Welcome to the Wallace lab!
Starting in a new place there is a lot to keep track of.
This page is intended to list all the essentials to get started.
Inclusivity
We have a strong commitment to an inclusive and safe working environment for all, described in the Inclusivity Statement.
Communication expectations
Talk to people! Ask questions! Answer questions! Admit when you don’t know the answer! All nicely, of course.
Most internal lab communication happens first either in-person or on slack.
Whenever it’s helpful to talk to someone “in person” or by call - ask to set it up.
If people who weren’t part of your in-person conversation would be helped by knowing about it, please post on the relevant channel on slack.
Most external communication happens on email. If you’re asking a lab business-related question, if in doubt cc Edward, if it’s about the wet lab space cc Liz.
If it’s scientific correspondence with a collaborator definitely cc Edward.
For wet-lab workers, please share your mobile phone number for use only in emergencies.
We keep the list of numbers on datastore, in wallace_rna/LabMemberContactNos.
We have a Wallace lab calendar on outlook; most events are posted there and some are listed on slack as well.
These are asynchronous communication channels - you don’t need to respond immediately - it’s not useful to be constantly “on call” and it’s bad for your mental health.
Set notification schedules on slack so that you aren’t disturbed when you’re focused on a task or you’re off work or asleep, and ignore emails then too.
However, please respond to email & slack messages within one ordinary working day, i.e. a weekday when you’re not on leave, nor at a conference or training session, nor doing a stressful experiment such as a timecourse.
If you don’t have a full response, it’s courteous to respond saying “I don’t know, can I get back to you tomorrow/next week/when I’ve done some reading”.
If you’re not working, set an autoreply to do that for you.
If you ask someone else a question and they don’t get back to you, ask again the next ordinary working day.
Access
The lab is in the Waddington building on King’s buildings campus. How to travel to the King’s Buildings. However, due to COVID-19 restrictions, you will have to discuss with Edward and the building manager how much your work requires building access before attempting to go there.
Get your student/staff card as soon as possible, from card services. To get access to the Waddington building, email synthsys administrator Julie Fyffe and cc Edward. If allowed after the opening hours use card then enter your card PIN (see card help) to access building.
Lack of access
Remote working is hard, whether due to COVID-19, or any other more specific reason.
We’ll talk about it and figure out the best solution we can.
Where do we belong?
Physically, we are in the Waddington building on the Kings’ Buildings campus, address and info on the contact page.
Organisationally, we are in the Institute of Cell Biology, which is part of the large and diverse School of Biological Sciences. In turn, SBS is part of the College of Science and Engineering. Most adminstrative stuff that lab members have to deal with is at school level, some at institute level.
Note: Before it got too large and was split up into the current institutes, there was an Institute of Cell and Molecular Biology (ICMB), which is still the name used for the seminar series.
We are affiliated with the Centre for Engineering Biology, formerly known as SynthSys. This is a vibrant research community of people who, like us, are interested in interdisciplinary studies of biological systems.
Engineering Biology has a nice fortnightly meeting, seminar series, socials, and lots of opportunities for collaboration and science talk.
Planning
We have a rhythm of meetings to support and communicate our work.
You can find timing information on the outlook lab calendar.
We currently (September 2023) have no COVID-19 related working restrictions.
Meetings within the lab
Everyone is expected to attend, where possible:
- Weekly lab meetings, currently Thursdays 15:00-17:00.
- Fortnightly 1-1 meetings with Edward, sign up in the lab calendar by agreement.
- Lab socials, occasionally.
For full details, see the meetings overview lab manual page.
Nearby seminars, happy hours, etc.
- Journal Club - this has sometimes run monthly, depending on the current level of enthusiasm in the group. It’s really rewarding when it works. (Attendance strongly encouraged, but on hiatus)
- Many Mondays, ICMB seminar (Attendance usually valuable)
- Alternate Wednesdays, ICMB internal seminars (Attendance encouraged) - this is the best way to learn about what other people in the institute are doing
- Alternate Thursday mornings: Engineering Biology Open Centre Meeting (9:30 talks; attendance encouraged) - this is the community meeting for engineering, synthetic, and systems biology colleagues
- Last Friday of the month: Engineering Biology happy hour (5pm drinks, 6pm Pizza; attendance rewarding).
