Commit fad6a0d8 authored by Craig Russell's avatar Craig Russell
Browse files

Updating documentation

parent c03459d0
......@@ -28,7 +28,7 @@ author = 'Craig Russell'
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [myst_parser]
]
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
......
# Welcome to MkDocs
<!-- # Welcome to MkDocs
For full documentation visit [mkdocs.org](https://www.mkdocs.org).
......@@ -14,4 +14,74 @@ For full documentation visit [mkdocs.org](https://www.mkdocs.org).
mkdocs.yml # The configuration file.
docs/
index.md # The documentation homepage.
... # Other markdown pages, images and other files.
... # Other markdown pages, images and other files. -->
<!-- ## Quick start -->
<!--
| | | |
|---:|:---|:---|
| [![Binder](https://binder.bioimagearchive.org/badge_logo.svg)](https://binder.bioimagearchive.org/v2/gh/ctr26/bia-binder-rclone/HEAD) | Mounting Biostudies using rclone | github.com/ctr26/bia-binder-rclone
| [![Binder](https://binder.bioimagearchive.org/badge_logo.svg)](https://binder.bioimagearchive.org/v2/gh/EBIBioStudies/biostudies-notebooks/HEAD) | Reading Biostudies images | github.com/EBIBioStudies/biostudies-notebooks |
| [![Binder](https://binder.bioimagearchive.org/badge_logo.svg)](https://gpu.binder.bioimagearchive.org/v2/gh/HenriquesLab/ZeroCostDL4Mic/master?urlpath=lab/tree/ipynb)| Running ZeroCostDL4Mic | github.com/HenriquesLab/ZeroCostDL4Mic |
| [![Binder](https://binder.bioimagearchive.org/badge_logo.svg)](https://gpu.binder.bioimagearchive.org/v2/gh/HenriquesLab/ZeroCostDL4Mic/master?urlpath=lab/tree/ipynb)| ↳ with a specific notebook |
| [![Binder](https://binder.bioimagearchive.org/badge_logo.svg)](https://binder.bioimagearchive.org/v2/gh/IDR/idr0079-hartmann-lateralline/HEAD) | Some IDR studies are availiable | github.com/IDR/idr0079-hartmann-lateralline |
| | | |
|---:|:---|:---|
| [![Binder](https://binder.bioimagearchive.org/badge_logo.svg)](https://binder.bioimagearchive.org/v2/gh/ctr26/bia-binder-rclone/HEAD) | Mounting Biostudies using rclone | github.com/ctr26/bia-binder-rclone
| [![Binder](https://binder.bioimagearchive.org/badge_logo.svg)](https://binder.bioimagearchive.org/v2/gh/EBIBioStudies/biostudies-notebooks/HEAD) | Reading Biostudies images | github.com/EBIBioStudies/biostudies-notebooks |
| [![Binder](https://binder.bioimagearchive.org/badge_logo.svg)](https://gpu.binder.bioimagearchive.org/v2/gh/HenriquesLab/ZeroCostDL4Mic/master?urlpath=lab/tree/ipynb)| Running ZeroCostDL4Mic | github.com/HenriquesLab/ZeroCostDL4Mic |
| [![Binder](https://binder.bioimagearchive.org/badge_logo.svg)](https://gpu.binder.bioimagearchive.org/v2/gh/HenriquesLab/ZeroCostDL4Mic/master?urlpath=lab/tree/ipynb)| ↳ with a specific notebook |
| [![Binder](https://binder.bioimagearchive.org/badge_logo.svg)](https://binder.bioimagearchive.org/v2/gh/IDR/idr0079-hartmann-lateralline/HEAD) | Some IDR studies are availiable | github.com/IDR/idr0079-hartmann-lateralline |
| | | |
|-|-|-|
| | > "Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum."_ | |
|
-->
## BioImageArchive BinderHub
BinderHub allows users to share reproducible interactive computing environments from code repositories.
