scientific-writer 2.2.1__py3-none-any.whl → 2.2.3__py3-none-any.whl

scientific_writer/.claude/skills/venue-templates/assets/journals/plos_one.tex

@@ -0,0 +1,317 @@
+% PLOS ONE Article Template
+% For submission to PLOS ONE and other PLOS journals
+% Last updated: 2024
+
+\documentclass[10pt,letterpaper]{article}
+
+% Packages
+\usepackage[top=0.85in,left=2.75in,footskip=0.75in]{geometry}
+\usepackage{amsmath,amssymb}
+\usepackage{changepage}
+\usepackage[utf8]{inputenc}
+\usepackage{textcomp,marvosym}
+\usepackage{cite}
+\usepackage{nameref,hyperref}
+\usepackage[right]{lineno}
+\usepackage{microtype}
+\usepackage{graphicx}
+\usepackage[table]{xcolor}
+\usepackage{array}
+\usepackage{authblk}
+
+% Line numbering
+\linenumbers
+
+% Set up authblk for PLOS format
+\renewcommand\Authfont{\fontsize{12}{14}\selectfont}
+\renewcommand\Affilfont{\fontsize{9}{11}\selectfont}
+
+% Title
+\title{Your Article Title Here: Concise and Descriptive}
+
+% Authors and Affiliations
+\author[1]{First Author}
+\author[1,2]{Second Author}
+\author[2,$\dagger$]{Third Author}
+
+\affil[1]{Department of Biology, University Name, City, State, Country}
+\affil[2]{Institute of Research, Institution Name, City, Country}
+
+% Corresponding author
+\affil[$\dagger$]{Corresponding author. E-mail: [email protected]}
+
+\date{}
+
+\begin{document}
+
+\maketitle
+
+% Abstract
+\begin{abstract}
+\noindent
+Write a structured or unstructured abstract of 250-300 words. The abstract should be accessible to a broad readership and should clearly state: (1) background/rationale, (2) objectives, (3) methods, (4) principal findings with key data, and (5) conclusions and significance. Do not include citations in the abstract.
+\end{abstract}
+
+% Introduction
+\section*{Introduction}
+
+Provide background and context for your study. The introduction should:
+\begin{itemize}
+    \item Present the rationale for your study
+    \item Clearly state what is currently known about the topic
+    \item Identify the knowledge gap your study addresses
+    \item State your research objectives or hypotheses
+    \item Explain the significance of the research
+\end{itemize}
+
+Review relevant literature \cite{smith2023,jones2022}, setting your work in context.
+
+State your main research question or objective at the end of the introduction.
+
+% Materials and Methods
+\section*{Materials and Methods}
+
+Provide sufficient detail to allow reproduction of your work.
+
+\subsection*{Study Design}
+Describe the overall study design (e.g., prospective cohort, randomized controlled trial, observational study, etc.).
+
+\subsection*{Participants/Samples}
+Describe your study population, sample collection, or experimental subjects:
+\begin{itemize}
+    \item Sample size and how it was determined (power analysis)
+    \item Inclusion and exclusion criteria
+    \item Demographic information
+    \item For animal studies: species, strain, age, sex, housing conditions
+\end{itemize}
+
+\subsection*{Procedures}
+Detail all experimental procedures, measurements, and interventions. Include:
+\begin{itemize}
+    \item Equipment and reagents (with manufacturer, catalog numbers)
+    \item Protocols and procedures (step-by-step if novel)
+    \item Controls used
+    \item Blinding and randomization (if applicable)
+\end{itemize}
+
+\subsection*{Data Collection}
+Describe how data were collected, including instruments, assays, and measurements.
