This template is similar to the writing log formatted for LaTeX. They share much of the same preamble. It is exported from org-mode through LaTeX to PDF. This file compiles by entering \textbf{C-c C-e l o} without using an init.el file (e.g., \textbf{emacs -Q logXXXX.org}), but you may have to export it twice to get all of the changes in the source file deployed in the PDF. You have to wait half a minute for the compiled document to appear. The compiling is faster in LaTeX and on Overleaf. This does not matter much because I mostly read and work with the org file when planning my writing session.
This template contains a table of contents, numbered outline, and an index that support navigating the document when it has been rendered into a PDF. The label and ref macros are part of LaTeX’s hyperlinking system. Items in the table of contents and in the index are hyperlinked to sites in the body of the writing log. You can navigate to different sections of the document by clicking on the file outline in this left column.
The comments in the GUIDNACE drawers are usually hidden to reduce the clutter in the document. The comments provide a quick access to suggested ways of using a section. Put the cursor on the title of the drawer and enter tab to open the drawer. Repeat to close the drawer. The GUIDANCE drawers are under a headline with a :noexport: tag.
What is the rationale for writing this paper? To help advance the field? To help win or renew a grant funding? To establish credibility in a new Describe in a paragraph of prose the target audience of this paper. The journal titles are enumerated in descending order of desirability. You have a plan B journal identified at the time of submission so that you can respond swiftly if the plan A journal rejects the paper.1. 2. 3. 4.
By listing projects that are closely and even somewhat distantly related to the project at hand, it is possible to identify some synergies that might otherwise be overlooked. For example, when working in a new area, it is often useful to capitalize on the investment made in reading in the new field by capturing those insights in the form of a review article or book chapter. If you use Overleaf, you can include a hyperlink to the project’s webpage.- - - -
In this section and in the next two sections, we assemble the key components of the paper. You may wonder why we did not do this in the manuscript document. We find it easier to keep this prose close to the other lists in the sections that follow these subsections. In other words, we are using the writing log as an incubator for the initial drafts of these components of the paper.We craft a two-paragraph introduction following the method of Lindsay (Lindsay 2020 Scientific Writing Thinking In Words 2nd Ed). We do this drafting in the writing log until we are satisfied that we have a vision of the project that is clear enough to proceed. At this point, we transfer the draft introduction to the main manuscript.
This section contains a list of the potential key results that are vital to addressing the central hypothesis. Usually, there are 4 to 6 key results. Yes, we can think about the nature of the results even before we have performed the experiments.We are not necessarily thinking about the expected results, but we can guess about the nature of the results with regard to whether they will be in the form of a table, a graph or an image. We then do an initial sorting of the results on the basis of how much weight they bear upon testing the central hypothesis. This sorting will be the order in which the results are presented, in contrast to the general tendency to deliver the results in the order in which we obtain the results. At this point, we might even draft an initial paragraph for the results section that outlines the order of the results. This initial paragraph helps to set the reader’s expectations about the results that follow. After this initial paragraph is assembled and the planned results are listed, we will transfer this text to the main manuscript.
1. 2. 3. 4. 5. 6.
After some years of experience in a particular field, one has a sense of the critical discussion points about how the proposed results will relate to the results from the work of others. The content of this discussion is supposed to be about the relationship of our results to those reported by others. Sometimes, we expand these discussion points into initial paragraphs. After we think this section is well-developed, we will transfer it to the main manuscript. The discussion section should contain new points of discussion. If you are writing a series of papers about a topic, it is all too easy to recycle old discussion points. Before making the transfer mentioned above, we will check the proposed discussion points against those we have published to avoid repeating ourselves and remind ourselves to review our new results against our prior discussion points. You can check this list against the discussion section of your current manuscript to ensure that you are raising new points or updating prior points while appropriately citing yourself. The new results may require that we update our published discussion points.1. 2. 3. 4. 5. 6. 7.
Titles of 3-7 words long are easier for people to remember. We generally iterate through enough titles to find one that is catchy. Sometimes, this requires generating a list of more than 100 titles. This work takes time and should not be delayed until the day of manuscript submission.1. 2. 3. 4. 5. 6. 7.
