Instrumentation for genomic computing with Bioconductor

Vince Carey

Harvard Medical School
Source: vignettes/challenges/instrumentation.Rmd

Abstract

We will use the collectl system, along with some functions available in the Rcollectl package, to analyze system resource consumption for various genomic computing tasks. Ultimately we want to have a system for estimating resource needs for genomic analysis activities.

Difficulty

Advanced.

Challenge leader(s)

Date added

This challenge was created on November 27, 2020

Topics

  • Instrumentation

Duration

A minimum of 1 hour(s) is recommended for this challenge.

Repositories

A list of GitHub repositories that participate in this challenge.

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repository stargazers latest.push
vjcitn/Rcollectl 0 2021-07-20 13:17:28

Guidelines

Fork the original repository Rcollectl, working on a branch of your fork, and submitting a pull request when your contribution is ready for review.

You may contribute new R markdown files or edit existing ones.

The basic aims are to

  • understand and explain how collectl can be used to monitor resource consumption on linux-like systems (and beyond?)
  • start collectl monitoring for a task such as RNA-seq differential expression analysis
  • carry out the task during the monitoring session
  • create the collectl report, and parse, model and interpret using Rcollectl tools (or creating new ones)
  • develop tools for modeling results from a sequence of progressively larger test runs to support general consumption estimation procedures