Lab Policies and Expectations

Torres-Dowdall Lab

Current as of 01/23/2024

Purpose

This compact document serves as a guideline of principles for the members of the Torres-Dowdall lab. It provides both practical information regarding safety training and lab etiquette, as well as expectations for all members of the Torres-Dowdall lab.

E-Signatures and Acknowledgement of Policies

Please type your name to acknowledge you’ve read these lab policies.

Expectations and Responsibilities

General Expectations and Responsibilities

The Torres-Dowdall Lab promotes a rewarding, engaging, collaborative, and supportive lab environment. In order to maintain a healthy work environment, there are general expectations for conduct in the lab.

• The Torres-Dowdall Lab is committed to diversity, inclusion, and mutual respect for one another. In this lab, we strongly believe that differences among individuals, whether it be related to race, ethnicity, culture, gender, age, nationality, socioeconomic status, sexual orientation, disability, religion, serve to enrich our lab environment. We strive to create an equitable environment, and we recognize that there are communities with histories of marginalization, particularly in scientific fields. As such, we are committed to listening to, learning from, and supporting all members of our lab.
• As we are committed to an environment of support and respect, all members are expected to participate in greeNDot Bystander Intervention Training upon joining the lab.

• There are trainings designed specifically for graduate and professional students, which are offered in the fall semester each year.
• Undergraduate training is offered regularly throughout the academic year.
• Please visit https://greendot.nd.edu/ for more information regarding training dates.

• In the case that any member of our lab commits incidents of bias, discrimination, and/or harassment, appropriate actions will be taken.

• Initial incidents should be reported to another member of the lab or directly to the PI.
• Subsequent incidents, or serious incidents, will result in a report made to the Office of Institutional Equity (OIE), as well as the Notre Dame Department of Biology.

• For information on how to report an incident, please see:

• https://equity.nd.edu/
• https://speakup.nd.edu/ 

• Repeated behaviors will result in termination from the lab.

• Mental and physical health matters. Maintaining a work-life balance can be difficult; if you are struggling, and are comfortable letting Julián (or another lab member) know, please do.

• There are several resources available on campus for mental and physical health:

• https://ucc.nd.edu/  
• https://studenthealth.nd.edu/ 
• https://uhs.nd.edu/ 

• If there are any cases of hostility or tension in the lab, do not hesitate to discuss these issues with Julián (or another member of the lab). We strive to create a healthy work environment, and do not want any lab member to feel uncomfortable.

• In the case another lab member confides in you, please be respectful.

• We are committed to the academic and professional growth of all members of the lab. When we are able, we will support our labmates with learning new skills, troubleshooting, giving feedback, etc. Current members of the lab are expected to equally contribute their skills and techniques to the training of new lab members.

• We have to understand that time and resources are limited, so take advantage of the knowledge available in the lab while being respectful of one another.

• Never stay quiet about any incident involving safety. If you are injured or potentially exposed to hazardous agents, follow proper lab safety procedures and inform others if necessary.
• Always clean up after yourself and be mindful of borrowing items from your fellow lab mates, particularly in shared lab spaces (Galvin 213, 036, and 052).
• Please be mindful of the lab schedule. Your own time, as well as the time of your lab mates, is valuable. Being on time for scheduled lab meetings, one-on-one meetings, etc. is expected.

Principal Investigator

In addition to adhering to the above expectations, the PI is also expected to:

• Give feedback on a timely basis, including:

• Feedback on project ideas, conference posters, talks, manuscripts, figures, and grants.
• Feedback should be given in a timely manner. Generally, this means feedback within 1-2 weeks. In the case a lab member has not received feedback from Julián by then, they should send a reminder/follow-up via Slack.

• Be available on a regular basis (either in person, over email, or via Slack) to discuss research and lab-related matters.
• Attend weekly lab meetings and one-on-one meetings with graduate students, full-time lab staff, and undergraduate students (when necessary).
• Support the career development of all members of the lab, and assist lab members in the preparation of the next steps of their careers.
• Prioritize the mental and physical health of all members of the lab.

