@saibolla/ada 0.1.2

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Files changed (1432) hide show
  1. package/.ada/SYSTEM.md +81 -0
  2. package/.ada/agents/researcher.md +69 -0
  3. package/.ada/agents/reviewer.md +92 -0
  4. package/.ada/agents/verifier.md +45 -0
  5. package/.ada/agents/writer.md +54 -0
  6. package/.ada/settings.json +32 -0
  7. package/.ada/themes/ada.json +85 -0
  8. package/.env.example +31 -0
  9. package/AGENTS.md +79 -0
  10. package/LICENSE +191 -0
  11. package/README.md +188 -0
  12. package/bin/ada.js +26 -0
  13. package/dist/bootstrap/sync.js +143 -0
  14. package/dist/cli.js +404 -0
  15. package/dist/config/paths.js +32 -0
  16. package/dist/index.js +10 -0
  17. package/dist/model/catalog.js +255 -0
  18. package/dist/model/commands.js +180 -0
  19. package/dist/pi/launch.js +33 -0
  20. package/dist/pi/package-presets.js +55 -0
  21. package/dist/pi/runtime.js +81 -0
  22. package/dist/pi/settings.js +108 -0
  23. package/dist/pi/web-access.js +74 -0
  24. package/dist/search/commands.js +12 -0
  25. package/dist/setup/doctor.js +126 -0
  26. package/dist/setup/preview.js +117 -0
  27. package/dist/setup/prompts.js +34 -0
  28. package/dist/setup/setup.js +98 -0
  29. package/dist/setup/update.js +133 -0
  30. package/dist/system/executables.js +38 -0
  31. package/dist/system/node-version.js +31 -0
  32. package/dist/system/open-url.js +35 -0
  33. package/dist/system/promise-polyfill.js +12 -0
  34. package/dist/ui/terminal.js +64 -0
  35. package/dist/web/launch.js +48 -0
  36. package/dist/web-search.js +1 -0
  37. package/extensions/docparser/constants.ts +62 -0
  38. package/extensions/docparser/deps.ts +584 -0
  39. package/extensions/docparser/doctor.ts +353 -0
  40. package/extensions/docparser/index.ts +9 -0
  41. package/extensions/docparser/input.ts +230 -0
  42. package/extensions/docparser/request.ts +67 -0
  43. package/extensions/docparser/schema.ts +82 -0
  44. package/extensions/docparser/tool.ts +305 -0
  45. package/extensions/docparser/types.ts +99 -0
  46. package/extensions/research-tools/alpha.ts +107 -0
  47. package/extensions/research-tools/header.ts +284 -0
  48. package/extensions/research-tools/help.ts +93 -0
  49. package/extensions/research-tools/project-scaffold.ts +64 -0
  50. package/extensions/research-tools/project.ts +123 -0
  51. package/extensions/research-tools/shared.ts +16 -0
  52. package/extensions/research-tools.ts +42 -0
  53. package/logo.d.mts +3 -0
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  55. package/metadata/commands.d.mts +46 -0
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  63. package/prompts/jobs.md +16 -0
  64. package/prompts/litreview.md +18 -0
  65. package/prompts/log.md +14 -0
  66. package/prompts/replicate.md +24 -0
  67. package/prompts/review.md +18 -0
  68. package/prompts/watch.md +16 -0
  69. package/scripts/build-native-bundle.mjs +349 -0
  70. package/scripts/check-node-version.mjs +35 -0
  71. package/scripts/patch-embedded-pi.mjs +588 -0
  72. package/scripts/prepare-runtime-workspace.mjs +162 -0
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+ % NSF Research Proposal Template
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+ % For NSF Standard Grant Proposals
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+ % Last updated: 2024
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+ % Based on NSF PAPPG (Proposal & Award Policies & Procedures Guide)
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+
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+ \documentclass[11pt,letterpaper]{article}
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+ % Required formatting
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+ \usepackage[margin=1in]{geometry} % 1 inch margins required
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+ \usepackage{times} % Times Roman font (11pt minimum)
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+ \usepackage{graphicx}
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+ \usepackage{amsmath}
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+ \usepackage{amssymb}
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+ \usepackage{cite}
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+ \usepackage{hyperref}
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+ \renewcommand{\headrulewidth}{0pt}
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+ \begin{document}
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+ % ====================
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+ % PROJECT SUMMARY (1 page maximum)
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+ % ====================
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+
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+ \section*{Project Summary}
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+
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+ \subsection*{Overview}
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+ 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.
