Lab Manual

Rennison Lab Manual

Table of Contents

Welcome

Lab Motto

Expectations and Responsibilities

Everyone

Principal Investigator

Postdoctoral fellows

Graduate Students

Lab Manager/ Research Technicians

Undergraduate Students

Code of Conduct

Guidelines, General Policies and Lab Events

Annual Retreat

Authorship

Celebrations

Deadlines and Feedback

Field Safety

Fish Care and Feeding

Hours

Lab Calendar

Lab Equipment

Meetings

Molecular Lab Cleanliness and Safety

Ordering and Lab Stocks

PI Office Hours

Recommendation Letters

Reproducibility and Data Management

Scientific Collection

Sick Days

Vacation

Work Life Balance

Lab Resources and Communication Channels

Slack

Google Calendar

Lab listserv

Wiki

Welcome

So, you have joined the Rennison lab at the University of California San Diego – we are glad to have you!

We are a group interested in the evolution and maintenance of biodiversity and study the relevant processes using methods from the fields of population genomics, theory, evolution and ecology.

During your time in the lab group we hope that you do at least four things:

1) Have fun and make new friends

2) Collect and explore interesting and exciting data

3) Develop new and useful skills

4) Learn a great deal about Evolutionary Ecology

This lab manual was inspired by several other lab manuals and builds upon some of the content from them (e.g. here and here).

Upon joining the lab you are expected to read the sections of manual relevant to you and sign a form indicating that you have done so.

Lab Motto

‘Team work makes the dream work’

Through collaboration our achievements equal infinitely more than the sum of our individual contributions.

Expectations and Responsibilities

Everyone

In order to maintain a work environment that is positive, engaging, safe, welcoming and rewarding there are several things we all must do:

The ‘big’ things:

• Support your lab-mates. Help them out (even if you aren’t ‘on the project’) and be a friendly ear when they need it. Science should be collaborative, not competitive. If you help others you can expect others to help you when you need it.
• Respect your lab-mates. Respect their personal space and preferences. Respect their culture, religion, beliefs and sexual orientation. Everyone should feel welcome in the lab and discrimination or harassment of any kind will not be tolerated.
• If you are struggling tell someone. Science is hard and your health and happiness are important! We are here to help, please don’t suffer alone.
• Work carefully. Rushing often leads to the wasting of resources and/or making mistakes. Mistakes happen – but they should not be because of carelessness or rushed work.
• If a mistake is made admit it, correct it and move on. This may require telling collaborators if you have already shown them results or if they are working with data downstream from where an error has been discovered.
• Honesty is the best policy, especially in science. It is never ok to plagiarize, tamper with data, fabricate data, or fudge results. Null or unexpected results are normal and still important. We can do important, cool and high impact science without resorting to these practices. This cannot be emphasized enough; academic misconduct will not be tolerated.
• If there is tension, conflict or hostility in the lab it needs to be resolved as soon as possible. If you don’t feel comfortable confronting the person in question or if the situation is escalating, tell Diana.
• If you have a problem with Diana and are comfortable telling her about it, please do so. If you aren’t comfortable then tell another lab member or another member of the department (for more serious issues).
• Treat animals in the field and lab with care and respect. It is a privilege to be able to conduct research on animals and they deserve to be properly cared for.

The ‘little’ things that keep things running smoothly:

• Keep the molecular lab and fish room tidy, and common areas uncluttered.
• Contribute in lab meeting and come prepared – especially if you are the primary presenter!
• Show up to scheduled meetings and be on time.
• Respect people’s time – attempt to answer/solve your own questions or problems before asking someone else.
• If you see something is not working, running low or empty either do something about it yourself or find someone else to take care of it – don’t just ‘pass the buck’.  

Principal Investigator

All of the above, and I will commit to:

• Supporting you scientifically, emotionally, & financially.
• Provide feedback on your work (ideas, posters, talks, manuscripts etc) in a timely manner.
• Be consistently available to you for in person meetings and via e-mail.
• Support your career development by introducing you to other researchers in the field, promoting (and crediting) your work in talks, writing recommendation letters, and letting you attend conferences as finances permit.
• Help you to prepare for the next step of your career (inside or outside of academia).
• Maintain an environment that facilitates physical and emotional well-being.