## Quick start
> [![Binder](https://binder.bioimagearchive.org/badge_logo.svg)](https://binder.bioimagearchive.org/v2/gh/ctr26/bia-binder-rclone/HEAD) &emsp; Mounting Biostudies using rclone
>
> [![Binder](https://binder.bioimagearchive.org/badge_logo.svg)](https://binder.bioimagearchive.org/v2/gh/EBIBioStudies/biostudies-notebooks/HEAD) &emsp; Reading Biostudies images
>
> [![Binder](https://binder.bioimagearchive.org/badge_logo.svg)](https://gpu.binder.bioimagearchive.org/v2/gh/HenriquesLab/ZeroCostDL4Mic/master?urlpath=lab/tree/ipynb) &emsp; Running ZeroCostDL4Mic
>
> [![Binder](https://binder.bioimagearchive.org/badge_logo.svg)](https://gpu.binder.bioimagearchive.org/v2/gh/HenriquesLab/ZeroCostDL4Mic/master?urlpath=lab/tree/ipynb) &emsp; ↳ with a specific notebook
>
> [![Binder](https://binder.bioimagearchive.org/badge_logo.svg)](https://binder.bioimagearchive.org/v2/gh/IDR/idr0079-hartmann-lateralline/HEAD) &emsp; Some [IDR](https://idr.openmicroscopy.org/) studies are availiable
>
> [![Binder](https://binder.bioimagearchive.org/badge_logo.svg)](https://binder.bioimagearchive.org/v2/gh/ctr26/basic-gpu-binder/HEAD) &emsp; Binder for machine learning using GPUs
## Services and capabilities
| Tier |URL|Flavour|Resources|
|:----:|:----:|:----:|:----:|
| 1 | [binder.bioimagearchive.org](binder.bioimagearchive.org)| Public Binderhub | 8Gb RAM, 4 vCPUs, Ephemeral|
| 2 | [login.binder.bioimagearchive.org](login.binder.bioimagearchive.org)| Persistent Binderhub | <16Gb RAM, <8 vCPUs, 15 GB Storage, Dask|
| 2 | [gpu.beta.binder.bioimagearchive.org](gpu.beta.binder.bioimagearchive.org)| Authenticated Binderhub | <32Gb RAM, <8 vCPUs, (1-2) GPUs, Ephemeral, Dask|
| 3 | [kubeflow.binder.bioimagearchive.org](kubeflow.binder.bioimagearchive.org)| Authenticated Kubeflow | n x (<32Gb RAM, <8 vCPUs), 15 GB Storage, (1-2) GPUs, Dask |
<!-- | 1 | binder.bioimagearchive.org/sandbox | Public Jupyterhub | 8Gb RAM, 4 vCPUs | -->
<!-- | 2 | beta.binder.bioimagearchive.org/github | Authenticated Jupyterhub | <32Gb RAM, <8 vCPUs, 15 GB Storage, (1-2) GPUs, Dask | -->
### To request access to Tier 2/3, please contact [bioimagearchive@ebi.ac.uk](mailto:bioimagearchive@ebi.ac.uk)
<!-- - [![Binder](https://binder.bioimagearchive.org/badge_logo.svg)](https://binder.bioimagearchive.org/v2/gh/ctr26/bia-binder-rclone/HEAD) Mounting Biostudies using rclone
- [![Binder](https://binder.bioimagearchive.org/badge_logo.svg)](https://binder.bioimagearchive.org/v2/gh/EBIBioStudies/biostudies-notebooks/HEAD) Reading Biostudies images
- [![Binder](https://binder.bioimagearchive.org/badge_logo.svg)](https://gpu.binder.bioimagearchive.org/v2/gh/HenriquesLab/ZeroCostDL4Mic/master?urlpath=lab/tree/ipynb) Running ZeroCostDL4Mic
- [![Binder](https://binder.bioimagearchive.org/badge_logo.svg)](https://gpu.binder.bioimagearchive.org/v2/gh/HenriquesLab/ZeroCostDL4Mic/master?urlpath=lab/tree/ipynb) ↳ with a specific notebook
- [![Binder](https://binder.bioimagearchive.org/badge_logo.svg)](https://binder.bioimagearchive.org/v2/gh/IDR/idr0079-hartmann-lateralline/HEAD) Some IDR studies are availiable
-->
# User Guide
## Services and capabilities
| Tier | URL | Flavour | Resources |
|:----:|:--------------------------------------:|:------------------------:|:----------------------------------------------------------:|
| 1 | binder.bioimagearchive.org | Public Binderhub | 8Gb RAM, 4 vCPUs |
| 1 | binder.bioimagearchive.org/sandbox | Public Jupyterhub | 8Gb RAM, 4 vCPUs |
| 2 | binder.bioimagearchive.org/github | Authenticated Jupyterhub | <16Gb RAM, <8 vCPUs, 15 GB Storage, Dask |
| 2 | gpu.beta.binder.bioimagearchive.org | Authenticated Jupyterhub | <32Gb RAM, <8 vCPUs, (1-2) GPUs, Dask |
| 2 | beta.binder.bioimagearchive.org/github | Authenticated Jupyterhub | <32Gb RAM, <8 vCPUs, 15 GB Storage, (1-2) GPUs, Dask |
| 3 | kubeflow.binder.bioimagearchive.org | Authenticated Kubeflow | n x (<32Gb RAM, <8 vCPUs), 15 GB Storage, (1-2) GPUs, Dask |
## Cluster(s) structure
Currently there are two Kubernetes clusters jointly (but not very intelligently) hosting the listed services on Embassy Cloud.
......
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