Welcome to the Laskowski Lab!
We are excited to have you as part of the Amazon Warrior team! We strive to build an inclusive, supportive, constructive and fun culture in our lab. We recognize that everyone will have different needs and requirements but also offer different expertise and skill sets. These shared and distributed experiences, skills and perspectives are an asset to our lab.
Each person in the lab plays an important role in contributing both to the science we do and the culture we strive to maintain. Each person in the lab is expected to read this manual – it provides useful information on how things are done in the lab, useful resources and expectations of all lab members.
TL;DR: This manual will give lots of important detail but essentially:
- Don’t be a jerk
- Don’t fabricate/fudge/alter data
1 – Onboarding
Whenever someone new joins the lab, there are a number of procedural things that need to be done. The new member should work with their direct supervisor (either a grad student, postdoc, tech or Kate) to make sure ALL of these things are completed prior to them spending time in the lab.
- Read this manual. The new lab member should then go through the manual together with their direct supervisor (this will be Kate for full-time lab members, or the supervising grad student, tech or postdoc for part-time lab members).
- Lab communication and data storage. Each person should be added to:
- The lab Slack (ask Kate to do this)
- The shared Google calendars (anyone with access should be able to share this): Amazon Warrior Team (main calendar – birthday, gone, lab meetings etc); Fish Room Schedule (to block parts of the fish room for experiments – update paper calendar on fish room door too); Tracking System Schedule
- The lab Box account (anyone with access should be able to share this)
- There are also a whole series of animal and safety trainings that must be completed upon your arrival in the lab (and prior to you conducting any experimental work).
2 – Lab values & culture
The Laskowski Lab is committed to creating a culture that actively recruits and supports people of diverse racial, ethnic, sexuality, gender, socioeconomic, and other backgrounds. We strive to create an environment that is free of bias, discrimination, and bigotry; an environment that promotes anti-racist thinking and actions; and an environment where all members are comfortable with speaking out and are dedicated to self-improvement.
We believe that a healthy, inclusive lab culture is built on three principles: communication, education, and action.
Our lab emphasizes clear and timely communication. Speak up about small difficulties before they become big problems. We strive to promote a supportive environment where people are comfortable giving and receiving constructive criticism. We want all members to feel empowered to call out discriminatory language or actions (be they intentional or unintentional); it is understood that a simple “that’s not cool” is a signal that your language is inappropriate. We work under the assumption of good intent in our interactions with others, but will own the impact of our actions.
We also support lab members in calling out discriminatory practices outside of our lab, as we believe this is a critical first step in uprooting entrenched racism, ableism, homophobia, trans-phobia, and bigotry in our community.
We are dedicated to constantly improving our allyship and we believe that education is an essential part of self-improvement. Our lab is committed to maintaining an evolving library of required anti-racist and anti-discriminatory readings (see ‘resources’ channel in the lab Slack). This library also contains relevant resources on reporting discrimination and improving diversity in academia.
We commit to attending regular anti-racist, anti-bias, and bystander intervention trainings. We promote attendance and participation in diversity-focused activities such as journal clubs and anti-racist panels at conferences. We also encourage members to regularly identify, examine, and challenge our existing biases through self-reflection and reading broadly.
We believe that taking action within academia and the Davis community are essential to combating bias. We strongly encourage all lab members to participate in outreach and activism. As a young lab, the Laskowski Lab is still laying the foundation for our long-term DEI efforts. However, we are committed to the following:
- First-Year Seminars and Course-based Undergraduate Research Experiences to provide in-depth discussion and hands-on research experience to Davis undergrads
- The creation of long-term science outreach programs with local middle and high schools.
- Development of summer support for research collaborations with HBCUs and MSIs.
- Graduate student participation in existing graduate group DEI efforts.
- Whenever possible, paying undergraduate students.
- Intentional, diversity-minded approach to lab recruitment.
3 – General protocols
- Intra-lab communication happens through Slack. You are expected to check your Slack as you would your email; and also to contribute to discussions that may be happening there. Emails are fine when we need to include outside people or for formal reasons. Use good slack etiquette – threads, descriptive tags for files. Read this for more info on how to use Slack effectively.
