Lab Guide

(Adapted from web pages of colleagues Meghan Duffy and Regina Baucom)

Group Philosophy

Our group is focused on you and your success. You define success and together we work towards it. We set realistic goals and you work efficiently to reach them. Remember, though, that work is not life. Don’t spend all your time in the lab. Try to reach your goals without averaging more than 40 hours a week on your work. Sometimes we must work long intense hours on a particular experiment, but offset those times with days you don’t come in at all. Have a life outside of work: exercise, eat well, have fun. Take vacations!

Safety First!

In doing your research, remember rule #1 (poached from the Duffy Lab), which is that “no sample is worth your life!” We take safety seriously. This means keeping up to date on your safety trainings, paying attention to your own instincts about whether your plan is safe, asking questions of me or other folks who’ve been in the lab longer than you have, and looking out for others as well as yourself.

If there is a true emergency, get yourself and others to safety and call 911 or (510) 642-3333. To report a hazardous spill, call (510) 642-3073. Then call Ellen and report through the SimmsLab #general Slack. If there is a lab emergency (e.g., some equipment is not working, there’s a mysterious puddle on the floor, a freezer or incubator is misbehaving), report through the SimmsLab #general Slack.

More safety info: There are signs on the lab doors that tell you about safety equipment and regulations. The fire extinguisher is by the printer. If you are ever unsure about whether something is safe or have concerns about safety, please ask! If you are concerned about the safety of a chemical you are using, please consult the safety data sheets available online. Other safety information is available at the Environmental Health and Safety (EH&S) website.

Expected conduct: Simms Group Code of Conduct

(much of this material comes from Dr. Davide Oppo's website)

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 members of the Simms Lab Group 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 is not a legal document; it supplements, but does not supersede Department, Campus, and University policies.

Diversity, Equity and Inclusivity: Enjoyable, high-quality research can only be conducted when you feel safe, secure, and supported. 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, religion, marital status, veteran status, genetic information, citizenship status, national origin, color, and/or any other criteria prohibited under applicable federal, state, or local law. We do not tolerate harassment by and/or of members of our group in any form, and we ask all members of the community to conform to the following Code of Conduct :

Code of Conduct
  1. All communication, be it online or in person, shall be appropriate for a professional audience, and be considerate of people from different cultural backgrounds. Sexual language and imagery are not appropriate at any time.
  2. Be kind to others and do not insult or put down others.
  3. Behave professionally. Targeted harassment and/or exclusionary jokes are not appropriate. Harassing behaviors include bullying, offensive verbal comments related to group identities, sexual images in public spaces, deliberate intimidation, stalking, following, harassing photography or recording, sustained disruption of discussions, inappropriate physical contact, and unwelcome sexual or other inappropriate attention.
  4. Group members asked to stop any harassing behavior are expected to comply immediately.
  5. Contribute to discussions in group meetings with a constructive, positive approach.
  6. Be mindful of talking over others during discussions and be willing to hear out the ideas of others.
  7. If you notice that someone else in the group is being harassed, or if you have any other concerns, please contact Ellen or the resources listed below.

Ellen will discuss the Code of Conduct with lab members who violate these rules, no matter how much they contribute to group productivity, or how specialized or needed their skill set. If inappropriate behavior persists after this initial discussion, formal processes, in line with UC Berkeley’s policies, will commence. To report an issue, please contact Ellen Simms. Be aware, however, that Ellen is a mandated reporter for certain kinds of behavior, which means that the institution will not allow her to treat certain kinds of reports as confidential. If you do not feel comfortable contacting Ellen directly, please feel free to contact whomever you think is more appropriate according to the specific case:

Links to relevant University policies, including codes of conduct:

Diversity and inclusivity benefits all of us. It makes everyone feel safer and more secure. Moreover, the greater the mix of people in our group, the greater the mix of skills, experiences, perspectives, and ideas we can collectively draw on. But we cannot fully achieve the benefits of diversity and equality without creating an inclusive environment.

Honesty & integrity are absolutely essential

Science cannot progress without honesty. Do the right thing. If you make a mistake (and we all do at some point), do your best to acknowledge it and to correct it if possible. If the mistake is science-related, record all the details in your lab notebook and notify your mentor and/or Ellen. We all make mistakes (Ellen has made some doozies – you can ask her about them). The most important thing is that we acknowledge them and record their effects. This allows us to take them into account when continuing the study and when looking at the data. We can use that information to adjust things in the future, if needed. Remember that we all build on each other’s data. 

