Getting Started in the Lab

Whether you are an undergraduate student, graduate student, postdoctoral associate/fellow, or associated research staff, starting in a new lab can be a daunting experience. The onboarding process is crucial for ensuring that newcomers feel comfortable and familiar with the lab’s procedures, protocols, and guidelines. As you get started you may have a number of questions or uncertainties about your role, your project, our research, or life at UCSF. Just remeber that we are here to support you every step of the way, so we encourage questions and feedback during the onboarding process.

New Lab Member Essentials

Important UCSF Sites

• Office of Diversity and Outreach: UCSF DEI policy
• My Access: UCSF Online Services
• UCSF PeopleConnect: Integrated portal for HR
• UCnet: Benefits
• UCPath: Payroll
• Campus Life Services: Information on UC discounts, perks, housing, community organizations etc
• DPBS Intranet

Onboarding Tasks

Introductions

• Make sure to take a moment to introduce yourself to other Andrews lab members. We will also introduce you to our collaborators in the Center for Population Brain Health and Memory and Aging Center.

Organize to collect your UCSF ID

• Get UCSF ID Card: Make an appoinment or drop-in at the Mission Bay Campus.

Lab Website

• Email Shea a headshot and short bio about your self to be included on the Andrews Lab Website.

Work Computer

This is a list of software you should install on your work computer. If something is mising please add it!

Required software to install

• IDE: VScode
• R: R, RStudio
• Terminal: iTerm2 or Warp
• Homebrew
  • Git: Cloning git repo’s requires using SSH. See Generating a new SSH key and adding it to the ssh-agent and Adding a new SSH key to your GitHub account
• VPN Pulse Secure: UCSF request access
• Reference Manager: Papers or others
• Slack:
• Office 365: UCSF request access
• Zoom: UCSF request access
• wifi: UCSFwpa - Secure Wireless

Advanced software to install - project dependent

• miniforge: A package manager that combines Mamba’s speed with Conda Forge’s environment management for easy software setup.
• Snakemake: A workflow management tool that automates data analysis pipelines using a Python-based language.
• Docker: A platform for packaging applications into containers to ensure they run consistently across different environments.

Optional software to install - Shea reguarly uses these

• Oh My ZSH: Bring some life to your terminal!
• zsh-autosuggestions: autocomplete commands
• Dropbox: Save everything in the cloud.
  
• iStat Menues: Better tracking of your computers resources
• tadam: Pomodoro timer for focusing
• Magnet: Better management of windows
• Bartender: Take control of your menu bar

Wynton Acount

Wynton is UCSF’s High Performance Cluster

• Request an account
• Once you have an acount read Compute section for Tips on using Wynton

List Servs

Global Email list serves that Shea needs to add new employees too.

• Calendar invites for Lab Meetings: Shea
• Center for Population Brain Health: Tamar Simone
• Memory and Aging Center: MAC ARF
• Institute of Human Genetics: Aubrey Carstension

Mobile

• Email: UCSF enrollment
• wifi: UCSFwpa - Secure Wireless

Materials to Review

As a new member in the lab, there may be several materials that you should read or study to get a better understanding of the lab’s research projects and protocols. The timeframe and sequence for reading or studying these materials will vary depending on the project(s) you will be working on. However, it’s important to make sure you have a basic understanding of the lab’s research and protocols before starting your work. It’s also essential to ask questions and seek help from Shea and/or lab members if you need clarification or assistance.

• Background Material: Joining the lab comes with an expectation of foundational knowledge. Our Reading List offers a selection of introductory papers to help you get started. Please consult with Shea to identify which topics are most pertinent to your research project.
• Technical Manuals: Each project will use specific software tools, Shea will guide you on specific papers to read.
• Grants: For those involved in grant-funded projects, Shea will provide you with the relevant grant details.
• Publications: Read some of the lab’s recent publications to get a sense of the research questions and methods used by the lab members.

Training Basics

At the end of the hiring process HR will have sent an “Welcome to the University of California, San Francisco” email outlining trainings that need to be completed. These include:

• HBS Timekeeping system
• Office Ergonomics
• HIPAA 101
• WarnMe
• UC Cyber Security Awareness Fundamentals
• UCSF Foundations of Diversity, Equity and Inclusion
• UC Preventing Harassment & Discrimination: for Non-Supervisors or UC Preventing Harassment & Discrimination: for Supervisors, Faculty, MSP if you supervise others.
• Document: COVID-19 Prevention Training
• Any other required training found in your required training

Read the Lab Handbook

Hey you are already doing this! When you are finished, please utilize Git to clone the repository and push a new commit adding your name to the Signatures page acknowledging that you have read and comprehended the contents of the Andrews Lab handbook.