+
+\subsection*{Statistical Analysis}
+Clearly describe statistical methods used:
+\begin{itemize}
+    \item Software and version (e.g., R 4.3.0, Python 3.9 with scipy 1.9.0)
+    \item Statistical tests performed (e.g., t-tests, ANOVA, regression)
+    \item Significance level ($\alpha$, typically 0.05)
+    \item Corrections for multiple testing
+    \item Sample size justification
+\end{itemize}
+
+\subsection*{Ethical Approval}
+Include relevant ethical approval statements:
+\begin{itemize}
+    \item Human subjects: IRB approval, protocol number, consent procedures
+    \item Animal research: IACUC approval, protocol number, welfare considerations
+    \item Field studies: Permits and permissions
+\end{itemize}
+
+Example: "This study was approved by the Institutional Review Board of University Name (Protocol \#12345). All participants provided written informed consent."
+
+% Results
+\section*{Results}
+
+Present your findings in a logical sequence. Refer to figures and tables as you describe results. Do not interpret results in this section (save for Discussion).
+
+\subsection*{First Major Finding}
+Describe your first key result. Statistical results should include effect sizes and confidence intervals in addition to p-values.
+
+As shown in Figure~\ref{fig:results1}, we observed a significant increase in [outcome variable] (mean $\pm$ SD: 45.2 $\pm$ 8.3 vs. 32.1 $\pm$ 6.9; t = 7.42, df = 48, p < 0.001).
+
+\begin{figure}[!ht]
+\centering
+% \includegraphics[width=0.75\textwidth]{figure1.png}
+\caption{{\bf Figure 1. Title of first figure.}
+Detailed figure legend describing what is shown. Include: (A) Description of panel A. (B) Description of panel B. Sample sizes (n), error bars represent [SD, SEM, 95\% CI], and statistical significance indicated by asterisks (* p < 0.05, ** p < 0.01, *** p < 0.001). Statistical test used should be stated.}
+\label{fig:results1}
+\end{figure}
+
+\subsection*{Second Major Finding}
+Describe your second key result, referencing Table~\ref{tab:results1}.
+
+\begin{table}[!ht]
+\centering
+\caption{{\bf Table 1. Title of table.}}
+\label{tab:results1}
+\begin{tabular}{lccc}
+\hline
+\textbf{Condition} & \textbf{Measurement 1} & \textbf{Measurement 2} & \textbf{p-value} \\
+\hline
+Control & 25.3 $\pm$ 3.1 & 48.2 $\pm$ 5.4 & -- \\
+Treatment A & 32.7 $\pm$ 2.8 & 55.1 $\pm$ 4.9 & 0.003 \\
+Treatment B & 41.2 $\pm$ 3.5 & 62.8 $\pm$ 6.2 & < 0.001 \\
+\hline
+\end{tabular}
+\begin{flushleft}
+Values shown as mean $\pm$ standard deviation (n = 20 per group). P-values from one-way ANOVA with Tukey's post-hoc test comparing to control.
+\end{flushleft}
+\end{table}
+
+\subsection*{Additional Results}
+Present additional findings as needed.
+
+% Discussion
+\section*{Discussion}
+
+Interpret your results and place them in the context of existing literature.
+
+\subsection*{Principal Findings}
+Summarize your main findings concisely.
+
+\subsection*{Interpretation}
+Interpret your findings and explain their significance. How do they advance understanding of the topic? Compare and contrast with previous studies \cite{brown2021,williams2020}.
+
+\subsection*{Strengths and Limitations}
+Discuss both strengths and limitations of your study honestly:
+
+\textbf{Strengths:}
+\begin{itemize}
+    \item Large sample size with adequate statistical power
+    \item Rigorous methodology with appropriate controls
+    \item Novel approach or finding
+\end{itemize}
+
+\textbf{Limitations:}
+\begin{itemize}
+    \item Cross-sectional design limits causal inference
+    \item Generalizability may be limited to [specific population]
+    \item Potential confounding variables not measured
+\end{itemize}
+
+\subsection*{Implications}
+Discuss the practical or theoretical implications of your findings.
+
+\subsection*{Future Directions}
+Suggest directions for future research.
+
+% Conclusions
+\section*{Conclusions}
+
+Provide a concise conclusion summarizing the main findings and their significance. Avoid repeating the abstract.
+
+% Acknowledgments
+\section*{Acknowledgments}
+
+Acknowledge individuals who contributed but do not meet authorship criteria, technical assistance, and writing assistance. Example: "We thank Dr. Jane Doe for technical assistance with microscopy and Dr. John Smith for helpful discussions."
