feat: biochemical-engineer skill package v0.1.0

2026-08-14 16:54:09 +02:00
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--- a/PROVENANCE.md
+++ b/PROVENANCE.md
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+# Data provenance — biochemical-engineer
+
+Where the content of this skill package comes from, counted by
+content items (tasks, competences, tools, evidence entries, curated
+knowledge). Rendered live by Gitea:
+
+```mermaid
+%%{init: {'theme':'base','themeVariables':{'pie1':'#f9a825','pie2':'#1e88e5','pie3':'#ff355e','pie4':'#d97757','pie5':'#8e24aa','pieOuterStrokeWidth':'0px','pieSectionTextColor':'#fff'}}}%%
+pie showData
+    title Content sources — biochemical-engineer
+    "ESCO (occupation & competences)" : 89
+    "O*NET (tasks & tools)" : 59
+    "Job boards (market evidence)" : 81
+    "Anthropic official Claude skills" : 5
+    "External AI skill packs (mapped)" : 141
+```
+
+| Source | Items | Share | Files |
+|---|---|---|---|
+| ESCO (occupation & competences) | 89 | 23.7 % | references/profile.md, references/skills.md |
+| O*NET (tasks & tools) | 59 | 15.7 % | references/tasks.md, references/tools.md |
+| Job boards (market evidence) | 81 | 21.6 % | references/market.md (full report) + "Market evidence" headline sections |
+| Wikipedia & AI expert curation | 0 | 0.0 % | glossary, literature, usecases, intake, quality, evals/ |
+| Anthropic official Claude skills | 5 | 1.3 % | references/ai-skills.md, section "anthropics/skills" (official Claude Code skills) |
+| External AI skill packs (mapped) | 141 | 37.6 % | references/ai-skills.md (per-source attribution inside) |
+| Stack Exchange practitioner Q&A (CC-BY-SA) | 0 | 0.0 % | references/practitioner-qa.md (per-entry attribution inside) |
+
+Licensing: O*NET (USDOL/ETA, CC BY 4.0) · ESCO (© European Union) ·
+job-ad evidence via official APIs (JSearch/Adzuna) · Wikipedia content
+paraphrased with source URLs — never copied · external AI skills are
+linked, not copied (Apache-2.0/MIT/source-available, see ai-skills.md).
--- a/SKILL.md
+++ b/SKILL.md
@@ -0,0 +1,61 @@
+---
+name: biochemical-engineer
+description: "Occupational skill for the role 'biochemical engineer' (also: enzyme engineer, biochemical engineering adviser, biochemical research engineer, biochemical process engineer, biochemical engineering specialist, tissue engineer). Use when the user asks for typical biochemical engineer work such as: Develop lab scale models of industrial scale processes, such as fermentation.; Provide technical or scientific guidance to technical staff in the conduct of biofuels research or development.; Prepare, or oversee the preparation of, experimental plans for biofuels research or development."
+---
+
+# Biochemical Engineer
+
+Biochemical engineers research on the field of life science striving for new discoveries. They convert those findings into chemical solutions that can improve the wellbeing of society such as vaccines, tissue repair, crops improvement and green technologies advances such as cleaner fuels from natural resources.
+
+## Core workflow
+
+1. Develop lab scale models of industrial scale processes, such as fermentation.
+2. Provide technical or scientific guidance to technical staff in the conduct of biofuels research or development.
+3. Prepare, or oversee the preparation of, experimental plans for biofuels research or development.
+4. Prepare biofuels research and development reports for senior management or technical professionals.
+5. Design or conduct applied biodiesel or biofuels research projects on topics, such as transport, thermodynamics, mixing, filtration, distillation, fermentation, extraction, and separation.
+6. Conduct experiments on biomass or pretreatment technologies.
+7. Conduct experiments to test new or alternate feedstock fermentation processes.
+8. Analyze data from biofuels studies, such as fluid dynamics, water treatments, or solvent extraction and recovery processes.
+
+## How to use this skill
+
+- Read [references/profile.md](references/profile.md) for the occupation profile and scope.
+- Consult [references/tasks.md](references/tasks.md) for the full task and activity inventory.
+- Check [references/skills.md](references/skills.md) for essential vs. optional competences.
+- Check [references/tools.md](references/tools.md) for the software commonly used in this role.
+- See [references/ai-skills.md](references/ai-skills.md) — matched external AI agent skills (per-source attribution).
+
+## Key competences (essential)
+
+- adjust engineering designs
+- advise on manufacturing problems
+- advise on nitrate pollution
+- analytical chemistry
+- apply for research funding
+- apply liquid chromatography
+- apply research ethics and scientific integrity principles in research activities
+- apply statistical analysis techniques
+- approve engineering design
+- biological chemistry
+- biology
+- communicate with a non-scientific audience
+- conduct research across disciplines
+- demonstrate disciplinary expertise
+- develop biochemical manufacturing training materials
+
+## Hot technologies
+
+- Microsoft SQL Server
+- Microsoft SQL Server Integration Services SSIS
+- SAP software
+- Adobe Illustrator
+- Epic Systems
+- Microsoft SQL Server Reporting Services SSRS
+- Oracle Java
+- Perl
+- Python
+- Microsoft Office software
+
+---
+*Sources: ESCO v1.2.1 (http://data.europa.eu/esco/occupation/f3e23761-0663-4ae0-97a2-0b2dd3fa38a1), O*NET 30.3 (11-9041.01). See manifest.json for licensing/attribution.*
--- a/manifest.json
+++ b/manifest.json
@@ -0,0 +1,202 @@
+{
+  "name": "biochemical-engineer",
+  "title": "biochemical engineer",
+  "version": "0.1.0",
+  "layer": "core",
+  "language": "en",
+  "generated": "2026-07-07",
+  "ids": {
+    "esco_uri": "http://data.europa.eu/esco/occupation/f3e23761-0663-4ae0-97a2-0b2dd3fa38a1",
+    "esco_code": "2145.1.1",
+    "isco_group": "2145",
+    "onet_soc": "11-9041.01",
+    "crosswalk_match": "closeMatch"
+  },
+  "sources": [
+    {
+      "name": "ESCO",
+      "version": "1.2.1",
+      "url": "https://esco.ec.europa.eu/"
+    },
+    {
+      "name": "O*NET",
+      "version": "30.3",
+      "url": "https://www.onetcenter.org/",
+      "license": "CC BY 4.0"
+    }
+  ],
+  "attribution": "This package includes information from the O*NET Database (v30.3) by the U.S. Department of Labor, Employment and Training Administration (USDOL/ETA), CC BY 4.0. skillfactor is not endorsed by USDOL/ETA. ESCO data (v1.2.1) (c) European Union, used per the ESCO download conditions: https://esco.ec.europa.eu/en/use-esco/download",
