scientific-writing

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Tool: SKILL.md [1/4] Description: --- name: scientific-writing description: "Core skill for the deep research and writing tool.

Tool: SKILL.md [2/4] Description: Ensure completeness and transparency by following established reporting standards. For comprehensive guideline details, refer to `references/reporting_guidelines.md`.

Tool: SKILL.md [3/4] Description: - Review terminology used in recent high-impact papers in the target journal - Note field-specific abbreviations, units, and notation systems - Identify preferred terms (e.g., "participants" vs.

Tool: SKILL.md [4/4] Description: Verify all citations are accurate and properly formatted 6.

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Tool: references/citation_styles.md [1/4] Description: # Citation Styles Guide ## Overview Citation styles provide standardized formats for acknowledging sources in scientific writing. Different disciplines prefer different styles, and journals typically specify which style to use. The five most common citation styles in science are AMA, Vancouver, APA, Chicago, and IEEE. ## Choosing the Right Style | Style | Primary Disciplines | In-Text Format | |-------|-------------------|----------------| |

Tool: references/citation_styles.md [2/4] Description: of work. (Year). Journal Name... ``` **No date**: Use (n.d.) ``` Smith, J. D. (n.d.).

Tool: references/citation_styles.md [3/4] Description: A., and B. B. Author.

Tool: references/citation_styles.md [4/4]

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Tool: references/figures_tables.md [1/4] Description: # Figures and Tables Best Practices ## Overview Figures and tables are essential components of scientific papers, serving to display data patterns, summarize results, and provide evidence for conclusions.

Tool: references/figures_tables.md [2/4] Description: - Using scatter plots for categorical data - Missing correlation statistics **Example applications:** - Correlation between biomarkers - Relationship between dose and response - Method comparison (Bland-Altman plots) ### Box Plots (Box-and-Whisker Plots) **Best for:** - Showing distributions and spread - Comparing distributions across groups - Identifying outliers **Design guidelines:** - Clearly define box elements (median, quartiles, whiske

### Image Manipulation **Allowed:** - Brightness/contrast adjustment applied to entire image - Color balance adjustment - Cropping (with notation) - Rotation **NOT allowed:** - Selective editing (e.g., enhancing bands in gels) - Removing background artifacts - Splicing images without clear indication - Any manipulation that obscures, eliminates, or misrepresents data **Ethical requirement:** Report all image adjustments in Methods section. ## Figure and Table Numbering ### Numbering System **Fig

- [ ] Meets journal's RGB/CMYK requirements? - [ ] Self-explanatory caption with all abbreviations defined? - [ ] Caption length within journal limits?

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Tool: references/imrad_structure.md [1/4] Description: # IMRAD Structure Guide ## Overview IMRAD (Introduction, Methods, Results, And Discussion) is the predominant organizational structure for scientific journal articles of original research. Adopted as the majority format since the 1970s, it is now the standard in medical, health, biological, chemical, engineering, and computer sciences.

Tool: references/imrad_structure.md [2/4] Description: Procedures - Describe what was done in chronological order - Include sufficient detail for replication - Use subheadings to organize complex procedures - Specify timing (e.g., "incubated for 2 hours at 37°C") - For surveys/interviews: describe instruments, validation, administration #### Measurements and Outcomes - Define all variables measured - Specify primary and secondary outcomes - Describe measurement instruments and their validity - I

Tool: references/imrad_structure.md [3/4] Description: attempted to minimize this through structured interviews." ``` ### Common Mistakes - Simply repeating results without interpretation - Over-interpreting findings or claiming causation without warrant - Ignoring inconsistent or negative findings - Failing to compare with existing literature - Introducing new data or methods - Generic or superficial discussion of limitations - Overgeneralization beyond the study population - Missing the "so wh

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Tool: references/reporting_guidelines.md [1/4] Description: # Reporting Guidelines for Scientific Studies ## Overview Reporting guidelines are evidence-based recommendations for what information should be included when reporting specific types of research studies. They provide checklists and flow diagrams to ensure complete, accurate, and transparent reporting, which is essential for readers to assess study validity and for other researchers to replicate the work. The EQUATOR Network (Enhancing

Tool: references/reporting_guidelines.md [3/4] Description: | ### Multiple Guidelines **Some studies may require multiple guidelines:** **Example 1:** Pilot RCT with qualitative component - CONSORT for quantitative arm - SRQR for qualitative component **Example 2:** Systematic review of diagnostic tests - PRISMA for review methods - STARD considerations for included studies ## Extensions and Adaptations Many reporting guidelines have extensions for specific contexts: ### CONSORT Extensions (exam

Tool: references/reporting_guidelines.md [4/4] Description: expected **Common issues leading to rejection:** - Missing required checklists (medical journals) - Insufficient methods detail for reproduction - Missing key information (randomization, blinding, power calculation) - No data/code availability statement when required **Methods statement examples:** **Journal (STROBE):** ``` This study followed STROBE reporting guidelines.

Malicious tool definition detected

Tool: references/writing_principles.md [1/4] Description: # Scientific Writing Principles ## Overview Effective scientific writing requires mastering fundamental principles that ensure clarity, precision, and impact.

- [ ] Are technical terms defined? - [ ] Is terminology consistent?

- [ ] Is spelling correct (including technical terms)? ## Tools for Improving Writing ### Grammar and Style Checkers - **Grammarly**: Grammar, style, clarity - **ProWritingAid**: In-depth writing analysis - **Hemingway Editor**: Readability, simplification - **LanguageTool**: Open-source grammar checker **Caution:** These tools don't understand scientific writing conventions.