Welcome

Welcome to the lab handbook for the Smith-Vidaurre Lab, or the Behavior IntegRated with Data Science (BIRDS) Lab. Dr. Grace Smith-Vidaurre is the head of the lab. At any point in time, other members of the Smith-Vidaurre (BIRDS) Lab may include postdoctoral researchers, graduate students, rotation students, research assistants or technicians, undergraduate students, and visiting scientists. This handbook is intended to be a resource for all current members of the lab, as well as prospective researchers and students who are interested in joining the lab. As you read this handbook, you’ll find information about general expectations for lab members, as well as information about how the lab operates. Everyone who joins the lab is expected to commit to the lab expectations and policies outlined here, which serve as a contract for how the research team will work together.

Our Primary Research

We commit to a shared goal of conducting creative, rigorous, and accessible science. In order to meet this goal, we are dedicated to building and maintaining an inclusive lab culture that supports and respects scientists from diverse backgrounds with varied interests and career goals. As a lab, we commit to sustaining an anti-racist working culture and a safe space for members of the queer community, as well as for scientists whose identities and experiences reflect many other axes of diversity, such as disability, citizenship status, and socioeconomic status. We also commit to maintaining a lab environment that is positive, engaging, rewarding, and constructive. We value high-quality, careful science over rushed and careless work.

Our lab is focused on three primary research areas:

  • How do animals use socially learned vocalizations? This research is currently focused on information encoding and recognition of individual identity and social affiliations. Our work relies on empirical research with parrots and songbirds, and also leverages simulation and modeling approaches.

  • How may animals’ early-life environments shape the learned vocalizations that they produce as adults, as well as the brain regions necessary for learned vocal production? This work relies on empirical research with songbirds and may also use modeling approaches.

  • The lab integrates data science approaches across projects that fall under the two lines of research above. We develop and test computational pipelines for collecting and analyzing empirical or simulated datasets. We engage in open-access methods development and are committed to data science training for lab members, as well as disseminating data science skills to students in the local and broader STEM community.

These three areas of research will form the lab’s primary focus areas until at least 2027. Dr. Smith-Vidaurre is open to discussing other research areas of interest with current and prospective lab members, especially if new research directions or study systems will benefit the local community at MSU or in Michigan, underrepresented groups in STEM, groups of people who have been historically discriminated against in the U.S.A., or scientific communities in the Global South. Lab members interested in other research questions and study systems will need to commit to pursuing independent funding and research permits after careful discussion with Dr. Smith-Vidaurre.

Why is Our Basic Science Important?

The lab works on basic science that is primarily focused on animal communication and behavior. Our primary research is not applied science, which means that we do not study direct applications of animal communication and behavior for the conservation or management of animal populations in captivity or the wild. However, this does not mean that our science has less impact or is less important than biomedical or more applied research. Our research on animal communication and behavior has direct connections to human language, and is a compelling way for the broader public to learn more about animals, in the spirit of fostering more curiosity and respect for the natural world around us. Contributing to the public’s perception of animals is an important way to contribute to how individuals and institutions change their behavior to prioritize resources for conservation purposes and community engagement with the natural world. The lab is committed to disseminating our research to the public in order to broaden the impact of our research.

Our research also creates opportunities for training and teaching the next generation of biologists and data scientists at different career stages. Scientists and students who work on research in our lab will leave with a deeper understanding of the scientific process, the exciting questions that drive the lab’s research, and how applying data science approaches to address these biological questions facilitates creative and rigorous research. Students in the local community who take classes taught by lab members, including Dr. Smith-Vidaurre, postdoctoral researchers, and graduate students, will also receive scientific and quantitative training that is important for different careers. This ability to reach many students in the community through research training and teaching is an exciting component of traditional academic careers.

Environment and Expectations

Everyone

In the Smith-Vidaurre (BIRDS) Lab, we are committed to conducting high-quality science as well as helping each other to grow as scientists. In addition to creating an inclusive lab culture, our intent is also to maintain a collaborative and communicative environment for all lab members. Everyone is encouraged to ask questions about the science that we do and read about. In this lab, we expect everyone to make mistakes, and we also expect everyone to own up to and address their mistakes so as to learn from them. Another important aspect of growing as a scientist is learning how to respond when someone disagrees with you, so we also encourage lab members to challenge someone’s ideas in constructive ways when you do not agree. For instance, focus on having constructive conversations that are centered on curiosity and questioning. Treating disagreement as a way to learn from someone else can help you adapt the way in which you explain your ideas.

Maintaining a collaborative interdisciplinary space is another important part of our lab’s environment. The lab is part of the Department of Integrative Biology, the Department of Computational Mathematics, Science, and Engineering, and the Ecology, Evolution, and Behavior program, and will regularly include lab members who are primarily working in biology, data science, or both areas. All lab members commit to maintaining a space that can foster interdisciplinary research and learning opportunities. This includes making space for anyone to ask basic questions, challenge ideas (not people), and discuss basic assumptions and terminology, as well as conceptual frameworks, as clearly as possible.

Big Picture

We aim to have fun as a lab while we work on creative and rigorous science. To be able to have fun while maintaining our professional focus, we all need to adhere to these general guidelines:

  • Work on questions that are exciting to you and that push the boundaries of your knowledge and the field
  • Be open to constantly learning new concepts and skills from every experience during your time in the lab
  • Be careful and do not rush your work. Double and triplecheck everything that you do, especially when preparing work for publication
  • If you make a mistake, own up to it and do what you need to address it, even if you found the mistake after a paper was submitted
  • Make time to critique your experimental design and analysis pipelines from many angles. Discuss and update your plans often with members of the lab and Dr. Smith-Vidaurre prior to investing time and resources in empirical data collection or computational research
  • Keep up to date on the latest research in our field, through literature databases, listservs, social media, and attending conferences
  • Be honest and do not engage in research misconduct
  • Support and respect your lab mates. This is a collaborative lab, not a competitive lab. When you help others, you can expect help in return
  • If you are struggling with anxiety, stress, and/or your mental and physical health in ways that affect your work, tell Dr. Smith-Vidaurre so that I can connect you to resources to help you through rough times
  • Hostility and tension will not be tolerated in this lab. When you encounter a situation like this, you should confront the person in question and tell Dr. Smith-Vidaurre. If you do not feel comfortable confronting someone else in the lab, you should still let Dr. Smith-Vidaurre know about the situation immediately
  • Please tell Dr. Smith-Vidaurre when you have a problem with her. If you are not comfortable telling her and the issue is serious, then you should reach out to the chair of the Department of Integrative Biology or the Office of the University Ombudsperson at Michigan State University (email: ombud@msu.edu, phone: (517) 353-8830)
  • Invest in your personal life, priorities, and hobbies outside of the lab. We can only do good science when we take good care of ourselves outside of work
  • In the spirit of prioritizing self-care in order to conduct good science, I strongly recommend that all lab members seek out mental health support prior to or immediately after starting to work in the lab. Therapy or other forms of mental health support are important to set up even when you are feeling stable/supported, so that you have resources immediately available whenever a crisis arises

Smaller Picture

On a day-to-day basis, the lab will run most smoothly when we keep the following in mind:

