Welcome to the Roberts Lab Handbook!
Our hope is this is a one-stop locale for relevant information. You can use navigation at the left, the search function, and a few quick pages of interest are highlighted below. If you see something needing updating, you should be able to click on the pencil on each page and go directly to the source to edit, or simply submit an issue. Do not hesitate to join the Discussion.
Lab Culture
Start here: Onboarding — phased checklist for new members.
Policies & agreements: Code of Conduct · Environment and Expectations · Lab Safety · Undergraduate Contract
How we work: Lab Communication · Project Management · Lab Notebooks · Data Management
Career & community: DEI Resources · External Communication and Funding
Guides
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Writing Scientific Manuscripts — structuring and writing papers (reference; use when drafting).
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Oral Presentations — planning, designing, and delivering clear scientific talks.
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How to Grad School (Outreach Slides) — outreach material for prospective graduate students.
Computing and Code
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Best Practices - Resources for thinking about open and reproducible scientific computing.
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Agentic Coding Tools - Guide to using AI-powered coding assistants like GitHub Copilot with VS Code, web interfaces, and integration with UW Klone HPC and Raven.
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Code Snippets - Useful code chunks for shell, R, and other common tasks.
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Computing Hardware - Computing resources we have available & links to help you begin learning.
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Lab Software - A list of software installed on lab computers.
Klone guides: Quick Start · Containers · Conda · New User · Logging in · Node Types · Data Storage and System Organization · File Transfers · Installing Programs · Running a job · RStudio Server · VS Code
Raven guides: Conda · RStudio Server
Databases and Catalogs
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Lab Inventory - Inventory guidance and links to the Roberts Lab Inventory System, purchasing log, freezer contents, histology samples, and primer database.
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Histology Databank Explorer - Search and browse catalogued histology samples, blocks, slides, and available images.
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Pubathon - Annual "pubathon" roster, links to and status of manuscripts.
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Digital Media - Where and how to store media including photos, videos and audio.
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Genomic Resources - Here we try to compile genomic resources such that they are readily available and somewhat described.
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Spotify Playlists - Lab-curated Spotify playlists.
Protocols
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Purchasing and Reimbursement - Procedure for purchases.
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Data Management - This page is intended to document all aspects of data management, from the day-to-day, formal NGS and proteomics plans, and general archiving options.
Lab protocols: Bullet Blender · Glycogen-Glo Assay · Guava Muse Cell Analyzer · qPCR · Resazurin Assay · Reverse Transcription · Water Quality Testing
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Alarm Information - Description of active alarms in the lab, how to configure, and what phone calls mean.
Bioinformatic Workflows
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Basics - Core fundamental bioinformatic workflows.
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DNA Methylation Analysis - Bismark, EpiDiverse, methylKit, and lab examples for bisulfite sequencing workflows.
Recently updated
Pages below were updated most recently in this handbook (refreshed on each site build from git history).
| Page | Date | Description |
|---|---|---|
| docs/Computing-Hardware.md | 2026-08-09 | fix: size status-light stale threshold to observed prober cadence |
| docs/javascripts/server-status.js | 2026-08-09 | fix: size status-light stale threshold to observed prober cadence |
| docs/stylesheets/server-status.css | 2026-08-08 | feat: add server status lights to Computing Hardware page |
| docs/Data-Management.md | 2026-08-06 | docs: link Histology Databank Explorer from data management plan |
| docs/histology-explorer/README.md | 2026-08-06 | docs: correct stale coverage numbers in explorer README |
| docs/Lab-Inventory.md | 2026-08-04 | docs: update inventory system references |
| docs/Offboarding.md | 2026-08-04 | docs: update inventory system references |
| docs/Purchasing-and-Reimbursement.md | 2026-08-04 | docs: update inventory system references |
| docs/index.md | 2026-08-04 | docs: update inventory system references |
| docs/Onboarding.md | 2026-07-30 | Add TUSK link to Onboarding tutorials |
Only the most recent 10 entries are displayed.