Flanagan Lab Manual


I hope this will be a fun and rewarding experience for both of us. Below is a little about what I expect from you and what you can expect from me as we conduct research together. This is an evolving document; if there’s anything here that you have questions about or disagree with, please see me at any time.

I aim to foster an environment of scientific excellence, personal development, and collaboration. I want you to be happy and productive while working with me, and this lab manual is a first point of reference for current lab members. I ask that you abide by the expectations written here unless we have had an explicit conversation agreeing to a change.

Collaborating means we both have a stake in the work – you get the opportunity to learn new skills and grapple with new ideas, and I get the opportunity to exchange ideas with you and benefit from your perspective. Also, I find that working together is more fun than toiling alone.

Safety and Equipment Operation

Safety is a first priority. It may seem obvious, but no matter what, you are always more important than the data or samples. Please do not take unnecessary risks in the lab, office, or field. You must complete all required safety training prior to working in the lab. If there is a serious emergency, dial security (0800 823 637) and Sarah (027 235 0900). Any non-emergency safety concerns should be brought to me, one of the technicians on the floor, or one of the SBS safety officers (Craig Galilee 33695150 or Bill Davison 33695170). You are expected to complete all of the required Health and Safety trainings required by the School of Biological Sciences and the University of Canterbury. More information on the required trainings can be found on the SBS LEARN site, by talking with me, and by consulting Craig Galilee (the SBS safety officer).

A portion of my research includes fieldwork, which comes with associated risks. This is not mandatory for all students, and if you are unable or unwilling to participate there will be no repercussions. If you do want to conduct fieldwork, we will discuss those risks before going out in the field. Always have at least two people out in the field at a time.

Please see me or a technician for instruction before using a new piece of equipment. And, if while working in the lab, you find you are unsure of some procedure, stop and ask me again! You can always call me at work, or at home. If you can’t reach me, wait until we talk before continuing. In addition, most of the equipment in the lab is shared and expensive to replace. So, of course, I expect all users to exercise care in operating the equipment, and to inform me or the appropriate technician of any potential problems immediately.

Work Ethic

Scientific research is hard work, requiring attention to detail, dedication, and perseverance. These qualities are measured by your ability to stay focused, plan your research tasks and manage your time, properly execute your work, and to finish a research project. Being efficient with your time is key, and does not necessarily correlate with the number of hours you are physically in the lab/field/office. It’s very easy to let your research work slide! Successfully completing a research project that you can be proud of while simultaneously retaining your sanity (and getting your other work done!) is not impossible – it just requires planning and regular effort. While I will meet with you weekly (see below), I will not nag you. You must set your work schedule and be committed to sticking to it.

The Flanagan lab does not institute fixed work hours. That being said, it is important to have interactions with lab members and other members of the School, which generally occurs from 10am-4pm. Lab members are generally expected to start with a 9am-5pm schedule, but this will shift over time as priorities change. Expectations about the number of hours worked per week differs for each type of lab member (see below), but in general most lab members are expected to treat research as their full-time job (i.e., 40 hours per week). This does not mean whiling away hours in the lab or office doing non-research tasks. If you are unproductive in the lab/office, you are welcome to find a more productive place to work. I set this example by generally working from 8am-5pm on weekdays and not showing up on the weekends (with exceptions).

Lab members are welcome to work from home if their current line of research allows it and you don’t miss any previously-scheduled lab meetings, school meetings, or other commitments. If you work from home, I request that you put it on the Flanagan-lab shared Google calendar so that I know where you are.

Vacation and Medical Leave

Your mental and physical health are very important – to you and to ensure your success in the lab. You are expected to take time off when needed. If you feel as though you need help, contact Student Care for free: https://www.canterbury.ac.nz/support/needtotalk/. I expect that you will observe official university holidays unless there is a valid reason not to (e.g., the fish need to be fed), and I expect you will also take additional holidays. Taking vacation should be discussed two weeks or more in advance with me, and it is your responsibility to find someone to cover any lab duties you are responsible for.


