Lab Manual

[Created by Dr. Fang Chen- 2025; Most Recently Revised – February 25]

Preface

This document intends to help all members in Chen Lab to best avoid mistakes and improve efficiency, quality, well-being, and safety by making the desired research culture of the lab explicit and clear. It lays out reasonable expectations for me and (current and potential) lab members. Its goal is to save us all from having to play the “guess-what-Dr. Chen’s-thinking” game, or worse, needless miscommunication and all the stress that can come from such. This manual will be constantly evolving in my research group here at CWRU. Nothing is unchangeable but I ask us all to respect the process and abide by the expectations written here unless we have had an explicit conversation that agrees to some change. I would also emphasize that the goal is not to have me be a micro-manager; in fact, by laying all this out I hope I can be the opposite and enable us all to just get on with our jobs and enjoy the pursuit of this amazing vocation!

What you can expect of me

1.       A clear vision on your project(s) and project(s) goals.

2.       Independence in research projects. As long as it fits broadly in the scope of my lab’s mission and I can afford it, you should be able to pursue it. To be clear: certain grants have certain deadlines and there may be long periods of time when I need you to focus exclusively on a specific project, but you will have latitude—especially if you can prove to me that you can handle multiple projects at once.

3.       Opportunity to publish papers, abstracts, review papers, etc. This is the currency of science. Please do not underestimate the importance of publishing.

4.       Following the Guidelines on Authorship and Acknowledgement per university policy.

5.       Opportunities to attend professional conferences.

6.       Funding to support your salary and research.

7.       Timely response on email, papers, recommendation letters, grant applications, etc.

8.       Regular meetings both for the entire group and one-on-one to discuss research roadblocks, solutions, career opportunities, etc.

9.       Scientific and professional guidance that furthers your progress toward your professional goals, always remembering that it is your life, not mine.

10.   Honest feedback that promotes your success.

11.   Treating all fairly and equitably.

12.   Always being professional and proceeding with caution in how I handle all situations and information.

13.   Giving credit where credit is due, especially in public presentation of any work done in the lab.

14.   Being a life-long mentor to the extent you choose to engage me in that role.

15.   Time away for personal time and travel. We will follow the University’s guidance of this.

What I expect of you

1. Work Ethic.

You work hard. I expect all to be self-motivated and for the number of hours worked to never be an issue. I ask that all be in the lab at least from 9 am – 6 pm so that interaction with your colleagues can occur for their and your benefit. You are responsible for solving personal issues that consistently prevent you from being on time. Success in academia is highly related to your workload. For PhD students who aim for a faculty position thereafter, I expect you to be in the lab at least 50 hours per week. Exceptions will be made to individuals showing excellent self-discipline and meeting deadlines and expectations for research progress. Weekends are primarily for relaxing and recharging but keeping the momentum going at work is important and I expect many will stop by the lab and/or do some work at home to move projects forward.

2. Absences.

Please let me know AND use the scheduling calendar or sticky notes if you will be out of the lab and the duration of and general reason for that absence (e.g., vacation, illness/health, conferences, etc.). As a general rule of thumb, I expect people to take no more than 2 weeks’ vacation a year unless milestones are met. Don’t come to me and ask for a 3-week vacation when you join the lab for only 3 months.  Please let me know a few weeks ahead of time when you will be out of lab and use the scheduling calendar.

Please leave contact information for emergencies (e.g., cell phone). I promise not to reach out unless dire circumstances.

3. Research Progress.

Your success is not tied to “getting experiments to work”, but it is tied to you doing work. I’m not overbearing, but I also will not understand if you keep coming to me month after month without progress. To make progress, it is important that you actually care about your research project. We all go through highs and lows in research, but I’m assuming you are doing postdoc/graduate school because you are genuinely interested in your research project and want to see it succeed. Publication reflects research progress. Below is the general measurement of research progress:

1)  BSTP and MSTP students should have at least one first author peer-reviewed research manuscript (not review) by the qualifying exam.

2)  Graduate students need at least 3 papers to graduate with the PhD.

3)  Postdocs need one first author research paper per year.

4. Finding a New Project.

Two brains are better than one, especially when creativity is the task.  My hope is that everyone will engage in a period of intense and collaborative thinking when they join the lab and periodically thereafter to conceive of a project that is:

           -original

           -important

           -interesting

           -complements other projects in the lab

           -meshes with the overall direction of the group and its funding base

I will help shape the project to meet these goals but expect that each person in the lab provides the creative spark behind their respective projects.

5. Clear communications.

           You ask questions if you don’t understand. This is critical. Please do not act like you know how to do something if you don’t. I may not know the answer, but we will work together to figure it out.

