The references/ directory linked to nonexistent mermaid_diagrams/ and
markdown_templates/ prefixes. Updated to the actual paths: diagrams/
for diagram type files and ../templates/ for document templates.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Platform-integration skill for running protein and small-molecule modeling
jobs on Tamarind Bio (app.tamarind.bio) via its public REST API or MCP server.
References-only design: it points at Tamarind's live sources (llms.txt,
openapi.yaml, docs.tamarind.bio, and live MCP discovery via listModalities /
listTags / getAvailableTools / getJobSchema) rather than bundling a parallel
client that drifts.
Files:
- SKILL.md: overview, auth, MCP and REST surfaces, the discover / schema /
validate / submit / poll / results loop, tool-choice guidance, batch
aggregation, status lifecycle, and error table.
- references/api_reference.md, tool_catalog.md, workflows.md, examples.md.
Examples validated against the live API.
Co-Authored-By: Azam Hussain <azam@tamarind.bio>
Bumped the project version in pyproject.toml to 2.50.0. Updated README and documentation to reflect the addition of new skills, increasing the total to 146. Adjusted version and skills badges for accuracy.
Enhanced the README and CONTRIBUTING files to reflect the inclusion of NVIDIA NemoClaw and Pi as supported platforms for installing Agent Skills. Updated metadata parsing details to ensure clarity on single-line JSON format compatibility across all mentioned hosts.
Updated multiple skills to include a new `required_environment_variables` field, specifying necessary credentials for improved integration and user guidance. Each skill now clearly outlines required and optional environment variables, enhancing setup and usage clarity. Skills affected include autoskill, benchling-integration, biopython, bioservices, citation-management, clinical-decision-support, clinical-reports, dnanexus-integration, exa-search, hypothesis-generation, infographics, latex-posters, literature-review, markitdown, modal, neuropixels-analysis, omero-integration, open-notebook, parallel-web, peer-review, pptx-posters, pymatgen, pyzotero, research-lookup, rowan, scholar-evaluation, scientific-schematics, and scientific-slides.
* Sync citation-management skill with claude-scientific-writer updates
Port the citation management and verification enhancements from the
claude-scientific-writer repo (commits 4bede21 and 93dff38):
- Add Phase 2.5: Metadata Enrichment via Web Search — mandatory scan
for incomplete BibTeX entries (missing volume, pages, DOI) with web
search strategies to fill gaps before formatting. Commands adapted
to this repo's parallel-cli convention.
- Add venue-based citation count standards (Nature/Science 35-50+,
ML/CS conferences 30-45+, literature reviews 40-65+, medical
journals 30-45+) and diverse-referencing guidance.
- Add mandatory post-writing reference checks: no unresolved
citations, no unused bibliography entries, venue-level citation
counts, complete metadata.
- Upgrade validate_citations.py with --venue, --min-count, and
--manuscript flags: enforces venue citation standards and
cross-checks manuscript citations (Markdown/LaTeX) against the
BibTeX file to detect unresolved or unused references.
- Expand citation_validation.md Issue 3 with mandatory web search
workflow for incomplete metadata.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* Add venue-templates cross-references to literature-review and peer-review
Port the venue-templates skill cross-references from
claude-scientific-writer: literature-review gains a Venue-Specific
Writing Styles section pointing at the style guides, and peer-review
gains a pointer to reviewer_expectations.md for calibrating review
standards to the target venue. The venue-templates skill and all
referenced files already exist in this repo.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* Bump metadata.version to 1.1 for updated skills
Per CONTRIBUTING.md, increment metadata.version in the same PR that
updates a skill. All three skills pass the Agent Skills reference
validator (agentskills validate).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Co-authored-by: Claude Fable 5 <noreply@anthropic.com>