  • Participate in all lab and community events regularly. Undergraduate students will not be expected to attend lab meetings regularly unless their class schedule permits attendance
  • Adhere to the lab’s general working hours (see below) to help maintain a collaborative work culture. This is especially important for lab members who are working remotely
  • Discuss plans to work from home, or to take vacations early and often with me. Vacation policies will vary depending on your role in the lab, but I need to know when you plan to take vacation well beforehand. If your plans for vacation overlap with a critical deadline, or a push towards a critical deadline, for a task or goal to which you have previously committed, then I reserve the right to ask you to change your vacation plans
  • Be on time for our weekly individual and group meetings. A regular habit of tardiness is a form of disrespect because everyone’s time in the lab is valuable. When you are running a group meeting, you should arrive 15 - 20 minutes beforehand to set up
  • Respect lab members’ quiet working time. The lab will have workspaces that are desks in a shared office and well as desks in a fully open space. Generally, all of these spaces are considered primarily quiet working spaces, so you should not talk loudly or play music in any of these spaces (unless we are all in a group meeting together). Do not interrupt people when they are working unless it’s a real emergency
  • If you want to talk with someone in the lab during working hours, then invite them to go on a walk, or to get a tea, coffee, or lunch near campus. These breaks are fun ways to brainstorm with lab members and to get to know each other better, without interrupting others who want to work in a quiet space
  • Take care of yourself when you are sick, and talk to Dr. Smith-Vidaurre about plans to work from home. A mild cold can become worse and take up much more of your time if you don’t take care of yourself immediately. It’s also not good practice to expose your lab members to illness
  • Talk to Dr. Smith-Vidaurre immediately if you are feeling burnt out
  • If you are the last person in any of the lab spaces, make sure the door is locked and no one else is inside when you leave. If you are leaving a space without animals, then also make sure that the lights and A/C units are turned off
  • The lab needs to be kept clean and tidy, so clean up spills, crumbs, and other messes in all shared and individual spaces. Common areas should not be cluttered, so put equipment back where it belongs when you’re done for the day
  • Take care of the lab’s shared equipment, including kitchen and research equipment, and the lab bike
  • The lab bike should always be kept inside of the lab’s space in Giltner Hall, unless you’re using it to work elsewhere on campus. When you take the lab bike elsewhere, make sure to lock it securely. Do not leave the lab bike outside overnight. If the lab bike needs to be serviced, talk to Dr. Smith-Vidaure and take the bike to the MSU bike store (which also has air pumps outside)

Code of Conduct

In order to build and maintain our intended lab environment, all Smith-Vidaurre Lab members, including visitors and remote researchers, are expected to act in accordance with the following code of conduct. We will enforce this code as needed. We expect cooperation from all lab members to help ensure a safe environment for everyone in the lab. We expect lab members to follow these guidelines at any lab-related event.

The lab is dedicated to providing a harassment-free experience for everyone, regardless of gender, gender identity and expression, age, sexual orientation, disability, physical appearance and hair/skin texture, body size or weight, race, accents, or religion (or lack thereof). We do not tolerate harassment of lab members in any form. Sexual language and imagery is generally not appropriate for any lab venue, including lab meetings, presentations, or discussions. However, as we work on biological questions, work-related discussions of topics that include animal reproduction are appropriate.

Harassment includes offensive verbal comments related to gender, gender identity and expression, age, sexual orientation, disability, physical appearance, body size, race, religion, sexual images in public spaces, deliberate intimidation, stalking, following, harassing photography or recording, sustained disruption of talks or other events, inappropriate physical contact, and unwelcome sexual attention.

Members asked to stop any harassing behavior are expected to comply immediately.

If you are being harassed, notice that someone else is being harassed, or have any other concerns, please contact Dr. Grace Smith-Vidaurre immediately. As a faculty member, Dr. Smith-Vidaurre is a mandatory reporter of prohibited conduct under the MSU Relationship Violence and Sexual Misconduct Title IX Policy. If Dr. Smith-Vidaurre is the cause of your concern and you need to seek official resources, then please contact Dr. Kevin McGraw, the chair of the Department of Integrative Biology (email: mcgrawk5@msu.edu), and Office of the University Ombudsperson at Michigan State University (email: ombud@msu.edu, phone: (517) 353-8830).

General Research Expectations

In the Smith-Vidaurre (BIRDS) Lab, we engage in research that relies on captive animal experiments and animal care, wet lab work, and computational approaches to collect, process, and analyze data. I expect all lab members to fully engage in learning the approaches and methods necessary to conduct research in the lab, ranging from caring for captive songbirds on campus, to assembling and deploying electronics technology for data collection, to learning basic molecular biology protocols as well as basic programming and data analysis skills.

Scientific Integrity

We hold everyone in the lab to the highest degree of scientific integrity. Research misconduct in any form, including data falsification and fabrication, as well as plagiarism, will not be tolerated. Please see MSU’s Research Integrity Office for more resources, including trainings that graduate students and others in the lab will be encouraged and/or required to complete.

Research misconduct often arises from the pressure to be productive and successful in academia. If this pressure is so acute that you feel it is impacting your progress and mental health, then you should reach out to Dr. Smith-Vidaurre to talk about strategies to move forward. Everyone in the lab faces this pressure, as well as our colleagues in the broader academic community. There is absolutely no excuse to engage in research misconduct. Research misconduct puts your career at great risk and is a massive disservice to yourself as well as our entire field.

Computing Skills

As the lab works on computational analyses of different types of behavioral, molecular, or simulated datasets, everyone in the lab will be expected to become competent in computing skills that include R, bash, Python, and GitHub for version control. For instance, common tasks that you should be able to accomplish include installing R and using RStudio to write/save scripts, as well as accessing directories and files from a bash shell. A common pipeline that you should use regularly is to use GitHub (through Git on the command line or RStudio, or through GitHub Desktop) to synchronize local and remote repositories of your different coding and writing projects.

Lab Notebooks and Reproducible Research

Lab notebooks are another requirement for all lab members. Everyone who is working on any research project in the lab is required to maintain an electronic lab notebook that they update in real time. Your electronic lab notebook should be one or several Markdown files that you maintain in a private GitHub repository. Your electronic lab notebook repository must always be shared with Dr. Smith-Vidaurre. Random checks of lab notebooks will occur during the first 2-3 months that someone is new to the lab, and possibly beyond. A PDF or Markdown file of your lab notebook must be emailed to Dr. Smith-Vidaurre immediately prior to biweekly lab meetings.

The standard practice in the lab will be to document your daily activities in your electronic lab notebook, which will serve as a log of what you have worked on over time. This standard practice means that you must allocate time to update your lab notebook during each working session, and to back-up your notebook regularly. For instance, if your day was focused on reading papers, document the titles of the papers that you read (and add the URL of the GitHub repository for your annotated bibliography, see below). If your day was focused on scanning the Internet to troubleshoot code or hardware issues, document the websites that you visited and your troubleshooting steps. On days when you worked on code development or data analysis, you should note what you did and the GitHub repository where you conducted the work. When you spent the day working on animal care or setting up experiments, make note of this, and upload images or scans of your more detailed notes from your physical notebook. Regardless of what you did on any one day, you should document your general steps, all details necessary for someone to reproduce your work > 5 years down the line (links, mistakes or variations on a protocol, etc), and what needs to be done next.

