Lab Handbook

Lab Manual Introduction

This lab manual was inspired by the excellent work of Dr. Mariam Aly (Columbia University) editorial, whose Nature editorial and lab manual provided the foundation for many of the ideas here.

Purpose

The goal of this manual is to:

Clearly outline policies, practices, expectations, and roles within the lab.
Promote transparency in lab operations.
Foster a positive, supportive, and comfortable environment for all members.

Like Dr. Aly’s manual, this is a work in progress, a living document that will evolve as the lab grows, new members join, and new situations arise. If you have suggestions for additions or clarifications, please reach out to me (Isabel, PI).

Philosophy

This manual is a starting point for a positive lab experience and for building strong mentor–mentee relationships. But success requires active investment from everyone. We should view this manual as a framework for growth, reflection, and mutual respect.

For New and Prospective Members

All new lab members are expected to read this manual. It may also be helpful for those who are considering joining the lab.

If you are a PI or trainee considering writing your own manual, you are welcome to use this document as a source. I also encourage you to explore the websites of Dr. Mariam Aly and Dr. Margaret Mars Brisbin (http://www.micolab-usf.com/), which served as key sources of inspiration for me.

Expectations and Responsibilities

These expectations apply to everyone in the lab: PI, postdocs, technicians, graduate students, undergraduates, and visiting researchers. They are organized into two categories: Broad View principles and Day-to-Day Guidelines.

Broad View

Research is demanding, yet it can also be rewarding and fulfilling. In the Marine Organic Chemistry Lab, we aim to foster an environment that is positive, supportive, inclusive, and respectful, one where each member can thrive and contribute meaningfully. To maintain this atmosphere, we commit to the following principles:

Work with passion and pride. Choose projects you care about, put in your best effort, and enjoy the process.
Prioritize care and accuracy. Double-check your work, build in sanity checks, and seek feedback. Precision is more important than speed.
Acknowledge mistakes openly. Mistakes are part of science. Sharing them helps everyone learn and prevents larger problems later.
Uphold academic integrity. Do not plagiarize, manipulate, fabricate, or omit data. Unexpected or null results are still valuable contributions.
Support your colleagues. Offer help with time- and labor-intensive tasks, and rely on others when you need assistance.
Respect one another. Value diverse strengths, needs, cultures, identities, and beliefs. Create a welcoming, inclusive space.
Prioritize well-being. If you are struggling, reach out. The lab is here to support your health and happiness, whether or not you wish to share details.
Address conflict quickly. Speak with Isabel or a trusted faculty/administrator if tension arises. Respectful resolution is essential for a healthy lab.
Communicate openly—even with the PI. If you have concerns about Isabel, raise them directly if comfortable; if not, reach out to another faculty member or administrator.
Maintain balance. Protect your physical and mental health, nurture relationships, and take time off without guilt. Productivity is not measured by hours at the bench.

Day-to-Day Guidelines

In addition to the big picture principles, here are some practical habits that keep our lab safe, efficient, and welcoming:

Keep the lab clean. Wipe surfaces with diluted Lab Detergent after use, tidy up spills immediately, label materials, and never leave dirty dishes in the sink.
Stay home if you’re sick. Your health, and preventing others from getting sick, comes first.
Respect work-life boundaries. Weekend, holiday, or late-night work is never required. Work when and where you are most productive.
Replace or report supplies. If you finish a reagent or consumable, replace it if possible or let Isabel know to reorder.
Secure the lab. Lock the door and turn off lights if you are the last one to leave.

Role-specific Expectations and Responsibilities

We all play different roles in the lab, but our shared goal is to support each other, do meaningful science, and grow as researchers. Below are expectations and responsibilities for each position.

Principal Investigator (PI)

As your PI, I commit to:

Support & Environment: Providing scientific and financial support while fostering a positive and inclusive work environment that promotes both success and happiness.
Timely Feedback: Offering constructive feedback on project ideas, figures, posters, talks, manuscripts, and applications in a timely manner.
Accessibility: Being available regularly for meetings and communication (both in-person and via email) to discuss research or anything else you’d like to raise.
Career Development: Helping you build your career by connecting you with colleagues, promoting your work, supporting conference attendance, and writing strong recommendation letters.
Next Steps: Assisting in your preparation for the next stage of your career, whether in academia, industry, or beyond.
Transparency: Sharing lab updates openly (grants, collaborations, manuscripts, etc.).