           You clarify any misunderstandings if you sense there might be one.

           Use sticky notes to convey message when the others are not around, for examples, when you put away packages with others’ names, when you need to use a shared equipment for a longer duration than usual etc.

6. Financial Stewardship.

           You keep expenses low. Every dollar counts. I’m not going to personally approve every purchase, but I’m going to ask you to keep track of your expenses and justify it. Learn about the other equipment in the department and shared resources from other groups. Biological experiments can get very expensive very quickly. Please plan them smartly. Please ask me about controls when you have doubts.

1)      Shared reagents.

We cannot afford for everyone to have his/her own tube of everything. Please do not set up your own stash of samples of common reagents. Before ordering new reagents, please check the inventory to see if we have any (exactly the same one or other reagents that can do the work) already. Maintaining stocks of shared reagents requires everyone to update their usage in the shared inventory list and order a replacement well before the stock is gone, typically when the second-to-last tube/bottle is nearly finished.

2)      Unique reagents.

Please store all unique reagents in a box that is clearly marked with your name. Please clearly label everything with the content name, date, and your name or initials. This is enormously helpful in figuring out the value of what’s in a tube, be it a purchased reagent or a home-grown one (it allows us to look up in your notebook more about it, differentiate between different versions of something and, in some instances, figure out who the tube might belong to). Obviously, this is not necessary for aliquoted tubes of ROUTINE reagents that are in YOUR clearly labeled box.

3)  Animals.

Our research requires tests in animals. Before testing with animals, it is important to optimize our materials. There must be a purpose higher than curiosity to motivate experiments in animals; there must be a real expectation that human and/or animals will benefit from the work through lives saved or disease ameliorated. All animal work requires approval, in advance, from the relevant panels at Stanford. It is crucial that all aspects of the approved protocols be followed and that anyone working with animals has completed all the required training.  Animal users are responsible for reading the protocols, following up the animals, knowing what is in them and what we are required and not allowed to do.

7. Grantsmanship.

You will apply for independent funding. This is a win-win because it saves me money and it shows your independence. I will work with you to identify funding opportunities.

8. Lab Culture/Environment.

We all spend a lot of time in the lab, and it can and should be a place where all enjoy coming to work. I expect all to be respectful and supportive of one-another and professional in all interactions in the lab and in all professional encounters.

Respect others by returning shared reagents/tools/equipment in a good/clean condition to the designated place after use, timely updating inventory list upon usage, taking care of your own mess (cleaning your own bottles etc.) after experiments, asking for permission to use other’s unique reagents/tools etc. Respect also requires you credit people based on their contributions.  

Addressing conflicts with professionalism. Disagreements will arise, of course, but I expect those to be resolved professionally and courteously. If you are tempted to raise your voice, don’t – please explain your position calmly and if no resolution is forthcoming, walk away. When both parties are calm, then return to the conversation, possibly out of the lab. While it is not how I would prefer to spend my time, I’d rather engage any dispute with the individuals concerned and help resolve it (individually or together) than to see the culture of the lab become one where overly heated arguing occurs.

No microaggression. Humor is a matter of taste and culture. Please be sensitive to others who may “laugh along” but underneath be very uncomfortable. Please be sensitive about swearing and “off-color” jokes, especially those that might be interpreted as sexist, racist, homophobic, etc. It is crucial that the work environment be safe and free from all harassment or discrimination. And “microaggressions” are a real thing – you might think you made an innocent comment or asked an innocuous question but the person you are speaking to, or that is over-hearing you, might have spent a lifetime dealing with such comments/questions and they can really add up.

Being positive often involves adopting an optimistic mindset, where you choose to focus on the good in situations and people. It reflects trust, gratitude, and a belief in the inherent goodness of people, which can foster healthier relationships and a more fulfilling outlook on life. True positivity includes both hope and wisdom. It's important to balance positivity with discernment to navigate life with an open heart while staying grounded in reality.

Being open is deeply connected to humility and a willingness to embrace growth. It means acknowledging that you could be wrong and that there’s always something new to learn—whether it’s about knowledge, technology, culture, or perspectives from others. This mindset fosters curiosity, adaptability, and a deeper understanding of the world and the people in it. Being open doesn’t mean abandoning your values or beliefs, but rather being willing to explore, question, and evolve.

Kindness is a powerful force that not only benefits others but also enriches your own life. You collaborate and help each other. This includes other people in other groups. Nothing kills productivity and collaborations faster than keeping secrets and attitude problems.

9. Safety.

           You will work carefully and safely in the laboratory. You will follow all University policies on general lab and chemical safety, waste disposal, PPE, biosafety, etc. I expect all members to complete their specific required safety training and keep records up to date as required by the university. You will ask me or the safety office if anything is not clear.