- Important lab documents are stored on Box (all data, lab protocols, etc). Do not alter or delete any files that you did not create without express permission of Kate (the PI)
- Documents where many people need to edit often can be shared on Google (e.g. calendar).
4 – Participation
This is your research experience and it’s up to you to be the motivating force behind it. We expect lab members to be active participants in the science that we do in the lab, and in the larger scientific academic world. Discuss ideas. Make connections. Don’t get tunnel-vision but learn and read broadly. Question everything.
- Share your thoughts! Share your ideas! Share your expertise! We are a collaborative lab that wants to see everyone in the lab succeed. There should not be real or perceived competition among lab-mates. We do not “scoop” each other or take credit for other’s work. Part of the reason we love science and research is that it is fun to do and fun to work with other people.
- Lab meetings – Grad students and postdocs will be expected to lead (at least) one lab meeting/quarter. If materials will be discussed at lab meeting (i.e. paper, or draft) then these need to be sent around to everyone at least 5 working days prior to lab meeting. You are always expected to participate in and contribute to discussions during lab meeting.
- Do not be afraid to disagree in lab discussions but do it respectfully. We disagree with ideas, not necessarily with people. Keep the focus on the science, not the person.
- Going to seminars – go to at least one per week (more in your first year as a grad student). Even if they seem slightly outside your wheelhouse, it is important to learn about what other fields are doing and you sometimes get great ideas!
- Meeting with speakers – grad students and postdocs should be meeting with seminar speakers A LOT. If not every week, then probably every other week. Even if they don’t study something directly related to you. Get used to talking about your ideas with people and “thinking on your feet”. You never know when/how different connections might help you out!
- Conferences – assuming the lab has money, each grad student and postdoc will be funded to attend at least one academic conference per year. If an undergrad has taken a large role in a project and would like to attend, then this is also a possibility. Conferences are fun, but don’t forget that they are professional too. You are expected to use your time wisely at the conference (see relevant talks, meet new people, etc). You’ll be expected to give a summary of the cool things you learned/saw at a conference after you return (if the entire lab did not attend). If you want to attend other things (like workshops, or short-courses) just ask and we’ll see how well it fits and if we can find a way to get you there.
- Social lab culture – while not required, we encourage all lab members to participate in outside lab activities (quarterly lab dinners, or lab lunches, for example) to help build trust and camaraderie among lab-mates.
5 – Interactions among lab members
Each person in our lab has something to contribute. Some of us may work together in formal collaborations; some may only interact socially. Each person is deserving of respect and should be treated as such. Every person in the lab has responsibility for maintaining a clean, productive and supportive environment in our shared spaces.
- Stay home if you’re not feeling well! Seriously. We all know that remote work is completely feasible at this point.
- Sick/Covid expectations – Each quarter, we will meet to discuss and decide what our masking policy will be. Even when universal masking policies loosen, it should be general protocol and common courtesy to your fellow labmates that you wear a mask when you have had a higher likelihood of exposure. While the general rule is that if you are sick you should stay home, if you are experiencing mild or recovering symptoms that don’t preclude work, please wear a mask while at work. Basically, we should view masks as another tool in our arsenal to limit spreading disease among ourselves.
- Be responsible. Mistakes will happen. You may forget to do something you promised someone you would do, or do something that you shouldn’t have. When this happens, own up to it. Our goal is not to be perfect, but to be honest and rigorous. Mistakes offer an excellent opportunity for growth and can sometimes help expose larger more systematic problems (e.g. we haven’t outlined a protocol clearly enough yet) and so addressing them can be helpful for everyone in the lab. The covering up of a mistake is almost always creates far more problems than the initial mistake ever would.
- Helping lab members with their research is always encouraged and honestly, expected. This can be done informally by offering feedback and advice or training someone is a skill you already know. When this help moves into a more formal collaboration, then discussions should happen early and often to outline the expectations of such collaborations. See our Authorship Guidelines for advice on this.
- Be courteous. Don’t have loud conversations in the office space, especially personal ones. Professional meetings (i.e. with a seminar speaker) are fine if that is the only space available, though it might be useful to look into reserving the department conference rooms for this is possible. Invest in noise-cancelling headphones and recognize that when folks are wearing theirs that they may not want to be disturbed.
