Hypothesis Generation
spacering-net/codeg
Structured hypothesis formulation from observations. An agent skill from spacering-net/codeg.
Practical advice for thriving in PhD programs and academic research
Install Grad School Guide
$ npx skills add wentorai/research-plugins --skill grad-school-guide -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install wentorai/research-plugins grad-school-guide --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/research/methodology/grad-school-guide .claude/skills/grad-school-guide && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "grad-school-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/research/methodology/grad-school-guide into .claude/skills/grad-school-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "grad-school-guide", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/wentorai/research-plugins/tree/main/skills/research/methodology/grad-school-guideType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add wentorai/research-plugins --skill grad-school-guide -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install wentorai/research-plugins grad-school-guide --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/research/methodology/grad-school-guide .agents/skills/grad-school-guide && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "grad-school-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/research/methodology/grad-school-guide into .agents/skills/grad-school-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "grad-school-guide", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add wentorai/research-plugins --skill grad-school-guide -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install wentorai/research-plugins grad-school-guide --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/research/methodology/grad-school-guide .cursor/skills/grad-school-guide && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "grad-school-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/research/methodology/grad-school-guide into .cursor/skills/grad-school-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "grad-school-guide", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/wentorai/research-plugins.git --path skills/research/methodology/grad-school-guide--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add wentorai/research-plugins --skill grad-school-guide -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install wentorai/research-plugins grad-school-guide --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/research/methodology/grad-school-guide .gemini/skills/grad-school-guide && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "grad-school-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/research/methodology/grad-school-guide into .gemini/skills/grad-school-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "grad-school-guide", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install wentorai/research-plugins grad-school-guideInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add wentorai/research-plugins --skill grad-school-guide -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/research/methodology/grad-school-guide .github/skills/grad-school-guide && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "grad-school-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/research/methodology/grad-school-guide into .github/skills/grad-school-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "grad-school-guide", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add wentorai/research-plugins --skill grad-school-guide -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install wentorai/research-plugins grad-school-guide --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/wentorai/research-plugins.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/research/methodology/grad-school-guide .opencode/skills/grad-school-guide && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "grad-school-guide" agent skill from https://github.com/wentorai/research-plugins/tree/main/skills/research/methodology/grad-school-guide into .opencode/skills/grad-school-guide/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "grad-school-guide", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
grad-school-guide- GitHub stars
- 298
- Used in
- 1 other repo
- Token cost
- ~2.1k tokens
- SKILL.md length
- 874 words
- Files
- 1
- Skills in repo
- 405
- Repo updated
- First seen
- Licence
- MIT
At a glance
Practical advice for thriving in PhD programs and academic research
- Works in 5 steps: Survey the landscape. Read 20-30 recent… → Identify gaps. Look for "future work"… → Narrow progressively. Topic -> Sub-topic… → …
- Tasks that involve Hypothesis generation
- SKILL.md covers Overview, Formulating Research Questions, Developing Hypotheses and… and Managing Your Advisor and…, plus 4 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Grad School Guide is an agent skill from wentorai/research-plugins. Practical advice for thriving in PhD programs and academic research
Its SKILL.md is about 2.1k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science, covering Hypothesis generation. The repository describes itself as: 350+ academic research skills, MCP configs, and plugins for Research-Claw and AI agents. The licence is MIT.
When your agent uses it
- Tasks that involve Hypothesis generation
Example prompts
- “/grad-school-guide”
Workflow steps
5 steps, taken from the first numbered list in SKILL.md.
- Survey the landscape. Read 20-30 recent papers in your area.
- Identify gaps. Look for "future work" sections and limitations.
- Narrow progressively. Topic -> Sub-topic -> Specific question.
- Phrase as a question. "Does X improve Y compared to Z in context W?"
- Test with the "so what?" check. If the answer is yes or no, does it matter?
What it can do on your machine
Read from SKILL.md and the folder at commit bf44b3c. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md.