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+
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+ \subsection*{Intellectual Merit}
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+ Describe how the project advances knowledge within its field and across different fields. Address:
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+ \begin{itemize}
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+ \item How the project advances understanding in the field
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+ \item Innovative aspects of the research
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+ \item Qualifications of the research team
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+ \item Adequacy of resources
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+ \end{itemize}
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+
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+ \subsection*{Broader Impacts}
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+ Describe the potential benefits to society and contributions to desired societal outcomes. Address one or more of the following:
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+ \begin{itemize}
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+ \item Advancing discovery and understanding while promoting teaching and learning
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+ \item Broadening participation of underrepresented groups in STEM
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+ \item Disseminating broadly to enhance scientific and technological understanding
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+ \item Benefits to society (economic development, health, quality of life, national security, etc.)
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+ \item Developing the scientific workforce and enhancing research infrastructure
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+ \end{itemize}
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+ \newpage
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+ % ====================
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+ % PROJECT DESCRIPTION (15 pages maximum)
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+ % ====================
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+
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+ \section*{Project Description}
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+
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+ \section{Introduction and Background}
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+ \subsection{Current State of Knowledge}
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+ Provide context for your proposed research. Review relevant literature and establish what is currently known in the field.
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+ \subsection{Knowledge Gap}
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+ Clearly identify the gap in current knowledge or understanding that your project will address. Explain why this gap is significant.
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+ \subsection{Preliminary Work and Feasibility}
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+ Describe any preliminary work that demonstrates the feasibility of your approach. Highlight your team's qualifications and prior accomplishments.
75
+
76
+ \section{Research Objectives and Hypotheses}
77
+ \subsection{Overall Goal}
78
+ State the overarching long-term goal of your research program.
79
+
80
+ \subsection{Specific Objectives}
81
+ List 2-4 specific, measurable objectives for this project:
82
+ \begin{enumerate}
83
+ \item \textbf{Objective 1:} Clearly stated objective
84
+ \item \textbf{Objective 2:} Second objective
85
+ \item \textbf{Objective 3:} Third objective
86
+ \end{enumerate}
87
+
88
+ \subsection{Hypotheses}
89
+ State your testable hypotheses explicitly.
90
+
91
+ \section{Research Plan}
92
+ \subsection{Objective 1: [Title]}
93
+ \subsubsection{Rationale}
94
+ Explain why this objective is important and how it addresses the knowledge gap.
95
+
96
+ \subsubsection{Approach and Methods}
97
+ Describe in detail how you will accomplish this objective. Include:
98
+ \begin{itemize}
99
+ \item Experimental design or computational approach
100
+ \item Methods and procedures
101
+ \item Data collection and analysis
102
+ \item Controls and validation
103
+ \end{itemize}
104
+
105
+ \subsubsection{Expected Outcomes}
106
+ Describe what results you expect and how they will advance the field.
107
+
108
+ \subsubsection{Potential Challenges and Alternatives}
109
+ Identify potential obstacles and describe alternative approaches.
110
+
111
+ \subsection{Objective 2: [Title]}
112
+ [Repeat same structure as Objective 1]
113
+
114
+ \subsection{Objective 3: [Title]}
115
+ [Repeat same structure as Objective 1]
116
+
117
+ \section{Timeline and Milestones}
118
+ Provide a detailed timeline showing when each objective will be addressed:
119
+
120
+ \begin{center}
121
+ \begin{tabular}{|l|p{3cm}|p{3cm}|p{3cm}|}
122
+ \hline
123
+ \textbf{Activity} & \textbf{Year 1} & \textbf{Year 2} & \textbf{Year 3} \\
124
+ \hline
125
+ Objective 1 activities & Months 1-6: ... & & \\
126
+ \hline
127
+ Objective 2 activities & Months 7-12: ... & Months 13-18: ... & \\
128
+ \hline
129
+ Objective 3 activities & & Months 19-24: ... & Months 25-36: ... \\
130
+ \hline
131
+ Publications & & Submit paper 1 & Submit papers 2-3 \\
132
+ \hline
133
+ \end{tabular}
134
+ \end{center}
135
+
136
+ \section{Broader Impacts}
137
+ \textit{Note: Broader Impacts must be substantive, not perfunctory. Integrate throughout proposal.}
138
+
139
+ \subsection{Educational Activities}
140
+ Describe specific educational activities integrated with the research:
141
+ \begin{itemize}
142
+ \item Curriculum development
143
+ \item Training of graduate and undergraduate students
144
+ \item K-12 outreach programs
145
+ \item Public science communication
146
+ \end{itemize}
147
+
148
+ \subsection{Broadening Participation}
149
+ Describe concrete efforts to broaden participation of underrepresented groups:
150
+ \begin{itemize}
151
+ \item Recruitment strategies
152
+ \item Mentoring programs
153
+ \item Partnerships with minority-serving institutions
154
+ \item Measurable outcomes
155
+ \end{itemize}
156
+
157
+ \subsection{Dissemination and Outreach}
158
+ Describe plans for broad dissemination:
159
+ \begin{itemize}
160
+ \item Open-access publications
161
+ \item Data and code sharing (repositories, licenses)
162
+ \item Conference presentations and workshops
163
+ \item Public engagement activities
164
+ \end{itemize}
165
+
166
+ \subsection{Societal Benefits}
167
+ Explain potential benefits to society:
168
+ \begin{itemize}
169
+ \item Economic development
170
+ \item Health and quality of life improvements
171
+ \item Environmental sustainability
172
+ \item National security (if applicable)
173
+ \end{itemize}
174
+
175
+ \subsection{Assessment of Broader Impacts}
176
+ Describe how you will measure the success of broader impacts activities. Include specific, measurable outcomes.
