JEFworks Lab Guide

This is a living document and subject to modifications. Please feel free to fork, modify, and make pull requests to introduce new policies or modify old ones. This document was last modified Sept 2023.

Lab policy regarding COVID-19

(as of April 2024)

Dear lab,

I wanted to provide an update on the lab masking/sick-leave policy as it has been a year since we deviated from the university’s policy. First of all, I wanted to thank you all for helping make our lab space an accessible environment that supports the health and welfare of all lab members.

Covid/flu/rsv levels based on wastewater monitoring has finally reached a low level in our community. We will be moving to masking-optional during group lab meetings where there is a large number of lab members and continuing with masking optional for students (and visitors) for one-on-one meetings.

That being said, I still do take it as my responsibility to minimize the risk factors that may contribute to you getting sick (be it with COVID, burn-out, or etc) while pursuing your research and educational goals.

We will continue to support lab members with unlimited sick days. Lab members will continue to be asked to stay at home if you feel acutely sick; your one-on-one meetings will be canceled and lab meeting attendance (including virtual) will be strongly discouraged for sick lab members to focus on recovery. We will continue to support flexible working hours and hybrid meetings in instances of more prolonged recovery periods.

The lab will continue to provide access to high quality masks for your general and personal use; please feel free to take them for your day-to-day activities, travels, hospital visits, or other events that may expose vulnerable populations.

The lab will also continue to prioritize outdoor group events.

I will continue to actively monitor the public health situation and encourage you all to do so as well. If you have any thoughts, questions, or concerns regarding this lab policy, I’d be happy to find a time to discuss further.

Thanks in advance to you all.

Roles and Expectations

Your role

You are expected to take responsibility for your research project and career development. You are expected to manage your time in order to achieve the research and career-related goals established during meetings with Prof. Fan and your research team. You are expected to be held accountable and to help hold other team members accountable to progress in these goals. Lab members are encouraged to seek out independent resources and one another to overcome any challenges that may impede progress in these goals. Challenges should be communicated to Prof. Jean Fan or appropriate team members to facilitate progress.

My role

My role as your mentor and advisor is to help you develop, refine, and progress towards your research and career goals, whatever they may be. It is my responsibility to do my part in maintaining a healthy relationship and clear, open communication with you and to hold you accountable to progress in your goals.

Lab Time

Flexible working hours

The exact hours members of the lab choose to work is up to them. We believe in each lab member’s ability to best manage their own schedules in a manner that enables them to efficiently and effectively meet their research goals and advance their careers. However, being on campus between 9:00am and 5:00pm most days will help facilitate collaborative working and lead to a more fulfilling research experience.

Holidays or notable absenses

Permission for holiday or other notable absenses is rarely required, but please respect key deadlines and respect that we work as a research team. It is important to take holidays, respect weekends (or time in lieu) and establish a sustainable work-life balance. But it is also important to respect the time and efforts of others, including collaborators, publishing editors, funders, and so forth, and to note that effective working will improve the quality of your research and career potential.

Please discuss your planned holidays or other notable absences with Prof. Fan for coordination purposes (in order to cancel one-on-ones, etc) and mark your days out of lab on a lab calendar as a courtesy to Prof. Fan and other lab members so that we can anticipate your absence and refrain from disturbing you.

Communication

For all communication methods, please respect people’s working patterns, and remember that other people will have different priorities and focus. Please give consideration to the timing of your correspondence with respect to what the recipient needs to do. No lab members are required nor should feel obliged to reply to messages outside of their typical work hours. Seeking out in-person discussions is strongly encouraged for urgent matters requiring immediate attention.

Group meetings

Weekly lab meetings will be held in person at a time to be determined to best accomodate the schedules of the majority of current lab members based on class schedules. We expect all lab members to attend and contribute to group meeting and journal club discussions if they are not otherwise engaged in research business (e.g. at conference, attending training or a lecture, or using a core facility). We ask for all lab members to participate in lab meetings and lab events in person. Hybrid options may be provided under special circumstances. Please discuss with Prof. Fan further if you need to join a lab meeting virtually.

One-on-one meetings

Weekly one-on-one meetings will be held in person with specific timing to be established for each member when they join the lab and modified as needed. Lab members are expected to be proactive in requesting additional one-on-one beyond typically scheduled meetings as needed by discussing with Prof. Fan and marking on the group scheduling calendar. Hybrid options may be provided under special circumstances. Please discuss with Prof. Fan further if you need to join a one-on-one meeting virtually.

We strive to respect the ability of fellow lab members to engage in distraction-free deep thinking and long periods of uninterrupted work.