- Clean up after yourself. Both in terms of kitchen/office spaces, and also in terms of experimental spaces. Return shared tools to their homes at the end of the day.
- Conflict resolution – If you are having difficulty interacting with another lab-mate, you are encouraged to find ways to communicate and resolve these problems with your lab-mates. As mentioned previously, we encourage clear and open communication. Say something before it becomes a bigger problem. Schedule a meeting with them to talk it out. Focus on listening to the other person to understand their perspective. We don’t all need to be best friends with each other but we do all need to be courteous and professional colleagues. If it is something that cannot be resolved between the two of you, please let Kate know and we will all work together to find a solution.
6 – Time spent in the office/lab
We value “whole humans.” We know that science is just one part of your life. We value folks that find harmony between their work life and their non-work life. We don’t judge others based on whatever balance they find. We do not value workaholism.
- You are trusted to manage your time productively and efficiently. There is no official schedule of when you are expected to be in the lab (exceptions: fish duty), but there are benefits to folks being in the same area for spontaneous interactions, e.g. during core work hours (10ish to 3ish). Working from home is completely allowed but this should generally only be 1 day/week (unless otherwise arranged with Kate).
- In terms of a typical work week, I encourage you to find the schedule that works best for you and do your best to work productively during those times. Just for reference, I truly work a 40 hour work week (sometimes less, very rarely more). That said, occasionally, experiments or analysis or writing may demand temporarily longer hours than we’d like. So when necessary push through as long as its for a limited time (i.e a few weeks) and with the expectation you’ll give yourself a well-earned break once the push is complete! If you feel like you are “pushing” for more than a few weeks, talk to Kate to figure out how to rearrange plans in a more sustainable way.
- Research assistants (e.g. undergrads) need to communicate with their direct supervisor (the grad student, postdoc or tech they are working with) about arranging their schedule. These schedules are more rigid as they are often made in consideration of experimental work. Research assistants are expected to arrive when agreed upon and give as much notice as possible if plans change.
- You do not need to tell Kate when you need to leave early or are taking a day off, just as you do not need to justify to lab-mates where you are. There are no gold stars given out for being the first one in or the last one out.
- Headphones indicate important work is happening so please respect other people’s desire to work uninterrupted.
- Holidays – You don’t need to tell Kate when you’re taking a day off, you are trusted to manage your time responsibly (exception: full-time lab techs). But if you are going to be gone for more than a long weekend, it is your responsibility to make sure that the appropriate people know (Kate & other folks involved in your work) and that you arrange to have any duties you may have covered. Send Kate a Slack message to confirm that your time off does not interfere with any lab duties and then put the days that you will be away in the shared Google calendar. Tell Kate who will be covering for your responsibilities (if necessary). In theory, holidays of any length are okay, but these should be made with consideration of your progress and any other responsibilities you may have. The longer the holiday, the more notice you should provide before you go.
- Science is a creative process so try to ride the wave of productivity. Some days will be really good and productive; some days won’t. Sometimes you need a break and it’s okay to give yourself that. Sometimes you need to learn new habits to increase productivity. If you feel like you’re not making progress and you don’t know how to do so, or you’re having lots of bad days strung together, then talk to Kate to build a plan to form healthy productivity habits.
7 – Interactions with Kate
Your relationship with me is critical for your success and so making sure that we communicate effectively is important to me! I want you to feel like you know what your expectations are; if you ever feel unsure that you are meeting my expectations, or even what they are, please ask me. I value open, honest communication – I will always tell you if I think improvements need to be made with your progress and I will never view any questions or concerns you may have as frivolous or “stupid”. If something isn’t working or isn’t right, speak with me – it’s better to fix a problem when it’s small than when it snowballs into something big.
- I follow an open-door policy. If my office door is open (even partially so) then feel free to stop by and chat. If my door is closed, then I am either not around or am unavailable. The best and most important part of my job is working with the lab members, so I love hearing from you!
- I do not expect you to be constantly available via email/Slack. I expect you to find what work hours work best for you and stick to those (which may or may not line up with mine). That said, I generally expect a response to a Slack message within the same day (ideally within half a day) as I use those for rapid communication, assuming of course you are working that day.