You might also accidentally break a large, unique flask, or a critical piece of equipment. Please don’t just hide the broken item or walk away from the disabled equipment. This just leaves the next person who needs that item or equipment to discover the problem at a very inconvenient point in their protocol. We all slip up and drop things. Please let your mentor (or Ellen) know about the problem as soon as it happens so that we can fix the equipment or replace the item. That said, please don’t use any equipment or items in the lab without receiving training on how to use them safely and appropriately! If you don’t know how to use something, please ask for help!

Finally, and most importantly, we also sometimes make mistakes in our interactions with others. Again, this is something we all do. An effective apology is very important for clearing the air and maintaining collegiality. If you’re unsure how to apologize, there are resources to help. It’s important to recognize your mistake and the pain it has caused, avoid justifying it, and show how you will learn from it and find better ways of interacting. We can all support each other as we navigate these difficult waters.

Be open to new ideas and perspectives 

People come into our group from lots of different backgrounds, which is part of our strength. One reason why it’s a strength is that people from different backgrounds bring different ideas and perspectives to the table, and those are really useful for doing good science. So, be open to new ideas and perspectives, and please contribute your ideas and perspectives! Finally, it can sometimes feel daunting to share your ideas, but remember that the worst thing that can happen is you learn something new (e.g., that what you were thinking won’t actually work, and why). The best thing that can happen is we learn from you how to improve our lab practices/science!

Be mindful of power imbalances

Academia is a highly structured system (and UC Berkeley is the most hierarchical institution that Ellen has ever experienced). This means that, broadly speaking, faculty have more power than anyone else, including staff. It also means that postdocs have more power than grad students, who have more power than undergrads. However, there are other things that create power imbalances, too, including race, gender, ethnicity, socioeconomic status, etc. It’s important for us to keep potential power imbalances in mind so that we do not put someone in a position where they don’t feel safe (for example, to say “no” to something or to voice a concern). If anyone in the lab is making you feel unsafe, please tell Ellen. If Ellen is making you feel unsafe, please tell the Integrative Biology Department Chair (or someone else you feel safe talking to).

Sharing is caring…

Everyone in the lab is expected to share protocols and other resources. We have a really supportive research group, which is wonderful! People help each other: For example, if someone has a big day for an experiment or doesn’t know how to use a piece of equipment or needs feedback on a talk, poster, or manuscript. I want the group to stay this way. Over time, try to make sure things balance out so that you are giving as much help as you are receiving. 

…except when it’s not

But please remember that, while we enjoy transmitting phages to rhizobia, we don’t want to transmit pathogens to each other. In other words: if you’re sick, please stay home. It’s good for your health, the work you do while ill won’t be good anyway, and staying home reduces disease transmission. This is even more important now in the time of COVID-19. Pay attention to campus COVID-19 updates and follow basic disease prevention protocols!

Approach your research and education with a growth mindset

Two things that can be a challenge for all of us are: 1) thinking we need to do things perfectly, and 2) feeling like there are certain things we are bad at and never will be good at. In reality, the more we work on something, the better we get at it. This article on growth mindsets (by Carol Dweck, who developed the concept, which is supported by work done in Cal’s IB department by the late Professor Marian Diamond.

Feedback: ask for it early and give it constructively

Remember that criticism is easier to take if it’s delivered in a sandwich, with positive feedback as bread and the (constructively phrased!) suggestions for improvement in the middle. The formula: compliment, suggestions, compliment.

I (Ellen) will help you edit and prepare grants, reports, dissertation chapters, posters, and presentations. I try to return drafts of papers within 7-14 days (longer if I am teaching a large class). Unless I specifically say otherwise, I want to see a draft of everything coming from this lab before it is submitted, no matter how minor (conference abstract, poster, paper, grant, etc) — this helps us maintain quality and helps ensure our success rate.

Work at times that work for you (but also make sure you get enough sleep, exercise, and breaks)

Find the hours that work for you to work, and make sure you are leaving time for non-work activities. It’s good to be in the lab during typical work hours some of the time (partly so you can interact with lab mates), but it’s totally fine if you take some time during “normal” work hours to do other things (including exercise, meet a friend, see a therapist, etc.)

However, it’s important to note that work-life balance and self-care benefit substantially from planning ahead. Ellen has to admit that she is not the best model for planning ahead, so you can protect yourself by taking the initiative.