Collaborations

Lab members are encouraged to seek out and identify biological labs and clinical colleagues who may be interested in mutually beneficial collaboration opportunities. However, new collaborations should be discussed with Prof. Fan prior to accepting the project in order to ensure appropriate negotiation of authorship, funding, and other trainee priorities.

We expect all data, code, and relevant lab materials to be shared upon publication and to the Open Access standard to the best of our abilities.

Unpublished lab materials, including but not limited to software, data, manuscript drafts, and grants can be presented and shared with others outside the lab with approval from Prof. Fan and other corresponding author collaborators (if any) on the project.

Manuscript writing

Group members are expected to complete a check-list document for each manuscript they submit: click to download. This check-list is provided to help facillitate a minimum standard (both written and ethical) of the group’s output and level of communication to co-authors and collaborators.

Authorship

We aim for authorship to be inclusive of everyone who has made a substantial contributions to the conception or design of the work or the acquisition, analysis, or interpretation of data for the work AND upholds their responsibility in drafting the work or reviewing it critically for important intellectual content, approving the final version to be published, and agreeing to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

A “substantial contributions” can include, but is not limited to:

generating data where data generation requires understanding the project aims and tailored batch designs (beyond standard lab chores such as mouse colony maintenance)
analyzing data where data analysis requires understanding the project aims and custom scripts (beyond standard lab chores such as server maintenance)
providing software support through the development of new functionalities beyond previously published functionalities
providing cell-type annotations by incorporating expert biological domain knowledge

Contributions that do not meet the criteria of ‘substantial contributions’ can still be acknowledged. Alternatively, contributions that do meet the criteria of ‘substantial contributions’ can be moved to acknowledgements at the request of the contributor if they are not interesting in upholding additional responsibilities such as drafting the work, approval the final version, etc. Students are advised to discuss their contributions to various projects and collaborations in their regular one-on-one meetings for Prof. Fan’s awareness.

Please see ICMJE’s Uniform Requirements for Manuscripts Submitted to Biomedical Journals for more information.

Code of Conduct

We value the participation of every member of our community and want to ensure everyone has an enjoyable and fulfilling experience, both professionally and personally. Accordingly, all lab members are expected to show respect and courtesy to others at all times. We create our culture and our culture is inclusive.

Please note that this code of conduct supplements, and does not trump, Department and University level policies for your level of employ or study.

Inclusion and diversity

We value an inclusive and diverse research environment to support each individuals development and research, and to promote robust decision making and high quality research. All group members are thus dedicated to a harassment-free experience for everyone, regardless of gender identity and expression, sexual orientation, disability, physical appearance, body size, race, age, and/or religion. We do not tolerate harassment by and/or of members of our group in any form and we also all members to support each other in upholding the following principals:

All communication, be it online or in person, should be appropriate for a professional audience, and be considerate of people from different cultural backgrounds.
Be kind to others, and do not insult or put down other group members. We acknowledge that we will grow as a team, and learn from each other.
Behave professionally. Remember that harassment and sexist, racist, or exclusionary jokes are not appropriate.
Harassment includes offensive verbal comments related to gender identity, sexual orientation, disability, physical appearance, body size, race, religion, sexual images in public spaces, deliberate intimidation, stalking, following, harassing photography or recording, sustained disruption of discussions, inappropriate physical contact, and unwelcome sexual attention.
Participants asked to stop any harassing behaviour are expected to comply immediately.

Prof. Fan will discuss the code of conduct with lab members who violate these rules. If inappropriate behaviour persists after this initial discussion, formal processes, in line with Johns Hokins University’s work practice policies, will commence.

Scientific Integrity and Ethics

We expect lab members to be honest in scientific communications both within and outside the lab. We expect that lab members will design experiments in a manner that minimizes both bias and self deception. We expect that lab members will keep agreements, be careful, and share their code and results openly with the scientific community. We expect that credit will be given where credit is due, including in scientific writing. Plagiarism is not tolerated and it is your responsibility to know the definition and scope of plagiarism. While a full enumeration of ethical considerations is outside of the scope of this document, please don’t hesitate to raise any questions or concerns that you have at any point with Prof. Fan. Any perceived cases of scientific misconduct by lab members should be brought to Prof. Fan’s attention immediately in a private meeting. Please see university policies for research misconduct and training resources for responsible conduct of research for more information.

Remember: “The whole is greater than the sum of its parts”

Thanks for being a part of the team!

This lab guide borrows heavily and is modified from others courtesy of MicroMicEng (Ben Britton), The Fertig Lab (Elana Fertig), and others.

Released as CC-BY 4.0.