+  "counts": {
+    "tasks": 18,
+    "dwas": 9,
+    "skills_essential": 60,
+    "skills_optional": 28,
+    "software": 31
+  },
+  "enrichment_ai_skills": {
+    "generated": "2026-07-14",
+    "method": "deterministic mapping (ISCO prefix + title/competence keywords)",
+    "sources": {
+      "anthropics/skills": {
+        "repo": "https://github.com/anthropics/skills",
+        "commit": "f6656c1",
+        "license": "Apache-2.0; the document skills (docx/pdf/pptx/xlsx) are source-available \u2014 see the LICENSE.txt in the upstream skill folder",
+        "skills": 2
+      },
+      "davila7/claude-code-templates": {
+        "repo": "https://github.com/davila7/claude-code-templates",
+        "commit": "fa79251",
+        "license": "MIT",
+        "skills": 12
+      },
+      "brycewang-stanford/Auto-Empirical-Research-Skills": {
+        "repo": "https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills",
+        "commit": "85bf545",
+        "license": "CC-BY-4.0",
+        "skills": 12
+      },
+      "K-Dense-AI/claude-scientific-skills": {
+        "repo": "https://github.com/K-Dense-AI/claude-scientific-skills",
+        "commit": "4d97e29",
+        "license": "MIT",
+        "skills": 12
+      },
+      "K-Dense-AI/scientific-agent-skills": {
+        "repo": "https://github.com/K-Dense-AI/scientific-agent-skills",
+        "commit": "4d97e29",
+        "license": "MIT",
+        "skills": 12
+      },
+      "foryourhealth111-pixel/Vibe-Skills": {
+        "repo": "https://github.com/foryourhealth111-pixel/Vibe-Skills",
+        "commit": "34429a8",
+        "license": "Apache-2.0",
+        "skills": 12
+      },
+      "fcakyon/claude-codex-settings": {
+        "repo": "https://github.com/fcakyon/claude-codex-settings",
+        "commit": "44b7c00",
+        "license": "Apache-2.0",
+        "skills": 1
+      },
+      "OpenRaiser/NanoResearch": {
+        "repo": "https://github.com/OpenRaiser/NanoResearch",
+        "commit": "7144364",
+        "license": "MIT",
+        "skills": 1
+      },
+      "Orchestra-Research/AI-research-SKILLs": {
+        "repo": "https://github.com/Orchestra-Research/AI-research-SKILLs",
+        "commit": "773a529",
+        "license": "MIT",
+        "skills": 1
+      },
+      "zechenzhangAGI/AI-research-SKILLs": {
+        "repo": "https://github.com/zechenzhangAGI/AI-research-SKILLs",
+        "commit": "773a529",
+        "license": "MIT",
+        "skills": 1
+      },
+      "zebbern/claude-code-guide": {
+        "repo": "https://github.com/zebbern/claude-code-guide",
+        "commit": "d2c5280",
+        "license": "MIT",
+        "skills": 1
+      },
+      "nexu-io/open-design": {
+        "repo": "https://github.com/nexu-io/open-design",
+        "commit": "4b66023",
+        "license": "Apache-2.0",
+        "skills": 2
+      },
+      "ferdinandobons/startup-skill": {
+        "repo": "https://github.com/ferdinandobons/startup-skill",
+        "commit": "a5f97c3",
+        "license": "MIT",
+        "skills": 1
+      },
+      "sanjay3290/ai-skills": {
+        "repo": "https://github.com/sanjay3290/ai-skills",
+        "commit": "3619692",
+        "license": "Apache-2.0",
+        "skills": 1
+      },
+      "claude-world/director-mode-lite": {
+        "repo": "https://github.com/claude-world/director-mode-lite",
+        "commit": "9d0c333",
+        "license": "MIT",
+        "skills": 1
+      },
+      "open-gitagent/opengap": {
+        "repo": "https://github.com/open-gitagent/opengap",
+        "commit": "d7a8e2e",
+        "license": "MIT",
+        "skills": 1
+      },
+      "jeremylongshore/claude-code-plugins-plus-skills": {
+        "repo": "https://github.com/jeremylongshore/claude-code-plugins-plus-skills",
+        "commit": "e112938a",
+        "license": "MIT",
+        "skills": 1
+      },
+      "makenotion/claude-code-notion-plugin": {
+        "repo": "https://github.com/makenotion/claude-code-notion-plugin",
+        "commit": "9847f2a",
+        "license": "no explicit license \u2014 referenced by link only",
+        "skills": 1
+      },
+      "a5c-ai/babysitter": {
+        "repo": "https://github.com/a5c-ai/babysitter",
+        "commit": "44a5d58b",
+        "license": "MIT",
+        "skills": 1
+      },
+      "alirezarezvani/claude-skills": {
+        "repo": "https://github.com/alirezarezvani/claude-skills",
+        "commit": "0241f43",
+        "license": "MIT",
+        "skills": 1
+      },
+      "wanshuiyin/Auto-claude-code-research-in-sleep": {
+        "repo": "https://github.com/wanshuiyin/Auto-claude-code-research-in-sleep",
+        "commit": "eb5c9d7",
+        "license": "MIT",
+        "skills": 2
+      },
+      "BrianRWagner/ai-marketing-skills": {
+        "repo": "https://github.com/BrianRWagner/ai-marketing-skills",
+        "commit": "f36b34f",
+        "license": "no explicit license \u2014 referenced by link only",
+        "skills": 1
+      }
+    },
+    "total_skills": 80,
+    "tiers": {
+      "core": 78,
+      "adjacent": 2
+    }
+  },
+  "provenance": {
+    "items": {
+      "esco": 89,
+      "onet": 59,
+      "jobads": 81,
+      "wiki_ai": 0,
+      "anthropic": 5,
+      "ai_skills": 141,
+      "stackx": 0
+    },
+    "share_percent": {
+      "esco": 23.7,
+      "onet": 15.7,
+      "jobads": 21.6,
+      "wiki_ai": 0.0,
+      "anthropic": 1.3,
+      "ai_skills": 37.6,
+      "stackx": 0.0
+    },
+    "method": "content items per source category"
+  },
+  "collar": "white",
+  "computer_work": true
+}
--- a/references/ai-skills.md
+++ b/references/ai-skills.md
@@ -0,0 +1,274 @@
+# External AI agent skills — biochemical-engineer
+
+Proven, publicly available AI agent skills mapped to this occupation.
+Nothing is copied from the sources: every entry is a name, a one-line
+summary and a link to the upstream skill package. Each section names
+its source repository, commit, license and retrieval date.
+
+**Tiers:** `core` = the skill directly exercises a top market hard
+skill, tool or method (from gated job-ad evidence) or an essential
+ESCO competence of this occupation; `adjacent` =
+plausibly useful, secondary. Entries are capped at 12 per source
+and 80 in total per occupation (core first,
+strongest matches survive); everything beyond the caps is excluded
+and logged in the pipeline audit trail, not in this package.
