logProjectXver0.4.tex

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\title{Writing Log for Project \#\#\#\#, Ver0.5}
\author{Blaine H. M. Mooers \\University of Oklahoma Health Sciences}

\pgfplotsset{compat=1.18} 

\makeindex

\begin{document}
\maketitle
\tableofcontents


\section*{Introduction}


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.
When the tex file is being viewed on Overleaf, the file outline will appear in the left column.
You can navigate to different sections of the document by clicking on the file outline in this left column.

\paragraph*{Version 0.3} is a massive restructuring into four sections for improved clarity and simplicity.
The comments in the sections below can be commented out with a good text editor or by inserting a percent sign at the start of each line.
Some of the explanatory text some may have value in the future.
You can always comment out the lines that contain the explanatory text by inserting a percent sign at the start of each line.
In Overleaf, you would can select the block of text and then enter command-/ to comment out the block.



\section{Project initiation}
\subsection{Rationale for this article}
\label{sub:why}

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 field for my lab?


\subsection{Audience for the paper}
\label{sub:audience}
Describe in a paragraph of prose the target audience of this paper.



\subsection{Potential target journals for submission}
\label{sub:target-journals}

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.

\be
  \item 
  \item
  \item
  \item
\ee


\subsection{Related projects}
\label{sub:related-projects}

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.

\begin{itemize}
  \item
  \item 
  \item 
  \item 
\end{itemize}

\subsection{Draft Introduction}
\label{subsec:Introduction}

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.

\subsection{Potential results}
\label{subsec:Results.}

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.

\begin{enumerate}
  \item 
  \item
  \item
  \item
  \item
  \item
\end{enumerate}


\subsection{Potential discussion points}
\label{subsec:futureDiscussion}

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.

\subsection{Prior discussion points}
\label{subsec:priorDiscussion}
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.


\begin{enumerate}
  \item 
  \item
  \item
\end{enumerate}



\subsection{Potential titles}
\label{sub:titles}

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.


\begin{enumerate}
  \item 
  \item 
  \item
\end{enumerate}



\subsection*{Potential Keywords}
\label{sub:keywords}

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.              
\be
    \item open science
    \item 
    \item 
\ee

\subsection*{Potential Abstract}

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.



\subsection{Abbreviations}
\label{sub:abbrev}

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.


\begin{quote}
   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.
\end{quote}

Abbreviations are also listed at the end of the manuscript.

\begin{description}
    \item[abbrev] its expansion 
    \item[abbrev] its expansion 
    \item[abbrev] its expansion 
    \item[abbrev] its expansion 
\end{description}



\subsection{Potential collaborators: name; institution;e-mail}
\label{sub:collaborators}

\bi
\item 
\item
\ei




\subsection{Potential competitors: name; institution;e-mail}
\label{sub:competitors}

\bi
\item
\item 
\ei



\subsection{Potential reviewers: name; institution;e-mail}
\label{sub:reviewers}

\be
    \item 
    \item
\ee


\subsection{Draft cover letter}
\label{sub:coverletter}

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 after 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.

\subsection*{Inventory of data}

A common problem when working on a paper intermittently is to remember where you stored the data and the code needed for its analysis.
It can be difficult to find these items because they may be stored in folders with names that are not so obvious.
For example, a database or set of code may be utilized in two projects, but copies may not be made for both projects.
Ideally, these items are stored in the project folder.

However, these items may have emerged or evolved long before the paper was conceived. 
Moving these items to the current project folder may be awkward.
One does not want to make duplicates needlessly, nor does one want multiple versions to sprout up.
You can make symbolic links from the project folder to the data and code locations. 
However, it would probably be prudent to store information about the location of these files in the writing log as a backup should the symbolic links become accidentally deleted or broken.

You can store the locations of the data and code in the writing log so that you can quickly find these items.
They can be stored in the form of a two-column table.

\subsection*{Data}

\begin{table}
    \centering
    \begin{tabular}{cc}
        Description & Location\\
        \toprule
         & \\
         & \\
         & \\
         & \\
         & \\
         & \\
         & \\
         \bottomrule
    \end{tabular}
    \caption{Project's data storage locations.}
    \label{tab:my_label}
\end{table}

\subsection*{Inventory of released data}

\subsection*{Code}


\begin{table}
    \centering
    \begin{tabular}{cc}
        Description & Location\\
        \toprule
         & \\
         & \\
         & \\
         & \\
         \bottomrule
    \end{tabular}
    \caption{Project's computer code storage locations.}
    \label{tab:my_label}
\end{table}