Postdoctoral Researchers

In addition to the general lab guidelines, postdocs are expected to:

Develop an independent research direction that builds on lab strengths while moving toward future independence.
Keep a detailed lab notebook (paper).
Mentor students (graduate and undergraduate) when needed, fostering their growth as scientists.
Share your work through conferences and seminars.
Apply for grants and fellowships to support your research.
Begin preparing for your next career step (academic or non-academic). The job application process can be intense. Ask for help, share your progress, and let the lab cheer you on.

Graduate Students

Graduate students are expected to:

Develop and carry out your dissertation research, which should include at least one (M.Sc.) or three (Ph.D.) substantial, connected projects. Much of your work will be independent, but guidance and collaboration are always available.
Keep a detailed lab notebook (paper).
Mentor undergraduates in the lab and involve them in data collection where appropriate.
Present your work at conferences and SEOE events.
Apply for fellowships and awards to support your training.
Think critically about your career path, academia (research or teaching), government (NOAA, USGC, state agencies, etc), industry (biomedical, etc.), science writing, data science, etc., and talk to Isabel about aligning your training with your goals.
Stay on top of SEOE deadlines (proposal defense, qualifying exams, thesis submission, etc.). The PI can help you plan, but meeting deadlines is ultimately your responsibility.
Prioritize research time, coursework, teaching, and outreach, but remember that your research is what it gets your degree (Ph.D. or M.Sc.).

Undergraduate Students

Undergraduates are expected to:

Assist lab members with data collection, analysis, and lab maintenance (e.g., cleaning glassware, etc.).
Keep a detailed lab notebook (paper).
Establish a weekly schedule with your graduate student or postdoc mentor to ensure consistent progress.
If earning course credit, attend lab meetings when possible, give at least one presentation, and submit a final research write-up by semester’s end.

Code of Conduct

In addition to upholding the Carolinian Creed, all members and visitors of the Marine Organic Chemistry Lab are expected to maintain the highest standards of research ethics, integrity, and collegiality to foster a welcoming, respectful, and productive community for everyone. The lab is committed to equity, inclusivity, and adherence to Civil Rights and Title IX policies; harassment of any kind will not be tolerated. This includes, but is not limited to, behavior targeting gender, gender identity or expression, age, sexual orientation, disability, physical appearance, body size, race, ethnicity, national origin, or religion (or lack thereof). Harassment may take many forms, including offensive verbal comments, displaying inappropriate or sexual images, intimidation, stalking, following, unwelcome photography or recording, sustained disruptions, inappropriate physical contact, or unwelcome sexual attention. Anyone asked to stop harassing behavior must comply immediately, and concerns can be reported to Isabel or through the university’s reporting channels.

Scientific Integrity

Research Misconduct

We expect everyone in the lab to conduct research with honesty and integrity. Fabrication, falsification, and plagiarism are serious violations and are not permitted. Because this is also a core expectation of SEOE and USC, all lab members must read and follow the university’s policies on responsible conduct of research.

Reproducible Research

As both lab policy and a requirement of most universities, funding agencies, and scientific journals, all research must be reproducible. This means:

Data must be made publicly available alongside publications.
Lab notebooks should be detailed, organized, and readable (paper).
Protocols must be strictly follow, any deviations should be recorded in the lab notebook and inform to Isabel.
Methods sections in theses and manuscripts should include enough detail for others to replicate results.

To ensure data quality, all spreadsheets must be well-documented, properly organized, and available in the Lab share-drive.

Authorship

Authorship decisions aren’t always straightforward, and disagreements can arise. To keep the process fair and transparent for everyone, we use the APA guidelines as our standard:

“Authorship credit should reflect the individual’s contribution to the study. An author is considered anyone involved with initial research design, data collection and analysis, manuscript drafting, and final approval. However, the following do not necessarily qualify for authorship: providing funding or resources, mentorship, or contributing research but not helping with the publication itself. The primary author assumes responsibility for the publication, making sure that the data are accurate, that all deserving authors have been credited, that all authors have given their approval to the final draft; and handles responses to inquiries after the manuscript is published.”

