scientific-writer 2.1.1__py3-none-any.whl → 2.2.2__py3-none-any.whl

scientific_writer/.claude/skills/venue-templates/assets/grants/nih_specific_aims.tex

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+% NIH Specific Aims Page Template
+% THE MOST CRITICAL PAGE OF YOUR NIH PROPOSAL
+% 1 page maximum - strictly enforced
+% Last updated: 2024
+
+\documentclass[11pt,letterpaper]{article}
+
+% Formatting
+\usepackage[margin=0.5in]{geometry}  % 0.5 inch minimum margins
+\usepackage{helvet}  % Arial-like font
+\renewcommand{\familydefault}{\sfdefault}
+
+\usepackage{setspace}
+\usepackage{color}
+\usepackage{soul}  % For highlighting (remove in final version)
+
+% Remove page numbers (optional)
+\pagestyle{empty}
+
+\begin{document}
+
+% Optional: Highlight template text to remind yourself to replace
+% Remove \hl{} and color in final version
+\definecolor{highlight}{RGB}{255,255,200}
+\sethlcolor{highlight}
+
+% ====================
+% SPECIFIC AIMS PAGE
+% ====================
+
+\begin{center}
+\textbf{\large Your Project Title Here: Concise and Descriptive}
+\end{center}
+
+\vspace{0.3cm}
+
+% OPENING PARAGRAPH: The Hook and Gap
+% 2-3 sentences establishing significance and the knowledge gap
+
+\textbf{[Disease/condition]} affects \textbf{[number]} people worldwide and results in \textbf{[burden: mortality, morbidity, cost]}. \textbf{[Current treatment/understanding]} has improved outcomes, but \textbf{[limitation/gap]} remains a critical barrier to \textbf{[desired outcome]}. Understanding \textbf{[specific mechanism/relationship]} is essential for \textbf{[future advance: therapy, prevention, diagnosis]}.
+
+\vspace{0.2cm}
+
+% LONG-TERM GOAL
+% 1 sentence on your overarching research vision
+
+Our \textbf{long-term goal} is to \textbf{[overarching vision: develop cure, understand mechanism, improve treatment]} for \textbf{[disease/population]}. 
+
+\vspace{0.2cm}
+
+% OBJECTIVE AND CENTRAL HYPOTHESIS
+% 1-2 sentences on what THIS proposal will accomplish
+
+The \textbf{objective} of this proposal is to \textbf{[specific objective for this project]}. Our \textbf{central hypothesis} is that \textbf{[clearly stated, testable hypothesis]}.
+
+\vspace{0.2cm}
+
+% RATIONALE
+% 2-3 sentences explaining WHY you expect success (preliminary data!)
+
+This hypothesis is based on our \textbf{preliminary data} showing that \textbf{[key preliminary finding 1]} and \textbf{[key preliminary finding 2]}. These findings suggest that \textbf{[mechanistic explanation or expected outcome]}.
+
+\vspace{0.2cm}
+
+% TRANSITION TO AIMS
+% 1 sentence introducing the specific aims
+
+To test this hypothesis and achieve our objective, we will pursue the following \textbf{Specific Aims}:
+
+\vspace{0.3cm}
+
+% ====================
+% SPECIFIC AIM 1
+% ====================
+
+\noindent\textbf{Specific Aim 1: [Concise, active verb title describing what you'll do].}
+
+\textit{Working Hypothesis:} \hl{State testable hypothesis for this aim.}
+
+We will \textbf{[approach/method]} to determine \textbf{[what you'll learn]}. We will use \textbf{[model system/approach]} to test whether \textbf{[specific prediction]}. 
+
+\textbf{Expected Outcome:} We expect to find that \textbf{[predicted result]}. This outcome will demonstrate that \textbf{[significance of finding]} and will be \textbf{[positive/negative/innovative/transformative]} because \textbf{[why it matters]}.
+
+\vspace{0.3cm}
+
+% ====================
+% SPECIFIC AIM 2
+% ====================
+
+\noindent\textbf{Specific Aim 2: [Title of second aim].}
+
+\textit{Working Hypothesis:} \hl{Testable hypothesis for Aim 2.}
+
+Building on Aim 1, we will \textbf{[approach]} to \textbf{[objective]}. We will employ \textbf{[method/technique]} in \textbf{[model/population]} to test the hypothesis that \textbf{[specific prediction]}.
