GSA
GSA Bioinformatics
Internship Program
Intern Onboarding

Welcome to GSA Internship

Everything you need to get started — lab expectations, coding standards, GitHub workflow, and conduct guidelines.

github.com/gsabioinfointernship/onboarding

Lab Guidelines

Expectations, communication & meeting structure

Mission & Expectations

  • Dedicate at least 4 hours daily to research and group participation.
  • Mentors provide feedback, project planning, and career guidance.
  • Abstract submissions require mentor review one week before deadlines.
  • Oral presentations must first be presented to the team for feedback.
  • Authorship follows ICMJE standards. Plagiarism is not tolerated.
  • Maintain a safe, respectful, and harassment-free environment.
  • Maintain strict compliance with national and international ethical and copyright standards in all research activities.
  • Interns must not be engaged with any other organization during the internship — academic thesis work is the only permitted exception.

Communication

  • Primary platform: Slack. Join #general, #meeting, and #random channels.
  • Maintain active GitHub and Slack accounts throughout the internship.
  • Use official email for all formal work correspondence.

Meeting Schedule

  • Weekly scrum kick-off — every Friday at 8:30 AM.
  • Demo day — every Saturday at 8:30 AM (3-minute accomplishment update).
  • Research meetings — third Friday of each month (rotating meeting lead).
  • Weekly group meeting — every Sunday night, 9:00–11:00 PM, via Zoom/Google Meet/Teams (mandatory).

Good Practices

Reproducibility, code quality & data stewardship

Reproducibility

  • All research must be technically reproducible — identical code runs yield consistent results.
  • Avoid GUI-based tools (e.g., Excel) for data manipulation. Use code-based workflows instead.
  • Use renv to capture exact R package versions for reproducible environments.
  • Achieve reproducibility through Makefiles, shell scripts, and peer-reviewed code.

Code Quality

  • Languages: Python and R for analysis and visualization.
  • Use descriptive variable names (e.g., genomeList, not gl).
  • Write context-rich comments — explain why, not just what.
  • Make incremental Git commits after each successful analysis step.
  • All code goes through pull request review before merging.

Project Structure

  • README.md — project documentation at the root.
  • R/ or scripts/ — analysis scripts.
  • input/ — source datasets (read-only, never modified).
  • output/ — generated results and figures.
  • Use RStudio Projects instead of setwd() for portable file paths.

Data Governance

  • Keep read-only copies of all source data with secure backups.
  • Document metadata and experimental design before starting analysis.
  • Generated data must be uploaded to repositories (GEO, SRA) upon publication.
  • Statistical analysis must use R, Python, or Jamovi — Excel is not acceptable.

GitHub Guidelines

Workflow, branching & collaboration

Standard Workflow

  • Fork the repository to your personal GitHub account.
  • Clone your fork locally and create a feature branch.
  • Commit changes with clear, descriptive commit messages.
  • Push to your fork and open a Pull Request to the main repository.
  • Wait for peer review and approval before merging.

Key Concepts

  • Fork — your personal copy of a repository.
  • Clone — download a repository to your local machine.
  • Commit — a snapshot of your changes.
  • Push — upload local commits to GitHub.
  • Pull — download updates from the remote repository.
  • Branch — an independent line of development.
  • Pull Request (PR) — a proposal to merge your changes.
  • Upstream — the original repository; Origin — your fork.

Repository Rules

  • All work lives inside the GSA Bioinformatics Internship GitHub organization.
  • Private repositories require a minimum of two authorized users.
  • Default license: BSD-2-Clause Plus Patent License.
  • Publicly available data scripts must be version-controlled.

Social Media Policy

Professional conduct & representation

Professional Standards

  • Maintain a professional and respectful tone across all platforms.
  • Do not share confidential research data, health data, or unreleased findings.
  • Use official email for all formal work correspondence — not personal inboxes.
  • Obtain authorization before communicating externally on behalf of GSA.
  • Do not express personal opinions that could be mistaken for organizational positions.

Platforms Covered

  • These guidelines apply to Messenger, WhatsApp, Telegram, and all social media platforms.
  • Any public-facing communication that references GSA or the internship falls under this policy.

Violation Consequences

  • 1st offense — Verbal warning and counseling.
  • 2nd offense — Written warning and mandatory training.
  • 3rd offense — Suspension of social media privileges or role reassignment.
  • Severe violations — Potential termination and law enforcement notification.

Living Document

These guidelines evolve over time. Check the GitHub repository for the latest version. Questions? Reach out via Slack #general.