Postdocs

In addition to adhering to the above expectations, postdocs are also expected to:

• Develop their own independent line of research.
• Train and mentor other members of the lab (both undergraduate and graduate).
• Present their work at departmental events, at other labs, and conferences.
• Apply for grants.
• Apply for jobs (academic or otherwise) when you are ready.

Graduate Students

In addition to adhering to the above expectations, graduate students are also expected to:

• Develop your own dissertation research. Your dissertation should include at least three substantial, publishable projects that address the overarching research question.

• This research plan should be developed during your first year of graduate school.
• By the end of your third semester, you should have a working draft of your dissertation, which should have received feedback from Julián at least once.

• Mentor undergraduate students, either when they assist with your projects or begin their own independent research projects.
• Present your work at our lab meetings, departmental events, at other labs, and at conferences.

• This includes regularly presenting at Biofrass and in the Jones-TD Lab “Fish Meeting.”
• PhD students should present at least twice per year in the lab’s weekly meeting.
• PhD students should attend at least one conference per year beginning in their second year.

• Regularly attend departmental seminars, Biofrass, and thesis defenses. Attending lunches with seminar speakers is preferred, particularly when their research interests considerably overlap with those of the lab.
• Apply for grants. It is a valuable experience to learn how to write a grant, and may offer the chance to take time off from TA duties.
• Think about what you want for your career (whether it be in academia, industry, science writing, or otherwise) and talk to Julián about this to ensure you are getting the appropriate training for your career goals.
• Make sure all departmental requirements are being met annually.

• Some important milestones are:

• Select your Advisory committee by the end of your 3rd semester
• Defend the written component of your Candidacy Comprehensive Examination (CCE) by the end of the 4th semester.
• Defend the oral component of your Candidacy Comprehensive Examination (CCE) by the end of the 5th semester.

• Please see https://biology.nd.edu/graduate/graduate-requirements/ for more information.

• Prioritize research; coursework and TAing are important aspects of graduate school, but ultimately your research should be highest priority as it is required to earn a PhD and will prepare you for the next stage of your career.
• Participate in the husbandry of the fish in the lab. Proper scheduling is necessary to ensure the fish are being fed (including on weekends) and water changes occur on a regular basis. Husbandry should not fall on one lab member; it is a shared responsibility. In the case you are not able to come in, you are responsible for finding a substitute. If you are asked to be a substitute, please be considerate and understand it is your responsibility to help with husbandry.
• PhD students should commit to writing every day for at least half an hour (anything related to research, including making figures, writing grants, proposal writing, etc.).
• PhD students should commit to read every day for at least half an hour (scientific literature).
• Occasionally, you will be required to be in the lab on weekends, especially as our lab involves the care of live specimens; however, keep in mind that maintaining a work-life balance is important, and try to give yourself time to rest and recharge (and have fun!) on the weekends.
• Graduate students can expect 3 weeks of vacation. More time off is possible, but will be discussed on a case-by-case basis with Julián (and depends on student progress and personal considerations). Please note that spring break and fall break are undergraduate holidays, and in the case you TA it may be a requirement for you to stay on campus during this time.
• Goal setting meetings will occur both as a lab and one-on-one on a per semester basis.

• If general and academic expectations are not met, a one-on-one conversation with Julián will be held. If you continue to fail to meet expectations, the issue will be discussed with the BIOS Director of Graduate Studies (if this occurs within the first three semesters) and with the committee if it is after the third semester.

• Policy on One-on-One Meetings:

• Weekly one-on-one meetings should be scheduled at a time mutually agreed upon by Julián and the mentee.
• In certain circumstances, a different meeting frequency (e.g., twice a week or once every two weeks) can be arranged, provided both the mentee and Julián agree.
• Meetings are expected to last no more than one hour.
• Mentees should prepare an agenda prior to the meeting, outlining the topics they wish to discuss.
• Julián should have editing rights to the agenda to add any additional discussion items.

