I have been working on creating Docker images for a number of bioinformatics tools that I used on a regular bases. In addition to just having functional Docker images to run different workflows, I am also adding step-by-step instructions on how to access the Docker container and how to generate the input and output files using each tool. If a well-documented Docker image already exists for a bioinformatics tool I use regularly, I’ll just add a link in the Resources page. Below, you can find instructions on how you can make your own Docker images and brief description of the Docker images I created.

Table of contents
  1. DiffDock
  2. AlphaFill
  3. P2Rank
  4. PanPPI
  5. PhylogenyZ
  6. Chainsaw
  7. Evolocity

DiffDock

DiffDock can be used to run molecular docking analyses of specified small molecules and a given protein structure.

Docker Hub GitHub Dockerfile

AlphaFill

AlphaFill can be used to transplant ligands from experimental structures to predicted structures based on structure similairty. This AlphaFill Docker image can be used to run the stand-alone version of AlphaFill. Additional instructions and details are provided in the Docker Hub page.

Docker Hub GitHub Dockerfile

P2Rank

Docker Hub GitHub Dockerfile

PanPPI

A Python Dash web-app that I built to explore the PanPPI data we generated using the maize pan-genomes, as explained in this G3:Genes|Genomes|Genetics paper. Currently there is only a Docker image for the Dash app with the maize data included, but I am planning to add a Docker image for running the analysis workflow for custom pan-genomes and custom data.

Docker Hub GitHub Dockerfile

PhylogenyZ

An environment to run simple phylogenetic analyses, meant primarily for building protein trees. The general workflow I use is: (1) protein alignmnet using FAMSA, (2) alignment trimming using ClipKIT, and (3) building the phylogenetic tree using IQ-TREE2.

Docker Hub GitHub Dockerfile

Chainsaw

An Docker image for running Chainsaw, a protein domain segmentation based on a given PDB structure.

Docker Hub GitHub Dockerfile

Evolocity

An Docker image for running Evolocity, a Python package that calculates evolutionary velocity using protein languages. This Docker container comes with the default esm1b_t33_650M_UR50S and esm1b_t33_650M_UR50S-contact-regression pre-trained models downloaded so it takes a bit more space.

Docker Hub GitHub Dockerfile