GW-SMHS-BIOC6223

Repository for BIOC-6223 Bioinformatics graduate students midterm project

Purpose

1. Provide students the opportunity to expand their knowledge and learn an additional tool, GitHub: a free code sharing and publishing service where users can host open source projects. There is robust help documentation available on GitHub.

2. Facilitate support and feedback on midterm deliverables. As students are posting their BCOs, they will be receiving direct and actionable feedback in the form of issues.

By the end of this project, students should feel comfortable utilizing GitHub as a means of issue resolution in a collaborative environment.

Getting Started

BCO

Each student will need to:

1. Download their BCO from the BioCompute Editor onto their local machine
2. Rename it "Firstname_Lastname_BCO Number" (ex: Janisha_Patel_BCO_000010)
3. In the Student_BCOs folder, click Upload Files and select your saved BCO.
4. In the Commit changes section, please add a commit note("Upload J.Patel BCO") and in the description box indicate if your BCO is ready for review ("ready for review"). Your BCO will not be reviewed unless this is clearly stated
5. Confirm your BCO was uploaded by returning to the Student_BCOs folder and refreshing.

Project Board / Issue Resolution

To better organize your issues, each student will need to create a Project Board. The project board will enable you to sort your tasks, plan your projects, automate your workflows, track your progress, share your status, and retire your work once complete.

1. In the Projects tab of this repository, Create a Project
2. Establish Project board name according to the template: "[fullname]" (Example: JanishaPatel)
3. Provide Project description
4. Select Project Template: "Basic kanban" (This template will establish columns for To do, In progress and Done. More documentation on project boards can be found here and here)
5. In the "Student-BCO" folder, upload your BCO.json (downloaded from BCO Editor) by the provided deadline
6. Once uploaded, your reviewer will be providing feedback in the form of issues, which you will have acccess to on your newly created Project Board.
7. You will be asked to resolve these issues prior to the 10/18, as the corrected BCOs will be your submission to the pFDA challenge. You can reply to the feedback for clarification or further discussion- however provide your reviewer at least 48 hours to respond. Meaning: the latest we can guarantee your comment will be addressed/answered in time for your submission will be 10/16.

Hit a blocker? Want to provide feedback

Create a GitHub issue, and select appropriate:

• label : "midterm: BCO editor" , "midterm: pipeline" , "midterm: pFDA challenge", "feedback" or if unsure of where your question falls: "midterm: general"
• assignee: "Jonathon Keeney", "Janisha Patel", or "Helen Ibeawuchi"
• project: "[fullname]"
• milestone: "BCO draft" , "Further Research", "Final BCO"

Need additional BioCompute help? https://github.com/biocompute-objects/BCO_Specification

Need additional GitHub help? https://guides.github.com/activities/hello-world/