Lab Managers and Full-Time Research Staff

In addition to adhering to the above expectations, lab managers and full-time research staff are also expected to:

• Work on your own research projects, developed with Julián’s help.
• Maintain protocols for the lab (writing them, updating them, etc.), and keep any required lab paperwork up to date and organized.
• Oversee the hiring, scheduling, and training of undergraduate research assistants.
• Maintain the lab website, lab calendar, and lab manual.
• Be in the lab on a regular basis, with flexibility depending on your out-of-work schedule.

Undergraduate Students

In addition to adhering to the above expectations, undergraduates are also expected to:

• Participate in the husbandry of the fish in the lab. Proper scheduling is necessary to ensure the fish are being fed (including on weekends) and water changes occur on a regular basis. Husbandry should not fall on one lab member; it is a shared responsibility. In the case you are not able to come in, you are responsible for finding a substitute. If you are asked to be a substitute, please be considerate and understand it is your responsibility to help with husbandry.
• Assist other lab members with data collection and analysis, or create your own independent project under the mentorship of another lab member.

• Authorship will be discussed with collaborators/mentors when appropriate.

• Develop a regular, weekly schedule and inform your mentors when you are not able to be in the lab.
• If you are earning course credit for research, you are expected to attend lab meetings if you are able, and maintain regular hours in the lab.

Code of Conduct:

Policies and Expectations

• The lab is committed to maintaining a positive and healthy professional environment. As a part of the code of conduct, all members are expected to act in accordance with the “General Policies and Expectations” outlined above.

Scientific Integrity

• The Torres-Dowdall lab, and the University of Notre Dame, is committed to research integrity. Research misconduct is not treated lightly. As such, fabrication, falsification, and plagiarism are serious violations of the University of Notre Dame’s Research Misconduct Policy. For more information on the policy governing misconduct in research, please see the link below:

• https://research.nd.edu/our-services/compliance/research-misconduct/ 

• Allegations of fabrication, falsification, and plagiarism are taken seriously by Julián. In addition to the misconduct being reported to the Vice President for Research (https://research.nd.edu/people/robert-bernhard/), you will meet with Julián to discuss the specific implications of your misconduct, which may include termination of your relationship with the lab.
• Your research should be reproducible. As such, your experimental design, data collection, and data analyses must be organized and well documented. Taking extensive notes, recording vital steps/observations in your lab notebook, and commenting out your analyses/code is necessary. Version control is also encouraged; using a personal GitHub account to keep track of all versions of your analysis is encouraged.

Lab resources:

Slack

• Slack is used for communication about lab-related matters.
• There are two Slack workspaces for the lab: one just for us (torres-dowdalllab.slack.com) and one shared with Stuart Jones’s lab (fish-club.slack.com).
• There are several channels in the torres-dowdall lab workspace. Please use the appropriate channel when sending (or looking for) a message:

• #all-members for lab announcements pertaining to full-time and part-time lab members
• #lab-meetings for notes or communication related to lab meetings
• #fish-duties for things related to lab fish and fish lab
• #general-restricted for all full-time lab members
• #grad-students for messages just among graduate students
• #purchases-and-receipts for confirming what you buy and what you get
• #random for non-work-related chatting

• Slack should be checked regularly during the work week (Monday through Friday) in order to stay updated on lab matters. Full-time lab members should download the Slack app on their computers and/or phones. Part-time lab members should also check Slack regularly.
• The weekends are your time, and you should not feel required to consistently check the Slack workspace. That being said, because our research involves the care and handling of live specimens, it is important that you are reachable in an emergency situation. Full-time lab members should exchange cell phone numbers with one another for this purpose.

GitHub

• The Torres-Dowdall GitHub can be found here:

• https://github.com/TD-Lab-NotreDame

• Please confirm with Julián before distributing data and code through the lab’s GitHub repository.
• Ask Hanna for information about how to access the lab’s GitHub repository.

Google Calendars

• The lab uses Google Calendars to coordinate schedules with one another. Currently, there are two shared lab calendars.

• Torres-Dowdall Lab Shared Calendar: this calendar is primarily used to schedule lab meetings, one-on-one weekly meetings, and other lab events. In addition, this calendar is where you should enter any planned vacations/dates you will be out of the office. 