One-on-one meetings

We will meet formally each week to discuss results, progress, ideas, and relevant literature. Please come to each meeting prepared for substantive discussion – at least 1 thing you’re ready to show me (a plot, data table, thoughts on a paper, etc.) and at least 1 question (which could also be a plot, data, etc.). These discussion points should be documented in your agenda, which must be made available 24 hours prior to the meeting. Please also be ready to propose what you want to accomplish in the upcoming week in light of your week’s workload, and what adjustments need to be made to your schedule. In return, I will be ready for discussion and ideas for new directions. Early on and during ‘crunch’ periods, we may meet more frequently than once a week.

Lab meetings

Lab meetings are an opportunity for the group to discuss lab issues, important news, upcoming events, and to discuss the research being conducted in the lab. The format will change based on the lab members, but students are expected to regularly present at lab meetings and everyone is expected to participate in discussions.

Open Door Policy

I have an open door policy and you can normally interrupt me with questions at any time. However, I too have deadlines to meet and classes to prepare, so please keep this in mind. If your question isn’t urgent, and can wait until our scheduled weekly meeting, you’ll have my undivided attention and you’ll likely get a more coherent answer.


The lab schedule will be maintained on the Flanagan-lab Google calendar. Timing for meetings will be scheduled when members join the lab, and members should immediately notify me if conflicts arise as soon as possible. Please make sure I am aware of any changes to regularly-scheduled meetings, and send me reminders when arranging any special meetings!


Managing deadlines is an incredibly important component of being a successful and organized academic. When there are deadlines, please make sure that your collaborators (including me!) are aware of upcoming deadlines, and keep bugging them (yes, me too!) as the deadlines approach. Also, add deadlines on the Flanagan-lab Google calendar with appropriate email reminders (1 week in advance, 1 day in advance, etc).

With hard deadlines, give me at least one week for tasks with low time requirements (e.g., revising conference abstracts, filling out paperwork, etc) and two weeks for tasks that take more time (e.g., letters of recommendation). Expect at least a month of back-and-forths on manuscript revisions, drafts of grant/fellowship applications, and your 1 year confirmation document and dissertation.

Lab notebooks

I expect you to keep a well-organized notebook. For your wetlab notebook, I expect your notebook to include hard copies of anything that can be printed out. I expect you to keep a similarly complete and organized set of notes regarding your code and analysis projects, either a hard-copy notebook or an electronic notebook. In both of these notebooks, you should record your mistakes and difficulties performing the experiment, and do not remove them from your notebooks! Use a single cross out and explain why it was an error. Make sure your lab notebook is interpretable by yourself, me, and other lab members – doing this will help others and your future self!


It is my hope that every student researcher who works in this lab is part of a scientific publication or presentation (poster or talk). My policy for co-authorship is that you must contribute significantly to at least 2 (and often 3) of the following 4 stages of a project: (1) Conceived original idea and started project (e.g., wrote proposal, obtained funding) (2) Conducted work, made laboratory measurements, and processed data (3) Synthesized data and interpreted results to the point where a manuscript could be written (4) Got a manuscript/poster into final, publishable form (e.g., written, edited, made figures) Typically, to be a first author, you must contribute significantly to at least 3 of the above stages, including doing most of (4).

If you’ve done most of the work for a project, I strongly encourage you to discuss with me being first author on a paper. If you leave the lab before finishing a project, we will agree upon a timeline for finishing and submitting a poster/manuscript for publication. If you leave a project unfinished for too long, I reserve the right to have someone else finish it and adjust authorship order accordingly. Finally, contributing to only one of the 4 stages of a project, or small parts of 2 stages, may result in being acknowledged in the Acknowledgements section of resulting publications.