+
+% References
+\section*{References}
+
+% Using BibTeX
+\bibliographystyle{plos2015}
+\bibliography{references}
+
+% Or manually formatted (Vancouver style, numbered):
+\begin{thebibliography}{99}
+
+\bibitem{smith2023}
+Smith JD, Johnson ML, Williams KR. Title of article. Journal Abbrev. 2023;45(3):301-318. doi:10.1371/journal.pone.1234567.
+
+\bibitem{jones2022}
+Jones AB, Brown CD. Another article title. PLoS ONE. 2022;17(8):e0234567. doi:10.1371/journal.pone.0234567.
+
+\bibitem{brown2021}
+Brown EF, Davis GH, Wilson IJ, Taylor JK. Comprehensive study title. Nat Commun. 2021;12:1234. doi:10.1038/s41467-021-12345-6.
+
+\bibitem{williams2020}
+Williams LM, Anderson NO. Previous work on topic. Science. 2020;368(6489):456-460. doi:10.1126/science.abc1234.
+
+\end{thebibliography}
+
+% Supporting Information
+\section*{Supporting Information}
+
+List all supporting information files (captions provided separately during submission):
+
+\paragraph{S1 Fig.}
+\textbf{Title of supplementary figure 1.} Brief description.
+
+\paragraph{S2 Fig.}
+\textbf{Title of supplementary figure 2.} Brief description.
+
+\paragraph{S1 Table.}
+\textbf{Title of supplementary table 1.} Brief description.
+
+\paragraph{S1 Dataset.}
+\textbf{Raw data.} Complete dataset used in analysis (CSV format).
+
+\paragraph{S1 File.}
+\textbf{Supplementary methods.} Additional methodological details.
+
+% Author Contributions (CRediT taxonomy recommended)
+\section*{Author Contributions}
+
+Use CRediT (Contributor Roles Taxonomy):
+\begin{itemize}
+    \item \textbf{Conceptualization:} FA, SA
+    \item \textbf{Data curation:} FA
+    \item \textbf{Formal analysis:} FA, SA
+    \item \textbf{Funding acquisition:} TA
+    \item \textbf{Investigation:} FA, SA
+    \item \textbf{Methodology:} FA, SA, TA
+    \item \textbf{Project administration:} TA
+    \item \textbf{Resources:} TA
+    \item \textbf{Software:} FA
+    \item \textbf{Supervision:} TA
+    \item \textbf{Validation:} FA, SA
+    \item \textbf{Visualization:} FA
+    \item \textbf{Writing – original draft:} FA
+    \item \textbf{Writing – review \& editing:} FA, SA, TA
+\end{itemize}
+
+(FA = First Author, SA = Second Author, TA = Third Author)
+
+% Data Availability Statement (REQUIRED)
+\section*{Data Availability}
+
+Choose one of the following:
+
+\textbf{Option 1 (Public repository):} 
+All data are available in the [repository name] repository at [URL/DOI].
+
+\textbf{Option 2 (Supporting Information):}
+All relevant data are within the paper and its Supporting Information files.
+
+\textbf{Option 3 (Available on request):}
+Data cannot be shared publicly because of [reason]. Data are available from the [institution/contact] (contact via [email]) for researchers who meet the criteria for access to confidential data.
+
+\textbf{Option 4 (Third-party):}
+Data are available from [third party] (contact: [details]) for researchers who meet criteria for access.
+
+% Funding Statement (REQUIRED)
+\section*{Funding}
+
+State all funding sources including grant numbers. If no funding, state "The authors received no specific funding for this work."
+
+Example: "This work was supported by the National Science Foundation (NSF) [grant number 123456 to TA] and the National Institutes of Health (NIH) [grant number R01-234567 to TA]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript."
+
+% Competing Interests (REQUIRED)
+\section*{Competing Interests}
+
+Declare any financial or non-financial competing interests. If none, state: "The authors have declared that no competing interests exist."