Authorship Practices in the Lab

The student or postdoc leading a project will normally be first author, if it leads also writing the manuscript. If you are unsure, discuss with Isabel.
Isabel will typically be the last author if the data was generated in the Marine Organic Chemistry Lab here at USC.
Isabel will typically serve as corresponding author, as she has a stable academic email and can direct inquiries appropriately. However, if there is a strong case, a student or postdoc may serve as corresponding author.
Students, postdocs, technicians, and collaborators who contribute significantly may be added to the author list. Order of authorship will be determined based on contribution and discussed openly with all parties.
If a project is handed off from one student or postdoc to another, first authorship may transfer to the new lead, unless co-first authorship is appropriate.

All authorship decisions will be discussed transparently, and lab members are encouraged to raise questions or concerns at any stage.

Lab Resources

Communication

The best way to get in touch with Isabel regarding projects or lab issues is via email. If you are having an emergency in or out of lab, don’t hesitate call or text Isabel.

Google Drive

The lab will have a common Google Drive (coming soon, stay tuned) for storing protocols, datasets, presentations, posters, etc. I hope we also create a Lab folder were we store all of the information you need to get started, including tasks that need to be done upon arrival, day-to-day housekeeping duties, forms and flyers, stats tips, information about accessing lab servers, etc. Lab members would edit it when they obtain information that will be useful for others to know! Let know Isabel if you want to help.

GENERAL POLICIES

Lab Presence and Flexibility

Being physically present in the lab (analytical lab and computer lab) is an important part of your training and contributions. The lab environment provides critical opportunities for collaboration, learning from peers, building professional relationships, and accessing resources efficiently. It also minimizes distractions that are common when working from home.

Although academia allows for more flexible scheduling than many professions, this position should still be treated as a full-time commitment (approximately 40 hours per week). Time spent in the lab should be the norm, not the exception. Remote work may be appropriate on occasion, such as when no meetings, experiments, or collaborative activities are scheduled, but working exclusively from home is not acceptable. Exceptions may be made for documented health concerns (e.g., COVID-19 or other medical circumstances).

Isabel Communication Outside Normal Hours

I sometimes work during nights or weekends. I usually try to schedule emails to arrive the following morning or on Monday, though this may not always work (sometimes I forget to do it).

Important: I do not expect you to respond outside of your normal working hours. Unless we have previously discussed an urgent situation (e.g., an upcoming grant deadline), there should be no need for immediate responses.

Deadlines and Respecting Time

While I occasionally work weekends, I aim to keep that to a minimum. To help me maintain a healthy work/life balance, please provide adequate notice for deadlines, such as recommendation letters, manuscript feedback, or other time-sensitive requests. This ensures I can deliver what you need without last-minute strain. Also, managing deadlines effectively is essential in academia because missing or rushing to meet a deadline doesn’t only affect you, it also impacts your collaborators and anyone whose support you.

Guidelines for Working with Isabel

Conferences
Provide at least 2 week’s notice for adding edits to conference abstracts, posters, presentations, or filling out paperwork. Presentations are highly encouraged!!
Letters of Recommendation
Provide at least 3-4 weeks’ noticefor letters of recommendation and include your latest CV. I will let you know, the next steps needed.
Manuscripts and revisions
Provide at least 3-4 weeks’ noticefor working onmanuscripts. If this is your first manuscript, I recommend to work with me by steps, section by section, to avoid unnecessary stress.

Meetings

Weekly Lab Meetings (1 hour)

Purpose: Receiving feedback from the group, discussing methods and new papers, check on lab maintenance, and exploring outreach activities. Meetings may also be used for practice talks (e.g., conferences, job talks) or joint sessions with other labs.

Expectations: each member is expected to present at least once per semester. Meetings are informal, but presentations should contribute something substantive to the group. All lab members are expected to attend every meeting (unless there is a valid reason such as illness, family needs, etc.). Undergraduates are encouraged to attend whenever possible, provided it does not conflict with class schedules.

Individual Meetings

At the start of each semester, we will establish a schedule for weekly or bi-weekly one-on-one meetings. Every full-time lab member (technicians, graduate students, and postdocs) will be assigned a ~1 hour time slot to meet with Isabel. If scheduling conflicts occur (e.g., due to travel), we will work to reschedule within the same week. If you have no pressing topics to discuss, you are welcome to cancel the meeting or simply stop by for a brief check-in.

Something missing? Please let Isabel know if there are items that should be added, if anything is unclear, or if you notice any typos.