Lab members who are conducting wet lab work or work with animals will be required to keep a physical lab notebook, and to regularly update their electronic lab notebook with photographs of their physical notebook as well.

All lab notebooks need to have an immediate backup, which you can create by updating a text file on your computer that you push to GitHub each day, among other options. Each lab notebook needs to have entries that are organized by date in reverse chronological order. See the lab onboarding checklist below for tutorials on how to use GitHub.

Across lab notebooks, each lab member should document what they have done in a manner such that someone else could replicate the work that you have done. Keeping a detailed lab notebook is critically important for reproducibility in research. In other words, if someone followed all of your steps and analyzed your very same dataset, they should obtain the very same result(s). Reproducibility is also important for replicability, which is in turn a critical part of science in general. Replicability means that if someone addressed the same research question with a similar experimental and analytical design, but with a different dataset, they should be able to obtain generally similar results. Both reproducibility and replicability are important for scientific progress, and we aim to produce research that is reproducible and replicable.

Finally, I expect lab members to take notes in your electronic lab notebook to document our discussions during our weekly individual meetings. You should include notes on research progress updates, our main discussion points, and next steps, as well as any outstanding questions that you have for me or others. These notes will be helpful for me to keep track of your progress and our discussions over time. Undergraduate students should also follow this rule for regular meetings with your direct supervisor.

Standard Operating Protocols

As a lab, we will develop standard operating protocols for animal care, wet lab, data processing, and possibly data analysis that all lab members can access via GitHub. Once you have written a protocol for an experiment or procedure, you can link to this protocol in all subsequent electronic lab notebook entries and note whether/which modifications you have made while running the protocol. Animal care protocols will require additional documentation and logging that lab members must keep up with.

Writing

Postdoctoral researchers, graduate students, and research assistants must build and maintain a regular writing habit. Writing is critical for doing science, from communicating our ideas and results to our colleagues and the broader public, to obtaining the funding necessary to do the science itself. As scientists, we need to be writing every single day. Writing can take many different forms, and we will discuss writing productivity regularly as a lab. Each lab member will also be expected to seek peer feedback on writing products from at least 1 other lab member prior to requesting constructive feedback from Dr. Smith-Vidaurre.

Lab members should use GitHub to organize and back-up their writing projects. You can create private GitHub repositories to hold Word, .txt, LateX or other files for a given writing project. To receive feedback from lab members and Dr. Smith-Vidaurre, you can add them as collaborators to the repository, and add and push any comments that they send (in a document itself with track changes and comments, via email, or other options). You can organize documents with feedback in a separate “Feedback” folder. By regularly committing and pushing your own changes to GitHub, you will create a record of the changes you have made to a single document, which will help you avoid creating many different files to document different drafts or versions of your project.

Organizing a writing project in this way is also important for backing up your work. You can also use the same GitHub repository for your writing project to hold code for data processing and analysis, making figures, and other documents for tasks relevant to a writing project (e.g. manuscript submission).

Undergraduate students are not expected to build a daily writing habit, but they will be expected to maintain an annotated bibliography on GitHub (see below).

Reading and Annotated Bibliographies

Maintaining and regularly updating an annotated bibliography is another research expectation for graduate students, research assistants, and undergraduate students. Reading papers from the literature and taking notes in an annotated bibliography is an important part of the writing process. Lab members should create a private repository on GitHub shared with Dr. Smith-Vidaurre that holds their annotated bibliography in a single file or across files. Annotated bibliographies should be kept in the form of an RMarkdown document(s) with headers to organize papers by general topic, and you should add the URL for your annotated bibliography repository in your electronic lab notebook whenever you read for a given project. Similar to electronic lab notebooks, annotated bibliographies will also be checked randomly during the first 2-3 months that someone is new to the lab, and possibly beyond.

Incorporating Writing Feedback

When incorporating feedback on your writing from peers or Dr. Smith-Vidaurre, you will be expected to reflect on the feedback prior to making changes to the structure, content, and writing style. This is easiest when you open a document with feedback alongside your own working version of the writing project. For those using Word or similar software, passively accepting changes (such as selecting “Accept Changes”) in a draft in which someone gave you feedback is unacceptable. Incorporating feedback yourself, and allowing yourself to reflect on feedback, is an important part of growing as a writer over time.

Artificial Intelligence

As a member of the lab, you need to learn how use generative artificial intelligence (AI) or other AI tools with a lot of careful thought and consideration. Lab members who want to use AI tools to scaffold their learning process for writing, coding, or other purposes must check in with Dr. Smith-Vidaurre before beginning to use these tools.

Using AI tools to replace any step of your work in the scientific process is not acceptable. However, it will be acceptable to use AI tools to support your learning process, as long as you communicate your use of these tools with Dr. Smith-Vidaurre. You must also demonstrate that you are using AI generated materials as a rough starting point, and that you are modifying the generated materials using your own creative and critical thinking. Given privacy concerns, it is also not acceptable to upload any sensitive material from the lab, including data, code for new software, or drafts of manuscripts or grant proposals, to any AI interfaces.

Deadlines

Deadlines are important for getting things done in an organized way in academia. All lab members should tell Dr. Smith-Vidaurre immediately about a deadline related to their research, and should check in with me periodically as the deadline draws nearer. You are not bugging me when you email me reminders. In fact, I prefer receiving frequent reminders about upcoming deadlines. Ideally, you will email me 1 month, 2 weeks, 1 week, 2 days, and 1 day before a deadline, unless I have already sent my feedback (or letter of recommendation).

For all research products with a hard deadline, you should plan to submit all documents at least 24 hours before the official deadline. When you are working towards a hard deadline that requires feedback on my end, like helping you polish a (short) writing product or job application materials, you should let me know at least 1 month beforehand so that I can give you multiple rounds of feedback. Longer writing products, such as independent fellowship applications, will need many more revisions over a longer period of time (at least 3 months before the deadline). When you are working towards a deadline that doesn’t require a lot of work (reading a polished abstract draft, signing paperwork), let me know at least 1 week ahead of time.

For research products with deadlines that will generally be internal, such as manuscript submissions, you should send outlines and drafts to Dr. Smith-Vidaurre as soon as you finish them. You should also follow up if I haven’t responded within in 1 week. Generally, given everything on my plate as a faculty member, my first response will be to outline when you can expect to receive my feedback.

All lab members, but especially graduate and undergraduate students early in their careers, should expect to undergo multiple rounds of revision of research products with Dr. Smith-Vidaurre. This rule of thumb applies to all research products that involve writing, including very short products like abstracts for conference presentations. Performing and communicating rigorous science requires many rounds of writing and revision. Writing is a critical skill that takes practice, and receiving and incorporating feedback through multiple revisions is a fundamental part of this learning process. I expect each lab member to take the initiative to map out writing timelines that include sufficient time to incorporate several rounds of feedback before a hard deadline.