+
+_Matched deterministically (ISCO group + title/competence keywords,
+tiered against market evidence + ESCO essentials) by
+`pipeline/p5_enrich_ai_skills.py` on 2026-07-14._
+
+## Source: anthropics/skills
+
+- Repository: [https://github.com/anthropics/skills](https://github.com/anthropics/skills) (commit `f6656c1`, retrieved 2026-07-14)
+- License: Apache-2.0; the document skills (docx/pdf/pptx/xlsx) are source-available — see the LICENSE.txt in the upstream skill folder
+
+| Skill | Tier | What it adds | Upstream |
+|---|---|---|---|
+| `docx` | adjacent | Use this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files) or Word templates (.dotx files). Triggers include: any mention of 'Word doc', 'word document', '.docx', '.dotx', or requests to … | [source](https://github.com/anthropics/skills/tree/main/skills/docx) |
+| `pdf` | adjacent | Use this skill whenever the user wants to do anything with PDF files. This includes reading or extracting text/tables from PDFs, combining or merging multiple PDFs into one, splitting PDFs apart, rotating pages, adding watermarks, creating … | [source](https://github.com/anthropics/skills/tree/main/skills/pdf) |
+
+## Source: a5c-ai/babysitter
+
+- Repository: [https://github.com/a5c-ai/babysitter](https://github.com/a5c-ai/babysitter) (commit `44a5d58b`, retrieved 2026-07-14)
+- License: MIT
+
+| Skill | Tier | What it adds | Upstream |
+|---|---|---|---|
+| `meta-analysis-engine` | core | Skill for conducting meta-analyses of research findings | [source](https://github.com/a5c-ai/babysitter/tree/44a5d58b/library/specializations/domains/science/scientific-discovery/skills/meta-analysis-engine) |
+
+## Source: alirezarezvani/claude-skills
+
+- Repository: [https://github.com/alirezarezvani/claude-skills](https://github.com/alirezarezvani/claude-skills) (commit `0241f43`, retrieved 2026-07-14)
+- License: MIT
+
+| Skill | Tier | What it adds | Upstream |
+|---|---|---|---|
+| `product-skills` | core | Use when coordinating product work across the 12 bundled product sub-skills (RICE, OKRs, UX research, design tokens, competitive teardown, analytics, experiments, discovery, roadmaps, spec-to-repo, landing pages, SaaS scaffolding) or the 4 … | [source](https://github.com/alirezarezvani/claude-skills/tree/0241f43/product-team/skills/product-skills) |
+
+## Source: BrianRWagner/ai-marketing-skills
+
+- Repository: [https://github.com/BrianRWagner/ai-marketing-skills](https://github.com/BrianRWagner/ai-marketing-skills) (commit `f36b34f`, retrieved 2026-07-14)
+- License: no explicit license — referenced by link only
+
+| Skill | Tier | What it adds | Upstream |
+|---|---|---|---|
+| `last30days` | core | Research any topic across Reddit, X, and web from the last 30 days. Get current trends, real community sentiment, and actionable insights in 7 minutes vs 2 hours manual research. | [source](https://github.com/BrianRWagner/ai-marketing-skills/tree/f36b34f/last30days) |
+
+## Source: brycewang-stanford/Auto-Empirical-Research-Skills
+
+- Repository: [https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills](https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills) (commit `85bf545`, retrieved 2026-07-14)
+- License: CC-BY-4.0
+
+| Skill | Tier | What it adds | Upstream |
+|---|---|---|---|
+| `claude-scientific-guide` | core | Ready-to-use agent skills for scientific research and engineering | [source](https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/85bf545/skills/43-wentorai-research-plugins/skills/research/methodology/claude-scientific-guide) |
+| `hud` | core | Diverga HUD (Heads-Up Display) management skill. Configure and manage the research project statusline display. Supports multiple presets: research, checkpoint, memory, minimal. Triggers: "hud", "statusline", "display settings | [source](https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/85bf545/skills/25-HosungYou-Diverga/skills/hud) |
+| `academic-baseline` | core | Use when working on any empirical academic research context — paper writing, data analysis, literature review, or any task involving citations, results, or publication artifacts. Establishes non-negotiable principles that govern all other … | [source](https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/85bf545/skills/60-regisely-superpapers/skills/academic-baseline) |
+| `methodology-skills` | core | 13 research methodology skills. Trigger: study design, methodology selection, scientific reasoning, mentoring. Design: rigorous methods frameworks covering qualitative, quantitative, and mixed approaches. | [source](https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/85bf545/skills/43-wentorai-research-plugins/skills/research/methodology) |
+| `law-skills` | core | 9 legal research skills. Trigger: legal research, case law analysis, regulatory compliance. Design: legal databases, citation networks, and judicial analytics tools. | [source](https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/85bf545/skills/43-wentorai-research-plugins/skills/domains/law) |
+| `psychology-research-guide` | core | Psychological research methods, experimental design, and analysis | [source](https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/85bf545/skills/43-wentorai-research-plugins/skills/domains/social-science/psychology-research-guide) |
+| `econ-audit` | core | Audit economic analysis outputs (fiscal briefings, macro briefings, market research, longlists, and other quantitative economic documents) against methodology standards, academic literature, and common errors. Runs structured checks across … | [source](https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/85bf545/skills/58-charlescoverdale-econstack/econ-audit) |
+| `publication-output` | core | This skill covers publication-quality tables and figures for academic research papers. Use when formatting regression results, summary statistics, Monte Carlo output, or research visualizations for LaTeX inclusion. Triggers on "table", … | [source](https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/85bf545/skills/11-James-Traina-compound-science/skills/publication-output) |
+| `research-ideation` | core | This skill should be used when the user asks to "brainstorm research ideas", "use 5W1H framework", "identify research gaps", "conduct gap analysis", "start research project", "conduct literature review", "define research question", "select … | [source](https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/85bf545/skills/33-Galaxy-Dawn-claude-scholar/skills/research-ideation) |
+| `results-analysis` | core | This skill should be used when the user asks to "analyze experimental results", "run strict statistical analysis", "compare model performance", "generate scientific figures", "check significance", "do ablation analysis", or mentions … | [source](https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/85bf545/skills/33-Galaxy-Dawn-claude-scholar/skills/results-analysis) |
+| `new-project` | core | Full research pipeline from idea to paper. Orchestrates all phases — discovery, strategy, analysis, writing, peer review, and submission. Use when starting a new research project from scratch. | [source](https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/85bf545/skills/16-hsantanna88-clo-author/dot-claude/skills/new-project) |
+| `core-api-guide` | core | Search and retrieve open access research papers via CORE aggregator | [source](https://github.com/brycewang-stanford/Auto-Empirical-Research-Skills/tree/85bf545/skills/43-wentorai-research-plugins/skills/literature/fulltext/core-api-guide) |
+
+## Source: claude-world/director-mode-lite
+
+- Repository: [https://github.com/claude-world/director-mode-lite](https://github.com/claude-world/director-mode-lite) (commit `9d0c333`, retrieved 2026-07-14)
+- License: MIT
+
+| Skill | Tier | What it adds | Upstream |
+|---|---|---|---|
+| `handoff-gemini` | core | Delegate long-context analysis, research, and large-document summarization to Google Gemini CLI (1M-token context) via non-interactive `gemini -p`, preserving Claude context. Use when the user says 'use gemini'/'hand off to gemini' or a … | [source](https://github.com/claude-world/director-mode-lite/tree/9d0c333/skills/handoff-gemini) |
+
+## Source: davila7/claude-code-templates