Below is a list of potential keywords. Abstracting services use the title and abstract to extract terms for searching. As a result, select keywords that are not in these two parts of the paper. Usually, there is a limit on the number of keywords, so we choose the keywords carefully. We make a long list of keywords and select the best ones.- open science
2. 3. 4. 5. 6. 7.
After filling in the above subsections, we are in a solid position to draft the abstract for the paper. This is just a draft and will be updated as the results emerge. However, going through this exercise is another way of visualizing the paper’s contents and helps to strengthen that vision. Such clarity is essential to maintain momentum. A common mistake is to delay the assembly of the list of acronyms and abbreviations. An incomplete list tells the reviewer that the authors assembled the manuscript in a hurry.Acronyms/Abbreviations/Initialisms should be defined the first time they appear in each of three sections: the abstract; the main text; the first figure or table. When defined for the first time, the acronym/abbreviation/initialism should be added in parentheses after the written-out form.
Abbreviations are also listed at the end of the manuscript.
- abbrev
- its expansion
- abbrev
- its expansion
- abbrev
- its expansion
- abbrev
- its expansion
- - - -
- -
1. 2. 3. 4. 5.
It is never too early to start writing the cover letter for a project. This letter is another form of summary that is part of the actualization of the project. If we have enough energy and time left over from completing the initialization of the writing project, we may proceed to drafting the cover letter. The advantage of doing so is to capture one’s excitement about the project. It is never too early to start this section. Work on it should not be delayed until the last minute because you risk overlooking somebody’s contribution.- - - - - -
It is never too early to start this section. Work on it should not be delayed until the last minute because you risk overlooking a funding source.- - - - - - - - -
This section catalogs the data to be used in the paper. You might start this section with the data management plan included in the supporting grant application. Then you might include updates to this plan as the project evolves.#+CAPTION[Stored data]: Projects’s stored data.
| Description | Location |
|---|---|
| SSRL images February 2024 | MooersHD11 |
| SSRL images August 2024 | MooersHD12 |
#+CAPTION[External software]: Projects’s required external software.
| Description | Location |
|---|---|
| CCP4 | iMac2 |
| Phenix | iMac3 |
#+CAPTION[Software repos]: Projects’s software repositories.
| Description | Location |
|---|---|
| Repo1 | GitHub |
| Repo2 | Codeberg |
#+CAPTION[Related videos]: Videos related to project.
| Description | URL |
|---|---|
- - - - - -
- - - - - -
- - - - - -
- - - - - - -
- - - - - - -
While it is useful to write about half of a manuscript in four hours in the first sitting without having done any experiments to provide a mental framework for the project and limit the scope, the work will need to be done. If the work is computational or experimental, many plans exist to get it done. Several plans must be developed to execute the work required to complete and submit the manuscript. These plans might not be written down many times, but it is probably quite useful to actually articulate them somewhere. These plans may not necessarily have to reside inside the writing log: A link to the plan in a plain text or an HTML file may be sufficient. Some of these plans are global in nature and may be applicable across all projects. Some plans may be specific to the project at hand and must be elaborated on. If these plans are relatively short, they could be included in the writing log, but if they are lengthy, it might be necessary to just provide a link to them.- Budget
- Relation to specific aims of funded grants.
- Secure funding for the research and manuscript.
- Timeline to do the required experiments to test the hypothesis.
- Secure access to required national laboratory resources at experimental stations (i.e., general user proposal and beamtime requests).
- Secure access to computing resources.
- Gather the appropriate information from the literature.
- Recruit collaborators
- Recruit lab members to do the work.
- Individual career development for lab members, including yourself.
- Biosafety.
- Authentication of key biological and chemical resources.
- Rigorous statistical sampling and data analysis
- Data management including backups and archives.
- Data sharing.
- The NIH PEDP.
- Advertising plan: posters, talks, seminars, YouTube videos, social media posts.
- Checklist for manuscript completion.
- Timeline and Milestones.
- Periodic assessments of the current state of the manuscript.
- - -
- [ ] Central hypothesis identified.
- [ ] Introduction drafted to define scope.
- [ ] Results ordered by relevance to the central hypothesis.
- [ ] Results imagined as figures and tables.
- [ ] Results outlined to the subsection level.
- [ ] Results outlined to the paragraph level.
- [ ] Figures have been conceptualized.