- I generally do not check my work communications after normal work hours (MF ~8-6) so you are welcome to send me communication during those times, but just know that I likely will not respond until I am back in my normal work day (exception: you should call me immediately if something is going horribly wrong in the fish room!)
- If you have a scheduled meeting with me, it is your responsibility to come prepared. For early grad students, this means updating your Powerpoint Log with the appropriate information for the meeting with me (this could include bullet points about topics we need to discuss, graphs of results to show me, etc). These updates should be made no later than the morning of your meeting with me.
- We will agree on deadlines for things together. It is your responsibility to get me things on time or let me know when things will be late and set a new (realistic) deadline
- It is my responsibility to get you feedback in a timely fashion. This will differ depending on what it is – some things I will try to get you back within a day or two (e.g. feedback on abstracts, emails, slack convos). Other things I will need longer (manuscript revisions) but I will always try to get feedback to you within two weeks as a general rule.
- Emergencies – contact me via my cell phone if/when emergencies arise (personal emergencies, or fish room related emergencies)
8 – Fish care & experimental space
Taking care of our fish colonies is one of our biggest responsibilities and privileges as scientists. Making sure the fish duties as performed as planned is critical because 1) our animals deserve to be as happy and healthy as possible, 2) keeping our stocks in good health is critical for our science and 3) we are bound by the rules of the Institutional Animal Care and Use Committee and everyone in the lab could face serious repercussions if our duties are not met.
- If you are taking care of fish, you are expected to attend fish training and read (and understand) the fish care manuals and SOPs (standard operating procedures). These are all found in the white binder in the fish room.
- Fish feeding – every full-time lab member is expected to share fish care and feeding duties. This will include weekends and some holidays. The fish must be checked EVERY SINGLE DAY. If you cannot make it in on your assigned day, it is your responsibility to contact the back-up person (and if that fails, contact Kate) and ensure that someone is there to check on them. Part-time lab members (e.g. hourly paid undergrads) can also participate in fish feeding, though this should be decided in discussion with Kate.
- If you see something wrong in the fish room – SAY SOMETHING. Nothing is “not your problem”.
- Never move experimental materials or delete data without express consent from the responsible person.
- Security – the door to the fish room needs to stay locked at all times. Check with Kate before bringing in any visitors to the fish room.
- Photos – taking photos of experimental set-ups is a good idea, but check with Kate before sharing them with anyone outside the lab.
- Getting access to the fish room. Before you can be added to the animal protocol, you need to complete the tasks listed in the 1- On-boarding section at the top of this manual.
9 – Data management
Protecting the data we collect is critical as it is the entire point of our lab existing. Our lab does science in as transparent, reproducible and rigorous way as possible. That is, you should conduct every step of your research as if someone is looking over your shoulder and be ready to justify why you did things the way you did, and bring the receipts to show that you did exactly what you said you did. The goal is to 1) document exactly how every piece of data was initially collected, 2) analyze those data transparently so that someone else could reproduce the exact same results if given your data and analyses and 3) publicly deposit all the evidence of this process.
- Lab notebooks:
- Keep a lab notebook. Every Amazon Warrior is required to have a hardcopy paper lab notebook. Anything that has to do with an experiment you run should be documented here.
- Pages should be dated and written in ink. Write down details of the experimental planning, scheduling, behavioral assay protocols, a priori hypotheses, outline of the projected steps of the analysis. Trust me, you will forget details and you may need to reference them after months or (several) years.
- The purpose of the lab notebook is to not only help you remember details of what you did and why months or potentially years later, but also as solid proof that we did the things the way we said we did.
- Know that at any moment, Kate may ask to see your lab notebook and she will expect it to be up to date, complete and well organized.
- Organize your lab notebook well – use tabs to start new sections. Write legibly. Keep a blank page at the beginning to fill in with Table of Contents.
- These lab notebooks should never be thrown out and will stay in the lab when you leave.
- Take photos of experimental set-ups. These are necessary for our own records, but also useful for presentations down the road.
- In videos, make sure to use unique file names and ideally, have a tag visible in the video itself with its identification.
- Create a schedule for every experiment. This will be especially useful if multiple people are collecting data and/or the experiment is staggered over time. Even if you are the only one collecting data, make a document showing what data are being collected on what days. This can be done in your lab notebook or in an online format (but always print out the schedule and then paste it in your lab notebook).