Postdoctoral Fellows

In addition to all of the above, you are also expected to:

• Develop and make progress in your own independent line of research. 
• Help to train and mentor students in the lab (undergraduate and graduate) when needed.
• Present your work at events within and outside of the university (e.g. international conferences, seminar series, departmental events).
• Apply for external funding. I will only hire you if I can support you for at least one year. However, it is in your best interest to gain experience writing grants and can help to extend your contract and/or free up lab funds for other uses.
• Challenge me (Diana) when I am wrong or when your opinion is different.
• Attend relevant departmental seminars whenever possible.

Graduate Students

In addition to all of the above, you are also expected to:

• Develop your dissertation research projects – for PhD students this should be at least 3 substantial projects that address a clearly defined question.
• Help to mentor undergraduate students in the lab as needed.
• Present your work at events within and outside of the university (e.g. international conferences, seminar series, departmental events).
• Apply for external funding to support your research (e.g. UCSD, NSF, SSE and SEB awards). It is useful experience applying for small grants and awards, looks good on the CV, and can give you more project freedom.  
• Prioritize your time towards research. Coursework and TAing are important but research is the core contribution towards your PhD.
• Ensure that you are aware of all departmental deadlines and degree requirements.
• Attend relevant departmental seminars whenever possible.

Lab Manager/ Research Technicians

In addition to all of the above, you are also expected to:

• Work on any of your own research projects (developed with Diana’s help).
• Maintain the aquatics lab facility.
• Help new lab members settle into the lab by answering whatever questions they have that you can answer or directing them to Diana as appropriate.
• Oversee hiring, scheduling and training of undergraduate research assistants.
• Maintain the lab website, update the lab manual, add events to the lab calendar.
• Assist lab members with data collection as necessary.
• Be in the lab or fish room on a regular basis. Your presence in on campus when others are around is essential. This means you probably shouldn’t work 7pm to 3am. 8 am to 4 pm or 10 am to 6 pm are more reasonable, with flexibility depending on your out-of-work schedule (e.g. personal appointments).

Undergraduate Students

In addition to all of the above, you are also expected to:

• Assist other lab members with data collection and analysis (unless you are working on your own independent project under the mentorship of another lab member, in which case you should work on that).  
• Develop a weekly schedule to spend time in the lab by talking to your mentor. You should be coming in every week and scheduling enough time to get your work done.

Code of Conduct

The lab, and the university, is an environment that must be free of harassment and discrimination. All members are expected to abide by the University of California San Diego policies on discrimination and harassment, which you can (and should) read about here and here.

Guidelines, General Policies and Lab Events

Annual Lab Retreat

• Each year as a lab we will plan an overnight ‘getaway’ to spend some time communing with nature, brain storming, bonding and enjoying each other’s cooking.  
• Note – there is also an annual division of biological sciences retreat, see details here.

Authorship

In my view there are two key requirements for being an author on a manuscript:

1. Contribute to the intellectual content of the manuscript in a meaningful way.

2. Contribute to the writing and/or editing of the manuscript in a meaningful way

• Note that “collect data”, “analyze data”, or “fund the study” aren’t on the list. Those are key components of a paper, but do not (on their own) necessarily warrant authorship.
• Most often one person will take on the main responsibility for writing the paper, and this person will be given first authorship.
• These authorship guidelines extend to me; I do not expect authorship automatically on all manuscripts coming out of my lab. It is conceivable (and probable) that manuscripts borne from independent side-projects or collaborations could be produced without myself having contributed sufficiently enough to warrant authorship. That is fine with me – I encourage my trainees to gain independence in publishing if that is desired!
• It is worth noting that there are countless opinions regarding authorship, and there are always borderline cases. When it comes to borderline cases I generally suggest airing on the side of generosity. When collaborating with other people, I tend to defer to their lab group’s criteria. However, it’s important that within our group, we are clear on the expectations for authorship and transparent from the beginning about authorship discussions and decisions. If you ever have any questions or issues, please come speak to me.