I reserve the right to pull a research product from a targeted submission deadline if I feel that you have not made sufficient time for or progress with revisions. All research products from the lab that require submission for publication or review by an external organization, such as manuscripts, conference abstracts, and grant proposals, must receive my final approval for submission beforehand. Lab members must also send me the final submitted version for my own records.

Authorship

We follow the MSU Guidelines on Authorship for scientific publications in peer-reviewed journals. In our field, the first and last authors on papers are the authors who led the research and the preparation of the associated paper. The last author is a senior member of the authorship team who provided the bulk of the resources and/or guidance to perform and publish the research. Generally, the postdoc or student who is leading the research can expect to be the first author on manuscripts prepared for submission, and Dr. Smith-Vidaurre will be the last author. There will be times when Dr. Smith-Vidaurre is the first author, however, and sometimes close collaborators will be senior authors. When starting a new project, we need to talk about authorship expectations, contributions, and order as early and as often as possible. This rule also applies when we are working on manuscripts in collaboration with other labs.

Lab members who have helped with research that is being prepared for publication may be added to the author list after discussion with all parties involved in the preparation of the manuscript. If a postdoc or student starts a project but then voluntarily hands it off to another lab member, they will likely be a second or middle-author on the resulting work, or possibly a co-first author. When a student or postdoc works on a core project in the lab but does not complete analysis or manuscript writing within 3 years following data collection, Dr. Smith-Vidaurre may reassign the project to another lab member to facilitate publishing in a timely manner. The student or postdoc who originally lead the project will still be a co-author, and their authorship position will need to be discussed carefully and respectfully.

Lab members who have contributed to research and are a co-author on a manuscript must remain responsive to email and complete their remaining authorship responsibilities in a timely manner throughout the process of manuscript preparation, submission, revision, and acceptance in order to retain their authorship status. Generally, co-authors must respond within 2 weeks to emails from the lead author or others in the group. The lead author will be responsible for setting deadlines for responses and task completion, as well as following up with co-authors for accountability, with support from Dr. Smith-Vidaurre.

You are always welcome to discuss authorship expectations with Dr. Smith-Vidaurre, especially if you are unsure of your authorship status or position, or if you would like to discuss changes. Authorship is a gray area that requires a lot of communication in order to be as ethical as possible. We strive to be inclusive with authorship so that we avoid “ghost” authorship. We aim to include researchers who contributed substantially to our work in the authorship group, and researchers who supported our efforts in our acknowledgments. In order to respect those did who make substantial contributions, we also strive to avoid “guest” authorship, or being overly inclusive in our authorship decisions.

Close Collaborators

The Smith-Vidaurre or BIRDS lab collaborates closely with the Hobson Lab at the University of Cincinnati, led by Dr. Elizabeth Hobson. Dr. Hobson and her lab members are our long-term collaborators on monk parakeet research at an external research site. Dr. Hobson’s lab focuses on animal sociality, including how animals use social information during naturalistic social interactions to make decisions, and how group social structures can emerge from individuals’ decisions. Our collaboration with the Hobson Lab makes it possible for us to integrate acoustic and social data collected from the very same individuals, which in turn makes it possible for us to address our lab’s primary research questions with the monk parakeet study system. Our lab is focused on the vocal communication and bioacoustics side of this long-term collaboration with the Hobson Lab. Graduate students and postdocs can have access to social data collected by the Hobson Lab for projects that our lab leads, but only in service of our lab’s questions related to vocal communication, and only after researchers in the Hobson Lab have had the chance to use their data for projects that they are leading. These guidelines also apply for Hobson Lab members who are interested in using acoustic data collected using our lab’s resources. There will be opportunities for lab members to receive training in data collection and analysis between the Smith-Vidaurre and Hobson labs, but participating in data collection alone will not automatically grant someone authorship on publications. How data is collected and used across our labs, as well as how authorship is granted, will be determined through frequent discussions with both Dr. Smith-Vidaurre and Dr. Hobson.

We also collaborate closely on modeling and acoustic communication projects with Dr. Vanessa Ferdinand at the University of Melbourne. Dr. Ferdinand’s lab works on complex cognition and communication, with a particular focus on cultural evolution, information theory, and lyrebird acoustic communication. Our collaborative research with Dr. Ferdinand is focused on leveraging computational approaches to study the evolution and maintenance of vocal learning, as well as other research directions. Smith-Vidaurre lab members can expect to be first authors on collaborative papers with Dr. Ferdinand when a lab member leads the data collection, analysis, and writing for a given project. When Dr. Ferdinand’s lab members lead these activities, then we will participate as supporting authors. Authorship roles and positions will be discussed early and often with Dr. Smith-Vidaurre and Dr. Ferdinand. Lab members should keep in mind that authorship roles and positions can change over time, and will ultimately be determined by Dr. Smith-Vidaurre and Dr. Ferdinand.

The lab’s collaborations are not limited to the collaborative research above, although we will publish more frequently with our close collaborators. All of our close collaborations are built on open communication as well as mutual trust and respect. I expect all members of the lab to continue maintaining this communication, trust, and respect in the long-term.

Working Hours

I expect lab members to generally work from 9am - 5pm US Eastern time on business days, unless discussed otherwise. We are working on research together as a team, and it is much easier to build and maintain a collaborative working environment, and to disseminate knowledge, when lab members engage in research at similar times of day. For remote researchers, this means that you will need to be available and respond in a timely manner over the different platforms that we use for lab communication (email, GitHub, Zoom, possibly others) during these working hours. For researchers working in person, you will have the flexibility to work from home 1 day each week, depending on whether your current project allows for remote work, as well as your general productivity in the lab. This general rule can be revisited with Dr. Smith-Vidaurre as lab members progress.

Reviews of Electronic Notebook: All researchers, regardless of whether you are working in person or remotely, should expect me to regularly check your electronic lab notebook, and should expect an email or in-person check-in from me if you are not keeping up with your daily lab notebook entries. I expect lab members to document our discussions during weekly individual meetings as well (see the electronic lab notebook section above). I will regularly review electronic lab notebooks during the first 2-3 months that someone works in the lab (and possibly beyond) to provide accountability as you establish this daily habit.

Weekend Work Expectations: Generally, I expect lab members to take weekends to recharge and rest, and I do not expect everyone to regularly work through the weekend. The exception will be rotating animal care duties for researchers working with songbirds on campus, or working with monk parakeets off-campus, since animal care cannot pause over the weekend. Songbird animal care duties will be spread across lab members working in person. Lab members who are helping with weekend animal care should discuss their weekly work schedule with Dr. Smith-Vidaurre to ensure that you are not getting burnt out. Another exception to working on weekends are times when we need to push to finish data analysis, writing, or other tasks in order to meet important and/or urgent deadlines for any one project. If you feel that you are pushing to complete tasks for a project over the weekend too often, please discuss this with Dr. Smith-Vidaurre immediately.

Flexibility and Trust: I need to be able to trust researchers in my lab in order to be flexible with my expectations around working hours, productivity, and time management. This trust is something that must be earned as we work together, and requires a dedication to mutual respect and effective communication.

