Developing Portable and Reusable Computational Biology Modules

Submission information

Submission Number: 128

Submission ID: 222

Submission UUID: cd8de520-0e28-466e-a8e8-5b70d5c39243

Submission URI: /form/project

Created: Tue, 11/16/2021 - 15:18

Completed: Tue, 11/16/2021 - 15:18

Changed: Thu, 04/28/2022 - 13:48

Remote IP address: 74.75.33.23

Submitted by: Chris Wilson

Language: English

Is draft: No

Webform: Project

Project Title Developing Portable and Reusable Computational Biology Modules

Program Northeast

Project Image {Empty}

Tags bioinformatics (277), data-reproducibility (578), docker (35), genomics (537)

Status Complete

Project Leader

Project Leader Chris Wilson

Email cwilson@mdibl.org

Mobile Phone 20772499187

Work Phone 207-288-9880

Project Personnel

Mentor(s) Bruce Segee

Student-facilitator(s) {Empty}

Mentee(s) {Empty}

Project Information

Project Description Modern genome-scale data typically requires multi-step, linked workflows for
complete analysis. While many open-source tools are freely available, they are
written across a range of frameworks and platforms (e.g., R, python, and
shell-scripts) that can be confusing or even conflicting to maintain on a single
system. As such, it is in the interest of the research community to develop
portable and reusable computational modules aimed at reducing the installation
and maintenance burden and expanding access to these tools without requiring a
wealth of systems-administration knowledge. This project involves the
development, debugging and maintenance of robust, reusable analysis modules for
computational biology workflows using Docker and Singularity.

Project Information Subsection

Project Deliverables {Empty}

Student Research Computing Facilitator Profile {Empty}

Mentee Research Computing Profile {Empty}

Student Facilitator Programming Skill Level Practical applications

Mentee Programming Skill Level {Empty}

Project Institution {Empty}

Project Address {Empty}

Anchor Institution NE-University of Maine

Preferred Start Date {Empty}

Start as soon as possible. Yes

Project Urgency Already behind3Start date is flexible

Expected Project Duration (in months) {Empty}

Launch Presentation {Empty}

Launch Presentation Date 12/14/2021

Wrap Presentation {Empty}

Wrap Presentation Date {Empty}

Project Milestones

Milestone Title: Initial suite of docker/singularity images
Completion Date Goal: 2022-01-14
Milestone Title: Demonstrate testing methodology
Completion Date Goal: 2022-01-21
Milestone Title: Wrap Presentation
Completion Date Goal: 2022-02-15

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What will the student learn? The student will learn consultative skills associated with being a research computing facilitator and will develop advanced skills required to develop portable modules including:
Advanced use of docker images and dependencies.
Scalability and robustness of command line tools
Bash scripting

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HPC resources needed to complete this project? {Empty}

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Final Report

What is the impact on the development of the principal discipline(s) of the project? {Empty}

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Is there an impact physical resources that form infrastructure? {Empty}

Is there an impact on the development of human resources for research computing? {Empty}

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