There are many interesting seminars in the school of biological sciences, listed on the website.
Engineering Biology, ICMB, and infectious disease seminars are also listed there.
Computing
There are a lot of different online tools, it’s hard to keep track of, this is the friendly guide.
University username (UUN)
First you’ll need your university email account including a UUN and password. For students, UUN will be your student number sXXXXXXX, for staff it will involve initials and some of your surname, like Vlad Sanchez’ might be vsanche1. Most university services are accessed through myed, and for myed and many other sites you will have to login using a system called “EASE” - this means using your username and password. For all the other tools, it will usually be best to sign up with your university @ed.ac.uk account.
There are many help pages available on these tools at information services, and you can ask questions via their IS helpline.
The university’s email goes by default to outlook, although it is possible to set up with other clients.
Outlook has the advantage of interfacing with the outlook calendar system, sharepoint, microsoft teams, and so on.
So, we use it for the lab calendar.
Printing
There is a printer connected to the university-managed system (edprint) in Waddington 2.08.
Your University ID card is needed to print, and you will have to put in UUN and password the first time to associate your account to your card.
In the past people had trouble being able to print, this seemed to fix the problem on Mac:
- Go on System Preferences -> Printers & Scanners, then remove the current EdPrintPull printer.
- Even if your computer is university managed, install EdPrintPull for the non-university managed computers edprint.
- Try printing, a pop-up where you have to put in your UUN and password will appear the first time.
- To check whether the printer will have your document, log in myprint and go on the Jobs pending release tab on the left. This will tell you whether your job has been uploaded and will save you a trip to the printer just to find your job is not there.
School of Biological Sciences info
SBS wiki has a lot of useful information, although some of it is hard to find and/or out of date.
Accounts to create
Slack - lab talk
Wallace lab slack workspace - this is where most of the lab talk happens. Sign up first so you can ask other questions there.
You’ll want to join several slack channels:
- #everyone
- #random
- #coding-help
- #papers
- #lab (if you work in the wet lab)
- #orders (if you work in the wet lab)
- #labnotebook (also if you work in the wet lab)
- maybe some other specific channels, ask around!
Outlook groups
These are email lists.
The 2nd floor lab group also accesses a space on microsoft teams, that is not really used.
VPN - off-campus access
For many off-campus options including Datastore, Eddie, and journal sites, you connect through the VPN (virtual private network).
Register for a VPN account using: information services vpn site.
Datastore - the university’s shared data storage space
DataStore is a file store for active research data, and is available to all research staff and postgraduate research students. To request access, there is a new link as of September 2020.
Please request access to the lab’s space, csce/datastore/biology/groups/wallace_rna a.k.a. smb://csce.datastore.ed.ac.uk/csce/biology/groups/wallace_rna. Edward authorizes access to this datastore storage area.
Mapping datastore drives on your computer
To access datastore drives as if they were on your computer (this needs checking):
- Click Start > Computer, select Map network drive and choose any available letter.
- In the Folder box, type the share’s path
\\sg.datastore.ed.ac.uk\csce\biology\groups\wallace_rna or (windows) smb://csce.datastore.ed.ac.uk/csce/biology/groups/wallace_rna
- Select Reconnect at logon and Connect using different credentials and click Finish.
- Enter your username in the format ED\username and put in your University password.
- Select Remember my credentials and press OK.
People & Money - buying lab stuff and computer stuff
NEED TO UPDATE PROCUREMENT INFO REGARDING P&M
Expenses
For expenses (e.g. conferences, outreach, travel) it is now addressed by the People and Money system.
Currently (September 2022) most staff and students have access, it seems to work.
PhD students should email Andrea Shulz in SBS finance office (and cc Edward if that helps).
Grant budgets
Currently it’s still very difficult to check grant budgets due to the People & Money debacle.
Your work will be funded by specific grant codes, check with Edward.
Email guidelines below.
Please cc Edward on all grant and finance-related emails.