+
+- Repository: [https://github.com/davila7/claude-code-templates](https://github.com/davila7/claude-code-templates) (commit `fa79251`, retrieved 2026-07-14)
+- License: MIT
+
+| Skill | Tier | What it adds | Upstream |
+|---|---|---|---|
+| `scientific-critical-thinking` | core | Evaluate research rigor. Assess methodology, experimental design, statistical validity, biases, confounding, evidence quality (GRADE, Cochrane ROB), for critical analysis of scientific claims. | [source](https://github.com/davila7/claude-code-templates/tree/fa79251/cli-tool/components/skills/scientific/scientific-critical-thinking) |
+| `latex-posters` | core | Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication. Includes layout design, color schemes, multi-column formats, … | [source](https://github.com/davila7/claude-code-templates/tree/fa79251/cli-tool/components/skills/scientific/latex-posters) |
+| `denario` | core | Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, … | [source](https://github.com/davila7/claude-code-templates/tree/fa79251/cli-tool/components/skills/scientific/denario) |
+| `research-engineer` | core | An uncompromising Academic Research Engineer. Operates with absolute scientific rigor, objective criticism, and zero flair. Focuses on theoretical correctness, formal verification, and optimal implementation across any required technology. | [source](https://github.com/davila7/claude-code-templates/tree/fa79251/cli-tool/components/skills/ai-research/research-engineer) |
+| `scientific-writing` | core | Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process: (1) create section outlines with key points using research-lookup, (2) convert to flowing … | [source](https://github.com/davila7/claude-code-templates/tree/fa79251/cli-tool/components/skills/scientific/scientific-writing) |
+| `market-research-reports` | core | Generate comprehensive market research reports (50+ pages) in the style of top consulting firms (McKinsey, BCG, Gartner). Features professional LaTeX formatting, extensive visual generation with scientific-schematics and generate-image, … | [source](https://github.com/davila7/claude-code-templates/tree/fa79251/cli-tool/components/skills/scientific/market-research-reports) |
+| `scientific-slides` | core | Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design … | [source](https://github.com/davila7/claude-code-templates/tree/fa79251/cli-tool/components/skills/scientific/scientific-slides) |
+| `venue-templates` | core | Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues (Nature, Science, PLOS, IEEE, ACM), academic conferences (NeurIPS, ICML, CVPR, CHI), research posters, and … | [source](https://github.com/davila7/claude-code-templates/tree/fa79251/cli-tool/components/skills/scientific/venue-templates) |
+| `biomni` | core | Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR … | [source](https://github.com/davila7/claude-code-templates/tree/fa79251/cli-tool/components/skills/scientific/biomni) |
+| `citation-management` | core | Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to … | [source](https://github.com/davila7/claude-code-templates/tree/fa79251/cli-tool/components/skills/scientific/citation-management) |
+| `scientific-brainstorming` | core | Research ideation partner. Generate hypotheses, explore interdisciplinary connections, challenge assumptions, develop methodologies, identify research gaps, for creative scientific problem-solving. | [source](https://github.com/davila7/claude-code-templates/tree/fa79251/cli-tool/components/skills/scientific/scientific-brainstorming) |
+| `brenda-database` | core | Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway analysis. | [source](https://github.com/davila7/claude-code-templates/tree/fa79251/cli-tool/components/skills/scientific/brenda-database) |
+
+## Source: fcakyon/claude-codex-settings
+
+- Repository: [https://github.com/fcakyon/claude-codex-settings](https://github.com/fcakyon/claude-codex-settings) (commit `44b7c00`, retrieved 2026-07-14)
+- License: Apache-2.0
+
+| Skill | Tier | What it adds | Upstream |
+|---|---|---|---|
+| `paper-search-usage` | core | This skill should be used when user asks to "search for papers", "find research papers", "search arXiv", "search PubMed", "find academic papers", "search IEEE", "search Scopus", or "look up scientific literature". | [source](https://github.com/fcakyon/claude-codex-settings/tree/44b7c00/plugins/paper-search-tools/skills/paper-search-usage) |
+
+## Source: ferdinandobons/startup-skill
+
+- Repository: [https://github.com/ferdinandobons/startup-skill](https://github.com/ferdinandobons/startup-skill) (commit `a5f97c3`, retrieved 2026-07-14)
+- License: MIT
+
+| Skill | Tier | What it adds | Upstream |
+|---|---|---|---|
+| `startup-design` | core | Design, validate, and plan a startup from scratch. Covers market research, competitive analysis, business model, brand identity, product definition, financial projections, and validation experiments. Trigger when the user has a startup … | [source](https://github.com/ferdinandobons/startup-skill/tree/a5f97c3/startup-design) |
+
+## Source: foryourhealth111-pixel/Vibe-Skills
+
+- Repository: [https://github.com/foryourhealth111-pixel/Vibe-Skills](https://github.com/foryourhealth111-pixel/Vibe-Skills) (commit `34429a8`, retrieved 2026-07-14)
+- License: Apache-2.0
+
+| Skill | Tier | What it adds | Upstream |
+|---|---|---|---|
+| `denario` | core | Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, … | [source](https://github.com/foryourhealth111-pixel/Vibe-Skills/tree/34429a8/bundled/skills/denario) |
+| `scientific-reporting` | core | Write research/technical reports with strong structure + figure standards. Supports Markdown/HTML/PDF outputs (Quarto optional), executive summary, methods, results, discussion, and reproducibility appendix. | [source](https://github.com/foryourhealth111-pixel/Vibe-Skills/tree/34429a8/bundled/skills/scientific-reporting) |
+| `scientific-brainstorming` | core | Open-ended scientific ideation partner. Use for research gaps, mechanism exploration, interdisciplinary connections, assumptions, possible research directions, and lightweight literature matrix or A+B paper-combination idea mapping. For … | [source](https://github.com/foryourhealth111-pixel/Vibe-Skills/tree/34429a8/bundled/skills/scientific-brainstorming) |
+| `scientific-slides` | core | Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design … | [source](https://github.com/foryourhealth111-pixel/Vibe-Skills/tree/34429a8/bundled/skills/scientific-slides) |
+| `slides-as-code` | core | Build research slides with text-first source (Slidev/Marp/Reveal/Quarto) and reproducible export (PDF). Includes structure, figure reuse rules, and quality checklist for top-tier scientific presentations. | [source](https://github.com/foryourhealth111-pixel/Vibe-Skills/tree/34429a8/bundled/skills/slides-as-code) |
+| `citation-management` | core | Comprehensive citation management for academic research. Resolve bibliographic identifiers, extract accurate metadata, validate citations, deduplicate references, and generate properly formatted BibTeX entries. This skill should be used … | [source](https://github.com/foryourhealth111-pixel/Vibe-Skills/tree/34429a8/bundled/skills/citation-management) |
+| `statistical-analysis` | core | Statistical analysis toolkit. Hypothesis tests (t-test, ANOVA, chi-square), regression, correlation, Bayesian stats, power analysis, assumption checks, APA reporting, for academic research. | [source](https://github.com/foryourhealth111-pixel/Vibe-Skills/tree/34429a8/bundled/skills/statistical-analysis) |
+| `openalex-database` | core | Query and analyze scholarly literature using the OpenAlex database. This skill should be used when searching for academic papers, analyzing research trends, finding works by authors or institutions, tracking citations, discovering open … | [source](https://github.com/foryourhealth111-pixel/Vibe-Skills/tree/34429a8/bundled/skills/openalex-database) |
+| `scholar-evaluation` | core | Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem formulation, methodology, analysis, and writing with quantitative scoring and … | [source](https://github.com/foryourhealth111-pixel/Vibe-Skills/tree/34429a8/bundled/skills/scholar-evaluation) |