177
+
178
+ \section{Results from Prior NSF Support}
179
+ \textit{Required if PI or co-PI has received NSF funding in the past 5 years}
180
+
181
+ \subsection{Award Title and Number}
182
+ Award Number: NSF-XXXXX, Amount: \$XXX,XXX, Period: MM/YY - MM/YY
183
+
184
+ \subsection{Intellectual Merit}
185
+ Summarize research accomplishments and findings from prior award.
186
+
187
+ \subsection{Broader Impacts}
188
+ Describe broader impacts activities and outcomes from prior award.
189
+
190
+ \subsection{Publications}
191
+ List publications resulting from prior NSF support (up to 5 most significant):
192
+ \begin{enumerate}
193
+ \item Author, A.A., et al. (Year). Title. \textit{Journal}, vol(issue), pages.
194
+ \end{enumerate}
195
+
196
+ \newpage
197
+
198
+ % ====================
199
+ % REFERENCES CITED (No page limit)
200
+ % ====================
201
+
202
+ \section*{References Cited}
203
+
204
+ \begin{thebibliography}{99}
205
+
206
+ \bibitem{ref1}
207
+ Author, A.A., \& Author, B.B. (2023). Article title. \textit{Journal Name}, \textit{45}(3), 123-145.
208
+
209
+ \bibitem{ref2}
210
+ Author, C.C., Author, D.D., \& Author, E.E. (2022). Book title. Publisher.
211
+
212
+ \bibitem{ref3}
213
+ Author, F.F., et al. (2021). Another article. \textit{Nature}, \textit{590}, 234-238.
214
+
215
+ % Add more references as needed
216
+
217
+ \end{thebibliography}
218
+
219
+ \newpage
220
+
221
+ % ====================
222
+ % BUDGET JUSTIFICATION (3-5 pages typical)
223
+ % Note: Budget is submitted separately in NSF's systems
224
+ % This justifies the budget requests
225
+ % ====================
226
+
227
+ \section*{Budget Justification}
228
+
229
+ \subsection*{A. Senior Personnel}
230
+ \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.
231
+
232
+ \textbf{Co-PI Name (X\% academic year):} Justify role and effort.
233
+
234
+ \subsection*{B. Other Personnel}
235
+ \textbf{Postdoctoral Researcher (1.0 FTE, Years 1-3):} Justify need for postdoc, qualifications required, and role in project. Salary: \$XX,XXX/year.
236
+
237
+ \textbf{Graduate Student (2 students, Years 1-3):} Justify need, training opportunities, and project contributions. Stipend: \$XX,XXX/year per student.
238
+
239
+ \textbf{Undergraduate Researchers (2 students/year):} Describe research training opportunities. Hourly wage: \$XX/hour.
240
+
241
+ \subsection*{C. Fringe Benefits}
242
+ List fringe benefit rates for each personnel category as determined by institution.
243
+
244
+ \subsection*{D. Equipment (\$5,000+)}
245
+ \textbf{Instrument Name (\$XX,XXX):} Justify need, explain why existing equipment inadequate, describe how it enables proposed research.