Please use SBS.FinanceBusinessPartners@ed.ac.uk for all enquiries relating to:
- Salary forecasting, coding and costings
- Budget reports, coding and approvals
- Journals (moving income or expenditure between budgets e.g. corrections)
- Planning, budget setting and forecasting
- Financial modelling
- Endowments, donations and non-research restricted grants
- Year-end accounting
Our colleagues David and Tracy in the Business Support team also have a shared mailbox. Please use SBS.Business-Support@ed.ac.uk for emails relating to:
- Transaction queries (invoices, expenses etc)
- Requesting access to P&M procurement app
- Advice for raising requisitions on P&M
- Expenses claims for visitors / non-staff
- Raising sales invoices to external bodies
- Feedback on SBS P&M SharePoint site
RSpace - Electronic lab notebook
Rspace - this is the electronic lab notebook that is used by everyone who works in the wet lab.
To get an account, email data.support@ed.ac.uk and cc Edward, subject: Add user to Wallace lab Rspace, and include your UUN.
Subsequent logins go through EASE.
There is a lot of help available, e.g. new user tutorial, RSpace helpdocs.
We have guidelines for how to write lab notebook entries to go in the lab manual, feel free to discuss with others in the lab too.
Linking RSpace to datastore
Please link your datastore to RSpace as well. You can set this up by following this Youtube video: Linking RSpace ELN to Datastore at University of Edinburgh.
Please note that if the SSH key registration does not work properly the first time, click the hyperlink under your login name in the main panel of RSpace to reregister the key.
Then, navigate to the Wallace lab data store - csce_datastore_biology_groups_wallace_rna_data.
From here, choose the files/folders you would like to add.
They will be shown in your lab book page wherever you have placed the link. To download the files - click on the filename in the lab book page, click the “i” button that pops up underneath and then click download.
protocols.io - protocol sharing
We use protocols.io to write, share, edit protocols. It’s a great site! Create an account with your @ed.ac.uk email address. Ask to join the Wallace lab for Fungal RNA group.
protocols.io integrates with RSpace and also with slack. This means that you can link your lab notebook page to the protocol you used, discuss a protocol with the rest of us, and so on.
protocols.io, like RSpace, is a service that we pay for access to via an institutional subscription. Don’t be embarrassed to ask for help, we are paying for that service.
For really big analysis needs, we tend to use Eddie from ecdf. They have all the power you need, helpful tutorials, etc.
Often it is helpful to run medium-sized jobs on bifx, the server at the Wellcome Centre for Cell Biology. Ask Edward about this.
ORCID
ORCID provides a persistent digital identifier (an ORCID iD) that you own and control, and that distinguishes you from every other researcher. Set one up, it will be useful.
git, github, gitlab
We use git extensively as version control software, to share data and code within the lab and across the world. Even the lab website is hosted on github. Please create a github account. Then, create your team page on the lab website as described in the README.md.
Flic Anderson made a workshop on github flow, tailored for our everyday git and github needs.
Also see this good enough practices list of other git resources.
You can ask for help on the lab slack #coding-help channel.
The University also has something similar, a private instance of gitlab, which we sometimes use, and which uses the UUN/EASE login.
Email lists to join
Edinburgh manages mailing lists through the mlist server.
Please join:
wallacelabrna - easy way to send email to everyone in the lab, we use it for some shared accounts.engbio - the centre for engineering biology (formerly Synthsys) email list.waddington_occupants - anyone who occupies any space in the Waddington building.icmb - the institute for cell biology, etc.
To join these, it is often easiest to email Julie Fyffe, Centre for Engineering Biology administrator, and cc Edward.
Depending on your interests, you may also wish to join:
Software to install on your local computer
- R: https://cran.rstudio.com/
- Rstudio: https://www.rstudio.com/products/rstudio/download/
- tidyverse R packages: https://www.tidyverse.org/
- Python: the cool kids install this with miniconda nowadays
- Snapgene: https://www.snapgene.com/ - SynthSys has a licence, email Tomasz Zielinski for info
- Inkscape: https://inkscape.org/
- Zoom: use the university’s service
- Surely there must be some others?
