DRAFT: Lab policy document - Cuddington-Lab/documents Wiki

Cuddington Lab Policy

PI: Kim Cuddington

Department of Biology, University of Waterloo, Waterloo, ON

https://www.ecotheory.ca

Version 0, June 2022

(Update by Kim Cuddington)

This document is being created using Silan, M., Bellemin, R., Dujols, O., Sparacio, A., Adetula, A., & IJzerman, H. (2021). CO-RE Lab Lab Philosophy v5. Retrieved from https://doi.org/10.31234/osf.io/6jmhe as a reference

Preamble

In order for research to be fun and productive, we need rules of conduct and practice to ensure inclusivity, fair dealing and collegiality. At the same time, research is hard work, and therefore those that do not work, disrupt work, falsisfy work, or even attempt to take credit for the work of others, have no place in this space. This document is a set of guidelines to make research happen in the best way possible.

First things (could be a redirect to a new doc)

  1. If you are brand new to the lab, one of the first things to do is to read this document and make a list of questions. We will attempt to answer these during our introductory lab meeting at the beginning of each semester. There, you will meet everyone, and learn about their research as well.
  2. There are forms and training related to safety and funding that need to be completed before you can work in the lab. Please see the list here: https://github.com/Cuddington-Lab/documents/wiki/Onboarding-for-New-Lab-Techs:-Training-and-Safety-Forms
  3. If you are receiving a salary, human resources will need information. Follow the procedures here: https://isc.uw.edu/wp-content/uploads/2017/06/Edit-Accu-Time-Entry-Quick-Guide.pdf
  4. If you are just starting as a graduate student, you will need to to various things such as get a UWaterloo ID card, attend TA training etc. Please see the information here: https://uwaterloo.ca/chemistry/graduate-students/checklist-new-graduate-students. Biology specific academic information is here https://uwaterloo.ca/biology/graduate-studies/biology-graduate-handbook
  5. The lab archives conversations on our slack channel cuddingtonlab.slack.com. If you have not already been added, please email the PI.
  6. You will need a github account http://www.quantitative-biology.ca/git-and-github.html#install-the-git-application-on-your-machine and an email address. Currently the lab calendar is housed on google, so a gmail account may be useful. Set up instructions here:https://support.google.com/mail/answer/56256?hl=en

How we do research

Inclusivity

The lab should be a safe place for all good researchers, regardless of age, ethnicity, gender identity, sexual identity and orientation, body size, political affiliation, religion, or level of experience. However, at the same time, we must acknowledge that research is the process of questioning every detail of modelling, experiment, graphing and writing. Every member of the lab should be able to critique the research of every other member of the lab (including – or especially – that of the PI). In all cases this critique must be productive, delivered in a pleasant and collegial manner, and under no circumstances fall into _ad hominem _attacks.

Similarly, every member of the lab, regardless of identity, is entitled to a safe space in which to conduct research. Therefore all aspects of lab practice, procedures and policies can be questioned, and should be revised when they are found to negatively impact the inclusive and safe environment we are endeavouring to create.

Question everything, and respect everyone.

Health and Safety

  1. In case of injury. Location of first aid kit
  2. hazardous material spill
  3. broken glass
  4. Safety training requirements: Please see the list here: https://github.com/Cuddington-Lab/documents/wiki/Onboarding-for-New-Lab-Techs:-Training-and-Safety-Forms
  5. working with biological hazards (e.g. invasive species, giant hogweed)
  6. Contact numbers:
  • Police
  • First aiders in department
  • Fire deputy
  • Mental health issues
  • Workplace violence
  • Maintenance and repairs

Conflict resolution

Professional conduct

No sleeping in the lab or making kraft dinner on the bunsen burner

Money stuff other than salary

Purchases

Travel

Open Science and Reproducibility

Lab routine and procedures

Weekly checkin

Quantitative skills

Inclusivity training

Community outreach

Authorship and timely publication

Funding

Role expectations

Working Hours,Vacation,Integration at the University,and Unexpected Events

What we research

Overarching questions

Our research has two major themes:

  1. when are non-equilibrium dynamics important for understanding and managing ecological systems, and

  2. how does the tendency of organisms to modify their physical environment alter our understanding of these dynamics.

These are BIG topics which guide our research on more constrained or applied questions such as a) what is the impact of temperature variation, autocorrelation or other patterning on population dynamics? b) how do far from equilibrium age structures modify the expected impact of invasive species? or c) when do engineering predators benefit their prey? As a sideline, we also consider questions in philosophy of science such as: what is simplicity and how does it relate to model selection in biology?

Methods

Our lab uses quantitative methods study study ecological phenomena. We employ and develop mathematical, computational and statistical techniques, and so the primary objective for lab members is to develop expertise in at least one of these areas. While we certainly do complete experiments, this is not our primary focus, and frequently projects will be entirely theoretical, will use pre-existing data, or will involve capturing big data from various sources.

There are many published training materials available to help with the acquisition of quantitative skills, and the undergrad courses BIOL 457 Community Ecology, BIOL 458 Quantitative Ecology, and BIOL 367 Mathematical Methods in Biology offer a fair amount of this training. In house, we have a culture of directly instructing both our lab members, the department, and others through open educational resources (see https://www.quantitative-biology.ca/)

Foundational readings

To learn more about the big picture of our lab research the following readings may be useful

Ten simple rules for tackling your first mathematical models: A guide for graduate students by graduate students (see https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008539)

An Empiricist’s Guide to Using Ecological Theory (see https://www.journals.uchicago.edu/doi/full/10.1086/717206)

Previously developed methods and code

Previously collected data