Code of Conduct

University of Canterbury provides a Code of Conduct for students and for staff, with which everyone in the Flanagan lab is expected to comply. To ensure that all lab members have a productive and safe environment for everyone, I also expect everyone to follow the additional Code of Conduct items found here.

The lab is dedicated to providing a harassment-free experience, regardless of gender, gender identity and expression, age, sexual orientation, disability, physical appearance, body size, race, or religion (or lack thereof). Harassment of lab members will not be tolerated. Harassment can include making offensive comments verbally or using digital means (e.g., email, Facebook, Twitter), and can also include other problematic conduct such as stalking, inappropriate touching, and sabotaging work progress.

If you experience Code of Conduct violations, contact me immediately. I will help you navigate the appropriate next steps to take. If you would rather contact someone else, reach out to Tammy Steeves (PhD coordinator), Daniel Stouffer (masters’ coordinator) or Elissa Cameron (4th year coordinator), or reach out to the Equity and diversity centre at UC. Lab members asked to stop any harassing behaviour are expected to immediately comply.


I expect everyone in this group to maintain high ethical standards. It should go without saying, but don’t compromise data, fabricate results, or plagiarize any piece of writing. As a very general rule of thumb, copying 100 words of text from another source without acknowledging it is plagiarism. This is the upper end of what most people consider plagiarism. If you have any questions about what I mean, see me anytime. You also have an ethical duty to acknowledge that our work here is collaborative, and is rarely yours alone. I would not write a paper, give a poster, or deliver a talk without acknowledging your contribution to our joint work and I expect the same of you. I encourage you to give presentations (talks or posters) about our work, but ask you to consult me before agreeing to do so. This is standard practice in science: co-authors must approve the release of joint work and should be listed together at the beginning of the talk, poster, paper, etc.

Animal Ethics Approval is required for all work on vertebrates (and a few invertebrates), including pipefish. You are expected to seek the appropriate approval for the work that you are conducting in the lab. I will help you with this, but I expect that you will be aware of the animal ethics requirements and will take a leading role in acquiring approval for your experiments (this especially pertains to graduate students).

Implicit Bias

Implicit bias refers to the attitudes or stereotypes that affect our understanding, actions, and decisions in an unconscious manner. These implicit associations develop over the course of a lifetime starting at an early age through exposure to direct and indirect messages. Everyone has implicit biases, and the first step is to recognize them. You are encouraged to assess your own implicit biases. If you feel anyone in the lab is acting in a biased or unfair way, please let me know.

Data Management

Lab Data

Lab data should be stored both on a local hard drive and an external hard drive, and all raw data and associated metadata should be regularly backed up. You notes and analysis codes are crucial resources for the lab, and these must be available upon request. Before leaving the lab for good, and upon completion of projects, old datasets must be backed up (we will work out archiving protocols when the time comes).

Open Science

The Flanagan lab is committed to responsible and open scientific practices. That means that lab members are expected to share their code and data with others, both within and outside the lab. Within the lab, sharing code can happen whenever you like. The appropriate time to share data and code outside of the lab is generally only once the lab has finished working on it – however, this should be discussed with me and all lab members involved in the projects.

All lab members are expected to have a GitHub profile, which should be linked to the lab’s GitHub account. Code should be uploaded to GitHub and changes should be regularly committed and pushed to the website. Repositories such as such as dryad and the Short Read Archive will be used to make data publicly available at the time of publication of papers. The lead author is responsible to archive data unless other arrangements are made.


Expectations of all Lab Members

We want everyone in the Flanagan lab to be honest, humble, happy, and healthy. You are expected to have a proactive attitude and contribute to the lab, bringing your enthusiasm and creativity with you. All lab members are expected to treat each other with respect and dignity, and harassment or scientific misconduct of any kind will not be tolerated (see Code of Conduct). It is common courtesy to keep common spaces clean and organized, and this is doubly true in the laboratory since we share space with others outside of our group. Acknowledge responsibility for your actions and avoid providing excuses for your behaviour.

