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mkdocs.yml
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mkdocs.yml
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site_name: User documentation
nav:
- Home:
- index.md
- Quick Start to the ODM:
- user-guide/quick-start/index.md
- Data in the User Interface:
- Data Consumer: user-guide/quick-start/consumer-gui.md
- Data Contributor: user-guide/quick-start/contributor-gui.md
- Administrator: user-guide/quick-start/admin-gui.md
- Data in API:
- Data Consumer: user-guide/quick-start/consumer-api.md
- Data Contributor: user-guide/quick-start/contributor-api.md
- Administrator: user-guide/quick-start/admin-api.md
- Key Concepts: user-guide/key-concepts/key-concepts.md
- Users, Roles, Permissions: user-guide/users-roles-permissions/users-roles-permissions.md
- Guides:
- User Interface Advanced Guide:
- user-guide/index.md
- About Genestack: https://genestack.com/
- Guide:
- user-guide/index.md
- Quick Start Guide: user-guide/doc-odm-user-guide/quickstart_user.md
- User Setup: user-guide/doc-odm-user-guide/setup.md
- Create New Study: user-guide/doc-odm-user-guide/create-study.md
- Import Data on ODM: user-guide/doc-odm-user-guide/import-samples-spreadsheet.md
- Import Data Using API: user-guide/doc-odm-user-guide/import-data-using-api.md
- Import Data Using Python Script: user-guide/doc-odm-user-guide/import-data-using-python-script.md
- Exporting Data: user-guide/doc-odm-user-guide/exporting-data.md
- Cross-reference Mapping: user-guide/doc-odm-user-guide/xref-mapping.md
- Study Browser: user-guide/doc-odm-user-guide/studybrowser.md
- Metadata Editor: user-guide/doc-odm-user-guide/metadata-editor.md
- Template Editor: user-guide/doc-odm-user-guide/template-editor.md
- Curator Guide: user-guide/doc-odm-user-guide/curator_guide.md
- Metadata Versioning: user-guide/doc-odm-user-guide/versioning.md
- Sharing Studies: user-guide/doc-odm-user-guide/sharing.md
- Getting a Genestack API token: user-guide/doc-odm-user-guide/getting-a-genestack-api-token.md
- Supported File Formats: user-guide/doc-odm-user-guide/supported-formats.md
- Tools:
- odm-sdk:
- Installation: tools/odm-sdk/installation.md
- Configuration: tools/odm-sdk/configuration.md
#- Work from python:
- Work from terminal:
- Users:
- Users creation: tools/odm-sdk/terminal/users/user-creation.md
- Templates:
- Create or update template: tools/odm-sdk/terminal/templates/create-or-update-template.md
- Delete template: tools/odm-sdk/terminal/templates/delete-template.md
- Study:
- Uploading study: tools/odm-sdk/terminal/study/uploading-study.md
- Curation script: tools/odm-sdk/terminal/study/curation-script.md
- Sharing study: tools/odm-sdk/terminal/study/sharing-study.md
- Deleting study: tools/odm-sdk/terminal/study/deleting-study.md
- Loading from GEO: tools/odm-sdk/terminal/study/loading-from-geo.md
- Dictionaries and ontologies:
- Default dictionaries: tools/odm-sdk/terminal/dictionaries-and-ontologies/default-dictionaries.md
- Exporting ontologies from ODM: tools/odm-sdk/terminal/dictionaries-and-ontologies/exporting-ontologies-from-odm.md
- Creating new dictionary: tools/odm-sdk/terminal/dictionaries-and-ontologies/creating-new-dictionary.md
- Loading new ontology:
- tools/odm-sdk/terminal/dictionaries-and-ontologies/loading-new-ontology.md
- CSV dictionary format: tools/odm-sdk/terminal/dictionaries-and-ontologies/loading-new-ontology/csv-dictionary-format.md
- SKOS dictionary: tools/odm-sdk/terminal/dictionaries-and-ontologies/loading-new-ontology/skos-dictionary.md
- Generated:
- tools/odm-sdk/generated/index.md
- odm-api:
- Python:
- Installation: tools/odm-api/python/installation.md
- Example: tools/odm-api/python/example.md
- Generated:
- tools/odm-api/python/generated/README.md
- R:
- Installation: tools/odm-api/r/installation.md
- Example: tools/odm-api/r/example.md
- Generated:
- tools/odm-api/r/generated/README.md
- UI:
- Training Materials: ui/training-materials.md
- Release notes:
- v1.50 - v1.59: release-notes/v1.50-v1.59.md
- v1.40 - v1.49: release-notes/v1.40-v1.49.md
- v1.30 - v1.39: release-notes/v1.30-v1.39.md
- v1.20 - v1.29: release-notes/v1.20-v1.29.md
theme:
name: material
palette:
- scheme: default
primary: custom
accent: custom
toggle:
icon: material/brightness-7
name: Switch to dark mode
- scheme: slate
primary: custom
accent: custom
toggle:
icon: material/brightness-4
name: Switch to light mode
logo: assets/ODM-mono-white.png
favicon: assets/favicon.ico
features:
- announce.dismiss
- content.action.edit
- content.action.view
- content.code.annotate
- content.code.copy
# - content.code.select
# - content.tabs.link
- content.tooltips
# - header.autohide
# - navigation.expand
- navigation.footer
- navigation.indexes
# - navigation.instant
# - navigation.instant.prefetch
# - navigation.instant.progress
# - navigation.prune
- navigation.sections
- navigation.tabs
# - navigation.tabs.sticky
- navigation.top
- navigation.tracking
- search.highlight
- search.share
- search.suggest
- toc.follow
# - toc.integrate
extra:
version:
provider: mike
extra_css:
- stylesheets/extra.css
markdown_extensions:
- admonition
- pymdownx.details
- pymdownx.superfences
- attr_list
- md_in_html
- pymdownx.highlight:
anchor_linenums: true
line_spans: __span
pygments_lang_class: true
- pymdownx.inlinehilite
- pymdownx.snippets
- pymdownx.tabbed:
alternate_style: true
- tables
- pymdownx.superfences:
custom_fences:
- name: mermaid
class: mermaid
format: !!python/name:pymdownx.superfences.fence_code_format
- footnotes
- pymdownx.critic
- pymdownx.caret
- pymdownx.keys
- pymdownx.mark
- pymdownx.tilde
- pymdownx.emoji:
emoji_index: !!python/name:material.extensions.emoji.twemoji
emoji_generator: !!python/name:material.extensions.emoji.to_svg
- def_list
- pymdownx.tasklist:
custom_checkbox: true
- codehilite
- pymdownx.tabbed
- toc:
permalink: true