• Please give Julián a minimum of 3 weeks notice before you enter any planned out-of-office/vacation dates (either over Slack, email, or in person). Although the calendar is for keeping track of who is in/out of the office, it is not intended for “requesting” time off.
• Graduate students can expect 3 weeks of vacation. More time off is possible, but will be discussed on a case-by-case basis with Julián (and depends on student progress and personal considerations). Please note that spring break and fall break are undergraduate holidays, and in the case you TA it may be a requirement for you to stay on campus during this time.

• Fish Care: this calendar is used primarily for keeping track of daily/weekly fish husbandry responsibilities.

Google Drive

• The shared Google Drive is where we store and share lab resources and files.
• Full-time lab members will be added to the Google Drive upon joining the lab. Part-time lab members will have any relevant files/folders shared with them, and may be added to the shared Google Drive on a case-by-case basis.

General policies:

Lab Safety and Training

• All lab staff must undergo formal safety training that is provided by the University.
• Mandatory courses are:

• Accident/Injury Reporting & Access to Medical Records
• Fire Extinguisher

• Other courses to remain complaint are:

• Biosafety Training
• Laboratory Safety Initial Training
• AUTOCLAVE SAFETY TRAINING

• For those working in the fish room, you should also do

• Ladder Safety Training

• Everyone should also perform the Emergency Action Plan. This is associated with the department's emergency action plan (not in eNDeavor)
• In addition to safety training, individuals working with live specimens must undergo formal training through the IACUC/AALAS. In order to receive this training, individuals must email complian@nd.edu and request they are assigned the following trainings:

• Working with the IACUC
• Introduction to Wildlife
• Introduction to Fish
• AVMA Guidelines for the Euthanasia of Animals

• Informal training for lab protocols will be given on a case-by-case basis. As our lab is collaborative, it is expected that senior graduate students assist with the training of incoming graduate students. However, the training responsibility is not to fall on one individual. As such, discussions with Julián regarding training responsibilities are to be expected upon recruitment of new students.
• The use of proper PPE in the lab is to be expected. Individuals in the lab must sign and date the PPE verification form that is posted on the lab door.

• PPE may include lab coats, goggles, gloves, etc.
• PPE may vary based on the lab task performed.

• Graduate students on RAships, as well as lab managers, must receive training in buyND. To receive training as a graduate student, individuals must email training@nd.edu and request training for buyND. Non-student researchers/staff may sign up for training through Endeavor. See the following link for more information:

• https://buy.nd.edu/how-to-buy/ 

Lab Stock and Ordering

• Whenever we are close to running out of something, or we need to purchase a new item for the lab, please send a message in the #purchases-and-receipts slack channel.
• Lab managers and/or individuals on RAships are responsible for ordering materials for the lab. These individuals should be trained on buyND prior to ordering for the lab. See below for information on buyND training:

• https://buy.nd.edu/how-to-buy/ 
• https://buy.nd.edu/guides-and-videos/buynd-training-guide-and-videos/ 

• For non-routine restock orders or orders over $300 notify Julian for approval before placing the order.

Molecular Lab Cleanliness

• Common use areas should be kept clean and clutter free.
• No food or drink 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.

Fish Room (052) Cleanliness

• No food or drink should be in 052.
• Close-toed shoes should be worn in 052.
• As fish room duties involve water changes, wet floors are to be expected. Please exercise caution when in 052, and use towels/squeegees to remove excess water from the floors when possible.

• If you do use towels, please place them in the hamper by the door. Do not leave them for others to pick up.

• Please use the broom to sweep up any dropped fish food from the floor.

Lab Meetings

• Day of week/time for lab meetings will be determined at the beginning of each semester based on the majority availability of all lab members.
• Please strive to be on time for all scheduled meetings.
• Attendance at lab meetings is mandatory for all full-time lab members and undergraduates earning credit in the lab. For undergraduates not earning credit in the lab, it is mandatory schedule permitting.
• Lab meetings occur weekly and are 1-1.5 hours.
• Graduate students and post-docs are responsible for presentations every 2-3 months and undergraduate students once per semester (again, schedule permitting).
• Everyone is expected to participate in lab meetings: asking questions, providing constructive advice in a positive manner, etc. Students are expected to give and receive scientific criticism. Criticism is not personal, only professional.