If you are a new start and you don’t have an adequate laptop for your work, talk to Edward, and we will find a way to fix that.
The program or school funds laptops for all new PhD students.
Wet lab
There’s a number of accounts and setup tasks relevant to getting going in the wet lab. Safety comes first, although here it’s listed after.
Wet lab - Tablet
We have Android tablet computers that live in the lab that you can use to take notes, take pictures of experiments and upload them directly to your lab notebook by RSpace. Use this! First you will need to set up an account on the tablet kept in your bay.
Update: the Android tablets might actually not work. Ask if you need something.
There is also a windows tablet used to control the lab microscope (does that have accounts???)
Those are important because we are not allowed to use personal mobile phones in lab spaces in SBS, especially not in our Category 2 lab space.
Wet lab - synthsys scheduler
For use of many items of lab equipment - plate readers, fragment analyser, qPCR machine, and so on - you need an account on the synthsys scheduler. The page is accessible from campus or the VPN.
Plate readers tend to be in high demand, join the plate readers mailing list (how??). You may have to join the weekly “plate reader” booking meeting if you are going to use them regularly.
Wet lab - DNA sequencing
Sign up for a DNA sequencing account at MRC PPU in Dundee.
See routine sequencing info.
Wet lab - facilities
For fancy fluorescence microscopy, the Centre Optical Instrumentation Laboratory (COIL) is a Wellcome Trust funded facility containing the most up to date imaging equipment. COIL also has a scheduler that you need to sign up for to use.
The school has other facilities with great specialised equipment. Genomics, proteomics, etc.
Wet lab - other considerations (incomplete)
- opentrons pipetting robot
- centrifuges
- we have a tube labeling machine
- we have a lot of equipment, but lack a single list of all the stuff we have. Ask people!
Safety
We take safety seriously. If anyone were to be careless, there would be a number of ways to damage yourself or other people involving chemicals, explosions, and opportunistic pathogens. We must follow the health and safety guidance from the School as described in SBS wiki. We also need to learn about the risks, how big they are, how to avoid them, and generally how to take care.
Some examples of genuinely dangerous things that affect our work:
- Fungal pathogens such as Cryptococcus are dangerous to immunocompromised or pregnant people.
- It’s 2021, and we are still in the middle of the COVID-19 pandemic.
- Microwaves heating liquids can cause scalding, or if containers are sealed can cause explosions that can cause serious damage.
- Reagents for lysis and extraction, such as betamercaptoethanol, phenol, and trizol, melt flesh and cause burns. In large quantities they are lethal.
- You can set your hair on fire with a bunsen burner.
All these things can be low risk if thought about carefully. Know the risks and know the preventative measures. Discuss these with your colleages and with Edward.
If you notice anyone doing anything dangerous or risky, talk to them and talk to Edward.
Training
The Health and Safety Induction and the Buildings Induction are now on Learn. It can be a bit difficult to find things on Learn, the H & S one can be found by searching the course catalogue for “safety induction” and choosing the relevant one (e.g. PhD) and the buildings one by searching “SBS Buildings Induction”.
Once you have completed the buildings induction you should contact the building manager, who will send some building-specific info as well. Someone in the group should do a tour of the building with a view to fire safety, pointing out:
- Fire alarm activation points nearest the lab/office
- Fire escape routes and exits
- First aid kits, first aid room and how to contact a first aider
- The day and time of the fire alarm test
Risk assessments
In lab Waddington 2.18 we have a folder of risk assessments covering procedures. These should all be looked over. Those that affect your work must be read, understood, and signed, before you will be allowed to work in the lab. If there are any errors or omissions in the risk assessments, please alert Edward immediately.
Liquid nitrogen
The university has special training measures for Liquid Nitrogen, following a few nasty accidents. To sign up, get a code and information by emailing SBS safety, and cc Edward, with subject line “sign up for liquid nitrogen training”.
Edward’s Checklist
Fix missing things
Is there something that you needed to know that wasn’t covered here? Ask the lab on slack. Ask other people until you get an answer.
Then edit it on the website github, so that the next person who needs it can benefit too.