- [ ] Figures have been drafted.
- [ ] Figure legends have been drafted.
- [ ] Tables have been conceptualized.
- [ ] Tables have been drafted.
- [ ] Table legends have been drafted.
- [ ] Paragraphs in the Results section drafted.
- [ ] Results concluding sentences checked.
- [ ] Discussion points identified.
- [ ] Prior publications checked for Discussion points.
- [ ] Discussion paragraphs drafted.
- [ ] Discussion concluding sentences checked.
- [ ] Discussion subsections check with the central hypothesis.
- [ ] Citations have been entered.
- [ ] Citations have been checked.
- [ ] Bibliographic information has been checked.
- [ ] Accuracy of Bibliographic information checked.
- [ ] Citations have entries in the annotated bibliography.
- [ ] Abstract drafted.
- [ ] Supplemental materials assembled.
- [ ] The first draft is finished.
- [ ] Round 1 of rewriting finished.
- [ ] Round 2 of rewriting finished.
- [ ] Ready for reverse outline.
- [ ] Round 3 of rewriting.
- [ ] Solicit review by co-authors.
- [ ] Internal polishing editing.
- [ ] Ready for intense review by a professional writer.
- [ ] Intensive review revisions have been incorporated.
- [ ] Penultimate draft ready for internal proofreader.
- [ ] Penultimate review revisions incorporated.
- [ ] Manuscript ready for submission.
#+CAPTION[Milestones]: Timeline with milestones.
| Milestone | Target date | Achievement date |
|---|---|---|
| milestone 1 | date | date |
| milestone 2 | date | date |
| milestone 3 | date | date |
| milestone 4 | date | date |
| milestone 5 | date | date |
Accomplishments:
- - -
List the next task or action to be taken to move the project forward. The section is supposed to contain one to do item. It is the next task that needs to be done. The idea to determine in at the end of the current work session what the next action should be so that you do not have to spend time selecting the next action item when you return to the project. This idea came from David Allen, the author of “Getting things done”.I have to admit that I rarely do this task next. I generally reconsider all of the pending to-do’s at the start of my work session, and I often wind up identifying a new task that was not identified as the “Next Action” at the end of the last work session. Anyways, you do gain the peace of mind knowing that you have identified the next step, although you may not take it. If you do not use this section, go ahead and delete it.
These are the tasks that are thought to be required to get the project finished. The prioritizing of the tasks is the hard part. The book “Time Power” by Charles Hobbs provides helpful guidance on setting priorities. I use an unordered list below but you can use a list of TODO items and include this org file in the list of source files for the generation of TODOs in org agenda. I generally would have an overwhelming number of TODOs so I do not use org-agenda in this fashion.- - - - - -
Update your knowledge base if you found anything worth adding to it.- - - - - -
- - -
- - - -
- - - -
- - -
This section stores tasks that are related to the current project and that may be worth doing someday. Often these tasks are tangential to addressing the central hypothesis of the paper. This is a place for capturing those wonderful ideas. Sometimes these ideas blossom into new projects. This section can capture ideas that might be mentioned in terms of future work in the discussion section of the manuscript.- - -
- ???
- ???
- ???
- ???
- At start of work session, review the timeline, recent daily entries, next action item , and to-do list.
- Write the goal(s) for the current writing session as a means of engaging mentally in the work. This prose could be retained or deleted at the end of the work session.
- At the end of the work session, move finished items to an achievement list for the day.
- Move the unfinished items to the to-do list.
- Identify the next task or action.
- Update the wordcount.txt file, if you wrote anything.
- Update the project Sheet in the Writing Progress Workbook.
- Update your personal knowledge base.
- Chrome has the TextArea extension that is needed to run Grammarly in Overleaf.
- Use the shortcuts (new commands defined in the preamble) to save time typing.
- Where shortcuts are not possible, use templates.
- View Overleaf project with Chrome to be able to run Grammarly via the Chrome Grammarly extension.
- code Snippets can be mapped to voice commands in Voice In Plus.
You must install Grammarly and Textarea extensions for Chrome. With your project open in Overleaf, open the textarea icon in the upper right of your browser and check the checkbox. This will convert the PDF viewport into RichText. Hit the Grammarly icon. Grammarly will check the text in the RichText viewport. Corrections that you make in the RichText viewport are applied to your tex file in the left viewport. Note that the preamble of the document will cause the text to be spread out. You may have to scroll down a ways to see the document environment.