246
+
247
+ \subsection*{E. Travel}
248
+ \textbf{Domestic Conference Travel (\$X,XXX/year):} Justify conference attendance for dissemination (1-2 conferences/year for PI and students).
249
+
250
+ \textbf{Field Work Travel (\$X,XXX):} If applicable, justify field site visits.
251
+
252
+ \subsection*{F. Participant Support Costs}
253
+ \textit{If hosting workshop, summer program, etc.}
254
+
255
+ Stipends, travel, and per diem for XX participants attending [workshop/program name].
256
+
257
+ \subsection*{G. Other Direct Costs}
258
+ \textbf{Materials and Supplies (\$X,XXX/year):} Itemize major categories (e.g., chemicals, consumables, software licenses).
259
+
260
+ \textbf{Publication Costs (\$X,XXX):} Budget for open-access publication fees (estimate X papers @ \$X,XXX each).
261
+
262
+ \textbf{Subaward to Partner Institution (\$XX,XXX):} Justify collaboration and subaward amount.
263
+
264
+ \textbf{Other:} Justify any other costs.
265
+
266
+ \subsection*{H. Indirect Costs}
267
+ Calculated at XX\% of Modified Total Direct Costs (institution's negotiated rate).
268
+
269
+ \newpage
270
+
271
+ % ====================
272
+ % DATA MANAGEMENT PLAN (2 pages maximum)
273
+ % ====================
274
+
275
+ \section*{Data Management Plan}
276
+
277
+ \subsection*{Types of Data}
278
+ Describe the types of data to be generated by the project:
279
+ \begin{itemize}
280
+ \item Experimental data (e.g., measurements, observations)
281
+ \item Computational data (e.g., simulation results, models)
282
+ \item Metadata describing data collection and processing
283
+ \end{itemize}
284
+
285
+ \subsection*{Data and Metadata Standards}
286
+ Describe standards to be used for data format and metadata:
287
+ \begin{itemize}
288
+ \item File formats (e.g., HDF5, NetCDF, CSV)
289
+ \item Metadata standards (e.g., Dublin Core, domain-specific standards)
290
+ \item Documentation of data collection and processing
291
+ \end{itemize}
292
+
293
+ \subsection*{Policies for Access and Sharing}
294
+ Describe how data will be made accessible:
295
+ \begin{itemize}
296
+ \item Repository for data deposition (e.g., Dryad, Zenodo, domain-specific archive)
297
+ \item Timeline for public release (immediately upon publication, or within X months)
298
+ \item Access restrictions (if any) and justification
299
+ \item Embargo periods (if applicable)
300
+ \end{itemize}
301
+
302
+ \subsection*{Policies for Re-use, Redistribution}
303
+ Describe terms for re-use:
304
+ \begin{itemize}
305
+ \item Licensing (e.g., CC0, CC-BY, specific data use agreement)
306
+ \item Attribution requirements
307
+ \item Restrictions on commercial use (if any)
308
+ \end{itemize}
309
+
310
+ \subsection*{Plans for Archiving and Preservation}
311
+ Describe long-term preservation strategy:
312
+ \begin{itemize}
313
+ \item Repository selection (long-term, stable repositories)
314
+ \item Preservation period (minimum 3-5 years post-project)
315
+ \item Data formats for long-term preservation
316
+ \item Institutional commitments
317
+ \end{itemize}
318
+
319
+ \subsection*{Roles and Responsibilities}
320
+ Identify who is responsible for data management implementation.