+
+If competing interests exist, declare them explicitly: "Author TA is a consultant for Company X. This does not alter our adherence to PLOS ONE policies on sharing data and materials."
+
+\end{document}
+
+% Notes for Authors:
+% 1. PLOS ONE has no length limit - be concise but thorough
+% 2. Use Vancouver style for citations [1], [2], [3]
+% 3. Figures: TIFF or EPS format, 300-600 dpi
+% 4. All data must be made available (data availability statement required)
+% 5. Include line numbers for review
+% 6. PLOS ONE focuses on scientific rigor, not novelty or impact
+% 7. Reporting guidelines encouraged (CONSORT, STROBE, PRISMA, etc.)
+% 8. Ethical approval required for human/animal studies
+% 9. All authors must agree to submission
+% 10. Submit via PLOS online submission system
+

scientific_writer/.claude/skills/venue-templates/assets/posters/beamerposter_academic.tex

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+% Academic Research Poster Template using beamerposter
+% For conference presentations
+% Last updated: 2024
+
+\documentclass[final]{beamer}
+
+% Poster size and scale
+% Common sizes: a0, a1, a2, a3, a4
+% Custom size: size=custom,width=XX,height=YY
+\usepackage[size=a0,scale=1.24,orientation=portrait]{beamerposter}
+
+% Packages
+\usepackage[utf8]{inputenc}
+\usepackage{amsmath,amsthm,amssymb,latexsym}
+\usepackage{graphicx}
+\usepackage{booktabs,array}
+\usepackage{multirow}
+\usepackage{qrcode}  % For QR codes
+\usepackage{tikz}
+\usepackage{lipsum}  % For placeholder text (remove in final version)
+
+% Beamer theme
+\usetheme{Berlin}
+% Other themes: default, AnnArbor, Antibes, Bergen, Berkeley, Berlin, Boadilla, CambridgeUS, Copenhagen, Darmstadt, Dresden, Frankfurt, Goettingen, Hannover, Ilmenau, JuanLesPins, Luebeck, Madrid, Malmoe, Marburg, Montpellier, PaloAlto, Pittsburgh, Rochester, Singapore, Szeged, Warsaw
+
+% Color theme
+\usecolortheme{seahorse}
+% Other color themes: default, albatross, beaver, beetle, crane, dolphin, dove, fly, lily, orchid, rose, seagull, seahorse, whale, wolverine
+
+% Custom colors (Okabe-Ito colorblind-safe palette)
+\definecolor{OIorange}{RGB}{230,159,0}
+\definecolor{OIblue}{RGB}{86,180,233}
+\definecolor{OIgreen}{RGB}{0,158,115}
+\definecolor{OIyellow}{RGB}{240,228,66}
+\definecolor{OIdarkblue}{RGB}{0,114,178}
+\definecolor{OIvermillion}{RGB}{213,94,0}
+\definecolor{OIpurple}{RGB}{204,121,167}
+
+% Set custom colors
+\setbeamercolor{block title}{fg=white,bg=OIdarkblue}
+\setbeamercolor{block body}{fg=black,bg=white}
+\setbeamercolor{block alerted title}{fg=white,bg=OIvermillion}
+\setbeamercolor{block alerted body}{fg=black,bg=white}
+
+% Fonts
+\setbeamerfont{title}{size=\VERYHuge,series=\bfseries}
+\setbeamerfont{author}{size=\Large}
+\setbeamerfont{institute}{size=\large}
+\setbeamerfont{block title}{size=\large,series=\bfseries}
+\setbeamerfont{block body}{size=\normalsize}
+
+% Remove navigation symbols
+\setbeamertemplate{navigation symbols}{}
+
+% Title, authors, and affiliations
+\title{Your Research Title Here:\\A Concise and Descriptive Title}
+
+\author{First Author\inst{1}, Second Author\inst{1,2}, Third Author\inst{2}}
+
+\institute[shortinst]{
+\inst{1} Department of Science, University Name, City, State, Country\\
+\inst{2} Institute of Research, Institution Name, City, Country
+}
+
+% Footer
+\setbeamertemplate{footline}{
+  \leavevmode%
+  \hbox{%
+  \begin{beamercolorbox}[wd=.33\paperwidth,ht=4ex,dp=2ex,left]{author in head/foot}%
+    \hspace{1em}\usebeamerfont{author in head/foot}Contact: [email protected]
+  \end{beamercolorbox}%
+  \begin{beamercolorbox}[wd=.34\paperwidth,ht=4ex,dp=2ex,center]{title in head/foot}%
+    \usebeamerfont{title in head/foot}Conference Name 2024
+  \end{beamercolorbox}%
+  \begin{beamercolorbox}[wd=.33\paperwidth,ht=4ex,dp=2ex,right]{date in head/foot}%
+    \usebeamerfont{date in head/foot}University Logo\hspace{1em}
+  \end{beamercolorbox}}%
+  \vskip0pt%
+}
+
+\begin{document}
+
+\begin{frame}[t]
+\begin{columns}[t]
+
+% Left Column
+\begin{column}{.48\textwidth}
+
+% Introduction/Background
+\begin{block}{Introduction}
+\begin{itemize}
+    \item \textbf{Background:} Provide context for your research. What is the broader problem or area of study?
