CTML Lab Manual

Lab Culture

At CTML, we value a lab culture that is collaborative, supportive, inclusive, open, and free from discrimination and harassment. We believe that our lab thrives when all members feel safe and respected in sharing their ideas and opinions. Therefore, we encourage students and staff of all experience levels to respectfully share their honest opinions and ideas on any topic. If you feel confused or unsure about anything, including expectations, the collaboration process, your research, or communication with external funders or collaborators, please communicate with your advisor or other members of CTML.

Diversity, Equity, and Inclusion

The CTML is committed to cultivating a culture of diversity, equity, and inclusion. We aim to be a safe, supportive, and anti-racist environment in which students from diverse backgrounds are equally and inclusively supported in their education and training. We recognize that diversity takes many forms, including differences in race, ethnicity, gender, sexuality, socioeconomic status, religion, disability, and political affiliation. We strive to create an environment where all members feel valued and respected.

Protecting Human Subjects

At CTML, we take the protection of human subjects in research very seriously. All lab members working with human subjects data should complete CITI Human Subjects Biomedical Group 1 training and share their certificate with Andrew Mertens. Before starting work on any project, Andrew will add team members to relevant Institutional Review Board protocols to ensure they have permission to work with identifiable datasets.

Confidentiality is one of the most important aspects of protecting human subjects in our work. As a student supporting our data science efforts, you should:

• Understand and comply with project-specific policies about where data can be saved, particularly if the data include personal identifiers.
• Not share data with anyone without permission, including other members of the group who might not be on the same IRB protocol as you (check with Andrew first).
• Do not download identifiable data to your personal laptop or other computers, and make sure you are storing the data in a protected location allowed by the UCB IRB board (examples: Berkeley Box, Savio, or private servers like the Hubbard lab’s RedVelvet server.
• Talk to your supervisor if you have any concerns about proper practices.

Remember, data that looks like it does not contain identifiers might still be classified as data that requires special protection by our IRB or under HIPAA. Always proceed with caution and ask for help if you have any concerns about how to maintain study participant confidentiality.

We hope that this guide provides you with a helpful overview of the culture, policies, and procedures that are important to our lab. If you have any questions or concerns, please do not hesitate to reach out to Andrew or any other member of the lab.

Communication and coordination

One benefit of the academic environment is its schedule flexibility. This means that lab members may choose to work in the early morning, evening, or weekends. That said, we do not expect lab members to respond outside of business hours (unless there are special circumstances), but please try to response to messages within 1 business day, regardless of communication platform.

Slack

• Slack is most useful for internal communication with other Berkeley team members active on Slack and for coding questions.
• Use Slack for scheduling, coding related questions, quick check ins, etc. If your Slack message exceeds 200 words, it might be time to use email.
• Use channels instead of direct messages unless you need to discuss something private so that others on a project can track decisions/issues.
• Please make an effort to respond to messages that message you (e.g., @andrew) as quickly as possible.
• If you are unusually busy (e.g., taking MCAT/GRE, taking many exams) or on vacation please alert the team in advance so we can expect you not to respond at all / as quickly as usual and also set your status in Slack (e.g., it could say "On vacation") so we know not to expect to see you online.
• Please thread messages in Slack as much as possible.

Email

• Use email for longer messages (>200 words) or messages that merit preservation. Slack is harder to search and less stable long term, so if major decisions are made are analyses or manuscript drafting, those should be preserved in email.
• Use email for communicating with outside collaborators or directors (Maya, Mark, Alan)

Notion (and other task trackers)

• Consult with your direct superviser about the task tracker software of their choice.
• If using Notion (or similiar software):
  • Create a free account
  • Your supervisor will add new cards within our shared Notion board that outline your tasks.
  • The higher a card is within your list, the higher priority it is.
  • Generally, strive to complete the tasks in your card by the date listed.
  • Use checklists to break down a task into smaller chunks. Sometimes your supervisor will write this for you, but you can also add this yourself.
  • Move your card to the "Completed" list when it is done.

Google Drives

• We mostly use Google Drive to create shared documents with longer descriptions of tasks or to draft manuscripts or analysis plans when multiple collaborators are working on document.
• Google docs or sheets are the most useful collaborative tool for outside collaborators because they don’t require an account.

• Communication and coordination

  One benefit of the academic environment is its schedule flexibility. This means that lab members may choose to work in the early morning, evening, or weekends. That said, we do not expect lab members to respond outside of business hours (unless there are special circumstances), but please try to response to messages within 1 business day, regardless of communication platform.

This page covers expectations for Biostatistics Masters and PhD Students in the Center for Targeted Machine Learning

Conference Procedure

• Ask your supervisor before submitting an abstract to present at a confernce.
  • Make sure any identified co-authors have given their approval.
  • Share the abstract for co-author approval if submitting to a conference.
• Share posters or presentations with all co-authors at least two weeks before the conference to make sure to give them enough time to provide comments.

Authorship

• As the criteria for co-authorship can vary widely across disciplines, consult with your supervisor before determining author order and inclusion.
• As a general rule, follow the ICMJE guidelines to make sure all potential coauthors meet the criteria for coauthorship.
  • https://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authors-and-contributors.html
• All authors need a chance to comment on the work before manuscript submission.
• Determine authorship early in the research project to avoid conflict or misunderstandings.
• In general, the first author does most of the writing, but consult with your supervisor on a case-by-case basis.
• Co-first authorship should be determined by who led the drafting and submission process, not necessarily the original intellectual contribution.

PhD Expectations

• Biostatistics PhD handbook:

  Shareable-Biostats-Grad-Degree-Program-Handbook-2019-version-JCM.pdf

• CTML PhD students are expected to submit three papers for publication or have advanced drafts submitted within a timeline set in coordination with your advisor.

  • If research is led by a PhD student and used within

A graduate student research position is a fabulous opportunity to develop research skills and contribute to publications, but it is also a paid job with expectations in both output and conduct. To set clear expectations for each GSR position, we have devised a CTML GSR evaluation process.

In addition to this formal process, please communicate with your supervisor around questions or concerns. Each CTML GSR will be assigned one Project Leader (PL) in addition to their Faculty Supervisor (FS). Depending on the project, a GSR’s FS will also be their PL.

The PL and GSR are responsible for the GSR’s  goal & milestone setting for the year and monthly check-ins. If the PL has any concerns regarding the GSRs progress, the PL will conduct a  mid-year evaluation and/or schedule a conversation with the FS before the end of the semester.

Each Spring, the GSR will submit a self-evaluation that will be utilized during their annual evaluation with their FS. The purpose of the annual evaluation is to showcase growth as well as to create goals for next year. Afterwards, the GSR will be invite to submit an anonymous program evaluation to help improve CTML’s GSR program. The calendar below provides the annual evaluation cycle as well as links to program documents.

Links to external documents:

1. GSR Evaluation Calendar 
2. GSR task and expectation template
3. Faculty Supervisor Evaluation survey
4. Self evaluation
5. Annual evaluation