10. Integrity.

           You understand and follow all issues related to academic integrity including plagiarism and the responsible conduct of research.

11. Notebooks & Data Management.

You use LabArchives to keep careful records of all experiments and organize/store research data. While small data files can be uploaded to LabArchives, large data file should be uploaded to our shared BOX DRIVE. This is critical. Nothing is worse than getting something to work and then not being able to repeat it because of poor record keeping. You are welcome to make copies of your own notebooks to take with you when you leave but the originals must remain here, as required by the university. This includes both digital records and laboratory notebooks.

My general guidelines are:

1)      Use a separate notebook for each project.

2)      Date every experiment.

3)      Indicate the overall purpose of the experiment.

4)      Record full details of materials and methods. 

5)      Include calculations, even if it is a sloppy draft. These can be checked if there is a problem (ranging from how you made a 10 mM stock of some reagent to how you made a reaction mix).

6)      Present the key results and/or refer to any electronic database with the results. Include all original data.

7)      Describe your conclusions – write this for your, my and future lab-workers’ benefit.  Talk to us! State lessons learned, even if negative. Put models in to help you and others think about the work. It is also helpful to note which experiment/figures are in your papers and provide clear descriptions of how new parasite strains were made, isolated, and which clone(s) were used for your published research.

8)      Organize your data to a representable format timely, include all the details that can remind you how you did the experiment. You can use these organized data for your group presentation, manuscript figures, conference presentations, thesis etc. It will greatly improve your efficiency. Please upload them to related project in the LabArchives/BOX DRIVE.

12. Career Development.

I also expect you to be the master of your own fate. Graduate students: you oversee completing all the requirements for graduation. I won’t be keeping tabs on this. It is never too early to be thinking about what you want to do after you leave my lab. This will allow me to help you more when you are here to make that transition.  Postdocs: what will you do when you leave? Academia? Industry? Government? I will work hard to help you get what you want, but you have to articulate that to me. Early.

13. Conferences.

I expect you to present at least one professional conference annually. I will remind you which conferences to attend and you can also suggest conferences that are relevant to our research. I expect you to submit at least one abstract and present during these conferences. You should oversee the due dates of abstracts submission, registration, prepare and practice your presentations, etc. I expect to review your posters and go over your talks to provide input and to be sure that I know what we are saying/showing publicly. Please archive final copies of all presentations on the LabArchives/BOX DRIVE.

·       Posters.

LESS IS MORE. Posters should be very light, generally in bullet format and with relatively few words.  Don’t reformat a paper into a poster, with tons of words and details. People passing by need to see a short summary to decide if this is something that they want to take the time to look at in detail. Conclusions/”take-home messages” are also essential. Posters should also be ingestible without you as a guide. This is because posters typically stay up for much longer than the period that you are required to stand beside them and people should be able to peruse them and take away the most important points.

·   Research talks.

Unless you have given essentially the same talk before, please plan to practice with whomever from the group can come (please invite everyone). Likewise, please try to make time to attend such practice talks and give input. Since most of us don’t like to be hypocritical, it is useful to criticize and then apply those criticisms of others to your own talk. I also recommend inviting someone from outside the lab to the talk to catch the omission of things that we all take as “given” but others don’t (e.g., use of lab-specific jargon, system-specific “insider” knowledge, etc.). Including work by others in the lab can often strengthen a talk, whether those data were obtained as part of a collaborative effort or just something someone else has obtained. Regardless, please:

1) Always talk to the person concerned and be sure to get their explicit permission to include their (or your “collective”) results in your talk.

2) Always acknowledge the person’s contribution verbally during the talk and in writing on the relevant slide(s); including a photo of the person helps remind you to do this and helps people in the audience seek out the person to learn more about the result.

Do homework before the conference, please plan in advance about sessions that could be interested and related to our research as well as people to network with to facilitate your research and career development. Attendance at sessions is clearly key and I strongly recommend taking good notes as the amount of information flowing in can be overwhelming and impossible to retain.

The resulting network will enormously facilitate your research both in terms of information learned and the ease of obtaining reagents when those occasions arise. To meet people, you may need to GET OUT OF YOUR COMFORT ZONE!!  I strongly recommend sitting at meals with people you don’t know. Do this for at least one, preferably two meals a day. Meaning, don’t hang out with folk you do know! Introduce yourself to those you sit next to and ask, “what do you work on” and be prepared to do likewise although I suggest answering with “I work on HOW or WHAT…” – pose it as a question you are answering so you don’t just say “I’m trying to knock-out…” Another good conversation-starter at meetings is asking someone “What’s the most interesting (coolest?) thing you’ve heard so far?” One reason people don’t like to sit with people they don’t know is that it feels rude to abandon those you do know. So, make a pact with those friends and maybe explain that “Dr. Chen says we have to sit with people we don’t know for at least one meal each day so let’s split up for this one and compare notes later.”