+
+\textbf{Expected Outcome:} These studies will reveal \textbf{[predicted finding]}. This is significant because \textbf{[impact on field/understanding]}.
+
+\vspace{0.3cm}
+
+% ====================
+% SPECIFIC AIM 3 (OPTIONAL)
+% ====================
+
+\noindent\textbf{Specific Aim 3: [Title of third aim].}
+
+\textit{Working Hypothesis:} \hl{Testable hypothesis for Aim 3.}
+
+To translate findings from Aims 1-2, we will \textbf{[approach]} to determine \textbf{[translational objective]}. We will \textbf{[method]} using \textbf{[clinically relevant model/patient samples]} to test whether \textbf{[translational prediction]}.
+
+\textbf{Expected Outcome:} We anticipate that \textbf{[result]}, which will provide \textbf{[proof-of-concept/validation/mechanism]} for \textbf{[therapeutic/diagnostic/preventive strategy]}.
+
+\vspace{0.3cm}
+
+% ====================
+% PAYOFF PARAGRAPH
+% ====================
+
+% 2-3 sentences on IMPACT, INNOVATION, and FUTURE DIRECTIONS
+
+\textbf{Impact and Innovation:} This project is \textbf{innovative} because it \textbf{[novel aspect: new concept, method, approach, application]}. The proposed research is \textbf{significant} because it will \textbf{[advance the field by...]} and will ultimately lead to \textbf{[long-term impact: improved treatment, new therapeutic target, diagnostic tool]}. Upon completion of these studies, we will be positioned to \textbf{[next steps: clinical trial, mechanistic studies, therapeutic development]}.
+
+\vspace{0.5cm}
+
+% ====================
+% ALTERNATIVE STRUCTURE (if preferred)
+% ====================
+
+% Some successful Specific Aims pages use this alternative structure:
+% - Open with hook (same as above)
+% - State long-term goal and objective (same)
+% - Present central hypothesis with 2-3 supporting pieces of preliminary data
+% - Then state: "We will test this hypothesis through three Specific Aims:"
+% - List aims more concisely (1-2 sentences each, plus expected outcome)
+% - Conclude with payoff paragraph emphasizing innovation, significance, impact
+
+\end{document}
+
+% ====================
+% TIPS FOR WRITING SPECIFIC AIMS
+% ====================
+
+% 1. START WITH A HOOK
+%    - Open with the big picture: disease burden, societal cost, mortality
+%    - Use compelling statistics
+%    - Make it clear why anyone should care
+
+% 2. IDENTIFY THE GAP
+%    - What's currently known?
+%    - What's the critical barrier or unknown?
+%    - Why does it matter?
+
+% 3. STATE YOUR HYPOTHESIS EXPLICITLY
+%    - Clear, testable hypothesis
+%    - Not "We hypothesize that we will study..." (that's not a hypothesis!)
+%    - "We hypothesize that [mechanism] causes [outcome]"
+
+% 4. SHOW PRELIMINARY DATA
+%    - Demonstrate feasibility
+%    - Prove you're not starting from scratch
+%    - Build confidence in your approach
+
+% 5. THREE AIMS (TYPICALLY)
+%    - Can be 2 or 4, but 3 is most common
+%    - Aims should be related but somewhat independent
+%    - Failure of one aim shouldn't sink the whole project
+%    - Aims can build on each other (Aim 1 → Aim 2 → Aim 3)
+
+% 6. EACH AIM SHOULD HAVE:
+%    - Clear title (active verb)
+%    - Working hypothesis
+%    - Approach/method
+%    - Expected outcome
+%    - Significance/impact
+
+% 7. END WITH PAYOFF
+%    - Innovation: What's new/different?
+%    - Significance: Why does it matter?
+%    - Impact: What will change?
+%    - Future: Where does this lead?
