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tamarind

Access a collection of open-source molecular design and structural biology tools on the Tamarind Bio platform, via its REST API or MCP server — no local GPUs required. Tamarind bundles popular open-source models for structure prediction (AlphaFold, Boltz, Chai, ESMFold), protein, binder, and de novo design (RFdiffusion, ProteinMPNN, BoltzGen), antibody and nanobody design and developability, protein-ligand docking (DiffDock, Autodock Vina), binding-affinity prediction, MSA generation, and molecular dynamics. Use when the user mentions Tamarind or tamarind.bio, wants to run any of these open-source tools in the cloud, references app.tamarind.bio/api or the x-api-key header, or needs to submit batches of sequences for structural or biophysical characterization.

Quality

92%

Does it follow best practices?

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SecuritybySnyk

Passed

No findings from the security scan

The canonical home for this skill is tamarind in K-Dense-AI/scientific-agent-skills

SKILL.md
Quality
Evals
Security

Quality

Content

85%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

An exceptionally well-engineered skill body: executable end-to-end code, explicit validation checkpoints and error-recovery loops for single jobs, batches, and chaining, and a clean one-level-deep reference structure. The only weakness is redundancy — several high-value footguns (bare-filename S3 scoping, the `source` field, full-list /tools behavior) are repeated two to three times, inflating token cost without adding information.

Suggestions

Consolidate the bare-filename-vs-email-prefix rule into one canonical statement in "File inputs" and cross-reference it from the Foot-gun and validateJob-notes paragraphs, instead of explaining it three times in the same section.

Deduplicate the `source: "static-fallback"` explanation, which appears in both "Job settings, schemas, and validation" and the "validateJob notes" — keep one and link the other.

State "REST /tools returns the full list; filter client-side" once (e.g., in "Discovering tools") and trim its restatements in the Core workflow comments and tool_catalog reference.

DimensionReasoningScore

Conciseness

Mostly efficient and rich in non-obvious platform knowledge Claude cannot know (response shapes, bare-filename S3 scoping, batchStatus polling), but the same footguns are restated multiple times: the bare-filename-not-email-prefix rule appears three times within "File inputs" (list item 1, the Foot-gun paragraph, and the validateJob notes), the `source: "static-fallback"` explanation appears in both "Job settings, schemas, and validation" and "validateJob notes", and "REST /tools returns the full list; filter client-side" is repeated across Core workflow, Discovering tools, and tool_catalog.md. This is more than the 'minor instances' of anchor 4, so it sits at anchor 3: could be meaningfully tightened by consolidating each repeated rule into one canonical statement.

3 / 5

Actionability

Fully executable, copy-paste-ready coverage of the common cases: a complete discover→submit→poll→download Python script with a real sequence and payload, a runnable batch polling loop with terminal-status and aggregation-error handling, a curl auth example, MCP tool signatures with argument lists, and exact response shapes and error strings ("The following files have not been uploaded: <email>/<file>"). Matches anchor 5; not score 4 because the examples cover the core single-job, batch, file-input, and chaining cases with no gaps.

5 / 5

Workflow Clarity

The canonical loop is stated explicitly ("Always follow discover → schema → validate → submit → poll → results") and echoed in numbered code comments, with an explicit pre-submit validation checkpoint ("Always `validateJob` (MCP) before submitting — it's the reliable guard") and feedback loops for error recovery (error-code table mapping to actions, `getJobLogs` on `Stopped`, break on all terminal statuses, raise on `AggregationFailed`). Batch operations — the rubric's cap trigger — are fully covered by validate-before-submit and batchStatus polling, so the workflow cap does not apply. Matches anchor 5.

5 / 5

Progressive Disclosure

The body is an overview of behaviors and gotchas that appropriately delegates bulk material to four real, one-level-deep reference files (examples.md, api_reference.md, tool_catalog.md, workflows.md — all present in ./references/), each clearly signaled inline and summarized with its purpose in the closing "Reference files" section. No nested reference chains, and no API-reference dump inlined in the body (the endpoint table lives in api_reference.md). Matches anchor 5.

5 / 5

Total

18

/

20

Passed

Description

100%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

The description is exemplary: third-person, concise, and comprehensive on capabilities with named tools, plus an explicit 'Use when…' clause carrying concrete platform, artifact, and tool-name triggers. It matches the rubric's top anchors on all four dimensions with no fluff or over-claims.

DimensionReasoningScore

Specificity

Enumerates multiple concrete capability areas with named tools — "structure prediction (AlphaFold, Boltz, Chai, ESMFold)", "protein, binder, and de novo design (RFdiffusion, ProteinMPNN, BoltzGen)", "antibody and nanobody design and developability", "protein-ligand docking (DiffDock, Autodock Vina)", "binding-affinity prediction, MSA generation, and molecular dynamics" — plus the two access surfaces ("via its REST API or MCP server") and batch submission. Coverage is comprehensive across the platform's capability space, matching the anchor-5 example's breadth; not score 4 because no capability area is conspicuously missing.

5 / 5

Completeness

Explicitly answers what ("bundles popular open-source models for structure prediction… docking… binding-affinity prediction, MSA generation, and molecular dynamics") and when ("Use when the user mentions Tamarind or tamarind.bio, wants to run any of these open-source tools in the cloud, references app.tamarind.bio/api or the x-api-key header, or needs to submit batches of sequences"), exactly mirroring the anchor-5 good example. Not score 4 because the when-clause is already fully explicit with concrete trigger phrases.

5 / 5

Trigger Term Quality

Natural triggers span the platform name and URLs ("Tamarind or tamarind.bio", "app.tamarind.bio/api"), the auth artifact ("the x-api-key header"), tool names users actually say (AlphaFold, DiffDock, ProteinMPNN, RFdiffusion), capability nouns ("structure prediction", "docking", "binding-affinity prediction", "MSA generation"), and intent phrases ("run any of these open-source tools in the cloud", "submit batches of sequences"). This matches anchor 5's comprehensive synonym coverage; not score 4 because both the colloquial and technical phrasings users would naturally emit are present.

5 / 5

Distinctiveness Conflict Risk

Clear niche — the Tamarind Bio cloud platform — with distinct triggers (tamarind.bio, app.tamarind.bio/api, x-api-key) that no other skill would claim; generic tool names are explicitly channeled to "run… in the cloud", separating it from local-install skills. Minimal conflict risk per anchor 5.

5 / 5

Total

20

/

20

Passed

Validation

87%

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 14 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

metadata_field

'metadata' should map string keys to string values

Warning

frontmatter_unknown_keys

Unknown frontmatter key(s) found; consider removing or moving to metadata

Warning

Total

14

/

16

Passed

Repository

synthetic-sciences/openscience

Path

backend/cli/skills/biology/tamarind/SKILL.md

Reviewed

Table of Contents

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