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
github.comkarpathy.github.iostearnslab.yale.edubigaidream.gitbooks.iomicrosoft.com
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Grad School Guide loads about 2.1k tokens when it runs. Until then it costs about 21 tokens; SKILL.md has 874 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
The full file from wentorai/research-plugins at commit bf44b3c, republished under its MIT licence (© wentorai). 874 words, ~2,122 tokens.
Download SKILL.mdSave it as
.claude/skills/grad-school-guide/SKILL.md (or your agent's skills folder).- name
- grad-school-guide
- description
- Practical advice for thriving in PhD programs and academic research
Graduate School Research Guide
Overview
Graduate school -- particularly a PhD program -- is a multi-year commitment that demands not only technical skills but also effective research methodology, advisor management, paper writing strategies, and career planning. The difference between thriving and merely surviving often comes down to having the right mental models and practical frameworks for the research process.
This guide distills wisdom from the awesome-grad-school repository (450+ stars, maintained by the Polo Club of Data Science at Georgia Tech) and supplements it with actionable frameworks for formulating research questions, developing hypotheses, structuring a theoretical framework, and managing the end-to-end research lifecycle. The advice here applies broadly across STEM and social-science disciplines.
Whether you are an incoming PhD student, a mid-program researcher seeking to improve your productivity, or an advanced candidate preparing for the job market, this skill provides concrete tools for each stage of the journey.
Formulating Research Questions
A strong research question is the foundation of any good paper. It should be specific, answerable, and significant.
The FINER Criteria
| Criterion | Description | Example Check |
|---|---|---|
| Feasible | Can be answered with available resources | Do you have the data, compute, and time? |
| Interesting | Engages the research community | Would peers read this at a top venue? |
| Novel | Not already answered | Has OpenAlex/CrossRef search been done? |
| Ethical | Follows research ethics standards | Does it require IRB approval? |
| Relevant | Advances the field meaningfully | Does it connect to open problems? |
From Topic to Question: A Step-by-Step Process
- Survey the landscape. Read 20-30 recent papers in your area.
- Identify gaps. Look for "future work" sections and limitations.
- Narrow progressively. Topic -> Sub-topic -> Specific question.
- Phrase as a question. "Does X improve Y compared to Z in context W?"
- Test with the "so what?" check. If the answer is yes or no, does it matter?
Example progression:
Topic: Natural language processing
Sub-topic: Low-resource language translation
Gap: Few-shot methods underperform on morphologically rich languages
Question: Can morphological decomposition improve few-shot translation
quality for agglutinative languages?Developing Hypotheses and Theoretical Frameworks
From Question to Hypothesis
A hypothesis is a testable, falsifiable prediction derived from your research question:
- Directional: "Method A will achieve higher BLEU scores than Method B on agglutinative language pairs."
- Non-directional: "There will be a significant difference in BLEU scores between Method A and Method B."
- Null (H0): "There is no significant difference in BLEU scores between Method A and Method B."
Building a Conceptual Model
A conceptual model maps the relationships between your key variables:
Independent Variable Moderator Dependent Variable
[Morphological [Language [Translation
Decomposition] ------> Typology] -----> Quality (BLEU)]
| ^
| Mediator |
+-------> [Vocabulary |
Coverage] --------------------+Document your conceptual model with:
- Constructs: The abstract concepts (e.g., "translation quality").
- Operationalizations: How you measure each construct (e.g., BLEU, COMET scores).
- Relationships: Hypothesized causal or correlational links.
- Boundary conditions: Where the model applies and where it does not.
Managing Your Advisor and Research Workflow
Communication Frameworks
The Weekly Update Email:
Subject: Weekly Update - [Your Name] - Week of [Date]
1. ACCOMPLISHED THIS WEEK
- Completed experiment X with results Y
- Drafted Section 3 of the paper
2. BLOCKERS
- Need access to GPU cluster for large-scale runs
- Waiting on co-author feedback on Section 2
3. PLAN FOR NEXT WEEK
- Run ablation study on components A, B, C
- Begin writing Section 4
4. DISCUSSION ITEMS FOR MEETING
- Should we include dataset Z in our evaluation?