321
+
322
+ \end{document}
323
+
324
+ % ====================
325
+ % ADDITIONAL DOCUMENTS (submitted separately in NSF system)
326
+ % ====================
327
+
328
+ % 1. BIOGRAPHICAL SKETCH (3 pages per person)
329
+ % - Use NSF-approved format (SciENcv or NSF template)
330
+ % - Professional preparation
331
+ % - Appointments
332
+ % - Products (up to 5 most relevant, up to 5 other significant)
333
+ % - Synergistic activities
334
+
335
+ % 2. CURRENT AND PENDING SUPPORT
336
+ % - All current and pending support for all senior personnel
337
+ % - Use NSF format
338
+ % - Check for overlap with proposed project
339
+
340
+ % 3. FACILITIES, EQUIPMENT, AND OTHER RESOURCES
341
+ % - Describe available facilities and equipment
342
+ % - Computational resources
343
+ % - Laboratory space
344
+ % - Other resources supporting the project
345
+
346
+ % ====================
347
+ % FORMATTING CHECKLIST
348
+ % ====================
349
+
350
+ % ☐ Margins: 1 inch on all sides
351
+ % ☐ Font: Times Roman 11pt or larger (or equivalent)
352
+ % ☐ Line spacing: Single spacing acceptable
353
+ % ☐ Project Summary: 1 page, includes Overview, Intellectual Merit, Broader Impacts
354
+ % ☐ Project Description: 15 pages maximum
355
+ % ☐ References Cited: No page limit, consistent formatting
356
+ % ☐ Biographical Sketches: 3 pages per person, NSF-approved format
357
+ % ☐ Budget Justification: Detailed and reasonable
358
+ % ☐ Data Management Plan: 2 pages maximum
359
+ % ☐ Current & Pending: Complete and accurate
360
+ % ☐ Facilities: Adequate resources described
361
+ % ☐ Broader Impacts: Substantive and integrated throughout
362
+ % ☐ All required sections included
363
+
364
+ % ====================
365
+ % SUBMISSION NOTES
366
+ % ====================
367
+
368
+ % 1. Submit through Research.gov or Grants.gov
369
+ % 2. Follow your institution's internal deadlines (usually 3-5 days before NSF deadline)
370
+ % 3. Obtain institutional approval before submission
371
+ % 4. Ensure all senior personnel have NSF IDs
372
+ % 5. Budget prepared in NSF's system (separate from this document)
373
+ % 6. Check program-specific requirements (may differ from standard grant)
374
+ % 7. Contact Program Officer for guidance (encouraged but not required)
375
+
@@ -0,0 +1,171 @@
1
+ % Nature Journal Article Template
2
+ % For submission to Nature family journals
3
+ % Last updated: 2024
4
+
5
+ \documentclass[12pt]{article}
6
+
7
+ % Packages
8
+ \usepackage[margin=2.5cm]{geometry}
9
+ \usepackage{times}
10
+ \usepackage{graphicx}
11
+ \usepackage{amsmath}
12
+ \usepackage{amssymb}
13
+ \usepackage{hyperref}
14
+ \usepackage{lineno} % Line numbers for review
15
+ \usepackage[super]{natbib} % Superscript citations
16
+
17
+ % Line numbering (required for submission)
18
+ \linenumbers
19
+
20
+ % Title and Authors
21
+ \title{Insert Your Title Here: Concise and Descriptive}
22
+
23
+ \author{
24
+ First Author\textsuperscript{1}, Second Author\textsuperscript{1,2}, Third Author\textsuperscript{2,*}
25
+ }
26
+
27
+ \date{}
28
+
29
+ \begin{document}
30
+
31
+ \maketitle
32
+
33
+ % Affiliations
34
+ \noindent
35
+ \textsuperscript{1}Department Name, Institution Name, City, State/Province, Postal Code, Country \\
36
+ \textsuperscript{2}Second Department/Institution \\
37
+ \textsuperscript{*}Correspondence: [email protected]
38
+
39
+ % Abstract
40
+ \begin{abstract}
41
+ \noindent
42
+ Write a concise abstract of 150-200 words summarizing the main findings, significance, and conclusions of your work. The abstract should be self-contained and understandable without reading the full paper. Focus on what you did, what you found, and why it matters. Avoid jargon and abbreviations where possible.
43
+ \end{abstract}
44
+
45
+ % Main Text
46
+ \section*{Introduction}
47
+ % 2-3 paragraphs setting the context
48
+ Provide background on the research area, establish the importance of the problem, and identify the knowledge gap your work addresses. Nature papers should emphasize broad significance beyond a narrow specialty.
49
+
50
+ State your main research question or objective clearly.
51
+
52
+ Briefly preview your approach and key findings.
53
+
54
+ \section*{Results}
55
+ % Primary results section
56
+ % Organize by finding, not by experiment
57
+ % Reference figures/tables as you describe results
58
+
59
+ \subsection*{First major finding}
60
+ Describe your first key result. Reference Figure~\ref{fig:example} to support your findings.
61
+
62
+ \begin{figure}[ht]
63
+ \centering
64
+ % Include your figure here
65
+ % \includegraphics[width=0.7\textwidth]{figure1.pdf}
66
+ \caption{{\bf Figure title in bold.} Detailed figure caption explaining what is shown, experimental conditions, sample sizes (n), statistical tests, and significance levels. Panels should be labeled (a), (b), etc. if multiple panels are present.}
67
+ \label{fig:example}
68
+ \end{figure}
69
+
70
+ \subsection*{Second major finding}
71
+ Describe your second key result objectively, without interpretation.