Note that you must supply the full file paths. Also, note the order of the arguments to bibConvert. The third argument is the file type of the first. The fourth argument is the file type of the second argument.
For a template annotated bibliography, see https://github.com/MooersLab/annotatedBibliography.
- Escape with a forward slash the following: &, _, %, and #.
- Title case the journal titles.
- Replace unicode characters with LaTeX code: e.g., replace Å with Å. Not all LaTeX document classes are compatible with unicode.
- The primes have to be replaced with ‘.
- The vertical red rectangles with a white dot in the middle should be replaced with a whitespace.
- There are two styles in the bibtex world: bibtex and biblatex. We are using bibtex. It is simpler. It has fewer fields.
- Use Google Scholar bibtex over Medline or PubMed biblatex.
- Often the error is in the bibitem entry above the one indicated in the error messages.
- All interior braces must by followed by a comma, including the last one.
- When stumped, replace the entry with a fresh one from Google Scholar.
The following is copied from the Crystal Journal’s author guidelines.
A graphical abstract (GA) is an image that appears alongside the text abstract in the Table of Contents. In addition to summarizing the content, it should represent the topic of the article in an interesting way. The GA should be a high-quality illustration or diagram in any of the following formats: PNG, JPEG, EPS, SVG, PSD or AI. Written text in a GA should be clear and easy to read, using one of the following fonts: Times, Arial, Courier, Helvetica, Ubuntu or Calibri. The minimum size required for the GA is 560 \(×\) 1100 pixels (height \(×\) width). When submitting larger images, please, keep to the same ratio.
I usually make the mistake of treating the graphical abstract as an afterthought. Then there is no time to make one during submission of the manuscript. This can lead to delays or to the journal converting one of your sub-figures into a graphical abstract. A good example of a graphical abstract is found here.
The writing progress notebook enables the tracking of progress on a project basis [fn:3]. The Notebook automatically updates sums of words written and minutes spent across all projects on a given day. It only takes a few seconds to enter the number of words written and the time spent for a specific project on that project’s Google Sheet. If you have Voice In plus activated, say the words “open sheet 37” to have the worksheet for project 37 opened in the web browser. If not, click on this direct link to the Google Sheet in the compiled PDF of this writing log [fn:4].
If you maintain a knowledge base like a Zettelkästen in org-roam or
Obsidian or Notion, you might consider adding literature notes and
permanent notes at the end of a work session [fn:5] [fn:6]. The name of
the index for this project is XXXXXXXXX. Enter Control-c n f to find
this project note. This knowledge base can store information that you
may want to use eventually in the paper.
These notes that you may add might be in the form of what are called permanent notes that include new insights or plans for the work. These thoughts are not directly linked or derived from any particular reference in the literature. Another kind of note is known as a citation note or literature note is derived from a specific reference. This kind of note will contain the BibTeX cite key.
Although such notes can be stored in an annotated bibliography (https://github.com/MooersLab/annotatedBibliography), I seem less likely to utilize this information while working on a manuscript because the annotated bibliographies are in a different document. Because it is out of sight, the annotated bibliography is also out of mind.
The advantage of keeping these bits of knowledge inside the writing log is that you can link the entries made in the daily log section to these bits of knowledge by using the label and ref macros of LaTeX. You can also set up label and ref pairs between to-do items and the bits of knowledge. Some of these notes may refer to a particular reference, so you can include the cite key with these notes if the reference has been included in the BibTeX library file sourced at the bottom of this file.
I usually source the BibTeX library file that I am using in the annotated bibliography for a particular project. Keeping these items together in one document will improve the odds that you act upon the collected information, reducing the mental bandwidth you have to commit to managing this writing log.
Another approach I use sometimes is to include such information on lines that have been commented out in the manuscript’s tex document near where I want to utilize that information. I must admit that this approach can become a little unwieldy if the comments span many lines.
If you use the Pomodoro method, you would probably want to commit the last one or two poms of a work session on a writing project to update your knowledge base. If you have been lagging on doing such updates, you may want to commit four to six poms to this kind of work; you might have to do this over multiple days if you have fallen behind.