- Timeline for submission to [Conference]Research Productivity System
| Practice | Cadence | Tool |
|---|---|---|
| Daily progress log | End of each day | Plain text file or Notion |
| Literature reading | 2-3 papers/week | Zotero + annotations |
| Experiment tracking | Per run | Weights & Biases or MLflow |
| Writing | 30 min daily minimum | LaTeX or Markdown |
| Advisor meeting prep | Weekly | Structured update email |
| Research talks | Monthly (lab meeting) | 15-min presentation |
Paper Writing Strategy
The Reverse-Outline Method
- Write bullet points for each section (1-2 sentences per paragraph).
- Order bullets by logical flow.
- Expand each bullet into a full paragraph.
- Revise for transitions and coherence.
Show full SKILL.md (346 more words)Show less
Section-by-Section Tips
- Introduction: Open with a concrete problem, not "In recent years..."
- Related Work: Organize by theme, not chronologically. Compare approaches, do not just list them.
- Methods: Write so a competent researcher can reproduce your work.
- Results: Lead with the most important finding. Use tables for exact numbers, figures for trends.
- Discussion: Address limitations honestly. Reviewers respect self-awareness.
Handling Rejection
Paper rejection is a normal part of academic life. The awesome-grad-school community recommends:
- Allow 24-48 hours to process emotions. Do not respond immediately.
- Categorize each review comment as: (a) valid and fixable, (b) valid but requires new experiments, (c) misunderstanding to clarify, or (d) subjective disagreement.
- Create an action plan for addressing category (a) and (b) items.
- Resubmit to the next venue with improvements, not just the same paper.
Career Planning
Timeline for a 5-Year PhD
| Year | Focus | Milestones |
|---|---|---|
| 1 | Coursework + exploration | Pass qualifying exam, identify area |
| 2 | First project + first paper | Submit to workshop or conference |
| 3 | Core research + publications | 1-2 papers at top venues |
| 4 | Thesis writing + job market prep | Draft thesis proposal, internship |
| 5 | Defense + job search | Submit thesis, interview |
Building Visibility
- Maintain a personal academic website with publications and blog posts.
- Present at conferences and workshops.
- Share preprints on arXiv before publication.
- Engage constructively on academic social media.
Best Practices
- Start writing early. The paper is not separate from the research -- writing clarifies thinking.
- Build a library of reusable code. Experiment templates, plotting scripts, and data loaders save hours on each project.
- Invest in relationships. Collaborators, mentors, and peers are your most valuable resource.
- Take care of your health. PhD burnout is real. Set boundaries and maintain activities outside research.
- Read broadly. Some of the best ideas come from adjacent fields.
- Track your accomplishments. Maintain a running CV and a "brag document" for annual reviews and job applications.
References
- awesome-grad-school -- Curated grad school advice (450+ stars)
- A Survival Guide to a PhD -- Andrej Karpathy
- Modest Advice for New Graduate Students -- Stephen Stearns, Yale
- De-Mystifying Good Research -- Fei-Fei Li
- How to Write a Great Research Paper -- Simon Peyton Jones
© wentorai, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in skills/research/methodology/grad-school-guide of wentorai/research-plugins.
Open the folder on GitHubat commit bf44b3c
Used in 1 other repository
We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in wentorai/research-plugins, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Grad School Guide next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Grad School Guide this skillwentorai/research-plugins | 298 | 1 repos | ~2.1k | Automated safety check: Pass | MIT | |
| Hypothesis Generationspacering-net/codeg | 3.9k | 14 repos | ~3.6k | Automated safety check: Notes | MIT | |
| Nature Paper CardYuan1z0825/nature-skills | 47k | 2 repos | ~2.1k | Automated safety check: Pass | Apache-2.0 | |
| Hypothesis GenerationK-Dense-AI/claude-scientific-writer | 2.4k | 2 repos | ~3.9k | Automated safety check: Pass | MIT | |
| Good QuestionRimagination/good-question | 305 | 1 repos | ~4.3k | Automated safety check: Pass | MIT | |
| High Stakes Analytics Decision Lablimingrui679-design/high-stakes-analytics-decision-lab | 1k | — | ~2.2k | Automated safety check: Pass | MIT |
Similar skills
Nature Paper Card
Yuan1z0825/nature-skills
Builds a structured deep-reading card for one scientific paper, covering methods, how experiments support claims, limitations and research ideas, with a script to prepare the source.
