*, *helm-bibtex*, *ivy-bibtex*, or the like can help find the right citekey from inside Emacs.\n3. You can edit org-mode files in other text editors. Many text editors support syntax highlighting for org-mode. VS Code has a package that provides additional support. To get the most out of utilizing org-mode, it is best to utilize it inside of Emacs. Org-mode is now built into GNU Emacs. You can utilize org-mode without configuring the `init.el` file. You can achieve the same effect by starting your current Emacs with the `-Q` flag, which skips reading your `init.el` file. The editing and building of an `init.el` file to extend the features of Emacs can be an activity trap. Frustration associated with errors late during the editing of this file led to Emacs having a reputation for being difficult to master.\n\n## Postscript Oct 10, 2022\nMy approach was developed independently of another [solution](https://github.com/fangohr/template-latex-paper-from-orgmode/issues/4) found here. \n\n## Postscript May 16, 2023\nI had upgraded my operating system to Ventura, but I had not properly migrated my MacPorts. I found that I was missing the breakcities.sty file.\n\n## Postscript October 11, 2024\n\nI often print manuscripts before traveling to edit them while airborne.\nThe papers tend to get mixed up between projects.\nI added a header that clarifies which project a page belongs to.\n\n## Related sites\n\n- [Writing log template in Org-mode](https://github.com/MooersLab/writingLogTemplateInOrg)\n- [Writing log template in LaTeX](https://github.com/MooersLab/writingLogTemplate)\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- [Workbook for 2022 for tracking time spent and words written by project](https://github.com/MooersLab/writingProgress2022)\n- [Slideshow template in LaTeX](https://github.com/MooersLab/slideshowTemplateLaTeX)\n- [Annotated bibliography Template in LaTeX](https://github.com/MooersLab/annotatedBibliography)\n- [Diary for 2022 in LaTeX](https://github.com/MooersLab/diary2022inLaTeX)\n- [Diary for 2023 in LaTeX](https://github.com/MooersLab/diary2023inLaTeX)\n- [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- [The writer's law](https://github.com/MooersLab/thewriterslaw)\n\nNote that [latex-emacs profile](https://github.com/MooersLab/latex-emacs) has functions for converting LaTex lists into org-markdown lists.\n\n\n## Update history\n\n|Version        | Changes                                                                                                                                   | Date                        |\n|:--------------|:------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------|\n| Version 0.2   |   Added badges, funding, and update table.                                                                                                | 2024 May 21          |\n| Version 0.3   |   Updated main.org so it can compile without configuration from an init.el file.                                                          | 2024 August 18      |\n| Version 0.4   |   Fixed issues with preamble. Put comments in drawers.                                                                                    | 2024 August 22       |\n| Version 0.5   |   Put preamble in a drawer.                                                                                                               | 2024 August 26       |\n| Version 0.6   |   Put GUIDANCE drawers under subheadings with no export tag.                                                                              | 2024 August 26        |\n| Version 0.7   |  Add urlx package to allow linebreaks in urls.                                                                                            | 2024 August 27        |\n| Version 0.7.1 | Added short author list, running title, and page of N pages format to header                                                            | 2024 October 11       |\n| Version 0.7.2 | Switch to Xelatex to enable the use of true Arial fonts.                                                                                | 2025 April 13       |\n\n## Sources of funding\n\n- NIH: R01 CA242845\n- NIH: R01 AI088011\n- NIH: P30 CA225520 (PI: R. Mannel)\n- NIH: P20 GM103640 and P30 GM145423 (PI: A. West)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmooerslab%2Fmanuscriptinorg","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmooerslab%2Fmanuscriptinorg","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmooerslab%2Fmanuscriptinorg/lists"}