A writer does the following:
- Schedules daily writing time on workdays; takes a relaxed approach on weekends.
- Shows up and writes during the scheduled writing time.
- Stands up and walks around every 25 minutes for no more than 5 minutes (i.e., uses the Pomodoro technique).
- Limits generative writing to 3-5 hours daily; spends the rest of the day on supportive tasks and other duties.
- Overcomes writer’s block by rewriting the last paragraph or reverse outlining a section.
- Keeps near a list of tricks for overcoming writer’s block.
- Manages their energy by doing generative writing first, rewriting second, and supportive tasks later in the day.
- Jumps into generative writing; does not wait to be inspired.
- Does generative writing when half-awake early in the day and editing and rewriting when fully alert, generally mid to late morning.
- Masters their writing tools without letting the tools master them.
- Writes without distractions (no YouTube videos, TV, radio, etc.; playing classical music is okay sometimes).
- Tracks the time spent and words written by project ID.
- Takes credit for time spent reading material related to the project, especially if finished by making an entry in an annotated bibliography.
- Uses a separate writing log for each writing project.
- Makes writing social when it is mutually beneficial.
- Reads and writes about writing at least once a fortnight.
- Keeps up on weasel words, wordy phrases, cliché, and other junk English; reviews this list quarterly to avoid their use.
- If a scientist, writes with precision, clarity, and conciseness. The order is in descending importance. Has memorized this list.
- Uses computerized writing tools responsibly, not blindly: Takes full responsibility for the final draft.
- Documents in writing log any use of AI to generate or paraphrase passages.
- Uses dictation software for some generative writing.
- Uses software tools like Grammarly, the LanguageTool, and the Hemingway.app to stimulate improvements in their writing.
- Knows enough about good writing to accept only useful suggestions.
- Does not blindly accept noun clusters, English contractions, and weasel words suggested by AI software.
- Uses copilot when exhausted to complete sentences.
- Uses the paraphrasing tool of some chatbots (e.g. TexGPT) cautiously and only to generate intermediate drafts.
- Reviews this list periodically.
Premises of the creed:
- Writing is any activity that advances a writing project. Most of the time spent on these writing activities does not involve generative writing.
- Generative writing is the most valuable activity: All other activities descend from it.
- Generative writing and editing use different parts of the brain, so they should be done at separate times.
- Generative writing is best done when half awake because your internal editor is not fully on so new ideas are more likely to emerge.
- Generative writing be done by dictation while commuting if planned before the commute.
- Editing is best done when fully awake because your internal editor will be activated. (Be careful; late-night editing can keep you awake later than intended and interfere with your sleep pattern.)
- Most of the time spent on actual writing involves rewriting.
- Planning is an important (underemphasized) component of writing.
- Writing includes any activity that advances a writing project.
- The word count does not capture most writing-related activities. Hence, the time spent on these activities must be tracked to document these efforts.
- Time tracking is an essential component of time management. It is hard to manage what you do not measure. **Writing involves a lot of time management!!**
- 90 minutes of generative writing per day on one project is the optimal length of time due to our [ultradian cycles](https://www.youtube.com/watch?v=ezT8kGzYOng). Thank you to my brother, Randall, for alerting me to this. Longer stretches of writing on one project are known as binge writing, which always leads to diminishing returns.
- Writing includes reading the papers that you cite and those that you do not wind up citing. This reading activity can rejuvenate your momentum and inspire new ideas. It is best done in the evening so your subconscious can work overnight with the new insights. **Writing involves feeding your subconscious: Feed our head!**. Reading is grossly underemphasized in writing books. Time should be scheduled for it else it is less likely to be done.
- Writing includes mundane tasks like managing bibliographic libraries and making figures; these are good afternoon activities.
- Writing includes data analysis.
[fn:1] https://github.com/MooersLab/writing-progress-2024-25
[fn:2] <a href=”file:“><insert link for specific sheet>
[fn:3] https://github.com/MooersLab/writing-progress-2024-25
[fn:4] <a href=”file:“><insert link for specific sheet>
[fn:5] https://wiki2.org/en/Zettelkasten
[fn:6] https://wiki2.org/en/Comparison_of_note-taking_software