Celebrations

• Birthdays will be celebrated with baked goods (or alternative treats if so desired) – so don’t forget to put that all important date in the lab calendar!
• PABs. Publications are something to be celebrated! Thus, they call for PABs – that is, ‘Publication Acceptance Beverages’. If you publish a paper it is the lab’s tradition that you provide a beverage of your choice (alcoholic or not) to share with your lab mates.
• Solstice – is there a better way to celebrate the longest and shortest days of the year than getting together as a lab? I think not – so plan for a summer BBQ and a winter get together!

Deadlines and Feedback

• If something is important and has a firm deadline it is crucial to tell your collaborators and people, whose help you need. You should tell the relevant people the deadline as soon as you know when it is and make sure to remind them as the date approaches. This also means you shouldn’t be afraid to ‘bug’ someone about it.
• Give Diana at least one weeks’ notice to do something with a hard deadline that doesn’t require a lot of time (e.g. reading a conference abstract, filling out paperwork).
• Give Diana at least two weeks’ notice for something that will take a moderate amount of time (e.g. letter of recommendation, award nomination).
• If you want feedback on something that will require multiple back-and-forth interactions between you and Diana (research statement, teaching statement, grant application) it would be best to start this process at least three weeks before the submission deadline.
• For manuscript submission and revisions (i.e. when there is no hard deadline) send drafts to Diana as soon as you have them and bug her to give you feedback if two weeks have passed.

Field Safety

• Don’t work alone.
• Let someone know when you are in the field, where you are working, and when you plan to return.
• Use relevant safety gear when necessary (e.g. life jackets).
• Make sure the first aid kit is in the truck.

Fish Care and Feeding

• You are the principal person responsible for the welfare of your own animals, 24 hours every day.
• Check all of your fish every day. If you are away, make sure you appoint someone to check your fish. Make sure everyone else in the lab knows who is your backup.
• If you see a problem with someone else’s animals, such as dead fish in the tank or filters not working, etc., then bring it to their attention immediately, or deal with the problem yourself if nobody is available. This can be difficult on weekends, especially if you planned only to feed the fish and get out of there quickly. But if you help others, they will help you. Put dead fish in falcon tubes with ethanol by the tank that contained them. Leave a note on the aquarium, a phone message, or an email, saying how you handled the situation.
• Keep the workspace clean. Keep the aisles of the wet lab free of hoses, rocks, equipment, and other debris.
• At all times it is necessary to work within the guidelines outlined within our animal care protocol.
• Check the feeding schedule to see when it is your turn.

Hours

• You are not expected to come into the lab on weekends or holidays (with the exception of the weekly designated fish feeders – details in the wiki). Don’t feel bad for taking time off work.
• In fact, there are no precise hours you are expected to keep. As long as you are getting your work done you can do it at whatever time of day you like. One of the benefits of academia is having flexibility in your work schedule
• In this vein, you are welcome to work ‘off campus’ when desired (i.e from home, a coffee shop etc).
• You are however expected to regularly attend the standard weekly on campus lab events and perform any fish duty you might have.

Lab Calendar

• The following should be added to the lab calendar:
  •  Planned absences for: extended vacations, field work or conference travel.
  • Your birthday!
  • Lab recreational events.

Lab Equipment

• Treat equipment with respect.
• During busy times sign up to use ‘in demand’ items (qPCR machine, microscope etc) this is done using the binders adjacent to each piece of equipment to avoid disappointment/double booking.
• If something isn’t working let the lab manager know so we can get it fixed!

Meetings

Individual Meetings

• At the beginning of each semester we will set a schedule for weekly meetings. Each full-time lab member (grad students, postdocs, technician) will have a one-hour long slot set aside to meet with Diana. This hour can be used however you find most valuable, this can include looking at data, discussing ideas, working through problems with an analysis, talking about future plans etc. If you feel there is nothing or little to discuss you are welcome to cancel the meeting or just drop in for a quick chat.
• Diana will meet with undergraduate students every other week (or according to need) – but post-docs and graduate students should meet with their undergraduate mentee on a more frequent basis.

