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 | |
| Tags | bioinformatics (277), data-reproducibility (578), docker (35), genomics (537) |
| Status | Complete |
| Project Leader | Chris Wilson |
| cwilson@mdibl.org | |
| Mobile Phone | 20772499187 |
| Work Phone | 207-288-9880 |
| Mentor(s) | Bruce Segee |
| Student-facilitator(s) | |
| Mentee(s) | |
| 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 Deliverables | |
| Project Deliverables | |
| Student Research Computing Facilitator Profile | |
| Mentee Research Computing Profile | |
| Student Facilitator Programming Skill Level | Practical applications |
| Mentee Programming Skill Level | |
| Project Institution | |
| Project Address | |
| Anchor Institution | NE-University of Maine |
| Preferred Start Date | |
| Start as soon as possible. | Yes |
| Project Urgency | Already behind3Start date is flexible |
| Expected Project Duration (in months) | |
| Launch Presentation | |
| Launch Presentation Date | 12/14/2021 |
| Wrap Presentation | |
| Wrap Presentation Date | |
| Project Milestones |
|
| Github Contributions | |
| Planned Portal Contributions (if any) | |
| Planned Publications (if any) | |
| 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? | |
| What will the Cyberteam program learn from this project? | |
| HPC resources needed to complete this project? | |
| Notes | |
| What is the impact on the development of the principal discipline(s) of the project? | |
| What is the impact on other disciplines? | |
| Is there an impact physical resources that form infrastructure? | |
| Is there an impact on the development of human resources for research computing? | |
| Is there an impact on institutional resources that form infrastructure? | |
| Is there an impact on information resources that form infrastructure? | |
| Is there an impact on technology transfer? | |
| Is there an impact on society beyond science and technology? | |
| Lessons Learned | |
| Overall results |