Lab guidelines

Welcome to the functional evolutionary genomics group at the University of Melbourne! This document sets out some of our basic tenets and policies, and is a great way to get oriented in the lab.

Lab culture and expectations:

Our lab is in the very fortunate position of sharing space with excellent experimental and computation research groups. We work closely with other groups in Melbourne Integrative Genomics and in the Centre for Stem Cell Systems, and both of these sets of people are great researchers you should always feel free to talk to. We also collaborate with some research groups in the School of BioSciences, with whom we have many research interests in common.

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.

Meetings and mentoring:

We use Slack for informal and quick communication within the lab – I will invite you to our lab’s slack when you join us in Melbourne. In an emergency, however, you should text or call me. My phone number is on every fridge and freezer in our wet lab, and on our shared slack. For bigger emergencies, you should call 000 first, and once you’re safe, me.

We have a joint group meeting with the Shim lab every two or three weeks where someone from either group presents their ongoing research; lab members working on iPSCs are also highly encouraged to attend the biweekly Wells lab/CSCS meeting. Beyond that, you will have one-on-one meetings with me once a week. In these meetings we’ll discuss your work, how it is going, what you might want to do next… etc. We also have a brief weekly wet lab meeting with members of the Wells lab where we discuss general issues with cell culture to make sure everyone is on the same page and aware of small issues – eg weird Matrigel batches or rumours of mycoplasma down the hall. All of these are detailed in our shared lab google calendar.

If you need me to do something for you, tell me about it, but also, tell the slack BusyBot to tell me about it: Just type /busybot [whatever] @igr [deadline] in our private slack channel. Please include a deadline, if there is one – otherwise I will assume it’s due sometime soon but perhaps not soon enough for your purposes. Also remember that I am not glued to my phone on weekends, holidays or evenings (and I don’t expect you to be either!), and I might well take a while to get back to you if I’m not in the office.

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 driving the nerdiest food truck in town. I am happy to support you in all of these, although you will probably want to find additional mentors that have more experience 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. Good record keeping is fundamental to robust science. I expect you to use github or bitbucket 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 me and bring to our lab meetings. Because we do a mix of computational and experimental work, most out of the box approaches don’t work well for us. We’re currently experimenting with both Benchling and Jekyll – they both have their benefits and drawbacks. You’re welcome to use either one of those for now (I will invite you to the relevant Benchling account and/or give you a five minute Jekyll intro), although eventually we will probably commit to only one. You can also experiment with the R package workFlowR, or try to convince me about switching to your own favourite tool. If you like to use pen and paper that’s fine too – take photos of your pages and upload them to Benchling or your Jekyll notebook. Once you delve deeper into computational analyses, I encourage you to explore the world of RStudio and interactive Shiny apps, but please keep in mind that while they are excellent means of presenting data, they’re not the best for guaranteeing reproducibility and your work should not depend on them.

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 twitter 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 the University’s website, gumtree, or, if you want to splurge, 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

The lab does not tolerate harassment, and welcomes all regardless of gender or gender identity, ethnicity, sexuality, age, nationality, religion or disability, and this code of conduct will be enforced. If you have concerns about someone else in the lab, you are always welcome to talk to me, if you feel comfortable doing it. If your concerns are about me, or feel uncomfortable discussing the issue with me, you should reach out to your advisory committee, or, if you don’t have one yet, to Devi Stuart-Fox, who is deputy chair for graduate education in BioSciences. Ultimately, you may also consider lodging a complaint or a grievance in keeping with University policy.

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.