Lab Meetings

• One-hour long Lab Meetings are held once a week at TBD time in TBD location.
• Lab members will take turns leading. A schedule assigning weeks will be created at the beginning of each semester.
• When it is your week to present you have the options of:
  • Leading the discussion of a journal article or topic of your choice.
  • Getting feedback on a manuscript you are working on.
  • Presenting an update on a in progress or completed project.
  • Giving a practice talk for an upcoming seminar, conference presentation or job talk.
• If leading the discussion of a journal article the paper should be sent to the lab email list at least 3 days before lab meeting to give adequate time for reading.

Molecular Lab Cleanliness and Safety

• Common use areas should be kept clean and clutter free.
• No food should be in the molecular lab.
• Field equipment should not be left lying around the molecular lab.
• All bottles containing liquids should be properly labeled.
• Dirty glassware should not be left in or around the sink.
• The attire you are wearing, and protective equipment used should match the task -> for example phenol-chloroform should be only handled in a fume hood and when wearing a lab coat, gloves and closed toe shoes.

Ordering and Lab Stocks

• If you use the last of something or notice stocks are low for a commonly used item note it on the lab white board so that it can be reordered.
• For non-routine restock orders or orders over $300 USD notify the lab manager or ask Diana for approval before placing the order.

PI Office Hours

• In addition to weekly meetings, you can most often find Diana in her office. Her door is almost always open; if it is, feel free to swing by for a chat. If her door is closed, assume that Diana is either gone, in a meeting in her office, or otherwise does not want to be disturbed – so please send a message rather than knocking.

Recommendation Letters

• If you have been in the lab for more than six months (it is difficult to really know someone if they have only been around a few months) you can count on Diana to write you a letter. Exceptions can be made if students or post-docs are applying for fellowships shortly after starting in the lab.
• If you need a letter, notify Diana of the deadline as soon as possible (see Deadlines for more guidance). Also send Diana your CV, and any relevant instructions for the content of the letter (e.g. what exactly it is for and where to send it). If the letter is for a faculty position, also include your teaching and research statements.

Reproducibility and Data Management

• In order to have confidence in our work, it is important that others are able to reproduce our results. Reproducible research is an essential component of science and an expectation for all projects coming out of the lab.
• To ensure reproducibility your analysis pipeline should be well organized and well documented. It therefore important to take extensive notes for each step of your analysis pipeline – this includes indicating any pre-processing of the data. It is also important to keep detailed notes on your experimental design. Your code should be clearly commented and in way that would be interpretable to someone else.
• All data, code and samples must be archived. See the lab wiki for the lab’s naming conventions and archive locations for each data/sample type.
• All raw sequence data and phenotype should be stored in at least two places at any time – see lab wiki for options.

Scientific Collection

• Always bring copies of our fish collection permits to the field.
• Call ahead when necessary for land owner permissions.
• Information on lakes is available from the Canadian Ministry of Environment using the Habitat Wizard application and the Fisheries Inventory.  
• Some of the fish we work on are endangered species and we are permitted to collect on a few. Fish deaths are therefore doubly tragic. Take good care of fish from them moment they are caught in a trap – don’t crowd them, keep out of water only briefly, and change the water regularly in holding containers. Keep them cool not chilled.
• Fish die more readily as the season progresses so plan to collect in April not June if at all possible.

Sick Days

• If you are sick stay at home unless it is absolutely 100% necessary to come in to work (e.g. an entire experiment will be ruined because you can’t find someone to cover for you). Nobody wants your germs. Take the time to rest or if you are feeling well enough to work find something you can do at home -writing, catching up on the literature, the list is usually endless…

Travel Budget

• PhD students that are presenting at a conference are eligible to receive $500 of annual travel support from the Division of Biological Sciences. I will provide at least an additional $500 per year towards the costs of conference related travel (maximum is funding and situation dependent).
• Post-doctoral fellows will receive at least $1000 per year for conference travel (maximum is funding and situation dependent).     