+
+% 8. COMMON MISTAKES TO AVOID
+%    - Too much background (this is not a mini-review)
+%    - Vague hypotheses or objectives
+%    - Missing expected outcomes
+%    - No preliminary data mentioned
+%    - Too ambitious (can't do it all in 5 years)
+%    - Not addressing innovation and significance
+%    - Poor logical flow between aims
+%    - Exceeding 1 page (auto-reject!)
+
+% 9. FORMATTING RULES (STRICTLY ENFORCED)
+%    - 1 page maximum (including all text, no figures typically)
+%    - Arial 11pt minimum (or equivalent)
+%    - 0.5 inch margins minimum
+%    - Any spacing (single, 1.5, double acceptable)
+%    - No smaller fonts allowed (even for superscripts/subscripts)
+
+% 10. REVISION STRATEGY
+%    - Write, get feedback, revise 10+ times
+%    - Every word must earn its place
+%    - Test on non-specialist colleagues
+%    - Read aloud to check flow
+%    - Have it reviewed by successful R01 holders
+%    - Mock study section review
+
+% ====================
+% EXAMPLES OF STRONG OPENING SENTENCES
+% ====================
+
+% DISEASE BURDEN APPROACH:
+% "Alzheimer's disease (AD) affects 6.7 million Americans and will cost $345 billion in 2023, 
+% yet no disease-modifying therapies exist."
+
+% MECHANISTIC GAP APPROACH:
+% "Despite decades of research, the molecular mechanisms driving metastasis remain poorly understood, 
+% limiting our ability to develop effective therapies for the 90% of cancer deaths caused by metastatic disease."
+
+% TRANSLATIONAL APPROACH:
+% "Current immunotherapies fail in 70% of patients with melanoma, largely because we cannot predict 
+% who will respond, highlighting an urgent need for biomarkers of treatment response."
+
+% ====================
+% REMEMBER
+% ====================
+
+% The Specific Aims page is often the ONLY page reviewers read carefully before 
+% forming their initial opinion. A weak Specific Aims page can doom an otherwise 
+% excellent proposal. Invest the time to make it compelling, clear, and concise.
+
+% Get feedback from:
+% - Successful R01 awardees in your field
+% - Grant writing office at your institution
+% - Colleagues who've served on NIH study sections
+% - Non-specialists (if they can't understand it, reviewers may struggle too)
+

scientific_writer/.claude/skills/venue-templates/assets/grants/nsf_proposal_template.tex

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+% NSF Research Proposal Template
+% For NSF Standard Grant Proposals
+% Last updated: 2024
+% Based on NSF PAPPG (Proposal & Award Policies & Procedures Guide)
+
+\documentclass[11pt,letterpaper]{article}
+
+% Required formatting
+\usepackage[margin=1in]{geometry}  % 1 inch margins required
+\usepackage{times}  % Times Roman font (11pt minimum)
+\usepackage{graphicx}
+\usepackage{amsmath}
+\usepackage{amssymb}
+\usepackage{cite}
+\usepackage{hyperref}
+
+% Single spacing (NSF allows single spacing)
+\usepackage{setspace}
+\singlespacing
+
+% Page numbers
+\usepackage{fancyhdr}
+\pagestyle{fancy}
+\fancyhf{}
+\rhead{\thepage}
+\renewcommand{\headrulewidth}{0pt}
+
+\begin{document}
+
+% ====================
+% PROJECT SUMMARY (1 page maximum)
+% ====================
+
+\section*{Project Summary}
+
+\subsection*{Overview}
+Provide a concise 1-2 paragraph description of the proposed research. This should be understandable to a scientifically literate reader who is not a specialist in your field.
+
+\subsection*{Intellectual Merit}
+Describe how the project advances knowledge within its field and across different fields. Address:
+\begin{itemize}
+    \item How the project advances understanding in the field
+    \item Innovative aspects of the research
+    \item Qualifications of the research team
+    \item Adequacy of resources
+\end{itemize}
+
+\subsection*{Broader Impacts}
+Describe the potential benefits to society and contributions to desired societal outcomes. Address one or more of the following:
+\begin{itemize}
+    \item Advancing discovery and understanding while promoting teaching and learning
+    \item Broadening participation of underrepresented groups in STEM
+    \item Disseminating broadly to enhance scientific and technological understanding
+    \item Benefits to society (economic development, health, quality of life, national security, etc.)
