1. StereoHub

1.1 StereoHub Architecture:

StereoHub: a comprehensive cloud platform for Stereo-Seq analysis, Single-Cell visualization, and CT segments annotation.

1. Github Team: https://github.com/StereoHub/

2. Source Repository: https://github.com/StereoHub/StereoHub

3. Documents: https://stereohub.github.io

4. Cloud Platform: http://43.242.96.52:5002

1.2 StereoHub Features:

1.2.1 Stereo-Seq Analysis

Pipelined single-slice analysis and time-based multi-slice analysis.

1.2.2 Single-Cell Seurat

Pipelined analysis and visualization of Single-Cell expression data based on Seurat.

1.2.3 Computed Tomography Slicer

Supports online labeling and feature extraction of DICOM data from CT and NMR.

1.3 StereoHub Develop or Deploy

1.3.1 Installing

# 1. git clone repository
git clone https://github.com/StereoHub/StereoHub.git
cd StereoHub

# 2. Install Environment
# 2.1 For Windows (Recommended)
.\env-win.bat

# OR

# 2.2 For Linux (Recommended)
bash env-linux.sh

# OR

# 2.3 Install Steps (Recommended)
# 2.3.1 Mamba Env Create and Activate
mamba create -n stereohub python=3.8
mamba activate stereohub

# 2.3.2 Shiny
mamba install -c conda-forge shiny=1.0.0 shinywidgets=0.3.2 IPython=8.12.2 ipywidgets=8.1.3

# 2.3.3 Utils
mamba install -c conda-forge numpy=1.23.5 pandas=1.5.3 matplotlib=3.7.1 faicons=0.2.2

# 2.3.4 Stereopy
mamba install stereopy=1.3.1 -c stereopy -c grst -c numba -c conda-forge -c bioconda -c fastai -c defaults

# OR

# 2.4 Conda Env Export and Create (Not Recommended)
conda env create -f stereohub.yml
conda activate stereohub

1.3.2 Run, develop and debug

# 1. For Windows
.\start-win.bat

# 2. For Linux
bash start-linux.sh

# 3. All Terminals
python -m shiny run \
  --host 127.0.0.1 \
  --port 5000 \
  --reload \
  --reload-includes "*.py,*.css,*.js,*.html,*.md" \
  --reload-excludes "*.png,*.pdf" \
  --log-level info \
  --app-dir "." \
  --launch-browser \
  --dev-mode \
  app.py

1.3.3 Deploy: Shinylive (WebAssembly + Pyodide) (Not Recommended)

Shinylive: Shiny + WebAssembly: https://shiny.posit.co/py/docs/shinylive.html

shiny create myapp

pip install shinylive
shinylive export myapp site
python3 -m http.server --directory site 5000

1.3.4 Deploy: Shiny-Server (Recommended)

Self-hosted deployments: https://shiny.posit.co/py/docs/deploy-on-prem.html

# 1. shiny-server
wget https://download3.rstudio.org/centos7/x86_64/shiny-server-1.5.22.1017-x86_64.rpm
sudo rpm -ivh shiny-server-1.5.22.1017-x86_64.rpm

# 2. stereohub environment
bash env-linux.sh

# 3. shiny-server home
cd /srv/shiny-server/
git clone https://github.com/StereoHub/StereoHub.git

# 4. shiny-server config
sudo vim /etc/shiny-server/shiny-server.conf

python /cluster/envs/miniconda3/envs/stereohub/bin/python;

run_as shiny;

server {
  listen 3838;

  # Define a location at the base URL
  location / {
    # Host the directory of Shiny Apps stored in this directory
    site_dir /srv/shiny-server;

    # Log all Shiny output to files in this directory
    log_dir /var/log/shiny-server;

    # An index of the applications available in this directory will be shown.
    directory_index on;
  }
}

# 5. shiny-server manage
sudo systemctl start shiny-server
sudo systemctl status shiny-server
sudo systemctl restart shiny-server

1.3.5 Deploy: Docker (Recommended)

# 1. Build, Run, Push
# 1.1 Setting services name, build, tag, port, volume, etc.
vim docker-compose.yml

# 1.2 Build stereohub and run container
docker compose up stereohub -d --build

# 1.3 Push stereohub
docker push omicsdocker/stereohub:1.1.0

# 2. Pull from DockerHub
# 2.1 Pull image with tag
docker pull omicsdocker/stereohub:1.1.0

# 2.2 Run service with port and name
docker run -d -p 3838:3838 --name stereohub omicsdocker/stereohub:1.1.0

1.3.6 Deploy: Singularity (Recommended)

# 1. Build Singularity Image File
# 1.1 Build based Docker local image
singularity build stereohub.sif docker-daemon://omicsdocker/stereohub:1.1.0

# 1.2 Build based Docker remote image
singularity build stereohub.sif docker://omicsdocker/stereohub:1.0.0

# 1.3 Build based singularity.def
singularity build stereohub.sif singularity.def

# 1.4 Run SIF
singularity run --bind /var/log/shiny-server:/var/log/shiny-server stereohub.sif
sudo singularity run --writable-tmpfs --bind /var/log/shiny-server:/var/log/shiny-server stereohub.sif

2. Stereo-Seq Technology:

a. STomics Stereo-Seq: https://stomics.tech

b. STomics Cloud: https://cloud.stomics.tech

c. STOmics Database: https://db.cngb.org/stomics/

d. ImageStudio, StereoMap: https://stomics.tech/products/BioinfoTools/OfflineSoftware

e. STomics Github: https://github.com/STOmics/

f. Stereopy: https://github.com/STOmics/Stereopy/

2.1 References

Ao Chen, Sha Liao, Mengnan Cheng, Longqi Liu, Xun Xu, Jian Wang. Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays. Cell, 2022, doi: https://doi.org/10.1016/j.cell.2022.04.003