22 Appendices
This chapter collects reference material: pointers to the templates, policies, and forms appendices; a glossary of terms; a resource list; and acknowledgments.
22.1 Appendix A — Templates
Reusable, fill-in templates live in templates. See the Templates appendix. They include:
- New Member Onboarding Checklist
- Project Pod Charter
- Individual Development Plan (IDP)
- Student Research Plan
- Manuscript Planning Sheet
- Authorship / Contributorship Agreement
- Data-Use and Access Checklist
- GitHub Repository Checklist
- Reproducible Analysis Checklist
- AI-Use Disclosure Form
- Conference Abstract Planning Sheet
- Weekly Meeting Agenda
- One-on-One Mentoring Meeting Template
- Stop / Start / Continue Feedback Form
- Offboarding Checklist
22.2 Appendix B — Standalone policies
Authoritative policy documents live in /policies. See the Policies appendix:
- Authorship & Contributorship Policy
- Data Governance Policy
- Responsible AI Use Policy
- Code of Conduct (also at repo root as
CODE_OF_CONDUCT.md)
22.3 Appendix C — Forms
Sign-and-submit forms live in /forms. See the Forms appendix:
- Onboarding Checklist
- Offboarding Checklist
- Manual Acknowledgment Form
22.4 Appendix D — Glossary
| Term | Meaning |
|---|---|
| Through-line | Exposure Science → Immune Bioactivity → Computational Forecasting → Equity-Focused Translation → Inclusive Workforce Development |
| Aliquary | FERMLLC sample-inventory platform (sibling in-house product): registration, freezer/box maps, barcode lookup, aliquot and freeze–thaw tracking — our inventory system of record (aliquary.com; Section 17.5) |
| Community-to-Clinic-to-Cloud | Our central narrative: measure environmental signals in communities → link to clinical/claims/biomarker outcomes → convert to equity-aware decision tools |
| Pod | A small, project-specific team with defined roles |
| IDP | Individual Development Plan |
| IAP | Individual Academic Plan (the PI’s strategic roadmap) |
| DUA | Data Use Agreement |
| ICMJE | International Committee of Medical Journal Editors (authorship criteria) |
| CRediT | Contributor Roles Taxonomy |
| CITI | Collaborative Institutional Training Initiative (research-ethics training) |
| Educational Biomarker Discovery Lab (EBDL) | The branch through which RIPLRT research is conducted within Lynn University |
| IRB | Institutional Review Board |
| Felix E. Rivera-Mariani, PhD, LLC | The parent legal entity (FL #L21000280781; PR #467494) under which the RIPLRT Institute operates; also the builder of Aliquary |
| Lynn University | Institutional home of the EBDL and of Lynn-affiliated members |
| RespRisk | The group’s respiratory-risk forecasting/decision-support workflow line |
| RIPLRT Bench | The Institute’s operational dashboard / workbench for day-to-day lab workflow (bench.riplrt.com; Section 11.3) |
| RIPLRT Institute | The research group as a whole, including all members and projects, operating under the LLC. |
| SMART goals | Specific, Measurable, Achievable, Relevant, Time-bound goals (12/36/60-month) |
| University of Puerto Rico (UPR) | Collaborating institution; home institution of UPR-affiliated mentees, who remain governed by UPR policy and IRB. |
22.5 Appendix E — Key resources and platforms
22.5.1 Lab platforms
| Platform | Role | URL | Data scope |
|---|---|---|---|
| Aliquary | Sample-inventory system of record (register, locate, track, export) | https://www.aliquary.com | De-identified sample/inventory metadata only; tenant-isolated; full export (Section 12.6) |
| RIPLRT Bench | Operational hub / workbench for day-to-day lab workflow | https://bench.riplrt.com | Operational status and workflow (exact modules and access tiers — placeholder; see Section 11.3) |
22.5.2 Other tools and resources
- Code & versioning: GitHub (Git), GitHub Projects
- Project management: ClickUp
- Documents: Google Drive / OneDrive
- Analysis & reporting: R/RStudio, Python, Quarto / R Markdown
- Lab notebook (experimental): eLabNext (when wet-lab / assay work applies; sample inventory is Aliquary)
- Structured data capture: Qualtrics, REDCap (if applicable)
- Open science / archiving: OSF, Zenodo, FigShare
- Datasets & repositories: Departments of Health claims & pharmacy; fungal-spore aeroallergen stations; BioLINCC; BioData Catalyst; All of Us Workbench; MESA; Framingham; AsthmaNet; NHANES, among others
- Methods: AI/ML, distributed lag models, mixed-effects models, GWAS, polygenic risk scores, SHAP explainability, causal mediation, multi-agent AI; equity-stratified analysis, among others
Workspace URLs, repository links, IRB links, account details, Aliquary tenant IDs, and RIPLRT Bench access tiers are confirmed during onboarding and recorded per project. Public versions of this manual should keep internal links and credentials out.
22.6 Appendix F — Acknowledgments
This 2026 manual builds on the 2018/2021 RIPLRT Lab Manual and the members, alumni, and writing mentors who created and maintained it. It was inspired by the open lab-manual movement and the broader community of research groups who share their handbooks so others can learn. We thank every RIPLRT member — past and present — who has contributed to making this group both a serious scientific program and a humane place to grow.
Maintained reproducibly with Quarto. See CHANGELOG.md for revision history and CONTRIBUTING.md to propose changes.