72
+
73
+ \subsection*{Third major finding}
74
+ Describe additional results as needed.
75
+
76
+ \section*{Discussion}
77
+ % Interpret results, compare to literature, acknowledge limitations
78
+
79
+ \subsection*{Main findings and interpretation}
80
+ Summarize your key findings and explain their significance. How do they advance our understanding?
81
+
82
+ \subsection*{Comparison to previous work}
83
+ Compare and contrast your results with existing literature\cite{example2023}.
84
+
85
+ \subsection*{Implications}
86
+ Discuss the broader implications of your work for the field and beyond.
87
+
88
+ \subsection*{Limitations and future directions}
89
+ Honestly acknowledge limitations and suggest future research directions.
90
+
91
+ \section*{Conclusions}
92
+ Provide a concise conclusion summarizing the main take-home messages of your work.
93
+
94
+ \section*{Methods}
95
+ % Detailed methods allowing reproducibility
96
+ % Can be placed after main text in Nature
97
+
98
+ \subsection*{Experimental design}
99
+ Describe overall experimental design, including controls.
100
+
101
+ \subsection*{Sample preparation}
102
+ Detail procedures for sample collection, preparation, and handling.
103
+
104
+ \subsection*{Data collection}
105
+ Describe instrumentation, measurement procedures, and data collection protocols.
106
+
107
+ \subsection*{Data analysis}
108
+ Explain analytical methods, statistical tests, and software used. State sample sizes, replication, and significance thresholds.
109
+
110
+ \subsection*{Ethical approval}
111
+ Include relevant ethical approval statements (human subjects, animal use, biosafety).
112
+
113
+ \section*{Data availability}
114
+ State where data supporting the findings can be accessed (repository, supplementary files, available on request).
115
+
116
+ \section*{Code availability}
117
+ If applicable, provide information on code availability (GitHub, Zenodo, etc.).
118
+
119
+ \section*{Acknowledgements}
120
+ Acknowledge funding sources, technical assistance, and other contributions. List grant numbers.
121
+
122
+ \section*{Author contributions}
123
+ Describe contributions of each author using CRediT taxonomy or similar (conceptualization, methodology, investigation, writing, etc.).
124
+
125
+ \section*{Competing interests}
126
+ Declare any financial or non-financial competing interests. If none, state "The authors declare no competing interests."
127
+
128
+ % References
129
+ \bibliographystyle{naturemag} % Nature bibliography style
130
+ \bibliography{references} % Your .bib file
131
+
132
+ % Alternatively, manually format references:
133
+ \begin{thebibliography}{99}
134
+
135
+ \bibitem{example2023}
136
+ Smith, J. D., Jones, M. L. \& Williams, K. R. Groundbreaking discovery in the field. \textit{Nature} \textbf{600}, 123--130 (2023).
137
+
138
+ \bibitem{author2022}
139
+ Author, A. A. \& Coauthor, B. B. Another important paper. \textit{Nat. Methods} \textbf{19}, 456--
140
+
141
+ 460 (2022).
142
+
143
+ % Add more references as needed
144
+
145
+ \end{thebibliography}
146
+
147
+ % Figure Legends (if not included with figures)
148
+ \section*{Figure Legends}
149
+
150
+ \textbf{Figure 1 | Figure title.} Comprehensive figure legend describing all panels, experimental conditions, sample sizes, and statistical analyses.
151
+
152
+ \textbf{Figure 2 | Second figure title.} Another detailed legend.
153
+
154
+ % Extended Data Figures (optional - supplementary figures)
155
+ \section*{Extended Data}
156
+
157
+ \textbf{Extended Data Figure 1 | Supplementary data title.} Description of supplementary figure supporting main findings.
158
+
159
+ \end{document}
160
+
161
+ % Notes for Authors:
162
+ % 1. Nature articles are typically ~3,000 words excluding Methods, References, Figure Legends
163
+ % 2. Use superscript numbered citations (1, 2, 3)
164
+ % 3. Figures should be high resolution (300+ dpi for photos, 1000 dpi for line art)
165
+ % 4. Submit figures as separate files (TIFF, EPS, or PDF)
166
+ % 5. Double-space the manuscript for review
167
+ % 6. Include line numbers using \linenumbers
168
+ % 7. Follow Nature's specific author guidelines for your target journal
169
+ % 8. Methods section can be quite detailed and placed after main text
170
+ % 9. Check word limits and specific requirements for your Nature family journal
171
+