+| `designing-experiments` | core | Design experiments and quasi-experiments before analysis. Use when choosing study design, treatment/control structure, outcomes, assumptions, validation plans after scientific experiment failure, or which of DiD, ITS, synthetic control, or … | [source](https://github.com/foryourhealth111-pixel/Vibe-Skills/tree/34429a8/bundled/skills/designing-experiments) |
+| `scientific-critical-thinking` | core | Evaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading frameworks (GRADE, Cochrane Risk of Bias), or teaching critical analysis. Best … | [source](https://github.com/foryourhealth111-pixel/Vibe-Skills/tree/34429a8/bundled/skills/scientific-critical-thinking) |
+| `exploratory-data-analysis` | core | Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. … | [source](https://github.com/foryourhealth111-pixel/Vibe-Skills/tree/34429a8/bundled/skills/exploratory-data-analysis) |
+
+## Source: jeremylongshore/claude-code-plugins-plus-skills
+
+- Repository: [https://github.com/jeremylongshore/claude-code-plugins-plus-skills](https://github.com/jeremylongshore/claude-code-plugins-plus-skills) (commit `e112938a`, retrieved 2026-07-14)
+- License: MIT
+
+| Skill | Tier | What it adds | Upstream |
+|---|---|---|---|
+| `windsurf-cascade-context` | core | Manage Cascade context window and memory for complex projects. Activate when users mention "cascade context", "ai memory", "context management", "large codebase navigation", or "multi-session development". Handles context optimization and … | [source](https://github.com/jeremylongshore/claude-code-plugins-plus-skills/tree/e112938a/plugins/saas-packs/skill-databases/windsurf/skills/windsurf-cascade-context) |
+
+## Source: K-Dense-AI/claude-scientific-skills
+
+- Repository: [https://github.com/K-Dense-AI/claude-scientific-skills](https://github.com/K-Dense-AI/claude-scientific-skills) (commit `4d97e29`, retrieved 2026-07-14)
+- License: MIT
+
+| Skill | Tier | What it adds | Upstream |
+|---|---|---|---|
+| `hugging-science` | core | Use when the user is doing AI/ML work in a scientific domain such as biology, chemistry, physics, astronomy, climate, genomics, materials, medicine, ecology, energy, engineering, math, drug discovery, protein design, weather modeling, … | [source](https://github.com/K-Dense-AI/claude-scientific-skills/tree/4d97e29/skills/hugging-science) |
+| `latex-posters` | core | Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication. Includes layout design, color schemes, multi-column formats, … | [source](https://github.com/K-Dense-AI/claude-scientific-skills/tree/4d97e29/skills/latex-posters) |
+| `scientific-brainstorming` | core | Creative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary connections, challenging assumptions, or identifying research gaps. Best for early-stage research planning when you do not … | [source](https://github.com/K-Dense-AI/claude-scientific-skills/tree/4d97e29/skills/scientific-brainstorming) |
+| `scientific-writing` | core | Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research-lookup then (2) convert to flowing … | [source](https://github.com/K-Dense-AI/claude-scientific-skills/tree/4d97e29/skills/scientific-writing) |
+| `research-lookup` | core | Look up current research and scientific information across three backends: fast web search via parallel-cli (default), the Parallel Chat API for deep multi-source synthesis, and Perplexity sonar-pro-search for scholarly paper searches. … | [source](https://github.com/K-Dense-AI/claude-scientific-skills/tree/4d97e29/skills/research-lookup) |
+| `market-research-reports` | core | Generate comprehensive market research reports (50+ pages) in the style of top consulting firms (McKinsey, BCG, Gartner). Features professional LaTeX formatting, extensive visual generation with scientific-schematics and generate-image, … | [source](https://github.com/K-Dense-AI/claude-scientific-skills/tree/4d97e29/skills/market-research-reports) |
+| `scientific-slides` | core | Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design … | [source](https://github.com/K-Dense-AI/claude-scientific-skills/tree/4d97e29/skills/scientific-slides) |
+| `venue-templates` | core | Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues (Nature, Science, PLOS, IEEE, ACM), academic conferences (NeurIPS, ICML, CVPR, CHI), research posters, and … | [source](https://github.com/K-Dense-AI/claude-scientific-skills/tree/4d97e29/skills/venue-templates) |
+| `autoskill` | core | Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing scientific-agent-skills, and draft new skills (or composition recipes that chain existing ones) for the patterns not yet covered. Use … | [source](https://github.com/K-Dense-AI/claude-scientific-skills/tree/4d97e29/skills/autoskill) |
+| `citation-management` | core | Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to … | [source](https://github.com/K-Dense-AI/claude-scientific-skills/tree/4d97e29/skills/citation-management) |
+| `exa-search` | core | Web toolkit powered by Exa, tuned for scientific and technical content. Use this skill when the user needs to search the web or fetch/extract URL content. Covers: web search (semantic lookups, research, current info — with optional … | [source](https://github.com/K-Dense-AI/claude-scientific-skills/tree/4d97e29/skills/exa-search) |
+| `scholar-evaluation` | core | Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem formulation, methodology, analysis, and writing with quantitative scoring and … | [source](https://github.com/K-Dense-AI/claude-scientific-skills/tree/4d97e29/skills/scholar-evaluation) |
+
+## Source: K-Dense-AI/scientific-agent-skills
+
+- Repository: [https://github.com/K-Dense-AI/scientific-agent-skills](https://github.com/K-Dense-AI/scientific-agent-skills) (commit `4d97e29`, retrieved 2026-07-14)
+- License: MIT
+
+| Skill | Tier | What it adds | Upstream |
+|---|---|---|---|
+| `hugging-science` | core | Use when the user is doing AI/ML work in a scientific domain such as biology, chemistry, physics, astronomy, climate, genomics, materials, medicine, ecology, energy, engineering, math, drug discovery, protein design, weather modeling, … | [source](https://github.com/K-Dense-AI/scientific-agent-skills/tree/4d97e29/skills/hugging-science) |
+| `latex-posters` | core | Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication. Includes layout design, color schemes, multi-column formats, … | [source](https://github.com/K-Dense-AI/scientific-agent-skills/tree/4d97e29/skills/latex-posters) |
+| `scientific-brainstorming` | core | Creative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary connections, challenging assumptions, or identifying research gaps. Best for early-stage research planning when you do not … | [source](https://github.com/K-Dense-AI/scientific-agent-skills/tree/4d97e29/skills/scientific-brainstorming) |
+| `scientific-writing` | core | Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research-lookup then (2) convert to flowing … | [source](https://github.com/K-Dense-AI/scientific-agent-skills/tree/4d97e29/skills/scientific-writing) |
+| `research-lookup` | core | Look up current research and scientific information across three backends: fast web search via parallel-cli (default), the Parallel Chat API for deep multi-source synthesis, and Perplexity sonar-pro-search for scholarly paper searches. … | [source](https://github.com/K-Dense-AI/scientific-agent-skills/tree/4d97e29/skills/research-lookup) |
+| `market-research-reports` | core | Generate comprehensive market research reports (50+ pages) in the style of top consulting firms (McKinsey, BCG, Gartner). Features professional LaTeX formatting, extensive visual generation with scientific-schematics and generate-image, … | [source](https://github.com/K-Dense-AI/scientific-agent-skills/tree/4d97e29/skills/market-research-reports) |
+| `scientific-slides` | core | Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design … | [source](https://github.com/K-Dense-AI/scientific-agent-skills/tree/4d97e29/skills/scientific-slides) |
+| `venue-templates` | core | Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues (Nature, Science, PLOS, IEEE, ACM), academic conferences (NeurIPS, ICML, CVPR, CHI), research posters, and … | [source](https://github.com/K-Dense-AI/scientific-agent-skills/tree/4d97e29/skills/venue-templates) |