+    \item Developing the scientific workforce and enhancing research infrastructure
+\end{itemize}
+
+\newpage
+
+% ====================
+% PROJECT DESCRIPTION (15 pages maximum)
+% ====================
+
+\section*{Project Description}
+
+\section{Introduction and Background}
+\subsection{Current State of Knowledge}
+Provide context for your proposed research. Review relevant literature and establish what is currently known in the field.
+
+\subsection{Knowledge Gap}
+Clearly identify the gap in current knowledge or understanding that your project will address. Explain why this gap is significant.
+
+\subsection{Preliminary Work and Feasibility}
+Describe any preliminary work that demonstrates the feasibility of your approach. Highlight your team's qualifications and prior accomplishments.
+
+\section{Research Objectives and Hypotheses}
+\subsection{Overall Goal}
+State the overarching long-term goal of your research program.
+
+\subsection{Specific Objectives}
+List 2-4 specific, measurable objectives for this project:
+\begin{enumerate}
+    \item \textbf{Objective 1:} Clearly stated objective
+    \item \textbf{Objective 2:} Second objective
+    \item \textbf{Objective 3:} Third objective
+\end{enumerate}
+
+\subsection{Hypotheses}
+State your testable hypotheses explicitly.
+
+\section{Research Plan}
+\subsection{Objective 1: [Title]}
+\subsubsection{Rationale}
+Explain why this objective is important and how it addresses the knowledge gap.
+
+\subsubsection{Approach and Methods}
+Describe in detail how you will accomplish this objective. Include:
+\begin{itemize}
+    \item Experimental design or computational approach
+    \item Methods and procedures
+    \item Data collection and analysis
+    \item Controls and validation
+\end{itemize}
+
+\subsubsection{Expected Outcomes}
+Describe what results you expect and how they will advance the field.
+
+\subsubsection{Potential Challenges and Alternatives}
+Identify potential obstacles and describe alternative approaches.
+
+\subsection{Objective 2: [Title]}
+[Repeat same structure as Objective 1]
+
+\subsection{Objective 3: [Title]}
+[Repeat same structure as Objective 1]
+
+\section{Timeline and Milestones}
+Provide a detailed timeline showing when each objective will be addressed:
+
+\begin{center}
+\begin{tabular}{|l|p{3cm}|p{3cm}|p{3cm}|}
+\hline
+\textbf{Activity} & \textbf{Year 1} & \textbf{Year 2} & \textbf{Year 3} \\
+\hline
+Objective 1 activities & Months 1-6: ... & & \\
+\hline
+Objective 2 activities & Months 7-12: ... & Months 13-18: ... & \\
+\hline
+Objective 3 activities & & Months 19-24: ... & Months 25-36: ... \\
+\hline
+Publications & & Submit paper 1 & Submit papers 2-3 \\
+\hline
+\end{tabular}
+\end{center}
+
+\section{Broader Impacts}
+\textit{Note: Broader Impacts must be substantive, not perfunctory. Integrate throughout proposal.}
+
+\subsection{Educational Activities}
+Describe specific educational activities integrated with the research:
+\begin{itemize}
+    \item Curriculum development
+    \item Training of graduate and undergraduate students
+    \item K-12 outreach programs
+    \item Public science communication
+\end{itemize}
+
+\subsection{Broadening Participation}
+Describe concrete efforts to broaden participation of underrepresented groups:
+\begin{itemize}
+    \item Recruitment strategies
+    \item Mentoring programs
+    \item Partnerships with minority-serving institutions
+    \item Measurable outcomes
+\end{itemize}
+
+\subsection{Dissemination and Outreach}
+Describe plans for broad dissemination:
+\begin{itemize}
+    \item Open-access publications
+    \item Data and code sharing (repositories, licenses)
+    \item Conference presentations and workshops
+    \item Public engagement activities
+\end{itemize}
+
+\subsection{Societal Benefits}
+Explain potential benefits to society:
+\begin{itemize}
+    \item Economic development
+    \item Health and quality of life improvements
+    \item Environmental sustainability
+    \item National security (if applicable)
+\end{itemize}
+
+\subsection{Assessment of Broader Impacts}
+Describe how you will measure the success of broader impacts activities. Include specific, measurable outcomes.