After the conference, please do a review presentation to the whole group as it is essential for the others to learn from your attendance. 

14. Departmental Seminars and Retreats.

I believe that communication within a department is invaluable in making the most of the community of scientists we are a part of. Selfishly, there is much to be learned from others, often unexpectedly. In addition, input to others is always useful. Hence, I expect you to attend all department seminars except in very unusual circumstances. For the same reason, I expect all to attend at the department retreats except in extraordinary circumstances. I also expect you to take advantage of these great opportunities to practice your presentation and networking skills. So, please submit abstracts and present whenever possible.

15. Lab Meetings.

Attendance. I expect all members that are not on vacation to attend lab meetings ON TIME except in truly extraordinary circumstances. Participation is required by asking questions, sharing your thoughts with the group. Don’t be shy about sharing “stupid” ideas – they may not be so insane and will help the creative process. Likewise, please be mindful that everyone in the room deserves an equal opportunity to talk. Some are more reticent to do so and need some “space” to offer an opinion.  Please don’t dominate the conversation and feel free to continue giving input after the meeting, one-on-one with the speaker.       

Presentation. Please send the final Powerpoint to me by 10 minutes before the presentation so I can take notes on them during the meeting.  Also, I expect these presentations to be

1) professional. Obviously, they can be informal but that does not mean unprofessional.  Be proud of your work.  Professionalism also means no “F-bombs” or other swearing. Treat all questions as worthy of a considered response, regardless of whether you feel the questioner should know the answer. 

2) Clear. Introduce the question/background, even if you’re sure everyone must remember it from the last meeting.  Odds are they don’t, and it can never hurt to remind them and you of the real point of the experiments.  Remind us of any key aspects that underlie your work.

3) Rigorous. It is crucial that you be the most critical of your own data. You will never hang for understating a conclusion, but you may (metaphorically speaking) for overstating it. 

4) Time-aware.  Only you know what you hope to teach and learn from others. Be mindful of the time and don’t hesitate to say, “that’s very useful input but I’d like to continue this particular conversation off-line and now move on as I need your help with some work I’ve yet to describe, even more.”

16. One-on-one Meetings.

Scheduled. I set aside an hour to meet with everyone weekly or biweekly.  I will try to give as much notice of any change as possible but occasionally, I learn of a meeting or seminar that I need to attend on short notice and ask your understanding. I expect the same of you and will likewise understand if things unavoidably change. Sometimes I am coming from the other side of campus and will be a few minutes late but will always try to call if it will be more than a few minutes. Sometimes, a meeting in my office will be on the verge of some scientific epiphany and I may ask for another few minutes when you come to my door. I promise not to abuse your gift of a few more minutes to me and one of your colleagues. If my door is shut and you’re not sure if I’m with someone, please knock – it is often the case that I’m working on something that needed concentration or just got off a phone call and am anxiously waiting for your arrival!

Spontaneous. The scheduled meetings are only the minimum of the interaction I expect to have with you.   Always feel free to stop by.  If my door is open, come on in.  If it’s closed then consider the bar raised in terms of how important the conversation needs to be but don’t consider this an absolute “do not disturb”; I won’t be shy about saying I’m in a meeting (in case it’s not obvious when I open the door). And always feel free to shoot me an email or text message to set up a time for an extra meeting (so you don’t have to take a chance on my being around when you’d like to meet).

17. Weekly Reports (for Scheduled One-on-one Meetings). 

Please:

1)      Send a PowerPoint update that describes your progress since our last formal meeting by the night before, or, at the latest, 8:00 a.m. on the day of our scheduled one-on-one meeting.  I use the time after breakfast to read these and actually THINK about the work.  It is MUCH harder to do that when coming in cold to the conversation.

2)      Name the report – YYYYMMDD-xxFCmtg where xx are your initials.

3)      Please use a first slide that has the date prominently displayed. I then take that slide set and merge it to the end of a slide set that has all your slides.  That way, we can easily scroll up to look at data from past weeks and the date slide serves as a rough time signature.

4)      State the title and goal of each project on a separate slide.  Obviously, this won’t change most weeks, but it is very helpful to me and probably not bad for you, to see what you are really trying to accomplish with the work.  And it “costs” nothing to have those slides repeated in the cumulative slide deck.

