jinko-context

Jinkō Context

Use this skill to explain Jinkō's shared mental model and vocabulary. Keep answers practical: the goal is to help a user or agent navigate Jinkō artifacts without confusing project organization, scientific content, and immutable versions.

PREREQUISITE: The folder-management example needs an initialized jinko-sdk connection and an SDK satisfying its metadata.requires_sdk range. Run the jinko-sdk-setup skill (../jinko-sdk-setup/SKILL.md) and proceed only once its check passes. A session code can be exchanged only once, so call get_session_code again before this skill's own SDK process. If that skill is not found, install it from novainsilico/jinko-skills.

Navigation and Version Management

Jinkō project navigation behaves much like working in a Git repository, but for scientific modeling artifacts instead of source-code files.

• A Project is like the repository: it is the boundary for a concrete scientific modeling effort, including references, data, models, protocols, trials, reports, and collaboration history.
• Folders are like repository directories: they organize related project items by workflow, experiment, disease area, evidence package, or analysis thread. The folder API is an organizational surface; a folder is not a Project Item.
• Project Items are like tracked files or domain objects in the repository: each item has an SID and represents a Jinkō artifact such as a model, protocol, trial, data table, reference, output set, or document.
• Snapshots are immutable states exposed by versioned Jinkō core-item APIs. The latest state is head. Do not assume every Project Item type exposes snapshots; use the resource's SDK/API surface to determine whether snapshot identity exists.

This Git-like structure makes Jinkō easier for agents to navigate because agents can separate three questions:

• Where is the work organized? Look at the project and folders.
• Which artifact is being discussed? Identify the project item.
• Which exact state of a versioned artifact matters? Use its explicit version or snapshot surface, or use head when the user wants the latest state.

Use Project, Project Item, and Snapshot rather than generic words like workspace, file, upload, save, version, revision, or commit unless you are explicitly making the Git analogy.

Domain Language

Project: A concrete scientific modeling effort with its own References, data, modeling artifacts, and reports. Avoid: workspace, case, study folder.

Folder: An organizational container inside a project used to group related project items. Folders support navigation and workflow hygiene; they do not replace item identity or snapshot identity. Avoid: Project Item or directory when speaking to end users unless making the Git analogy.

Project Item: A named Jinkō object inside a project, such as a Reference, model, protocol, trial, data table, output set, or document. Its SID is the preferred user-facing identity. Versioned types can retain that identity across versions. Avoid: file, asset, object when precision matters.

Snapshot: An immutable state of a Jinkō model, protocol, trial, or other resource whose core-item API exposes snapshots. It enables exact version access; it is not a universal property of folders or every Project Item type. Avoid: revision, save, version, commit except when explaining the analogy.

Reference: A Project Item that holds a source PDF, usually a scientific paper, and its bibliography metadata, such as the DOI. It is the evidence for extraction and modeling. The Jinkō API type name of this item is Source. Avoid: source, document, file, upload. Use Source only for the API type name.

Extract: A Project Item that holds one selected textual, rectangular, formula, or data-table object from one Reference. It can carry a formulation that states the evidence, such as a parameter value, clinical endpoint, or mechanism statement, and a classification (Statement, Hypothesis, or Data). Avoid: note, snippet, untracked fact.

Highlight: A located piece of evidence inside an Extract. It links to its position in the Reference PDF. A Highlight is not a Project Item. Avoid: annotation, quote.

Model: A Jinkō-compatible executable representation of the biological or pharmacological mechanism being modeled. Avoid: model file, script.

Protocol: The Jinkō artifact that defines trial arms, interventions, dosing or treatment conditions, and simulation timing. Avoid: study design, scenario file.

Trial: The Jinkō artifact that combines a protocol, model, output sets, and data tables for simulation or comparison. Avoid: run, simulation setup.

Calibration: The stage that adjusts model parameters so simulations fit selected experimental evidence. Avoid: fitting, tuning.

Calibration Candidate: A model-intrinsic parameter proposed for calibration. It may be marked with a toCalibrate model tag. Avoid: free parameter, tuned knob.

Virtual Population: A generated population of parameterized virtual subjects used for in-silico trial execution. Avoid: cohort, sample.

Traceability Link: The link from a model, dataset, or report assertion back to the Extract, Reference, or explicit assumption that justifies it. Avoid: reference (that term names the Project Item), citation, provenance.

Modeling Context: The full scientific, protocol, trial, Reference, and artifact background needed to build or refine a Jinkō Model. Avoid: extraction catalog, model input bundle.

Relationships

• A Project contains one or more Project Items.
• A Folder organizes Project Items within a Project.
• Some versioned Project Items expose Snapshots through their core-item APIs.
• A Snapshot captures one immutable core-item state; consult the resource API rather than assuming one exists.
• A Reference supports one or more Extracts.
• An Extract comes from one Reference and holds its evidence as one or more Highlights.
• A Highlight links to its position in the Reference PDF.
• A Model represents executable biological or pharmacological mechanisms.
• A Protocol defines arms, interventions, and timing used by a Trial.
• A Trial uses a Protocol, a Model, output sets or measures, and optional transformed data overlays.
• A Calibration uses selected evidence and outputs to adjust Calibration Candidates.
• A Virtual Population provides parameterized virtual subjects for Trial execution.
• A Traceability Link connects Project Items, Model components, Trial outputs, data tables, and reports back to Extracts, References, or explicit assumptions.
• A Modeling Context gathers the relevant References, Extracts, Traceability Links, Models, Protocols, Trials, and reports needed to make a modeling decision.

Response Guidance

• Translate user language into Jinkō language when it improves precision.
• Preserve the Git analogy for orientation, but do not imply Jinkō is literally Git.
• Distinguish stable SID identity from immutable snapshot identity where that resource exposes snapshots.
• Use head/latest only when the user wants the current state; name snapshots when exact reproducibility matters.
• When the user needs to inspect, create, or change folders, read references/folder-management.md and use its bundled script or the SDK calls it names rather than improvising API calls.
• Route implementation tasks to the relevant skill: jinko-reference, jinko-model, jinko-protocol, jinko-trial, jinko-vpop, jinko-data-table, or jinko-sdk-setup.