+    \item \textbf{Gap:} What is currently unknown or inadequately addressed?
+    \item \textbf{Objective:} Clearly state your research question or hypothesis
+    \item \textbf{Significance:} Why does this work matter?
+\end{itemize}
+
+\vspace{0.5cm}
+\textbf{Hypothesis:} State your main hypothesis clearly in one sentence.
+\end{block}
+
+\vspace{1cm}
+
+% Methods
+\begin{block}{Methods}
+
+\textbf{Study Design:} Brief description of overall approach.
+
+\vspace{0.5cm}
+
+\textbf{Participants/Samples:}
+\begin{itemize}
+    \item Sample size: n = XX
+    \item Key characteristics
+    \item Inclusion/exclusion criteria
+\end{itemize}
+
+\vspace{0.5cm}
+
+\textbf{Procedures:}
+\begin{enumerate}
+    \item Data collection procedure
+    \item Experimental intervention or measurement
+    \item Analysis approach
+\end{enumerate}
+
+\vspace{0.5cm}
+
+% Optional: Methods flowchart
+\begin{center}
+\begin{tikzpicture}[node distance=1.5cm, auto,
+    box/.style={rectangle, draw, fill=OIblue!20, text width=8cm, text centered, minimum height=1cm}]
+    \node [box] (step1) {Step 1: Participant Recruitment};
+    \node [box, below of=step1] (step2) {Step 2: Baseline Assessment};
+    \node [box, below of=step2] (step3) {Step 3: Intervention};
+    \node [box, below of=step3] (step4) {Step 4: Follow-up Assessment};
+    \node [box, below of=step4] (step5) {Step 5: Data Analysis};
+    
+    \draw [->] (step1) -- (step2);
+    \draw [->] (step2) -- (step3);
+    \draw [->] (step3) -- (step4);
+    \draw [->] (step4) -- (step5);
+\end{tikzpicture}
+\end{center}
+
+\textbf{Statistical Analysis:}
+\begin{itemize}
+    \item Statistical test used (e.g., t-test, ANOVA, regression)
+    \item Software: R 4.3.0, Python 3.9
+    \item Significance level: $\alpha = 0.05$
+\end{itemize}
+
+\end{block}
+
+\end{column}
+
+% Right Column
+\begin{column}{.48\textwidth}
+
+% Results
+\begin{block}{Results}
+
+\textbf{Finding 1: Main Result}
+
+\vspace{0.5cm}
+
+% Figure 1
+\begin{figure}
+\centering
+% \includegraphics[width=0.9\textwidth]{figure1.pdf}
+\caption{Figure 1. Main result showing significant effect. Error bars represent standard deviation. * p < 0.05, ** p < 0.01, *** p < 0.001.}
+\end{figure}
+
+\vspace{0.5cm}
+
+\textbf{Finding 2: Secondary Analysis}
+
+\vspace{0.5cm}
+
+% Table or second figure
+\begin{table}
+\centering
+\caption{Summary of key results}
+\begin{tabular}{lcccc}
+\toprule
+\textbf{Condition} & \textbf{Mean} & \textbf{SD} & \textbf{n} & \textbf{p-value} \\
+\midrule
+Control & 25.3 & 3.1 & 30 & -- \\
+Treatment A & 32.7 & 2.8 & 30 & 0.003 \\
+Treatment B & 41.2 & 3.5 & 30 & < 0.001 \\
+\bottomrule
+\end{tabular}
+\end{table}
+
+\vspace{0.5cm}
+
+\textbf{Finding 3: Additional Observation}
+
+Describe third key finding with reference to supporting data.