I am committed to helping you develop skills and expertise that will facilitate your career goals, whatever they are and regardless of your current stage. Therefore, I expect you to be open with me about your goals, questions, and concerns so that we can help you along your career path. You are in control of your career and your degree, so I expect you to be vocal about the support that you need. In a similar vein, I expect you to stay on top of your key deadlines. I will do my best to help you but it is ultimately your responsibility.

Postgraduate Students are expected to take ownership of their projects and be the driving force behind their projects. You are expect to be (or become) the expert on the research that forms the background of your project and on related publications (recent and historical). The goal of the lab is to place all graduate students and postdocs on their desired career paths, and I will help facilitate opportunities for you to develop the skills that you need to be successfully launched on your career (such as mentoring, grant writing, giving talks, publishing papers, and managing projects). I expect you to discuss your goals with me on a regular basis and clearly communicate what you need.

I will work with all postgraduate students to choose appropriate projects. I expect students to get established in the lab by working on a project that I think is feasible, and then as you gain experience in the lab that we will give riskier projects a try. Because we have a multidisciplinary working environment, I expect all students to have research projects that use at least two of the lab’s approaches. Students are expected to seek out opportunities to present your research, including within SBS, at regional conferences, and at international meetings—not to mention job talks. Be prepared to give a practice presentation to the lab at least one week ahead of time so that the lab can provide you with feedback.

Summer Research Scholarship Students: The goal of your participation in the Summer Research Scholarship is “to give senior students experience in research, to encourage them to pursue postgraduate study.” (https://www.canterbury.ac.nz/get-started/summer-school/summer-scholarships/). My interpretation of this is that by participating in this program you are interested in pursuing postgraduate study, or at the very least a career involving research. Also keep in mind that your work is a component of the overall work in the lab, so it is likely that you will end up as a contributor to a scientific paper in some shape or form (as a co-author or at least in the acknowledgments).

I expect you to treat the Summer Research Scholarship as a full-time job. At the end of the summer you will be expected to participate in the Summer Research Scholarship Conference, in which you give a 5-minute presentation about your project. It is your responsibility to create this presentation, but I expect that you will prepare it sufficiently in advance for me to be able to help you practice and improve the presentation. Remember that your work is collaborative; I expect you to acknowledge the contributions of others at some stage during your presentation.

Support Letters are extremely important for getting new positions, grants, and awards. You can count on me to write you a letter if you have spent substantial time working in the lab. I take letter-writing very seriously and I want to write you the strongest letter I possibly can for you. Therefore, I will make a point of asking you what aspects of your time in the lab you want highlighted. Do not hesitate to ask me for a letter! I want to know as soon as possible what the deadline is, the relevant instructions, and please send me an updated version of your CV. I may ask for additional information, such as specific aims for a grant or other application components. I highly encourage you to send me multiple reminders leading up to the deadline (and put the deadline as a reminder on the Flanagan-lab google calendar!).

Reviewing Papers is an important part of being a contributing member of academic society. We publish papers, which are peer reviewed, so we must review papers for others. We will aim to review 2-3 papers for every paper we submit. Since you as lab members will likely be lead authors on the papers we write, reviewing other researchers’ work is an essential part of your training. I will expect you to assist with reviewing papers. To help with your training, you and I will review the paper independently, and I will subsequently give you feedback on the review. You will ALWAYS be acknowledged to the editor for your contribution. If you receive an invitation to review, I encourage you to accept it if it is within your field of expertise – but I expect you to consult with me for advice, especially if we have not yet done one or two collaborative review yet.

Adapted from Michael Harrison Hsieh, “Undergraduate Researcher Contract”, Savio Chan, “Chan Lab Manual”, Lisa Gilbert, “Undergraduate Researcher Expectations”, Barbara Tewksbury “Research Student Guidelines and Expectations”, and Sarah Carmichael, “Undergraduate Research Contract”, and April Wright’s Code of Conduct.