Lab Meetings

Postdoctoral researchers, graduate students, and research assistants will generally be expected to participate in all lab meetings, unless discussed otherwise with Dr. Smith-Vidaurre. Lab members working remotely are expected to join these meetings via Zoom. Undergraduate students will be encouraged to attend lab meetings as their class schedule permits, and to join other meetings as they are able.

The lab’s group meetings will occur with different frequencies, with the purpose of providing regular feedback necessary for research activities, as well as professional development, and building an inclusive and equitable lab culture:

  • Weekly Individual Meetings (30 minutes): I aim to meet with postdoctoral researchers, graduate students, and research assistants once a week for individual meetings. These meetings will be 30 minutes long to facilitate a quick discussion of research progress and obstacles as well as short and long-term goals. See the section Specific Expectations for Different Team Members > Principal Investigator > Mentorship Approach for more details.

  • Weekly Lab Meetings (1 hour): These meetings will typically be focused around discussing research updates from each lab member and their planned activities for the next two weeks. We will also periodically use these lab meetings to discuss research papers published by other groups, or for professional development activities for the lab.

  • Bimonthly Diversity, Equity, and Inclusion Meetings (1 hour): This meeting will take the place of our regular lab meetings every other month. Our DEI meetings will be dedicated to discussing how we can continue to build and sustain an anti-racist lab and a safe space for queer scientists, as well as scientists whose identities and experiences reflect other axes of human diversity, such as disability, citizenship status, and socioeconomic status. We will also discuss how we can contribute to making the lab, our departmental community, and the broader scientific community more diverse, equitable, inclusive, and just spaces. These meetings will be particularly focused on broadening lab members’ understanding of how we can take action against systemic oppression in academia, and encouraging lab members to engage in their own process of self-education about the many barriers associated with different forms of oppression.

  • Weekly Writing Group (1.5 hours): We will meet each week for focused writing time as a team. Each lab member will bring one or multiple writing projects* that require steady progress. At the beginning of each meeting, we will each state the project that we are working on and our goal for the current writing session (up to 15 minutes). Everyone will work on their writing project(s) without interrupting others for ~1 hour, and then we will catch up about writing progress and obstacles in the last 15 minutes. Breaks will be encouraged for those who prefer to focus for short spurts rather than the full hour. Depending on the lab’s preferences, visitors from other labs at MSU may be invited to join us for this writing group.

  • Weekly Science Afternoon (1 hour, Fridays): Each week we will dedicate time to a casual meeting to work on projects or activities as a team. These meetings can include brainstorming new collaborative projects, debugging code, discussing a statistical analysis that someone wants to learn, or providing feedback on lab members’ figures in preparation for publication, among other topics. Visitors from other labs at MSU or other institutions can be invited to join us.

  • Practice Presentations (scheduled as needed): Practicing presentations for conferences, invited seminars, or academic job interviews is critically important for growing as a scientist. Practicing your presentation in front of your lab members is an excellent way to receive invaluable constructive feedback that can help improve the content and delivery of your presentation. All lab members who present at conferences are expected to schedule practice presentations with the lab at least 1 week prior to the conference itself, and to incorporate the lab’s feedback into the final version of their presentation. Postdoctoral researchers who want constructive feedback on their job talk(s) are encouraged to practice their talk with the lab as well. As a general rule of thumb, we will allocate 45 minutes of feedback for presentations that are 15 - 50 minutes, and 30 minutes of feedback for presentations under 15 minutes (posters and lightning talks).

* Writing projects will vary across members of the lab. Depending on your career stage, a writing project could consist of a manuscript, a grant proposal, a thesis proposal, standard operating protocols for the lab, or documentation of open-access software. For all lab members, writing tasks for these weekly writing groups will vary depending on the type and stage of your project. For instance, if you are contributing to a collaborative manuscript in the lab, a good writing task could be to write up the methods that you used to collect or analyze data, or to write a first draft of the introduction. If you are not contributing to a manuscript yet, you can instead work on writing up a standardized operating protocol for the experiments or tasks you are working on in the lab, or reading a paper and writing a short summary of the paper in an annotated bibliography.

Project Management

Everyone in the lab will be expected to learn how to use GitHub for version control and project management, and to regularly use GitHub across their different projects. Each lab member leading a project in the lab will be responsible for setting up and maintaining a GitHub repository(ies) and project management structure for their research team. GitHub is a valuable tool for coordinating collaborative research, tracking changes to files over time by different team members, and providing cloud backups of files. The skills that you learn from using GitHub are also highly transferrable to other careers, particularly in data science and any form of team science. Lab members will be expected to set up and maintain GitHub repositories for projects that include different amounts of writing and coding, spanning from grant proposals (mostly writing with some code for figures) to manuscripts (writing and code for data analysis and figures) to software development (primarily source code but also tutorials and documentation). See the sections above for electronic lab notebooks, writing projects, and annotated bibliographies for more information.

GitHub repositories can also be used with GitHub’s project and activity tracking tools to facilitate project management (such as creating Issues, assigning them to team members, and arranging them in Kanban-board style project by different project milestones). Lab members can use either GitHub’s project management tools online or they can use other project management tools, such as Click-Up. Regardless of the tools used for project management, once the lab member leading a project has decided on the platform that they will use, everyone contributing to the project must commit to regularly engaging with the project management interface.

Code and Data Storage and Management

Lab members are expected to help maintain code and data storage and access pipelines for all projects in the lab. All raw data will be privately stored for both the long-term and immediate short-term access, and will be made open-access to the broader public after the completion of a project or grant. Processed data may also be stored for private short-term access, and upon the completion of a project, for public long-term access. Code used for our research, including but not limited to data processing, data analysis, making figures, and methods development, will be made open-access upon the completion of a project, or at earlier stages, depending on the project. Lab members leading a project must regularly discuss their plans for short and long-term code and data storage and availability with Dr. Smith-Vidaurre. All lab members will be expected to read and abide by standard operating protocols for code and data storage and access in the lab, and to attend data ethics and management training as needed.

The lab’s code and data storage and access guidelines are determined by Dr. Smith-Vidaurre, as well as other Principal Investigators involved in our collaborative research (see above). The lab’s protocols and expectations for how lab members store, share, and document code and data are also shaped by the agencies that fund our research.

Conferences

All lab members are encouraged to regularly present their research at local, regional, national, and/or international conferences. Lab members who are not comfortable traveling should discuss alternatives with Dr. Smith-Vidaurre, including how to participate in virtual conferences. Undergraduate students, newer members of the lab, and lab members with preliminary results will be encouraged to attend local and regional conferences, while more senior lab members will be expected to present at national and international conferences.

Lab members who are interested in attending a conference must discuss their plans with Dr. Smith-Vidaurre at least 2 months prior to the abstract submission date for the given conference. My ability to support your registration, travel, and lodging for conferences will depend on whether or not you are presenting research, as well as the funding that I have available. I expect all lab members who are interested in attending a conference to apply for travel awards or other funding (either internal or external opportunities) to at least partially support the costs of conference attendance. When attending a conference, I also expect you to cover the costs of your own meals throughout the conference.

