ParticleChromo3D+: a Web Server for ParticleChromo3D Algorithm for 3D Chromosome Structure Reconstruction

Access on: http://ParticleChromo3D.online

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OluwadareLab, University of Colorado, Colorado Springs

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Build Status

Developers:
              David Vadnais
              Department of Computer Science
              University of Colorado, Colorado Springs
              Email: dvadnais@uccs.edu

Contact:
              Oluwatosin Oluwadare, PhD
              Department of Computer Science
              University of Colorado, Colorado Springs
              Email: ooluwada@uccs.edu

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1. Content of folders:

• configs: Python Dependencies
  
• exampleIfs: Synthetic and Real Hi-C datasets examples.
  
• flask: Source Code and utility's used.
  
• help: Example scripts to help a user get started with our webserver.
  
• results: Output structures generated for all the experiments performed.
  
• website: front end code

2. Hi-C Data example data in this study:

The GM12878 cell Hi-C dataset, GEO Accession number GSE63525, was downloaded from GSDB with GSDB ID: OO7429SF

3. Input matrix file format:

Square Matrix Input format: The square matrix is a tab seperated N by N intra-chromosomal contact matrix derived from Hi-C data, where N is the number of regions of a chromosome.

Or convert using the convert endpoint after uploading the Sparse Matrix as a TSV (three-column) file format.

4. Dependencies Installation:

With Docker

Docker

Without Docker

See config/requirements.txt

5. Usage - Docker

Base usage

• Download latest image
  • Via the GitHub web interface here: https://github.com/OluwadareLab/ParticleChromo3D_Plus/actions
• Load the image with
  • docker image load -i particlechromo3d_image.tar.gz
• Run the container with
  • docker run -d -p 5001:5001 -p 8080:8080 -e SERVICE_EMAIL=${YOUR_SVC_EMAIL} -e HOSTNAME_BE=${YOUR_URL} -e SERVICE_EMAIL_KEY=${KEY} particlechromo3d:latest

Build/extend the image

In the base folder build the image with docker build -t particlechromo3d:latest .

Then run the container with docker run -d -p 5001:5001 -p 8080:8080 -e SERVICE_EMAIL=${YOUR_SVC_EMAIL} -e HOSTNAME_BE=${YOUR_URL} -e SERVICE_EMAIL_KEY=${KEY} particlechromo3d:latest

Volumes (Persisting Data)

Working with volumes:

• docker volume create ${VOLUME_NAME}

• docker volume inspect ${VOLUME_NAME}

• docker volume ls

• docker volume rm ${VOLUME_NAME}

• docker run -d -p 5001:5001 -p 8080:8080 -e SERVICE_EMAIL=${YOUR_SVC_EMAIL} -e HOSTNAME_BE=${YOUR_URL} -e SERVICE_EMAIL_KEY=${KEY} particlechromo3d:latest

7. Usage - Direct:

In lieu of using docker flask/Ps.py can be run directly through:

• python Ps.py ${INPUT_MATRIX}

Use python Ps.py --help to find out more about the run options.

8. Publication:

Vadnais, David, and Oluwatosin Oluwadare. "ParticleChromo3D+: A Web Server for ParticleChromo3D Algorithm for 3D Chromosome Structure Reconstruction." Current Issues in Molecular Biology 45.3 (2023): 2549-2560.

Vadnais, D., Middleton, M. & Oluwadare, O. ParticleChromo3D: a Particle Swarm Optimization algorithm for chromosome 3D structure prediction from Hi-C data. BioData Mining 15, 19 (2022). https://doi.org/10.1186/s13040-022-00305-x