Timelines

Speaking of planning ahead & deadlines: you should pass abstracts, proposals, manuscripts, etc. by Ellen before you submit them. This means that you need to factor in time for editing things before the deadline. Things like proposals and manuscripts often take many many drafts before they get submitted, so, if something has a deadline, we should work out a plan early in terms of when to have drafts ready by. For meeting abstracts, you should get those to Ellen at least two weeks ahead of the deadline. 

Related: if you need a letter of recommendation for something, please let Ellen know at least a month ahead of time. 

Writing

Many scientists find writing challenging. But good writing is a key skill that will improve any career. One key is to write frequently.

“Writing productivity research and advice can be summarized in a single sentence: In order to be productive we need frequent, low stress contact with a writing project we enjoy.”

Jolie Jensen, Write No Matter What: Advice for Academics

One way to write frequently is to set daily writing goals and keep them. Many writers set time-related goals involving a particular time of day and a duration. The feminist writing coach Jo Van Every recommends dividing your writing into three categories. The easiest to schedule is the 10-minute to 30-minute “short snatch,” which some writers call a pomodoro, named after the tomato-shaped kitchen timer they use to gauge the time. Another category is slightly longer chunks of time that you carve out of your busy schedule by putting it on your calendar. During the semester, when you are teaching or taking classes, it’s especially key to schedule these times on your calendar. Finally, really luxurious are those times of the year when you can dedicate entire days to writing. However, an entire day of writing need not be ten hours or even eight hours. Even Charles Darwin wrote only about four hours each day, and it’s really stunning how much he managed to publish. (Of course, Darwin had a wealthy wife to support and care for him, but they did have five children, with whom he spent quite a bit of time.) When you are not teaching (or taking classes), set aside time for full days (those 4-hr days) of writing (but, for both mental and physical health, be sure to take breaks in those days and between those days).

Clear writing is often a strong indication of clear thinking, so writing frequently also exercises your thinking cap.

Another trick when facing a blank page is to just start writing what you want to say, without regard to how you say it (Meghan Duffy calls this her Barf and Buff strategy). With this strategy, you will get your ideas down before you lose track of them. But, it also means that you need to go back and clean them up. Repeatedly. Again and again. Did I say that you should revise? Revise, revise, revise!

Some tricks for helping you edit. First, don’t edit as you write (I’m guilty of this, myself, though). It’s far better to put a document away for a few days or a week and then edit it. After I let a document “marinate,” I’m always amazed at all the hanging bits: the adjacent pieces that don’t really hang together, the jumps in logic that leave the reader hanging, the hanging ideas from the introduction that haven’t been wrapped up in the conclusion, etc. It’s really hard to remove the really lovely-sounding pieces that just don’t fit. Meghan Duffy writes a blog post on strategies for keeping useful bits of writing that don’t belong in the current manuscript or document.

When I edit your work, I will scribble and comment (digitally, these days) all over your drafts. This is not because you are a poor writer. It is because everyone, including me, needs to polish our writing.

Consider what is good enough

An important ability in science (and life!) is recognizing what is “good enough“. If you are sending a text to a friend, you do not need to word it as carefully as if you are writing a manuscript. A blog post doesn’t need as much attention as an article. If you are writing a manuscript or grant proposal, it’s more important that it be finished than that it be perfect.

So if we don’t need to be perfect but also want to get better at something, what can we do? Aim for improvement, not perfection. Aim to do one thing that you couldn’t do before.

Learning to manage your time

Try not to say, “Yes!” to too many things. Do the things about which you are passionate, but also the things that will help you reach your goals. A corollary to being the person who gets things done well (but not perfectly) and on time is that you will be asked to do more things. So, saying “Yes” less often might not work. This means that a key lesson to learn is when and how to say, “No.” Be gracious and thank the person who has asked you. A simple “No, thank you, it doesn’t fit my plans.” should suffice. Don’t feel that you need to give a reason for declining.

How I will help you

(Some of this has been modified from Professor Baucom's website).

Much of my job involves advocating on behalf of you. I write letters of reference for group members. I help group members get their work written up and published. I seek grants to fund the lab, buy supplies, pay post-docs, and (when possible) pay students. I clear the paths so that you can get your work done.