\subsection*{Relevant videos}

\be
\item 
\ee

\subsection*{Relevant blogs}

\be
\item 
\ee



\section{Daily entries}
\label{sec:dailyEntries}

\subsection{Daily protocol}
\label{sub:entry-protocol}

\be
\item At start of work session, review the timeline \ref{sub:benchmarks}, recent daily entries \ref{sub:daily-log}, next action item \ref{sub:next}, and to-do list \ref{sub:to-do}.
\item 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.
\item At the end of the work session, move finished items to an achievement list for the day.
\item Move the unfinished items to the to-do list \ref{sub:to-do}.
\item Identify the next task or action \ref{sub:next}.
\item Update the wordcount.txt file, if you wrote anything \ref{sub:zk}.
\item Update the project Sheet in the Writing Progress Workbook \ref{sub:WPsheet}.
\item Update your personal knowledge base \ref{sub:zk}.
\ee

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\subsection{Daily Log}
\label{sub:daily-log}


\subsubsection{2024 January 21}

Accomplishments:
\bi
\item 
\item
\item
\ei



\subsection{Update Writing Progress Notebook}
\label{sub:WPsheet}
The writing progress notebook enables the tracking of progress on a project basis \footnote{\url{https://github.com/MooersLab/writing-progress-2024-25}}.
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 \footnote{\url{<insert link for specific sheet>}}.

Update the sheet for this project with the total number of minutes spent on this project and the word count.
The word count is accessed in Overleaf under the menu pull-down.
The word count operation has to be applied to a recently compiled tex document.






\subsection{Update Zettelka\"sten in org-roam}
\label{sub:zk}
Update your knowledge base if you found anything worth adding to it.

If you maintain a knowledgebase like a Zettelka\"sten in org-roam or Obsidian or Roam or Notion, you might want to consider making additions a literature notes and permanent notes at the end of a work session.
The name of the index for this project is \verb|XXXXXXXXX|.
Enter \mintinline{emacs}{Control-c n f} to search for this project note.
This knowledge base can be used to store information that you may want to use eventually in the paper.

You could alternatively create a section at the bottom of this writing log for the purpose of storing this kind of information in a list.
Often such listed are very useful for the planning and for the development of the manuscript.
While such notes can be stored in an annotated bibliography (), I seem to be less likely to utilize this information while working on a manuscript because the annotated bibliographies in a different document.
Because it is out of sight, it is also out of mind.

The advantage of keeping these bits of knowledge inside of the writing log is that you can link entries made in the daily log section to these bits of knowledge by using the \verb||\label{}|| and \verb|\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 references so you can include the cite keys with these notes if reference has been included in BibTeX library file that is sourced at the bottom of this file.
I usually source the BibTeX library file that I am using in the annotated bibliography for a the particular project.
Keeping these items together in one document will improve the odds that you act upon the collected information, and it reduces the mental bandwidth that you have to commit to managing this writing log.

Another approach that I use sometimes is to include such information on lines that have been commented out in the manuscriprt's tex document near where I want to use that information.
I do have to admit that this approach can become a little unwieldy it if the comments wind up spanning many lines.
The clutter can be eliminated by using a section\ref{subsec:new-ideas} at the bottom of the writing log has discussed above .

These notes that you may add might be in the form of what are called \textbf{permanent notes} that include new insights or plans for for the work.
These thoughts are not directly linked or derived from any particular literature reference.
Another kind of note is known as a \textbf{citation note} or \textbf{literature note} and is directly derived from a specific reference.
These kind of notes will contain the BibTeX citekey.

If you are using the Pomodoro method, you would probably want to commit the last one or two poms of a work session on a writing project to the updating of 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 across multiple days if you have fallen behind.





\subsection{Timeline,  Benchmarks, or Both}
\label{sub:benchmarks}

This section is an outline of benchmarks or deadlines.
It uses the description environment of LaTeX.
In this environment, the dates are put in square braces.
They will be printed in bold.
It helps to visualize the next steps that need to be taken to move the project forward.
It is best to try to map out a timeline so that the project can continue to move forward.


\begin{description}
\item [Jan. 21]
\item [Jan. 21]
\item [Jan. 21] 
\item [Jan. 21] 
\item [Jan. 24] 
\item [Jan. 26]
\item [Jan. 26]
\item [Jan. 30] 
\item [Feb. 5] 
\item [Feb. 8]
\item [Feb. 9]
\end{description}

\subsection{Next action}
\label{sub:next}

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.


\subsection{To be done}
\label{sub:to-do}

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 helpful guidance.

\bi
\item 
\item 
\item 
\item 
\ei



\subsection{Word Count}
\label{sub:wordcount}
\index{word count}

The word count is stored in wordcount.txt.
The word count tends to approach a plateau in the latter stages of writing.

\begin{figure}[htp!]
  \centering
  \begin{tikzpicture}
    \begin{axis}[
      xlabel={Date},
      ylabel={Word Count Cumulative},
      % legend pos=south east,
      % legend entries={},
      ]
      \addplot table [x=Day,y=Words] {wordcount.txt};
    \end{axis}
  \end{tikzpicture}
\end{figure}

\begin{table}[ht]
  \centering
  \pgfplotstabletypeset[
  columns/Date/.style={column name=Date},
  columns/Day/.style={column name=Day},
  columns/Word/.style={column name=Words},
  ]{wordcount.txt}
  \caption{Date, day and wordcount.}
  \label{tab:my_label}
\end{table}