+
+\section{Results from Prior NSF Support}
+\textit{Required if PI or co-PI has received NSF funding in the past 5 years}
+
+\subsection{Award Title and Number}
+Award Number: NSF-XXXXX, Amount: \$XXX,XXX, Period: MM/YY - MM/YY
+
+\subsection{Intellectual Merit}
+Summarize research accomplishments and findings from prior award.
+
+\subsection{Broader Impacts}
+Describe broader impacts activities and outcomes from prior award.
+
+\subsection{Publications}
+List publications resulting from prior NSF support (up to 5 most significant):
+\begin{enumerate}
+    \item Author, A.A., et al. (Year). Title. \textit{Journal}, vol(issue), pages.
+\end{enumerate}
+
+\newpage
+
+% ====================
+% REFERENCES CITED (No page limit)
+% ====================
+
+\section*{References Cited}
+
+\begin{thebibliography}{99}
+
+\bibitem{ref1}
+Author, A.A., \& Author, B.B. (2023). Article title. \textit{Journal Name}, \textit{45}(3), 123-145.
+
+\bibitem{ref2}
+Author, C.C., Author, D.D., \& Author, E.E. (2022). Book title. Publisher.
+
+\bibitem{ref3}
+Author, F.F., et al. (2021). Another article. \textit{Nature}, \textit{590}, 234-238.
+
+% Add more references as needed
+
+\end{thebibliography}
+
+\newpage
+
+% ====================
+% BUDGET JUSTIFICATION (3-5 pages typical)
+% Note: Budget is submitted separately in NSF's systems
+% This justifies the budget requests
+% ====================
+
+\section*{Budget Justification}
+
+\subsection*{A. Senior Personnel}
+\textbf{PI Name (X\% academic year, Y summer months):} Justify percent effort and role in project. Summer salary calculated as X/9 of academic year salary.
+
+\textbf{Co-PI Name (X\% academic year):} Justify role and effort.
+
+\subsection*{B. Other Personnel}
+\textbf{Postdoctoral Researcher (1.0 FTE, Years 1-3):} Justify need for postdoc, qualifications required, and role in project. Salary: \$XX,XXX/year.
+
+\textbf{Graduate Student (2 students, Years 1-3):} Justify need, training opportunities, and project contributions. Stipend: \$XX,XXX/year per student.
+
+\textbf{Undergraduate Researchers (2 students/year):} Describe research training opportunities. Hourly wage: \$XX/hour.
+
+\subsection*{C. Fringe Benefits}
+List fringe benefit rates for each personnel category as determined by institution.
+
+\subsection*{D. Equipment (\$5,000+)}
+\textbf{Instrument Name (\$XX,XXX):} Justify need, explain why existing equipment inadequate, describe how it enables proposed research.
+
+\subsection*{E. Travel}
+\textbf{Domestic Conference Travel (\$X,XXX/year):} Justify conference attendance for dissemination (1-2 conferences/year for PI and students).
+
+\textbf{Field Work Travel (\$X,XXX):} If applicable, justify field site visits.
+
+\subsection*{F. Participant Support Costs}
+\textit{If hosting workshop, summer program, etc.}
+
+Stipends, travel, and per diem for XX participants attending [workshop/program name].
+
+\subsection*{G. Other Direct Costs}
+\textbf{Materials and Supplies (\$X,XXX/year):} Itemize major categories (e.g., chemicals, consumables, software licenses).
+
+\textbf{Publication Costs (\$X,XXX):} Budget for open-access publication fees (estimate X papers @ \$X,XXX each).
+
+\textbf{Subaward to Partner Institution (\$XX,XXX):} Justify collaboration and subaward amount.
+
+\textbf{Other:} Justify any other costs.
+
+\subsection*{H. Indirect Costs}
+Calculated at XX\% of Modified Total Direct Costs (institution's negotiated rate).