+| `autoskill` | core | Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing scientific-agent-skills, and draft new skills (or composition recipes that chain existing ones) for the patterns not yet covered. Use … | [source](https://github.com/K-Dense-AI/scientific-agent-skills/tree/4d97e29/skills/autoskill) |
+| `citation-management` | core | Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to … | [source](https://github.com/K-Dense-AI/scientific-agent-skills/tree/4d97e29/skills/citation-management) |
+| `exa-search` | core | Web toolkit powered by Exa, tuned for scientific and technical content. Use this skill when the user needs to search the web or fetch/extract URL content. Covers: web search (semantic lookups, research, current info — with optional … | [source](https://github.com/K-Dense-AI/scientific-agent-skills/tree/4d97e29/skills/exa-search) |
+| `scholar-evaluation` | core | Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem formulation, methodology, analysis, and writing with quantitative scoring and … | [source](https://github.com/K-Dense-AI/scientific-agent-skills/tree/4d97e29/skills/scholar-evaluation) |
+
+## Source: makenotion/claude-code-notion-plugin
+
+- Repository: [https://github.com/makenotion/claude-code-notion-plugin](https://github.com/makenotion/claude-code-notion-plugin) (commit `9847f2a`, retrieved 2026-07-14)
+- License: no explicit license — referenced by link only
+
+| Skill | Tier | What it adds | Upstream |
+|---|---|---|---|
+| `notion-research-documentation` | core | Searches across your Notion workspace, synthesizes findings from multiple pages, and creates comprehensive research documentation saved as new Notion pages. Turns scattered information into structured reports with proper citations and … | [source](https://github.com/makenotion/claude-code-notion-plugin/tree/9847f2a/skills/notion/research-documentation) |
+
+## Source: nexu-io/open-design
+
+- Repository: [https://github.com/nexu-io/open-design](https://github.com/nexu-io/open-design) (commit `4b66023`, retrieved 2026-07-14)
+- License: Apache-2.0
+
+| Skill | Tier | What it adds | Upstream |
+|---|---|---|---|
+| `kami-deck` | core | A lab-meeting deck on gut-microbiome links to sleep quality — the design, the results, the caveats, and the next experiment. Built as a decision-grade academic research deck for lab group, PI. | [source](https://github.com/nexu-io/open-design/tree/4b66023/design-templates/kami-deck) |
+| `html-ppt-zhangzara-monochrome` | core | A grant proposal on CRISPR base-editing for sickle-cell disease — the hypothesis, the approach, the milestones, and the risk. Built as a decision-grade academic research deck for grant review committee. | [source](https://github.com/nexu-io/open-design/tree/4b66023/design-templates/html-ppt-zhangzara-monochrome) |
+
+## Source: open-gitagent/opengap
+
+- Repository: [https://github.com/open-gitagent/opengap](https://github.com/open-gitagent/opengap) (commit `d7a8e2e`, retrieved 2026-07-14)
+- License: MIT
+
+| Skill | Tier | What it adds | Upstream |
+|---|---|---|---|
+| `research` | core | Researches a topic by breaking it into subtopics, gathering factual information with reasoning, and producing a structured summary with key findings and open questions. Use when the user asks to research, investigate, look up, summarize a … | [source](https://github.com/open-gitagent/opengap/tree/d7a8e2e/examples/lyzr-agent/skills/research) |
+
+## Source: OpenRaiser/NanoResearch
+
+- Repository: [https://github.com/OpenRaiser/NanoResearch](https://github.com/OpenRaiser/NanoResearch) (commit `7144364`, retrieved 2026-07-14)
+- License: MIT
+
+| Skill | Tier | What it adds | Upstream |
+|---|---|---|---|
+| `academic-plotting` | core | Generates publication-quality figures for ML papers from research context. Given a paper section or description, extracts system components and relationships to generate architecture diagrams via Gemini. Given experiment results or data, … | [source](https://github.com/OpenRaiser/NanoResearch/tree/7144364/skills/vendor-ai-research/academic-plotting) |
+
+## Source: Orchestra-Research/AI-research-SKILLs
+
+- Repository: [https://github.com/Orchestra-Research/AI-research-SKILLs](https://github.com/Orchestra-Research/AI-research-SKILLs) (commit `773a529`, retrieved 2026-07-14)
+- License: MIT
+
+| Skill | Tier | What it adds | Upstream |
+|---|---|---|---|
+| `academic-plotting` | core | Generates publication-quality figures for ML papers from research context. Given a paper section or description, extracts system components and relationships to generate architecture diagrams via Gemini. Given experiment results or data, … | [source](https://github.com/Orchestra-Research/AI-research-SKILLs/tree/773a529/20-ml-paper-writing/academic-plotting) |
+
+## Source: sanjay3290/ai-skills
+
+- Repository: [https://github.com/sanjay3290/ai-skills](https://github.com/sanjay3290/ai-skills) (commit `3619692`, retrieved 2026-07-14)
+- License: Apache-2.0
+
+| Skill | Tier | What it adds | Upstream |
+|---|---|---|---|
+| `deep-research` | core | Execute autonomous multi-step research using Google Gemini Deep Research Agent. Use for: market analysis, competitive landscaping, literature reviews, technical research, due diligence. Takes 2-10 minutes but produces detailed, cited … | [source](https://github.com/sanjay3290/ai-skills/tree/3619692/skills/deep-research) |
+
+## Source: wanshuiyin/Auto-claude-code-research-in-sleep
+
+- Repository: [https://github.com/wanshuiyin/Auto-claude-code-research-in-sleep](https://github.com/wanshuiyin/Auto-claude-code-research-in-sleep) (commit `eb5c9d7`, retrieved 2026-07-14)
+- License: MIT
+
+| Skill | Tier | What it adds | Upstream |
+|---|---|---|---|
+| `research-lit` | core | Search and analyze research papers, find related work, summarize key ideas. Use when user says "find papers", "related work", "literature review", "what does this paper say", or needs to understand academic papers. | [source](https://github.com/wanshuiyin/Auto-claude-code-research-in-sleep/tree/eb5c9d7/skills/research-lit) |
+| `research-wiki` | core | Persistent research knowledge base that accumulates papers, ideas, experiments, claims, and their relationships across the entire research lifecycle. Inspired by Karpathy's LLM Wiki pattern. Use when user says \"知识库\", \"research wiki\", … | [source](https://github.com/wanshuiyin/Auto-claude-code-research-in-sleep/tree/eb5c9d7/skills/research-wiki) |
+
+## Source: zebbern/claude-code-guide
+
+- Repository: [https://github.com/zebbern/claude-code-guide](https://github.com/zebbern/claude-code-guide) (commit `d2c5280`, retrieved 2026-07-14)
+- License: MIT
+
+| Skill | Tier | What it adds | Upstream |
+|---|---|---|---|
+| `vc-industry-research` | core | Generate professional primary market / venture capital industry research reports, including sector deep-dives, investment memos, and market analysis. Produces detailed PDF reports covering TMT, consumer, healthcare, and industrials. … | [source](https://github.com/zebbern/claude-code-guide/tree/d2c5280/skills/vc-industry-research) |
+
+## Source: zechenzhangAGI/AI-research-SKILLs
+
+- Repository: [https://github.com/zechenzhangAGI/AI-research-SKILLs](https://github.com/zechenzhangAGI/AI-research-SKILLs) (commit `773a529`, retrieved 2026-07-14)
+- License: MIT
+
+| Skill | Tier | What it adds | Upstream |
+|---|---|---|---|
+| `academic-plotting` | core | Generates publication-quality figures for ML papers from research context. Given a paper section or description, extracts system components and relationships to generate architecture diagrams via Gemini. Given experiment results or data, … | [source](https://github.com/zechenzhangAGI/AI-research-SKILLs/tree/773a529/20-ml-paper-writing/academic-plotting) |
--- a/references/market.md
+++ b/references/market.md
@@ -0,0 +1,111 @@
+# Market evidence report — biochemical-engineer
+
+Source: **60 real job ads** (JSearch API, countries: us 60), extracted into the MSSQL evidence store; as of 2026-07-09.
+This report contains extracted, aggregated facts only — no ad text is
+reproduced (copyright / platform terms).