Publishing

 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.

• Authorship will be discussed prior to the start, and upon completion, of any collaboration or mentorship. If the lead author of the paper finds that anyone who has collected data, analyzed data, or funded the study should not be given authorship, the lead author must give justification for this.
• 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 Julián. It is possible that independent side-projects or collaborations could produce publications. This should be discussed with Julián prior to submitting for publication.
• It is 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 Julián.

Old Projects

• If a full-time student or postdoc collects a dataset but does not analyze or write it up within 3 years of the data collection, Julián withholds the right to re-assign the project (if appropriate).
• If a student or postdoc voluntarily relinquishes their rights to the project prior to the end of the 3 year window, Julián may also re-assign the dataset to another individual or team.
• The purpose of this is to prevent data from remaining unpublished, while respecting the individual who collected the data initially.

Presentations

• Seek out opportunities to present your research, whether it is at departmental talk series and events, to other labs (within or outside of Notre Dame), at conferences, or to the general public.

• Graduate students are required to present once per calendar year. Although this presentation can be at the weekly seminar (Biofrass), it is encouraged to look for opportunities at conferences/departmental seminars/etc.

• Presentations should be prepared in advance. You are strongly encouraged to give practice presentations to the lab 1-2 weeks ahead of conference presentations, and 4-5 weeks ahead of time for job talks. Practice presentations can provide valuable feedback to help refine your talk, and thus should be strongly considered.

Deadlines

• Our lab values organization. Organization is important for your own productivity, as well as the productivity of the lab. This is essential because disorganization doesn’t just hurt you, it hurts your collaborators and people whose help you need. When it comes to deadlines, tell your collaborators as soon as you know when a deadline is, and make sure they are aware of it as it approaches. This extends to Julián as well.
• Give Julián at least one week's notice to do something with a hard deadline that doesn’t require a lot of time (e.g., reading/commenting on conference abstracts, filling out paperwork, etc).
• Give Julián at least two weeks’ notice (preferably more) to do something with a hard deadline that requires a moderate amount of time (e.g., a letter of recommendation).
• If you want feedback on research and teaching statements, or other work that requires multiple back-and-forth interactions between you and Julián before a hard deadline, give him as much time as you can; at the very least three weeks.
• For manuscript submissions and revisions (i.e., which either have no deadline at all or only a weak deadline), send drafts to Julián as soon as you have them. Be aware that it could take up to 3 weeks to get comments back.

• If Julián does not provide feedback within these 3 weeks, feel free to send reminder messages.
• In your one-on-one meetings with Julián, please let him know if you have any high-priority revisions needed, and he will attempt to send feedback in a timely fashion.

Recommendation Letters

• If you need a letter, notify Julián of the deadline as soon as possible.
• Send Julián any relevant information along with your request for a letter

• CV
• Teaching/research statements
• Relevant information for the content of the letter
• How to submit/send the letter

Sick Days

• If you are not feeling well, please stay home.

• Our lab looks out for one another. If you need someone to assist with an experiment/task in your absence, please notify someone in the Slack workspace.
• If you cannot find someone to assist you, and it is absolutely 100% necessary to come into work (and you are well enough to physically come to campus) please take proper precautions (hand-washing, mask-wearing, distancing, etc.).
• Otherwise, take the time to rest (or, if you are feeling well enough to work, find something you can do at home. Writing, reading, updating your CV, the list is endless…)

• This policy pertains to mental health as well. As a lab, we value both physical and mental well-being, and recognize the importance of occasional “mental health days.” You should not feel guilty for prioritizing your well-being.

• If you are struggling with mental health, please do not hesitate to speak with Julián. Although taking mental health days (when needed) is encouraged, if you find your work life is impacted regularly, this may be a sign of a more serious issue.
• There are several on-campus resources available for you if you are struggling with mental health:

• https://ucc.nd.edu/ 
• https://ucc.nd.edu/counseling-services/
• https://studentaffairs.nd.edu/be-well/ 
• https://preventsuicide.nd.edu/resources/