- If behavioral data will be collected in the main fish room or you need to use the molecular room/cryostat, then this needs to be listed on the lab calendar. We will discuss scheduling at the start of each quarter to make sure that everyone has access to the space and limit any conflicts between simultaneous experiments.
- Data handling & analysis:
- All data *must* be saved on the Laskowski Lab Box. Save it in your folder and use intuitive and clear file naming practices. This includes all raw and processed data. Data produced in the lab are jointly owned by you and the lab, so they MUST be saved on the lab Box.
- The Box is backed up but make sure to save your data somewhere else too – either locally on your own hard drive, or an external hard drive. The more copies the better (ask Kate about how she lost an entire summer’s worth of data if you don’t believe this happens).
- After your raw data is collected, it’s critical that you keep track of every step from data cleaning to analysis to final results. At a bare minimum you need to keep a copy of the “raw” data in an un-corruptible format (this can be paper data sheets, saved images of stained brains and/or a pdf version of a digital excel file).
- All data cleaning/transformations should be done in R and using version control – never write over datafiles but ‘save as’ and append the date in the format e.g. “Data_project_YYYYMMDD.csv”
- Final data analysis should be compiled in an Rmarkdown file that reproduces exactly the results that go in the paper.
- File management:
- Managing all the files related to a single project is difficult. It is important to use intuitive and informative names for your files and to organize them well in different subfolders.
- For each project create a folder with an informative name within your folder on Box. It is useful to create sub-folders for each major step of a project; a potential organization is listed below.
- Project Name
- Design – includes any schedules, diagrams, predictions etc you generated when you were designing the experiment
- Raw Data – includes the raw data, meta-data, and the saved ‘incorruptible’ formats. Once data is put in here it should not be handled again
- Analysis – includes the data file that you will perform data cleaning and analysis on. All R files, R Markdown files and figures can be saved here
- Manuscript – all files related to writing up your manuscript. Always a good idea to append the date (YYYYMMDD) to help keep track of manuscript versions
- Old files – this is optional, but I am loathe to delete just about any file in case you find you need it later. Instead I put all old files into a folder like this to keep.
- Project Name
- Public deposit:
- All data and analysis files will be publicly deposited when the paper is published so do all your work knowing that the public will be able to see it!
10 – Departing the Laskowski Lab
All good things must come to an end and eventually you will move on from the Laskowski Lab. To ensure that critical data is saved appropriately, and projects can continue smoothly, it’s important that your departure is well planned for.
- All data files and/or samples need to be appropriately labeled, including with detailed meta-data. Tell/show Kate and the lab manager where these files or samples are located.
- All project files should be well organized (as described above) including a final ‘README’ file that gives the broad overview of the status of the project (if leaving before a project is published).
- Talk to the lab manager and confirm with them you are leaving and when so they can remove you from our protocols. We generally allow lab alumni to stay on the lab Slack for a month after their end date to allow for easy communication until you get settled at your next place.
- Lab notebooks should be complete and will be left in the lab (you are welcome to take photos/scans with you).
- Equipment that was bought with lab or UC Davis funds need to stay in the lab. Communicate with Kate about which equipment this is. For laptops, you should remove any files (and all lab related files should already be stored on Box!) and then restore factory defaults so someone else can use the machine.
- Turn in keys to the EVE main office.
- Give Kate your new contact info so we can get in touch in case we have questions about the project and because we want to know what fun new things you are working on!
11 – Letters of recommendation
We are always happy to provide letters of recommendation for our stellar lab members! If you think you’ll be needing a letter of recommendation, then please make sure to follow these steps. This ensures that we have enough time to write an appropriate letter
- All letters must be requested at least 4 weeks prior to the due date. Ask Kate (and if appropriate, your supervising grad student/postdoc/tech) whether she thinks she can provide a strong letter. If you give less than 4 weeks lead time then Kate will try to fulfill the request but cannot guarantee that she’ll have time.
- If Kate agrees to write a letter, then write her an email that includes what the letter is for, provide instructions on where to send the letter, include your CV/application materials and highlight any details you think might be especially important to mention.
- Follow up with Kate about a week before the letter is due to remind her, if she hasn’t already told you that she has submitted the letter