Graduate students, research assistants, and undergraduate students who plan to present research while they are in the lab must share their conference plans and abstracts with me prior to submission. As trainees in the lab, your presentations and conduct at conferences still fall under my responsibility as a supervisor, even if you are presenting collaborative research that does not include me as an author. An exception to this rule is if you submitted work to present at a conference under the supervision of another PI prior to joining this lab.

Postdoctoral researchers who plan to attend conferences during your time in the lab should tell me beforehand, even if you plan to present independent research or previous work. I do not need to see the materials you submit beforehand, unless they are directly tied to your research in this lab.

Community Engagement

In addition to regularly attending lab meetings and other lab events, I expect lab members to regularly engage in community events and activities in the Department of Integrative Biology (IBIO), the Department of Computational Mathematics, Science, and Engineering (CMSE), and the Ecology, Evolution, and Behavior (EEB) program.

Seminars: All members of the lab, aside from undergraduate students, are expected to attend the biweekly IBIO seminar during the academic year, and to attend at least 2 seminars in the CMSE department each semester as well (the CMSE Colloquium, CMSE Seminar, or Topological Data Analysis Seminar). Lab members who are primarily employed through the CMSE department will be expected to attend CMSE seminars regularly, and to attend at least 2 seminars in IBIO each semester. Lab members are also expected to attend all of the EEB program seminars that are relevant to their research and/or interests. Undergraduate students are encouraged to attend seminars relevant to their interests and career goals as their schedules permit.

PhD and MS Defenses: I expect all graduate students in the lab to attend PhD and Master’s defenses of other students in their primary graduate program (IBIO/EEB or CMSE). Attending defenses is an important form of training for preparing for your own defense, and is also a very important source of support for other students in your graduate program.

Department Social Events: All lab members working in person should regularly attend social events hosted by the IBIO and CMSE departments, or the EEB program, regardless of the primary focus of your research.

All lab members are encouraged to engage with the local and broader STEM community and the public, especially to communicate your research. Lab members with independent fellowships will be expected to carry out their proposed activities for community engagement and broadening the impact of their research.

Safety and Wellbeing

Both safety and wellbeing are fundamental for doing good science. All lab members must complete required safety training through MSU in a timely manner. I expect that lab members will avoid working alone as much as possible, particularly outside of typical working hours (9am - 5pm US Eastern time during business days or weekend animal care on or off campus). In the spirit of growing as scientists and conducting creative and rigorous science, I encourage all lab members to regularly maintain their wellbeing and self-care routines in their lives outside of work. Lab members must take time to recharge and invest in their personal hobbies and priorities in order to work efficiently and maintain steady productivity in the lab.

Pushing yourself so hard that you regularly burn out, fail to make steady progress towards your goals, and/or begin to disappear from regular lab activities, is not considered good practice in the lab. This behavior will not be tolerated.

If you are in need of additional resources to manage stress, anxiety, or your general mental health, please reach out to the confidential counseling services offered by MSU or the Employee Assistance Program.

Please review the MSU Safety Tips for general safety guidelines and resources on campus, including guidelines for emergencies related to weather, hazardous materials, or an active shooter.

Lab Communication

The lab will primarily communicate during in person lab meetings or individual meetings (remote members will attend via Zoom), as well as over email, and through creating or responding to issue postings on GitHub. In the future, the lab may begin to use other platforms for regular lab communication.

Lab Duties

Each lab member will have a rotating set of lab duties that they must complete in a timely manner. These lab duties are critically important for ensuring that the lab’s work runs smoothly on a day to day basis, and each of us needs to contribute to these regular duties. Lab duties will typically be assigned at the start of the semester, and can include duties that range from maintaining the lab printer, cleaning the kitchen appliances or wet lab benches, tracking hazardous waste, chemicals, and safety training for lab members, reviewing lab members’ code, among other duties.

Animal Research Expectations

In the BIRDS lab, we will often rely on observational or experimental research with live animals, primarily parrots and songbirds. All of the lab’s animal research will be approved by an Institutional Animal Care and Use (IACUC) committee at MSU, and our animal research activities must be conducted with an approved and active IACUC protocol. All researchers working directly with animals must complete the mandatory animal research trainings in a timely manner, and must be added to an IACUC protocol before beginning work with animals. The misuse or mistreatment of animals will not be tolerated. You can read more about MSU’s general guidelines for animal research here.

Photos and Videos

Taking photos or video recordings of lab members can only be done with someone’s knowledge and consent. Everyone taking photos or videos of the lab must obtain consent beforehand, and again prior to sharing photos or videos more widely (such as on social media) in order to respect everyone’s comfort and privacy.

We work with animals in captivity and sometimes in the wild. Photos and videos of the animals that we use for research, or the spaces where this research is conducted, cannot be shared with anyone outside of the lab or posted on social media without checking in with Dr. Smith-Vidaurre beforehand.

Violations of Lab Expectations and Policies

Any lab member who has concerns about these general lab expectations or policies is welcome to discuss them further with Dr. Smith-Vidaurre. Anyone violating the lab’s expectations and/or policies will receive one warning and will then face consequences if they continue to violate these expectations or policies. The consequences faced will be determined by Dr. Smith-Vidaurre, unless the behavior in question or policy violation(s) have direct consequences through a graduate program or undergraduate research program, or legal consequences through MSU, the lab’s funding agencies, or other organizations that fund or oversee the lab’s research.

Specific Expectations for Different Team Members

Principal Investigator

Day-to-day

Research is the primary focus of my work each day, although my role will generally be to guide and fund research as a supervisor. As a Principal Investigator (PI), I supervise multiple projects in parallel, including projects conducted by a single or multiple students in the lab, as well as collaborative projects with other labs. As a faculty member, I also have numerous other responsibilities within and beyond the local community at MSU, including (but not limited to) committee work, teaching, and leadership in external initiatives.

On any given day, I will frequently switch from one task to another while I balance these varied responsibilities. All lab members can help me by ensuring that you reliably complete tasks and goals to which you have committed. I expect that each lab member will take the initiative to learn which decisions need my input and which decisions you can handle independently. Lab members are expected to respect the time that I have allocated for our individual and group meetings by showing up to these meetings on time, and by preparing for individual and group meetings beforehand to use our time effectively. Lab members need to be flexible with scheduling meetings given the many demands on my time. Finally, I expect lab members to commit to being flexible with your communication style in order to foster a good working relationship in the long-term.

Mentorship Approach

My approach to mentorship is to consider each member of the lab a unique individual with their own learning trajectory and career goals. Everyone in the lab will have direct access to mentorship from me in individual or group meetings, but the frequency of these meetings will depend on your career stage. All lab members will also have opportunities to receive mentorship from and provide mentorship to other researchers in the lab.

Generally, I aim to meet with postdoctoral researchers, graduate students, and research assistants once a week for individual meetings. These meetings will be 30 minutes long to facilitate a quick discussion of research progress and obstacles as well as short and long-term goals. Individual meeting times can be shortened or extended depending on a researcher’s needs and my own availability. Undergraduate lab members will meet weekly with their direct supervisor or research team leader, either a postdoctoral, graduate student, research assistant, or possibly a senior undergraduate student. I will meet with team leaders and their undergraduate mentee(s) at least 3 times each semester for additional research supervision.

