0. Preface & Thanks

This handbook has been inspired by, and copied verbatim, material from the following openly shared handbooks for academic groups:

  • CCT Data Science Team (University of Arizona) — Group Procedures book: https://cct-datascience.github.io/group-procedures/
  • EpiForecasts (London School of Hygiene & Tropical Medicine) — Lab manual: https://epiforecasts.io/lab-manual.html
  • Whitaker Lab (Alan Turing Institute) — Project Management repo: https://github.com/WhitakerLab/WhitakerLabProjectManagement and Onboarding repo: https://github.com/WhitakerLab/Onboarding
  • Bahlai Lab of Applied Computational Ecology (Kent State University) — Policies repo: https://github.com/BahlaiLab/Policies
  • Zipkin Quantitative Ecology Lab (Michigan State University) — Policies repo: https://github.com/zipkinlab/Policies (forked from, and with thanks to, the Bahlai Lab)
  • Data Diversity Lab (University of Arizona) — Lab documents: https://datadiversitylab.github.io/lab-documents/
  • WIN Physics Group (University of Oxford) — listed via the WIN Lab Handbooks initiative: https://www.win.ox.ac.uk/about/training/lab-handbooks
  • Weecology (University of Florida — Ernest & White labs) — group site: https://www.weecology.org/ and GitHub organisation: https://github.com/weecology

We thank all these labs, as well as the helpful list of Open Lab Handbooks by the CCT Data Science team: https://github.com/cct-datascience/open-lab-handbooks

1. Introduction & Welcome

Welcome message and group overview

Welcome to the Evolutionary Epidemiology Group. We work on infectious disease challenges, typically from an evolutionary perspective.

Mission statement / lab philosophy

We strive for great science, with a focus on collegiality, collaboration, and learning.

How to use the handbook

The handbook can be read by people thinking of joining the group, and should be read by all new members when they start. It can be referred to intermittently as needed. The handbook is intended to complement, not replace, official documentation by either the University of Edinburgh or London School of Hygiene and Tropical Medicine (LSHTM). The group handbook can be viewed as a live document, intended to be updated and adjusted to cater for the group’s needs. If you have a suggestion, please let KA know.

2. Group Structure & People

Overview

We are a distributed group. The PI (Katie, KA) has joint positions at The University of Edinburgh (80%) and LSHTM (20%). Group members are primarily affiliated with one of these institutions. At LSHTM, members are affiliated with the Centre for Mathematical Modelling of Infectious Diseases (CMMID) as well as their respective department and faculty. In Edinburgh, members are part of the the School of Population Health Sciences situated within the College of Medicine and Veterinary Medicine (CMVM). Unless otherwise agreed, Edinburgh-based members sit in Ashworth Laboratories (Kings Buildings), where we are graciously welcomed by the Institute for Ecology and Evolution (IEE).

Roles and responsibilities by position:

Everyone in the group should:

  • Support the work of other group members and offer help where you can.Contribute to group meetings and other group events.
  • Share your work openly and early
  • When someone asks for feedback or help, respond within a few days, even if just to say you can’t help right now.
  • When giving feedback, be constructive and focus on the work.

Principal Investigator (PI)

  • Be available both in person and via electronic communication, including regular meetings to discuss work and anything else group members would like to discuss.
  • Provide a broad perspective on work within the context of the group and the general direction of science.
  • Provide timely feedback on drafts of manuscripts, talks, grant proposals, etc.
  • Help identify next career steps, whether inside or outside academia, and provide support towards them.
  • Identify training opportunities and conferences and support group members in making the most of them.
  • Point out grant and fellowship opportunities and support respective applications
  • When changing priorities, communicate this to others whose work is affected.

Postdocs PhD students Masters project students

3. Meetings and seminars

Weekly group meetings

  • Our weekly group meetings are hybrid to allow both Edinburgh and LSHTM to engage equally. The goal of the meeting is to foster shared scientific inspiration and creativity through engagement, understanding, and mutual respect. To allow this goal. We all meet Tuesdays 2-3.30pm online (LSHTM) and in person (Edinburgh). We rotate chairs and presenters.
  • Each meeting starts with each member telling us for 1-2 minutes what they did during the previous week (with a slide if needed) and there will be an opportunity for others to ask questions.
  • Presenters can choose their own work, an idea, a research paper, a skill or a professional development topic they would like to lead a discussion on. If you require the group to read any material, please give them a week’s notice.
  • Slides are accessed through the google drive: xxxxx

    Individual meetings with PI

  • I meet with postdocs and students either weekly or fortnightly depending on our preference. We will agree on a meeting schedule at our first meeting, and check in regularly to update as needed.
  • After each meeting send a summary of the points raised and the action items via Discord (Edinburgh) or Slack (LSHTM).

Departmental / Centre / Institute seminars

  • Engagement with wider scientific seminars is a privilege of being part of a university and provides a vital part of scientific training and inspiration for early, mid and late career researchers. Postdocs and PhDs are expected to attend at least one seminar per week during their normal working week. Make sure you receive the following seminar invitations:
  • Edinburgh: Mathematical Biology seminars, Biology IIR and IEE seminars (weekly), Edinburgh Infectious Diseases, Usher Institute, Edinburgh Microbiology seminars / AMR Forum
  • LSHTM: IDE, CMMID (monthly meetings - mandatory)

4. Communication

Email etiquette

Please reply with 2 working days to emails. A gentle prompt can be sent within after 2 working days to get a reply from KA, and after one week to colleagues (unless more urgent).

Slack/Discord

Please use Slack (LSHTM) or Discord (Edinburgh) for all internal communication. A gentle prompt after 24h can be sent to get a reply from KA.

5. Conferences

Submitting your work for conferences is highly encouraged (either as a poster or an oral presentation). Before you do so, please remember the following: - Never submit an abstract before giving all authors the ability to opt in. Therefore, please send abstracts *a minimum of 2 weeks before abstract submission. In exceptional circumstances, if this is not possible, then send authors a notice when they will receive the abstract at least 2 weeks before the abstract deadline** - Always OK the author list with KA before sending to authors. For more information on this, see ‘authorship’. - Discuss conference attendance in good time (at least a month) with KA to confirm finances and scientific content. It is helpful to get an approximate cost for the conference is possible

6. Onboarding & Getting Started

First week/month checklist Required training and certifications Group space orientation Key contacts and resources Setting up accounts and access