+
+## Seniority distribution
+
+| Seniority | Ads | Share |
+|---|---|---|
+| mid | 38 | 63 % |
+| n/a | 8 | 13 % |
+| senior | 7 | 12 % |
+| junior | 6 | 10 % |
+| lead | 1 | 2 % |
+
+## Tools — full market ranking
+
+| # | Item | Ads | Share |
+|---|---|---|---|
+| 1 | Rosetta | 5 | 8 % |
+| 2 | Microsoft Excel | 3 | 5 % |
+
+## Hard skills — full market ranking
+
+| # | Item | Ads | Share |
+|---|---|---|---|
+| 1 | data analysis | 21 | 35 % |
+| 2 | biomedical engineering | 10 | 17 % |
+| 3 | project management | 10 | 17 % |
+| 4 | enzyme engineering | 7 | 12 % |
+| 5 | scale-up | 7 | 12 % |
+| 6 | troubleshooting | 7 | 12 % |
+| 7 | medical equipment management | 6 | 10 % |
+| 8 | process optimization | 6 | 10 % |
+| 9 | capital asset planning | 5 | 8 % |
+| 10 | healthcare technology management | 5 | 8 % |
+| 11 | process development | 5 | 8 % |
+| 12 | regulatory compliance | 5 | 8 % |
+| 13 | infrastructure planning | 4 | 7 % |
+| 14 | protein engineering | 4 | 7 % |
+| 15 | computational workflows | 3 | 5 % |
+| 16 | experimental design | 3 | 5 % |
+| 17 | hazard investigation | 3 | 5 % |
+| 18 | policy development | 3 | 5 % |
+| 19 | process validation | 3 | 5 % |
+| 20 | protein purification | 3 | 5 % |
+| 21 | technology transfer | 3 | 5 % |
+
+## Methods — full market ranking
+
+| # | Item | Ads | Share |
+|---|---|---|---|
+| 1 | quality assurance | 5 | 8 % |
+| 2 | AI methods | 4 | 7 % |
+| 3 | high-throughput screening | 4 | 7 % |
+| 4 | biochemistry | 3 | 5 % |
+| 5 | cGMP | 3 | 5 % |
+| 6 | computational biology | 3 | 5 % |
+| 7 | directed evolution | 3 | 5 % |
+| 8 | structural biology | 3 | 5 % |
+
+## Responsibilities — full market ranking
+
+| # | Item | Ads | Share |
+|---|---|---|---|
+| 1 | data analysis | 7 | 12 % |
+| 2 | equipment maintenance | 5 | 8 % |
+| 3 | experiment execution | 4 | 7 % |
+| 4 | program management | 4 | 7 % |
+| 5 | staff training | 4 | 7 % |
+| 6 | technology assessment | 4 | 7 % |
+| 7 | assay development | 3 | 5 % |
+| 8 | engineering support | 3 | 5 % |
+| 9 | finding presentation | 3 | 5 % |
+| 10 | pipeline definition | 3 | 5 % |
+| 11 | policy development | 3 | 5 % |
+| 12 | process improvement | 3 | 5 % |
+| 13 | regulatory compliance | 3 | 5 % |
+
+## Job title variants in the market
+
+| Title | Ads |
+|---|---|
+| Biomedical Engineer | 6 |
+| Supervisory Biomedical Engineer (Clinical) | 5 |
+| AI-Based Protein Design and Enzyme Engineering Postdoctoral Associate | 1 |
+| Biochemical Engineer | 1 |
+| Biomechanical Engineer | 1 |
+| Biomedical Engineer - Clinical | 1 |
+| Biomedical Engineer - Perioperative | 1 |
+| Biomedical Engineer (Clinical Specialist) at Brainlab, Inc. Tucson, AZ | 1 |
+| Biomedical Engineer / LMDI SME | 1 |
+| Biomedical engineer at US Veterans Health Administration Miami, FL | 1 |
+| Biomedical Engineer at Veterans Health Administration Chicago, IL | 1 |
+| Biomedical Engineer at Veterans Health Administration Miami, FL | 1 |
+| Biomedical Engineer at Veterans Health Administration North Chicago, IL | 1 |
+| Biomedical Engineering New Grads - Imaging Project Coordinator | 1 |
+| Biomedical Research Engineer for Global Health Devices | 1 |
+| Biomedical Technician II / Biomedical Engineering | 1 |
+| Biomedical/Biochemical Engineer Internship at MRICD | 1 |
+| Bioprocess Engineer | 1 |
+| Chemical & Bioengineering Lecturer — Ignite UG/Grad Teaching | 1 |
+| Chief, Biomedical Engineer at Veterans Health Administration Richmond, VA | 1 |
+| Enzyme Engineer & Wet Lab Scientist for DNA Synthesis | 1 |
+| Fermentation Process Engineer - Yield & Quality | 1 |
+| Fermentation Process Engineer I Kula Bio Kula Bio champions sustainable, biological solutions f[...] | 1 |
+| Immediate Scientist I (Chemistry, Biochemist, Biochemical Engineer) based out of West Point, PA at On-Board Companies West Point, PA | 1 |
+| Lead Biomedical Process Engineer: Fermentation & Aseptic | 1 |
+
+Methodology: entities extracted per ad ({hard_skills, tools, methods, responsibilities, seniority}), normalized, counted as DISTINCT ads per entity; report threshold ≥ 3 ads. Headline sections in skills.md/tools.md use the stricter ≥ 20 % threshold.
--- a/references/profile.md
+++ b/references/profile.md
@@ -0,0 +1,36 @@
+# Occupation profile — biochemical engineer
+
+- **ESCO URI:** http://data.europa.eu/esco/occupation/f3e23761-0663-4ae0-97a2-0b2dd3fa38a1
+- **ESCO code:** 2145.1.1
+- **ISCO-08 group:** 2145 — Chemical engineers
+- **O*NET-SOC:** 11-9041.01 — Biofuels/Biodiesel Technology and Product Development Managers (match: closeMatch)
+
+## Description (ESCO)
+
+Biochemical engineers research on the field of life science striving for new discoveries. They convert those findings into chemical solutions that can improve the wellbeing of society such as vaccines, tissue repair, crops improvement and green technologies advances such as cleaner fuels from natural resources.
+
+## Definition
+
+nan
+
+## Alternative labels
+
+- enzyme engineer
+- biochemical engineering adviser
+- biochemical research engineer
+- biochemical process engineer
+- biochemical engineering specialist
+- tissue engineer
+- biochemical technology engineer
+- biochemical technology engineering adviser
+- bio-fuel engineer
+- biochemical technology engineering consultant
+- bio-chemical engineer
+- biochemical researcher
+- biochemical engineering researcher
+- biochemical engineering consultant
+- biochemical engineering expert
+- biochemical technology engineering expert
+- metabolic engineer
+- process development engineer
+- biochemical technology engineering specialist
--- a/references/skills.md
+++ b/references/skills.md
@@ -0,0 +1,109 @@
+# Competences — biochemical engineer
+
+Source: ESCO v1.2.1 occupation-skill relations (http://data.europa.eu/esco/occupation/f3e23761-0663-4ae0-97a2-0b2dd3fa38a1).
