Lab guidelines

Welcome to the Human Genomics and Evolution group at St Vincent’s Institute! This document is a shorter version of our internal lab manual sets out some of our basic tenets and policies, and is a great way to get oriented in the lab and decide whether it would be a place where you can thrive.

Lab culture and expectations:

We are in the very fortunate position of being surrounded by excellent experimental and computation research groups. Within SVI, we work closely with Davis McCarthy’s BioCellGen group, and share an interest in genomics with the Human Immunology and T1D groups at SVI. We are also affiliate members of Melbourne Integrative Genomics at the University of Melbourne, and collaborate with some research groups at the University of Melbourne, with whom we have many research interests in common. Much of our work is collaborative by nature. Outside Melbourne, we rely on colleagues at other institutions to share resources, data and best practices. In particular, we are currently working closely with groups at the Mochtar Riady Institute for Nanotechnology in Indonesia, the Translational Genomics Institute in the USA, and the University of Toulouse in France. Irene also has a secondary appointment at the University of Tartu, in Estonia, and collaborates with researchers there, as well as mentoring PhD students.

Above all, my job is to support your time in the lab and ensure that it is as successful as it can be. I want you to do well, and I will try my hardest to make sure you have the resources you need, be that collaborators, reagents or training opportunities. In my lab you will be trained to become a creative, rigorous and independent scientist. In return, you should be willing to work hard, think on your own, challenge yourself and engage with other members of the lab and of MIG in constructive, productive and perhaps unexpected ways. Although you will have your own project, the lab is a collaborative environment where people learn from one another and help each other, and we all work together to ensure that atmosphere is maintained.

More broadly, I want you to succeed at whatever career you’ve chosen. That includes the ‘traditional’ PhD-postdoc-faculty job path, but it also includes all other paths open to you, whether that be moving into industry research, becoming an investment banker or owning a food truck. I am happy to support you in all of these, although you will probably want to find additional mentors that have more experience than me in these realms. To make sure you’re on track, we’ll also meet every 6 months or so to discuss your long term plans and your progress towards achieving them. So that these meetings are fruitful, I’ll ask you to complete Individual Development Plans in advance, which will form the basis of our ongoing conversations on these subjects.

Reproducibility, notebooks and communication:

All the work we do in the lab should be of high quality, transparent, and reproducible.

To help us achieve this, there are a few things we do as routine, and a few others we are experimenting with right now. Chief amongst these is making sure everyone thoroughly documents their research and securely stores their data. Good record keeping is fundamental to robust science. You are expected to use our group’s SVI gitlab group to store and version your code. Your repos should be updated frequently (at least once a day when you’re working exclusively on dry lab!), preferably with informative commit messages, and your code should be legible – remember that eventually it will all be made public!

Beyond proper documentation of your code, you should always keep a digital notebook that you can share with Irene and bring to our one-on-one meetings. This should use our local set-up for the workflowR package and our established project structures. If your work is not documented in this fashion, it does not exist. Experimental work should be documented using Lab Archives. This is SVI policy, and the only allowed way to document experimental work. If you wish, in addition, you can use a sharepoint Word doc hosted inside the lab drive to summarise your ongoing progress (transfer ownership to Irene).

Your cell culture work should be equally well documented. We work with multiple cell lines, and under the microscope they all look identical, so good record keeping and careful labelling are habits you need to embrace from day one – and I will nag you about this. All raw data – gel photos, rtPCR runs, immunostaining images, etc – should be saved. If you can’t show me the raw data, I will not believe the final result.

We also have some basic lab protocols that are common to all members, and some basic data processing best practices. The former are available on both Dropbox and as hard copies in the tissue culture room; the latter are [not written up anywhere yet]. Unless you have really good reasons not to, you should follow these at all times.

Science moves very fast these days. I encourage you to set up a bluesky account and follow people you find interesting, or whose work is relevant to your own. It’ll serve as a low-key networking opportunity, and it will also expose you to what other people are working on, talking about, and thinking about. It’ll help you stay current and catch things that you might otherwise not have spotted.

Living and working in Melbourne:

Beyond the wealth of academic opportunities at your feet, Melbourne is also a city very much worth exploring. Anything you want to do, you probably can (so far, in the lab we’ve dabbled in rock climbing, ukelele playing, ice skating, Japanese language classes and intramural football to list a few), and part of your time with us should include taking advantage of this. I expect – and encourage – you to have a work-life balance. No one wants you to burn out six months into your time in the lab because you’ve been working non-stop 14 hour days in an effort to impress me with your dedication. Relax! I’m already impressed!

If you’re moving to Melbourne from afar one of the first things you’ll want to consider is accomodation! You can look at things like gumtree, Fairyfloos, flatmates.com.au or, if you want to splurge, realestate.com.au. You should also feel free to reach out to current lab members for more on-the-ground advice. The University of Melbourne also has a guide to living in the city. Some of its recommendations are geared towards undergraduate students, but on the whole you should find plenty of relevant information there.

Harrassment and lab code of conduct:

All members of the lab, along with visitors, are expected to abide by this code of conduct whenever they are representing the lab in any capacity, including travelling to attend scientific meetings.

All members are expected to help ensure a safe work environment for everybody. 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, body size, race, or religion (or lack thereof). We do not tolerate harassment of lab members in any form. Sexual language and imagery are generally not appropriate for any lab venue, including lab meetings, presentations, or discussions. However, do note that we work on biological matters so work-related discussions of, e.g. 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 behaviour are expected to comply immediately. We expect members to follow these guidelines in all in-person, phone, or online communications, lab-related events, university events, conferences, etc. If you are being harassed, notice that someone else is being harassed, or have any other concerns, please contact Irene immediately. If you feel that another lab member is not following the code of conduct outlined here, then in a polite, neutral, and professional manner address this with the individual. However, if you do not feel comfortable doing this, or find it ineffective, inform Irene.

Getting help:

Sometimes you might have personal problems. You are under no obligation to discuss these with me, but if I can help you with them, I will. There are campus resources available to you and you should be neither afraid nor ashamed of making use of them. Staying healthy – physically and mentally – is fundamental if you’re going to enjoy your time in academia.