+
+\newpage
+
+% ====================
+% DATA MANAGEMENT PLAN (2 pages maximum)
+% ====================
+
+\section*{Data Management Plan}
+
+\subsection*{Types of Data}
+Describe the types of data to be generated by the project:
+\begin{itemize}
+    \item Experimental data (e.g., measurements, observations)
+    \item Computational data (e.g., simulation results, models)
+    \item Metadata describing data collection and processing
+\end{itemize}
+
+\subsection*{Data and Metadata Standards}
+Describe standards to be used for data format and metadata:
+\begin{itemize}
+    \item File formats (e.g., HDF5, NetCDF, CSV)
+    \item Metadata standards (e.g., Dublin Core, domain-specific standards)
+    \item Documentation of data collection and processing
+\end{itemize}
+
+\subsection*{Policies for Access and Sharing}
+Describe how data will be made accessible:
+\begin{itemize}
+    \item Repository for data deposition (e.g., Dryad, Zenodo, domain-specific archive)
+    \item Timeline for public release (immediately upon publication, or within X months)
+    \item Access restrictions (if any) and justification
+    \item Embargo periods (if applicable)
+\end{itemize}
+
+\subsection*{Policies for Re-use, Redistribution}
+Describe terms for re-use:
+\begin{itemize}
+    \item Licensing (e.g., CC0, CC-BY, specific data use agreement)
+    \item Attribution requirements
+    \item Restrictions on commercial use (if any)
+\end{itemize}
+
+\subsection*{Plans for Archiving and Preservation}
+Describe long-term preservation strategy:
+\begin{itemize}
+    \item Repository selection (long-term, stable repositories)
+    \item Preservation period (minimum 3-5 years post-project)
+    \item Data formats for long-term preservation
+    \item Institutional commitments
+\end{itemize}
+
+\subsection*{Roles and Responsibilities}
+Identify who is responsible for data management implementation.
+
+\end{document}
+
+% ====================
+% ADDITIONAL DOCUMENTS (submitted separately in NSF system)
+% ====================
+
+% 1. BIOGRAPHICAL SKETCH (3 pages per person)
+%    - Use NSF-approved format (SciENcv or NSF template)
+%    - Professional preparation
+%    - Appointments
+%    - Products (up to 5 most relevant, up to 5 other significant)
+%    - Synergistic activities
+
+% 2. CURRENT AND PENDING SUPPORT
+%    - All current and pending support for all senior personnel
+%    - Use NSF format
+%    - Check for overlap with proposed project
+
+% 3. FACILITIES, EQUIPMENT, AND OTHER RESOURCES
+%    - Describe available facilities and equipment
+%    - Computational resources
+%    - Laboratory space
+%    - Other resources supporting the project
+
+% ====================
+% FORMATTING CHECKLIST
+% ====================
+
+% ☐ Margins: 1 inch on all sides
+% ☐ Font: Times Roman 11pt or larger (or equivalent)
+% ☐ Line spacing: Single spacing acceptable
+% ☐ Project Summary: 1 page, includes Overview, Intellectual Merit, Broader Impacts
+% ☐ Project Description: 15 pages maximum
+% ☐ References Cited: No page limit, consistent formatting
+% ☐ Biographical Sketches: 3 pages per person, NSF-approved format
+% ☐ Budget Justification: Detailed and reasonable
+% ☐ Data Management Plan: 2 pages maximum
+% ☐ Current & Pending: Complete and accurate
+% ☐ Facilities: Adequate resources described
+% ☐ Broader Impacts: Substantive and integrated throughout
+% ☐ All required sections included
+
+% ====================
+% SUBMISSION NOTES
+% ====================
+
+% 1. Submit through Research.gov or Grants.gov
+% 2. Follow your institution's internal deadlines (usually 3-5 days before NSF deadline)
+% 3. Obtain institutional approval before submission
+% 4. Ensure all senior personnel have NSF IDs
+% 5. Budget prepared in NSF's system (separate from this document)
+% 6. Check program-specific requirements (may differ from standard grant)
+% 7. Contact Program Officer for guidance (encouraged but not required)
+