+
+## Essential
+
+- **adjust engineering designs** (skill/competence)
+- **advise on manufacturing problems** (skill/competence)
+- **advise on nitrate pollution** (skill/competence)
+- **analytical chemistry** (knowledge)
+- **apply for research funding** (skill/competence)
+- **apply liquid chromatography** (skill/competence)
+- **apply research ethics and scientific integrity principles in research activities** (skill/competence)
+- **apply statistical analysis techniques** (skill/competence)
+- **approve engineering design** (skill/competence)
+- **biological chemistry** (knowledge)
+- **biology** (knowledge)
+- **communicate with a non-scientific audience** (skill/competence)
+- **conduct research across disciplines** (skill/competence)
+- **demonstrate disciplinary expertise** (skill/competence)
+- **develop biochemical manufacturing training materials** (skill/competence)
+- **develop professional network with researchers and scientists** (skill/competence)
+- **disseminate results to the scientific community** (skill/competence)
+- **document analysis results** (skill/competence)
+- **draft scientific or academic papers and technical documentation** (skill/competence)
+- **engineering principles** (knowledge)
+- **engineering processes** (knowledge)
+- **ensure compliance with environmental legislation** (skill/competence)
+- **ensure compliance with safety legislation** (skill/competence)
+- **evaluate research activities** (skill/competence)
+- **examine engineering principles** (skill/competence)
+- **gas chromatography** (knowledge)
+- **gel permeation chromatography** (knowledge)
+- **genetics** (knowledge)
+- **good manufacturing practices** (knowledge)
+- **high-performance liquid chromatography** (knowledge)
+- **increase the impact of science on policy and society** (skill/competence)
+- **integrate gender dimension in research** (skill/competence)
+- **interact professionally in research and professional environments** (skill/competence)
+- **interpret 2D plans** (skill/competence)
+- **interpret 3D plans** (skill/competence)
+- **life sciences** (knowledge)
+- **manage chemical testing procedures** (skill/competence)
+- **manage findable accessible interoperable and reusable data** (skill/competence)
+- **manage intellectual property rights** (skill/competence)
+- **manage open publications** (skill/competence)
+- **manage personal professional development** (skill/competence)
+- **manage research data** (skill/competence)
+- **mentor individuals** (skill/competence)
+- **operate open source software** (skill/competence)
+- **perform project management** (skill/competence)
+- **perform scientific research** (skill/competence)
+- **promote open innovation in research** (skill/competence)
+- **promote the participation of citizens in scientific and research activities** (skill/competence)
+- **promote the transfer of knowledge** (skill/competence)
+- **publish academic research** (skill/competence)
+- **run laboratory simulations** (skill/competence)
+- **speak different languages** (skill/competence)
+- **statistical process control** (knowledge)
+- **synthesise information** (skill/competence)
+- **test samples for pollutants** (skill/competence)
+- **think abstractly** (skill/competence)
+- **toxicology** (knowledge)
+- **use chromatography software** (skill/competence)
+- **use technical drawing software** (skill/competence)
+- **write scientific publications** (skill/competence)
+
+## Optional
+
+- alternative fuels (knowledge)
+- analyse medication's impact on brain (skill/competence)
+- apply blended learning (skill/competence)
+- computational chemistry (knowledge)
+- cryopreservation (knowledge)
+- design pharmaceutical manufacturing systems (skill/competence)
+- develop biocatalytic processes (skill/competence)
+- develop food production processes (skill/competence)
+- develop pharmaceutical drugs (skill/competence)
+- evaluate pharmaceutical manufacturing process (skill/competence)
+- examine samples in dermatology (skill/competence)
+- fermentation processes of food (knowledge)
+- food materials (knowledge)
+- food science (knowledge)
+- food storage (knowledge)
+- nanomaterials (knowledge)
+- oxidation (knowledge)
+- packaging engineering (knowledge)
+- packaging processes (knowledge)
+- perform toxicological studies (skill/competence)
+- pharmaceutical chemistry (knowledge)
+- pharmaceutical drug development (knowledge)
+- pharmaceutical industry (knowledge)
+- pharmaceutical manufacturing quality systems (knowledge)
+- processes of foods and beverages manufacturing (knowledge)
+- scientific literature (knowledge)
+- synthetic biology (knowledge)
+- teach in academic or vocational contexts (skill/competence)
+
+<!-- market-evidence -->
+
+## Market evidence (job-ad analysis, 60 ads, as of 2026-07-09)
+
+Share of analyzed job ads mentioning the item (threshold ≥ 20 %). Source: JSearch/Adzuna APIs.
+
+### Hard skills
+
+- data analysis — **35 %**
+
+<!-- market-evidence -->
--- a/references/tasks.md
+++ b/references/tasks.md
@@ -0,0 +1,36 @@
+# Tasks & work activities — biochemical engineer
+
+Source: O*NET 30.3, occupation 11-9041.01 (Biofuels/Biodiesel Technology and Product Development Managers).
+
+## Task statements
+
+- **[Core]** Develop lab scale models of industrial scale processes, such as fermentation.
+- **[Core]** Provide technical or scientific guidance to technical staff in the conduct of biofuels research or development.
+- **[Core]** Prepare, or oversee the preparation of, experimental plans for biofuels research or development.
+- **[Core]** Prepare biofuels research and development reports for senior management or technical professionals.
+- **[Core]** Design or conduct applied biodiesel or biofuels research projects on topics, such as transport, thermodynamics, mixing, filtration, distillation, fermentation, extraction, and separation.
+- **[Core]** Conduct experiments on biomass or pretreatment technologies.
+- **[Core]** Conduct experiments to test new or alternate feedstock fermentation processes.
+- **[Core]** Analyze data from biofuels studies, such as fluid dynamics, water treatments, or solvent extraction and recovery processes.
+- **[Core]** Oversee biodiesel/biofuels prototyping or development projects.
+- **[Core]** Propose new biofuels products, processes, technologies or applications based on findings from applied biofuels or biomass research projects.
+- **[Supplemental]** Develop computational tools or approaches to improve biofuels research and development activities.
+- **[Supplemental]** Perform protein functional analysis and engineering for processing of feedstock and creation of biofuels.
+- **[Supplemental]** Develop separation processes to recover biofuels.
+- **[Supplemental]** Develop methods to recover ethanol or other fuels from complex bioreactor liquid and gas streams.
+- **[Supplemental]** Develop methods to estimate the efficiency of biomass pretreatments.
+- **[Supplemental]** Design or execute solvent or product recovery experiments in laboratory or field settings.
+- **[Supplemental]** Design chemical conversion processes, such as etherification, esterification, interesterification, transesterification, distillation, hydrogenation, oxidation or reduction of fats and oils, and vegetable oil refining.
+- **[Supplemental]** Conduct research to breed or develop energy crops with improved biomass yield, environmental adaptability, pest resistance, production efficiency, bioprocessing characteristics, or reduced environmental impacts.
+
+## Detailed work activities
+
+- Communicate green energy production information.
+- Develop operating strategies, plans, or procedures for green or sustainable operations.
+- Develop specifications for new products or processes.
+- Develop technical processes to improve the efficiency of biofuel production.
+- Direct green energy production operations.
+- Evaluate energy production data.
+- Model operational processes.
+- Supervise workers performing environmentally sustainable activities.
+- Test green technologies or processes.
--- a/references/tools.md
+++ b/references/tools.md
@@ -0,0 +1,37 @@
+# Tools & technology — biochemical engineer
+
+Source: O*NET 30.3 'Software Skills' for 11-9041.01.
+
+| Software | Category | Hot technology |
+|---|---|---|
+| Microsoft SQL Server | Data base management system software | yes |
+| Microsoft SQL Server Integration Services SSIS | Enterprise application integration software | yes |
+| SAP software | Enterprise resource planning ERP software | yes |
+| Adobe Illustrator | Graphics or photo imaging software | yes |
+| Epic Systems | Medical software | yes |
+| Microsoft SQL Server Reporting Services SSRS | Object or component oriented development software | yes |
+| Oracle Java | Object or component oriented development software | yes |
+| Perl | Object or component oriented development software | yes |
+| Python | Object or component oriented development software | yes |
+| Microsoft Office software | Office suite software | yes |
+| Linux | Operating system software | yes |
+| UNIX | Operating system software | yes |
+| Microsoft PowerPoint | Presentation software | yes |
+| Microsoft Visio | Process mapping and design software | yes |
+| Microsoft Project | Project management software | yes |
+| Oracle Primavera Enterprise Project Portfolio Management | Project management software | yes |
+| Microsoft Excel | Spreadsheet software | yes |
+| Microsoft Word | Word processing software | yes |
+| Fund accounting software | Accounting software |  |
+| Agilent ChemStation | Analytical or scientific software |  |
+| Fleet Asset Management and Optimization Solutions FAMOS PEPSE | Analytical or scientific software |  |
+| GE Energy GateCycle | Analytical or scientific software |  |
+| Dassault Systemes CATIA | Computer aided manufacturing CAM software |  |
+| Structure query language SQL | Data base user interface and query software |  |
+| Formula translation/translator FORTRAN | Development environment software |  |
+| National Instruments LabVIEW | Development environment software |  |
+| Email software | Electronic mail software |  |
+| Ab Initio | Enterprise resource planning ERP software |  |
+| Microsoft Dynamics | Enterprise resource planning ERP software |  |
+| Web browser software | Internet browser software |  |
+| Microsoft Great Plains Personal Data Keeper | Time accounting software |  |