\section{Future additions and tangents}
\label{sec:future}


\subsection{Ideas to consider adding to the manuscript}
\label{subsec:new-ideas}

\bi
    \item  
    \item  
    \item  
\ei


\subsubsection{Introduction}
\label{ssubsec:new-ideas:Intro}


\bi
    \item  
    \item  
    \item  
\ei

\subsubsection{Results}
\label{ssubsec:new-ideas:Results}

\bi
    \item  
    \item  
    \item  
\ei

\subsubsection{Discussion}
\label{ssubsec:new-ideas:Discussion}

\bi
    \item  
    \item  
    \item  
\ei

\subsection{To be done someday}
\label{subsec:someday}

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.


\bi
    \item  
    \item  
    \item  
\ei

\subsection{Spin off writing projects}
\label{subsec:spinoffs}

\begin{description}
    \item [ ]
    \item [ ]
    \item [ ]
    \item [ ]
\end{description}



\section{Guidelines, checklists, protocols, helpful hints}
\label{sec:guides}

\subsection{Tips for using Overleaf}
\label{subsec:guides:overleaf}


\be
\item Chrome has the TextArea extension that is needed to run Grammarly in Overleaf.
\item Use the shortcuts (new commands defined in the preamble) to save time typing.
\item Where shortcuts are not possible, use templates.
\item View Overleaf project with Chrome to be able to run Grammarly via the Chrome Grammarly extension.
\item code Snippets can be mapped to voice commands in Voice In Plus.
\ee 


\subsection{Protocol for running Grammarly in Overleaf}
\label{subsec:guides:grammarlyInoverleaf}

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.


\subsection{Guidelines for debugging the annotated bibliography} 
\label{subsec:guides:annotDebug}

For a templete annotated bibliography, see https://github.com/MooersLab/annotatedBibliography.

\be
\item Escape with a forward slash the following: \&, \_, \%, and \#. 
\item Title case the journal titles.
\item Replace unicode characters with LaTeX code: e.g., replace Å with \AA. Not all LaTeX document classes are compatible with unicode.
\item The primes have to be replaced with '.
\item The vertical red rectangles with a white dot in the middle should be replaced with a whitespace.
\item There are two styles in the bibtex world: bibtex and biblatex. We are using bibtex. It is simpler. It has fewer fields.
\item Use Google Scholar bibtex over Medline or PubMed biblatex. 
\item Often the error is in the bibitem entry above the one indicated in the error messages.
\item All interior braces must by followed by a comma, including the last one.
\item When stumped, replace the entry with a fresh one from Google Scholar.
\ee



\subsection{Graphical Abstract}
\label{subsec:guides:graphicalAbstract}


The following is copied from the Crystal Journal's \href{https://www.mdpi.com/journal/crystals/instructions#preparation}{author guidelines}.

\begin{quote}
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 $\times$ 1100 pixels (height $\times$ width). 
When submitting larger images, please, keep to the same ratio.
\end{quote}

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 \href{https://www.mdpi.com/2073-4352/11/3/273}{here}.


\subsection{Guidelines for benchmarks}
\label{subsec:guides:benchmarks}


\subsection{Guidelines for using Writing Progress Notebook}
\label{subsec:guides:wpnb}

The writing progress notebook enables the tracking of progress on a project basis \footnote{\url{https://github.com/MooersLab/writing-progress-2024-25}}.
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 \footnote{\url{<insert link for specific sheet>}}.




\subsection{Guidelines for using a personal knowledge base}
\label{subsec:guides:knowledgebase}

If you maintain a knowledge base like a Zettelka\"sten  in org-roam or Obsidian or Notion, you might consider adding literature notes and permanent notes at the end of a work session \footnote{\url{https://wiki2.org/en/Zettelkasten}} \footnote{\url{https://wiki2.org/en/Comparison_of_note-taking_software}}.
The name of the index for this project is \verb|XXXXXXXXX|.
Enter \mintinline{emacs}{Control-c n f} to search for this project note.
This knowledge base can store information you may want to use eventually in the paper.

These notes that you may add might be in the form of what are called \textbf{permanent notes} that include new insights or plans for the work.
These thoughts are not directly linked or derived from any particular literature reference.
Another kind of note is known as a \textbf{citation note} or \textbf{literature note} is derived from a specific reference.
This kind of note will contain the BibTeX cite key.

While such notes can be stored in an annotated bibliography (insert link), 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 of the writing log is that you can link entries made in the daily log section to these bits of learning by using the \verb|\label{}| and \verb|\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 keys with these notes if the reference has been included in the BibTeX library file that is 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 wind up spanning 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 across multiple days if you have fallen behind.


\section{Backmatter}

% Uncomment after you have installed an annotated Bibliography.
%\bibliography{annotatedBiblio/annot}

\printindex

\end{document}