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Quick start of PatMatch VICE app in DE

Goal

PatMatch-JupyterLab is a Dockerized version of the PatMatch software. PatMatch is a program for finding patterns in peptide and nucleotide sequences. It was written by [Yan et al. (2005)](https://www.ncbi.nlm.nih.gov/pubmed/15980466). The PatMatch VICE app makes it available in a Jupyter environment provided by Cyverse. PatMatch use and the convenience that comes with having PatMatch working inside the Jupyter environment with interactive Python are illustrated in a series of included Jupyter notebooks. A utility script for moving command line-based PatMatch results into Python is also demonstrated in the provided notebooks.

Because PatMatch-JupyterLab provides PatMatch inside Cyverse’s VICE app environment, there are these benefits.

  • PatMatch is available for sequence analysis or for educational purposes without installing.
  • The text-based output of PatMatch can be converted via the Jupyter environment to insights and visualizations that provide new perspectives.
  • Easily share results with your team, even those members without PatMatch installed.

In this quick start, we will show you how to launch the PatMatch VICE app in DE.

Prerequisites

Haven’t signed-up to Cyverse? Here you can select ``launch binder`` to get the same content on a more limited system where you cannot link to the Cyverse data repository or share with Cyverse-using colleagues.

Downloads, access, and services

In order to complete this tutorial you will need access to the following services/software

Prerequisite Preparation/Notes Link/Download
CyVerse account You will need a CyVerse account to complete this exercise Register

Platform(s)

We will use the following CyVerse platform(s):

Platform Interface Link Platform Documentation Learning Center Docs
Discovery Environment Web/Point-and-click Discovery Environment DE Manual Guide

Input and example data

In order to complete this quickstart you will need to have the following inputs prepared.

Note

The example input data (which contains data and Jupyter notebooks) will either already prefilled for you during app launch or obtained in the course of running the notebooks

Input File(s) Format Preparation/Notes Example Data
Fasta sequence and Jupyter notebooks
  • Fasta
  • Jupyter notebooks
 Input data can be a sequence files in FASTA format Example FASTA file can be viewed here

Get started: Launch NanoDJ

  1. Login to the Discovery Environment.
  2. Click on Apps window in the DE workspace and search for and run PatMatch-JupyterLab.

Tip

Alternatively you can clik this PatMatchJupyterLab logo button to directly launch the PatMatch VICE app.

  1. Under “Analysis Name” leave the defaults or make any desired notes.
  2. Click Launch Analysis. You will receive couple of notifications on the bell corresponding to job submission and running with the “Access your running analysis here”.
  3. Clicking on the “Access your running analysis” will open the PatMatch-JupyterLab in another tab in the browser after a brief building phase.

Note

You will be asked to authenticate again to the JupyterLab with your CyVerse username and password

  1. In the main JupyterLab interface, in the file browser pane on the left, double-click on index.ipynb.
  2. Click on a notebook description in the list to launch it.
  3. Finally, once you finish analysis, navigate to the Discovery Environment tab, select the Analysis window and select the analysis, click “save and complete analysis”. Upon clicking complete analysis, the analysis will be completed and all the outputs will be brought back to the analysis folder. Alternatively you can use iput -rPVT <folder name> command to transfer the data back to the data store.

Additional information, help

  • Full materials for the webinar is available here
  • See the original JupyterLab quick start
  • Contact CyVerse support by clicking the intercom button on the page.

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