Developing Portable and Reusable Computational Biology Modules

Project Title: Developing Portable and Reusable Computational Biology Modules  
Program:
Northeast (308)

Project Image: {Empty}
Tags:
bioinformatics (277), data-reproducibility (578), docker (35), genomics (537)

Status: Complete
Project Leader
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Project Leader:
Chris Wilson

Email: cwilson@mdibl.org
Mobile Phone: 20772499187
Work Phone: 207-288-9880

Project Personnel
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Mentor(s):
Bruce Segee (83)

Student-facilitator(s):
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Mentee(s):
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Project Information
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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.



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Project Deliverables:
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Project Deliverables:
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Student Research Computing Facilitator Profile:
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Mentee Research Computing Profile:
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Student Facilitator Programming Skill Level: Practical applications
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Anchor Institution: NE-University of Maine
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Start as soon as possible.: Yes
Project Urgency: Already behind3Start date is flexible
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Launch Presentation Date: 12/14/2021
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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



What will the mentee learn?:
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Final Report
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Lessons Learned:
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