Expectations of PI

Lab members can expect mentorship from me on their science, ranging from brainstorming of new ideas to preparing and submitting manuscripts for publication in peer-reviewed journals. The mentorship that I provide lab members will also include constructive feedback on grant proposals and presentations, and regular discussion about how I can support you to achieve your career goals. My goal is to support lab members who are interested in diverse careers inside or outside of academia. As I have more experience with academic careers, I can provide direct feedback and tips for lab members interested in traditional and alternative academic careers. However, I aim to also connect lab members to colleagues in my network with non-academic jobs, and can also support lab members pursue internal and external opportunities to learn more about non-academic jobs. I will work with each member of the lab to set up short and long-term research and career development goals at the beginning of each semester.

As the PI, I am responsible for decisions that impact many people in the lab. These decisions may sometimes cause conflict, or may be made in order to mediate or resolve conflict in the lab. Some of my decisions will be communicated in person during individual or group meetings, but often times I will communicate decisions over email. Given the number of emails I receive and respond to on a daily basis, my email communications are likely to be short and concise in order to be efficient. These short emails should not be interpreted as criticism or carelessness, and I welcome constructive feedback about how I can improve my communication with lab members.

Conflict Management and Resolution

You can expect my support as a PI for conflict mediation and resolution in the lab. I do expect lab members to take the initiative to immediately address conflict themselves, and to immediately communicate conflicts and your plan for addressing them directly to me. Interpersonal conflict can happen at any time for many reasons, but failing to step up to address conflict is not considered good practice in this lab. Allowing interpersonal conflict to fester for any reason will not be tolerated in the lab. Consequences for violating these general expectations around conflict are up to my discretion, and may include mandatory conflict management and resolution training for particular lab members or for the whole lab. If the conflict that you encounter is very serious, and you feel that you cannot approach me to discuss the conflict, then I encourage you to reach out to the Office of the University Ombudsperson at Michigan State University (email: ombud@msu.edu, phone: (517) 353-8830).

Letters of Recommendation

All members of the lab who are pursuing the next steps of their career should use this form to request letters of recommendation from me.

Given my limited time as a faculty member, I cannot write recommendation letters less than 2 weeks before a given letter is due. Please ensure that you request letters of recommendation well ahead of this 2 week deadline. The form above is designed to collect the information that I will need to write a strong letter of recommendation. After filling out this form the first time, there are several questions that you do not need to fill out for subsequent requests (for instance, information about when we first met).

My ability to write a strong recommendation letter is contingent on your performance, progress, and behavior in the lab. If I feel that I cannot write you a strong letter, then I reserve the right to decline to write you a letter at all.

Graduate Students

Gradudate school is hard for many different reasons, and it is hard in a different way for each person. Completing a graduate degree can also be very rewarding, but you need to have your own motivations very clear in order to overcome the difficult periods. I expect that graduate students joining the lab have their own clear motivations for wanting to complete a graduate degree, beyond external expectations from your personal and professional connections. Completing a graduate degree is something that you commit to for yourself, and is not something that you undertake in order to satisfy another person (including me).

A PhD or Masters degree is a long-term undertaking in which you invest in your own learning process. In this learning process, you will constantly push the limits of your own knowledge as well as your existing technical skills. I expect graduate students to keep their minds open to constantly learning from every experience, whether it be learning a new statistical analysis in a class, watching a seminar that you find boring, reading papers outside of your field, or receiving constructive criticism from myself or the lab. I expect graduate students to treat this learning process as building the foundation of your independent research program, meaning that you will be expected to design, carry out, and defend your own independent research.

In addition to committing to this intensive learning process, you will also be asked to wear many different hats. This is an important part of academic training, and is also transferrable to other careers. As a graduate student, you will need to learn how to balance developing, carrying out, and funding your independent research projects with contributing to collaborative research (inside or outside of the lab), attending regular individual and lab meetings to contribute to the lab’s culture, mentoring undergraduate students and/or research assistants, providing peer feedback to lab members on their writing products, providing peer feedback to scientists in the community (as a manuscript reviewer), and keeping up with your regularly assigned lab duties. You will also need to track/keep up with your responsibilities for the classes that you teach, the classes that you take as a student, your graduate degree requirements, and future career steps, among other responsibilities.

It is critical that graduate students in the lab learn how to manage their time and work effectively in order to avoid becoming overwhelmed and burning out. You need to invest time in your personal life, as well as time to recharge and keep up your self-care routines.

Graduate students are encouraged to regularly discuss their career goals with me so that I can sponsor you or connect you to opportunities for additional career development. For instance, graduate students interested in conducting postdoctoral research or pursuing research-intensive careers are encouraged to start publishing their research before their 3rd year as a student. Graduate students with these interests should also talk with me often during their last 2 years of their graduate program about how to find, consider, and pursue external postdoctoral research opportunities.

Performance Expectations

As a graduate student, your performance will be evaluated by your thesis supervisor (Dr. Smith-Vidaurre) as well as your graduate committee. You need to make progress on your thesis research while also completing the minimum requirements for the graduate program to which you were accepted. I expect that graduate students begin to publish their thesis chapters in peer-reviewed journals prior to their defense, but I do not expect all of your thesis chapters to be published at the time of your defense. Following your defense, we will need to continue working together to publish your remaining thesis chapters in peer-reviewed journals. I also expect graduate students to start building a track record of applying for and obtaining grant funding, including small research grants and independent research fellowships. All graduate students should start applying for independent funding no later than their second year. Graduate students eligible for national fellowships should start these applications before or during their first year in the graduate program.

Your performance as a graduate student is tied to how quickly and how well you learn to manage your time, which will also be conditional on the source of your stipend. Unless you have won a research fellowship, your stipend will likely come from working as a graduate teaching assistant (GTA) or graduate research assistant (GA). Graduate student stipends will vary depending on the source of the funding, and the responsibilities associated with these positions will vary as well. Regardless of the source of your stipend, you will be expected to meet performance expectations and research goals each semester. If your GTA or GA responsibilities are taking up too much time, then you need to inform Dr. Smith-Vidaurre immediately.

Research Credits and Classes

Each graduate student will be responsible for tracking their graduate degree requirements and regularly discussing their class and research credit plan with Dr. Smith-Vidaurre. Generally, newer graduate students will have a heavier class load than graduate students further along in their careers, who will primarily sign up for dissertation research credits.

Postdoctoral Researchers

I am interested in supporting postdoctoral researchers in my lab through grants as well as competitive fellowships to conduct independent research. Generally, I expect postdocs supported on grants to spend their time leading writing and data analysis, as well as preparing presentations and manuscripts to communicate and publish the lab’s core research. For postdocs who join the lab with independent funding, I expect you to spend time in similar ways (but on your independent research) while also picking up new skills from working in the lab.

I expect all postdocs to work closely with me to prepare manuscript drafts for the lab’s core research or your independent research conducted in collaboration with the lab. We will need to discuss authorship contributions and roles early and often. We should also discuss what parts of the research that you conduct in the lab should stay in the lab after you leave, and what parts of the research you can take with you. These conversations are especially critical for postdoctoral researchers with independent training fellowships who work on the lab’s main study systems.