Vacation

• Let Diana know if you are intending to be away on vacation. Vacations under 2 weeks don’t need ‘pre-approval’ from Diana. Vacation durations > 2 consecutive weeks should be discussed – ideally before plans are made.

Work Life Balance

• While there may be a period of time where you enjoy spending all of your time working (or feel like you must to meet a deadline), it is important to offset these periods with other relaxing and/or fulfilling endeavours. This is something I struggled deeply with during my own PhD. While I still don’t necessarily always strike the perfect balance, I aim to make time for the things in both my personal and professional life that bring me joy.  

“Don’t confuse having a career with having a life” – Hillary Clinton

Lab Communication channels

Slack

Slack will be used as the primary means of lab communication.

Notes on using the lab slack:

When posting messages or looking for updates, check the appropriate channel: #general for lab announcements, #lab-meetings for notes or communication related to lab meetings, #papers for sharing links to relevant papers and discussing them, #code-tips for sharing wisdom on code writing or asking (and answering) the coding questions of others, #stats to ask and answer questions about statistical analyses, and #random for non-work-related chatting that is best kept out of the work-related channels.

Try to keep each channel on topic, so that people can subscribe only to the channels that concern them. For messages to one person or a small group, use direct messages. If you have to send attachments (e.g., papers) or send messages that include out-of-lab recipients, use e-mail. If it’s an emergency and Diana isn’t responding on Slack, e-mail her.

Full-time lab members should install Slack on their computers and/or phones. Part-time lab members should also check Slack regularly. You should of course feel free to ignore Slack on evenings and weekends – and Diana probably will, too!

Google Calendars

The lab has two Google Calendars (contact Diana for access)

1. Rennison Lab calendar: used to keep track of lab events, birthdays and travel.

Listserv

We have a lab listserv for sending e-mails to the entire lab when necessary (address TBD). Contact Diana to get added to the lab listerv.

Wiki

The password protected lab wiki contains almost all the information you need while in the lab. There is information on the tasks needed to be done upon arriving in the lab. There are check lists and print outs for the fish facility. You will also find information on collecting, taking morphological measurements, setting up tanks, molecular protocols and links to on and off campus resources for things like mental health and diversity. If you are wondering how to do something this is probably a good place to start (full table of contents below). Lab members should contact Diana for access.

Wiki Table of Contents:

Analytical Skill Resources and Tips

Statistics

Coding

Animal Care Protocols

Animal Care Protocol PDF

General Stickleback Maintenance

Stickleback Euthanasia

Make crosses

Preserve sperm

Raise crosses

Static aquarium set up

Starting the nitrogen cycle for static tanks

Manage the nitrogen cycle on static tanks

Water testing static tanks

Normal water changes for static tanks

Troubleshooting static tanks

Recirculating tanks

Elastomer tagging

RFID tagging

Arriving in the lab

Collection Permit PDFs

Collection Site Information

Data Management and Repositories

Code

Freezers

Genomic Data

Naming Schemes

Phenotypic and Ecological Data

Physical samples

Diversity Resources

General

LGBTQIA+

Women

Diversions

External Mentorship and Support

Fieldwork

Disinfecting traps at the end of your field trip

What to bring to the field?

Where to stay in the field?

Where to trap fish?

Who to contact for lake access?

Funding Opportunities

Undergraduates

Graduate Students

Post-doctoral Fellows

Important phone numbers

Lake information

Mental Health Resources

Graduate and Undergraduate Students

Postdoctoral fellows

Molecular Protocols

Ordering Procedures

Shipping Live Fish or Eggs

Soft Skills Resources and Tips

Making a webpage

Making a CV

Oral and Poster Presentations

Reviewing Manuscripts

Teaching

 Writing

Specimen Protocols

Preserve fish for later for DNA work using 95% ethanol

Preserve fish in 10% formalin for morphological analysis

Stain fish for morphological analysis

Fish morphological measurements