Hypothesis Generation
K-Dense-AI/claude-scientific-writer
Formulate evidence-bounded scientific questions, candidate hypotheses, rival explanations, causal or associational claims, discriminating predictions, measurements, and preregistration-ready…
Good Question
Rimagination/good-question
A skill your agent uses when a researcher is choosing, framing, refining, or stress-testing a research question, hypothesis, thesis topic, project idea, grant direction, paper angle, or stalled…
High Stakes Analytics Decision Lab
limingrui679-design/high-stakes-analytics-decision-lab
Build or review source-backed descriptive, diagnostic, predictive, and prescriptive analysis for consequential decisions.
Claim-Driven Experiment Planner
zjYao36/Auto-Research-Refine
Turns a refined research proposal into a claim-to-evidence-to-run-order roadmap instead of a sprawling benchmark wishlist.
More from wentorai/research-plugins
All 405 skills in this repoAbstract Writing Guide
wentorai/research-plugins
Craft structured research abstracts that maximize clarity and journal acceptance
Academic Citation Manager
wentorai/research-plugins
Manage academic citations across BibTeX, APA, MLA, and Chicago formats
Academic Paper Summarizer
wentorai/research-plugins
Summarize academic papers with structured extraction of key elements
Academic Study Methods
wentorai/research-plugins
Evidence-based study techniques for academic learning and retention
Academic Tone Guide
wentorai/research-plugins
Adjust writing tone and register for academic audiences and venues
Academic Translation Guide
wentorai/research-plugins
Academic translation, post-editing, and Chinglish correction guide
Related
Categories
Questions about Grad School Guide
What does Grad School Guide do?
Practical advice for thriving in PhD programs and academic research. Grad School Guide is an agent skill from wentorai/research-plugins.
When should I use Grad School Guide?
Grad School Guide fits situations like: tasks that involve Hypothesis generation.
How do I install Grad School Guide in Claude Code?
Run `npx skills add wentorai/research-plugins --skill grad-school-guide -a claude-code`. Or copy the skill folder (skills/research/methodology/grad-school-guide in wentorai/research-plugins) into .claude/skills/grad-school-guide in your project. Claude Code loads it when a task matches its description.
How do I install Grad School Guide in Codex?
Run `npx skills add wentorai/research-plugins --skill grad-school-guide -a codex`. Or copy the skill folder (skills/research/methodology/grad-school-guide in wentorai/research-plugins) into .agents/skills/grad-school-guide in your project. Codex loads it when a task matches its description.
Can I use Grad School Guide in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add wentorai/research-plugins --skill grad-school-guide -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/grad-school-guide, .gemini/skills/grad-school-guide, .github/skills/grad-school-guide and .opencode/skills/grad-school-guide in your project.
What does Grad School Guide need to run?
SKILL.md names no scripts, command-line tools or credentials: Grad School Guide is instructions for the agent only.
Does Grad School Guide access the network?
SKILL.md names 5 domains. As links in the text: github.com, karpathy.github.io, stearnslab.yale.edu, bigaidream.gitbooks.io and microsoft.com. This is read from the text; nothing was executed.
Is Grad School Guide safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Grad School Guide use?
Grad School Guide is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Grad School Guide use?
About 2.1k tokens (SKILL.md is roughly 8.5k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Grad School Guide?
Skills that share tags, products or a category with Grad School Guide: Hypothesis Generation (spacering-net/codeg, 3.9k stars), Nature Paper Card (Yuan1z0825/nature-skills, 47k stars), Hypothesis Generation (K-Dense-AI/claude-scientific-writer, 2.4k stars) and Good Question (Rimagination/good-question, 305 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Grad School Guide?
wentorai (a GitHub user) maintains it in wentorai/research-plugins, which has 298 GitHub stars. The repository holds 405 skills in this directory. The repository was last updated on June 19, 2026.
Source: wentorai/research-plugins on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.