My goal is to create a scientific atmosphere that helps you learn, but I can’t teach you everything you need to know. Every project requires different skills and knowledge; I am not all-knowing and cannot be an expert in everything. However, if there is something you need to learn, I will point you in the right direction so that you can get there on your own. You also come to the group with a skill set and a body of knowledge. Part of being in a research group is sharing your gifts with your colleagues. Be generous with your own gifts and seek help from each other.

I try to meet weekly with every team to catch up on scientific progress. I don’t always succeed in this goal, especially when I’m teaching a large course or meeting a deadline. You and your team may have to be resourceful in my absence. Other ways to get feedback from me are during our weekly lab group meeting and via our lab slack, which I try to keep up with. Warning: I’ve gotten worse at responding to email as it has become overloaded with official notifications. You might need to slack me about a neglected email request.

I try to be direct with folks when I see areas that need improvement, but I’m not always good at that because I like to provide people with positive feedback. I will tell you when you have done a good job on big and little things. We celebrate when a paper or grant is submitted or accepted, someone gets a job, or graduates, etc. If your performance lags, we will work together to develop a performance improvement plan. This will usually entail weekly and monthly goals set in response to specific identified issues.

How to know that you are making progress

How can you know if you are making progress? It depends on your position in the group. If you are a graduate student, are you developing research ideas, applying for grants to enact your plans, taking courses (but not too may), collecting data, analyzing it, and writing up your results? Have you taken and passed your prelims (see here for a prelims study guide)? Are you mentoring and working with undergrads? Have we developed an individual mentoring plan? If you are a post-doc, you should be producing manuscripts that will help you to be successful on the job market. Are you helping to mentor others in the lab? If you are an undergraduate researcher, are you producing data, maintaining a clear, legible, lab notebook, cooperating with your team?

We support each other as professionals

I am equally committed to the success of everyone in the lab. This means that I endeavor to treat everyone equitably and I expect everyone else to do the same. We are not competing with each other; we are a team of collaborators. I do not want group members to resent one another, which hurts morale and harms the whole group. This means that if you are feeling left out, or not listened to, or that someone is taking over your project, or some other concern, I want to hear from you before you’ve gotten really angry or depressed. Keeping open communication channels will make it easier to express such concerns before they poison the group.

I value a professional atmosphere in our group. This is crucial to everyone’s success. Being professional is not about behaving stiffly or dressing in some particular way. It means that we interact with one another in a professional manner. We maintain healthy colleague-colleague & mentor-advisee boundaries.

I *do* want to know if you are dealing with a problem (physical or mental condition, negotiating economic or family issues), and may need to have time off to cope, but I do not want to overstep boundaries and pry into your private life. Further, while I care about your overall well-being, I am not a trained psychologist, physician, financial advisor, or life-coach. My advice on these fronts will be flawed. If you are struggling with general malaise that is hampering your work, or a mental/emotional block about your work, then you likely need life coaching or counseling, and it is your responsibility to pursue and follow through with help. I can point you to the appropriate university-related people that CAN help in this way, for example, see Faculty and Staff Assistance Program for staff (links to mental wellness, stress reduction, counseling and life coaching), and CAPS for graduate and undergraduate students. I can also suggest some books to read on this front, but again, NOT my wheelhouse, i.e., call in the professionals, not your PI!

Mental Health

There is increasing evidence that certain attributes of academic research, including graduate or postdoctoral studies, may challenge your mental health. Specific factors driving this include:

  • Low pay and quality-of-life issues
  • Feelings of isolation in your research; e.g. everyone has their own topic and it can often feel as if you are working alone
  • Uncertainty in your research, although it should be noted that, in research of all kinds, it is not just the outcomes that are uncertain, but the questions themselves!
  • Uncertainty in your future career
  • So-called “negative results”; i.e. at some point in your research it is likely that certain questions will be more challenging to answer than anticipated, or that you will feel you have spent days/months/years toiling with little to show
  • Burnout; i.e. feeling the need to work endless hours to make up for the above issues, and the subsequent exhaustion

All graduate students and many postdocs encounter most of these issues at some level. I strongly encourage everyone in the group to take an active and preemptive approach towards the maintenance of their mental health. I assure you that you have the time and resources needed for a highly successful PhD or postdoc project. If there is anything that is placing undue stress, or preventing you from performing at your potential, please do not hesitate to let me or the departmental graduate advisors know how we can help. You should also be familiar with campus resources for students and for employees. Every effort will be made to help you access the right support networks.