+
+\end{block}
+
+\vspace{1cm}
+
+% Discussion/Conclusions
+\begin{block}{Discussion \& Conclusions}
+
+\textbf{Main Findings:}
+\begin{itemize}
+    \item Summary of first key result
+    \item Summary of second key result
+    \item Summary of third key result
+\end{itemize}
+
+\vspace{0.5cm}
+
+\textbf{Interpretation:}
+\begin{itemize}
+    \item How do these findings advance understanding?
+    \item How do they compare to previous work?
+    \item What are the mechanisms or explanations?
+\end{itemize}
+
+\vspace{0.5cm}
+
+\textbf{Limitations:}
+\begin{itemize}
+    \item Acknowledge key limitations honestly
+    \item Discuss how they might affect interpretation
+\end{itemize}
+
+\vspace{0.5cm}
+
+\textbf{Future Directions:}
+\begin{itemize}
+    \item Next steps for research
+    \item Potential applications
+\end{itemize}
+
+\vspace{0.5cm}
+
+\begin{alertblock}{Key Takeaway}
+\textbf{One-sentence summary of most important finding or implication.}
+\end{alertblock}
+
+\end{block}
+
+\vspace{1cm}
+
+% References and QR Code
+\begin{block}{References \& Contact}
+
+\begin{minipage}[t]{0.65\textwidth}
+\small
+\textbf{Selected References:}
+\begin{enumerate}
+    \item Smith et al. (2023). \textit{Journal Name}, 45:123-130.
+    \item Jones \& Brown (2022). \textit{Another Journal}, 12:456-467.
+    \item Williams et al. (2021). \textit{Third Journal}, 8:789-801.
+\end{enumerate}
+
+\vspace{0.3cm}
+
+\textbf{Acknowledgments:} Funding from [Agency] Grant \#12345. Thanks to [collaborators].
+\end{minipage}
+\hfill
+\begin{minipage}[t]{0.3\textwidth}
+\begin{center}
+\qrcode[height=3cm]{https://yourlab.university.edu/paper}\\
+\small Scan for full paper\\and supplementary materials
+\end{center}
+\end{minipage}
+
+\end{block}
+
+\end{column}
+
+\end{columns}
+\end{frame}
+
+\end{document}
+
+% Notes for Poster Design:
+% 1. Font sizes (for A0 poster):
+%    - Title: 80-100pt
+%    - Authors: 60pt
+%    - Section headers: 50-60pt
+%    - Body text: 32-36pt (set by beamerposter scale)
+%    - Captions: 28-32pt
+% 
+% 2. Use colorblind-safe colors (Okabe-Ito palette provided)
+% 
+% 3. Keep text minimal - use bullets, not paragraphs
+% 
+% 4. Make figures large and clear
+% 
+% 5. Use white space effectively - don't crowd
+% 
+% 6. Test readability from 6 feet (2 meters) away
+% 
+% 7. Include QR code linking to paper, lab website, or supplementary materials
+% 
+% 8. Print at professional print shop (FedEx Office, university print center)
+% 
+% 9. Common poster sizes:
+%    - A0: 841 × 1189 mm (33.1 × 46.8 in)
+%    - 36" × 48" (914 × 1219 mm)
+%    - Check conference requirements!
+% 
+% 10. Compile with: pdflatex beamerposter_academic.tex
+