I also expect all postdocs in the lab to contribute to mentoring lab members at different career stages, including providing peer feedback on writing products and presentations, providing guidance on data collection or analysis given your own expertise, and providing feedback related to professional development, such as discussing your own career path with the lab. When you contribute to mentoring students in the lab who prepare manuscripts for publication, we also need to discuss authorship expectations early and often.

Postdocs joining the lab should discuss research performance and career development expectations with me as early and as often as possible. For postdoctoral researchers who are interested in academic careers, I can provide constructive feedback on academic job applications and opportunities to practice job talks. Postdocs interested in traditional academic careers are also encouraged to regularly discuss how I can support them to continue developing their independent research programs. For postdocs who are more interested in teaching-intensive careers or non-academic careers, I am committed to connecting you to resources at MSU and/or colleagues in my network who may be available for informational interviews. I am also open to postdocs taking time to pursue workshops or training opportunities that are important for their career goals.

Research Assistants

Research assistants in the lab will be expected to lead and/or contribute to core research projects in the lab, as well as to help the lab set up equipment, computational pipelines, standard operating protocols, and regular animal care duties to support new lines of research. Research assistants will also be expected to supervise and work with undergraduate students who are engaged in research and/or animal care, and to help graduate students who are leading their own research projects.

I encourage research assistants to regularly discuss their career goals with me so that I can connect you to opportunities for additional career development. Research assistants interested in graduate programs are encouraged to discuss their interests with me, so that we can talk about the possibility of joining the lab as a graduate student, or identifying potential graduate mentors and applying to graduate programs at other institutions.

Undergraduate Students

Undergraduate students can join the lab to work on research projects or animal care under the supervision of a research assistant, a graduate student, or a postdoctoral researcher, and possibly a senior undergraduate student. Undergraduate students who join the lab must be motivated, have sufficient time in their schedules to commit to at least 9 hours of work in the lab each week for at least a year, and must read and sign a contract prior to beginning their work in the lab.

Undergraduate students interested in graduate programs are encouraged to discuss their interests with their direct supervisor and Dr. Smith-Vidaurre. We can discuss the possibility of joining the lab as a graduate student, or identifying potential graduate mentors and applying to graduate programs at other institutions.

Onboarding Checklist

Please complete this checklist during your first week in the lab:

  • Complete all MSU safety trainings that are assigned to you
  • Set up your official MSU email if you haven’t already
  • Read the lab handbook and make notes of your suggestions and questions
  • If you are working in person, then obtain a key for Giltner Hall from the Integrative Biology Office (Natural Sciences Building, Room 203)
  • Set up a system to keep track of your time, including meetings and working hours. You can use Google Calendar or other tools, and it’s ok to change this over time to a platform that works best for you
  • Email Dr. Smith-Vidaurre with the following information:
    • Lab handbook: Are there things missing that you think could be added to the handbook? Are there areas where you think we should change our expectations as a lab? If you do not have suggestions about what to add or change, then please send me at least one question about the handbook to indicate that you have read and reflected on its contents
    • Recurring individual meeting: All lab members except for undergraduates should set up a recurring individual meeting with Dr. Smith-Vidaurre for the given semester or summer. In our very first individual meeting, we will discuss our respective goals and expectations for your time in the lab, including professional development goals. Undergraduate students should set up a recurring individual meeting with their direct supervisor, and ensure that Dr. Smith-Vidaurre can attend the very first meeting. Undergraduates’ direct supervisors will be in charge of scheduling periodic group meetings with Dr. Smith-Vidaurre following the first meeting
    • Lab calendar: Request access to the lab calendar, which we will use to track animal care and other duties as well as vacation time across lab members
    • Lab spreadsheet access: Request access to the lab emergency contacts and scheduling spreadsheets
    • Research space access: If you will work with the zebra finches on campus, remind Dr. Smith-Vidaurre that you need access to Food Safety & Toxicology
    • Listserv acccess: Let Dr. Smith-Vidaurre know that you want to be added to IBIO department, CMSE department, and/or EEB program listservs to receive regular updates (including seminars, socials, and other opportunities)
  • Add your emergency contact information to the lab’s resources
  • Add your availability to the lab scheduling spreadsheet so that Dr. Smith-Vidaurre can schedule lab meetings and individual meetings
  • If you are new to GitHub:
  • If you do not already use a reference manager, then make a Zotero (recommended) or EndNote account. Reference managers are important tools for actively reading the literature, as well as inserting citations and references for writing projects
  • If you are new to using R, RStudio, and R Markdown files, then check out the following Software Carpentry tutorial. You should read and complete the “Summary and Setup” overview, and section 1 “Introduction to R and RStudio”, as well as the subsections “Data analysis reports”, “Creating an R Markdown file” and “Basic components of R Markdown” in section 14 “Producing Reports with knitr”
  • Create a private GitHub repository for your electronic lab notebook in an R Markdown file and share the repository with Dr. Smith-Vidaurre (@gsvidaurre).
  • Create a private GitHub repository for your annotated bibliography in an R Markdown file and share the repository with Dr. Smith-Vidaurre
  • If you haven’t done so already, download at least 3 of the lab’s papers that are relevant to your own research (see Dr. Smith-Vidaurre’s Google Scholar profile). Read these, and add a short paragraph per paper to your annotated bibliography
  • Make a backup plan for your laptop (ideally every week)

Handbook Resources

Creative Commons License

The Smith-Vidaurre (BIRDS) Lab Handbook by Dr. Grace Smith-Vidaurre is licensed under CC BY-NC 4.0

Citation

Please cite this handbook if you found it useful for your own lab:

Smith-Vidaurre (BIRDS) Lab Manual. 2024. https://Smith-VidaurreLab.github.io/handbook/. Licensed under a Creative Commons Attribution - Attribution-NonCommercial 4.0 International License.

General Resources:

The Aly Lab, Larremore Lab, and Roberts Lab handbooks were useful guides for structure and content, as well as lab handbook resources made available by Tendler et al 2022. Some of the mentoring guidelines and expectations above were inspired by the University of Michigan Rackham Graduate School resources on mentoring. The code of conduct above was modified from Titus Brown’s Code of Conduct.

References

  1. Aly Lab Manual. 2024. https://github.com/alylab/labmanual. Licensed under a Creative Commons Attribution - NonCommercial 4.0 International License.

  2. Benjamin C. Tendler, Maddie Welland, Karla L. Miller, & WIN Handbook Team. (2022). Lab Handbook Resources. Zenodo. https://doi.org/10.5281/zenodo.7419211.

  3. Larremore Lab Manual. 2024. https://larremorelab.github.io/manual/.

  4. Roberts Lab Manual. 2024. https://robertslab.github.io/resources/.

  5. Original source and credit for Code of Conduct: http://2012.jsconf.us/#/about & The Ada Initiative. Please help by translating or improving: http://github.com/leftlogic/confcodeofconduct.com. This work is licensed under a Creative Commons Attribution 3.0 Unported License.