5)      Include any recent results in graphical format, and include any details that I might need to interpret the data.

6)      Describe short-term experimental plans.

7)      Feel free to include a prompt for any other items you wish to discuss (administrative, career development, personal, etc.)

18. Graduation (Ph.D. students only)

I expect all PhD students to graduate in about five years and, in worst case, no more than six years. This six-year limit is absolute; if more work needs to be done it is often possible to finish the PhD and stay on for a few months to wrap up the science.

19. Finishing in the lab.

Upon completion of your time in the lab, please:

1)      Leave lab notebooks and data in an organized, accessible, and recognizable form. You are welcome to take a copy of your notebooks and data, but the original must remain with me. 

2)      Leave a list of all reagents that might be useful to others, appropriately indexed and accessible to others. This is your “Where did they leave it” file. Please print a copy and give it to me as well as send an electronic version. Leave very clear explanations of what they are, how to use/recover (for cells). Often the name you initially call something and how you refer to it in your notebooks is different from what ends up being used in a paper. Please give us a key to “decode” that.

3)      Discard all materials that could truly be of no use to others and completely clean off your bench and empty your fridge and freezer spaces (with the exception, of course, of items described in your “Where did they leave it”).

4)      Consolidate important items to be kept so they take up as little space as possible.

5)      Bequeath useful items (i.e. antibody stocks) to a specific person so they are not forgotten, lost and undiscoverable in a box!

6)      Help me think about the direction your project should take in the future.

7)      Write up any unpublished results in a timely way and take responsibility for continuing to do such once away.

8)      “Check in” periodically through life. I care about all who have ever been in the lab and hope to maintain some level of contact forever. In addition, I am required to provide current status information to funders on a periodic basis (e.g., for training grants). And, lastly, it is fun (and a challenge) to keep the “Lab Alumni/ae” website up to date so that you all can keep in touch with each other and prospective applicants can see what kinds of careers people take as they move on. And, for the record, I am proud of every individual’s chosen direction, without exception. To state the obvious, it is your life and career, not mine or anyone else’s, so don’t let what you think I might think about your choice influence you in any way; I will support you regardless.

20. Other Tips from The Four Agreements:

·       Be impeccable with your word.

·       Don’t take anything personally.

·       Don’t make assumptions.

·       Always do your best.

Appendix A - Help Resources

Getting Help

Being an undergraduate student, graduate student, post-doc, or staff can be difficult at times, and for many with mental health or other health needs, it can be challenging to navigate the CWRU system. Below, please find a list of resources that may be helpful to you during your time at CWRU. These are compiled resources, and I haven’t had the opportunity to check all of them out - but hopefully this is a good starting point. I welcome additions to this list. 

Please know that I am always available to discuss issues that you feel comfortable sharing with her, and I will do my best to guide you to needed help/guidance.

• Mental Health Resources | University Wellness https://case.edu/wellness/campuswide-resources/mental-health-resources

• Counseling Services | Division of Student Affairs https://case.edu/studentlife/healthcounseling/

• Grief Services | Division of Student Affairs https://case.edu/studentlife/healthcounseling/counseling-services/grief-resources

Financial help

There are also Financial Aid Programs that are available for students, postdocs, and staff at CWRU.

• Financial Aid https://case.edu/financialaid/

• Child Care Programs | Human Resources https://case.edu/hr/worklife/child-care-programs

Appendix B - Required Training for Chen Lab (2025-02-03):

Please let Dr. Chen know if you are asked to do training that is unlisted below.

 To start:

1.   Laboratory Safety Training (initial) https://case.edu/ehs/training/laboratory-safety

2.   Biological Safety Training (initial) https://case.edu/ehs/training/biosafety-training

3.   Formaldehyde Training https://case.edu/ehs/training/formaldehyde

4.   Laser Safety Training https://case.edu/ehs/training/laser-safety

5.   LabArchives Training https://www.labarchives.com/resources#resources-getting-started.

To stay:

1.   Laboratory Safety Training (online refresher), every year

2.   Biosafety Retraining (Canvas), every year

3.   Laser Safety Training (online refresher), every 2 years

As needed (get the training related to your duties):

1.   Animal Resource Center (Canvas) – if you work with animals

2.   CAPS Online Courses (Canvas) – if you order lab supplies

3.   Hazardous Materials Shipment Training – if you need to ship out samples

4.   Ultraviolet Safety Training – if you do UV crosslinking

5.   Radiation Safety Training – if you work with radiation

6.   Respiratory Protection Training – if you use respirator

7.   X-Ray Safety Training – if you work with X-ray

Find more information:

1.   https://case.edu/ehs/training

2.   Canvas online courses