---
# System prepended metadata

title: Lab Handbook

---

# Lab Handbook

<!--Sections to be added:

-!! Skill Profiles!!


- Resources - MK and MHF had some ideas
- Eddie explainer. Not 'how to' but 'why it's set like this'
https://www.wiki.ed.ac.uk/display/ResearchServices/Job+Submission
- Guide on writing a paper
https://vimeo.com/524236482/74da4b1e0d
- Guide to writing a thesis
- Outline for students of the milestones expected by the institute.
- Specify naming conventions:
    - plasmids - see for oligos
    - oligos/primers - MJ suggested the pMJ001 and oMJ001 convetion. SC agrees.
    - filenames - agree upon a convention, final say by Kenny
    - project numbers -are these necessary?
    - library names for RNA-seq, CAGE, WGS etc.

-->

## Joining the lab

Welcome! You've joined the Baillie Lab and we're so happy you're here!

During your time in the lab group we hope that you:

1) Have fun and make new friends
2) Collect and explore interesting and exciting data
3) Develop new and useful skills
4) Learn a great deal about biology and medical biology.

If you have a preferred name or preferred pronouns let us know!

This lab manual was inspired by several other lab manuals and borrows heavily from several:

[here](https://github.com/alylab/labmanual/blob/master/aly-lab-manual.pdf)
[here](https://ccmorey.github.io/labHandbook/intro.html)
[and here](https://rennisonlab.com/lab-manual/)

It's also 'always unfinished'. It will be updated to answer questions we haven't thought of yet and to accommodate new lessons we learn along the way.


## What kind of lab are we?

Practically, we are an amphibious lab...part 'wet' (experiments in a laboratory) and part 'dry' (computer based work). Most of our projects have wet and dry components. 

Which you are will depend on your project. 

More broadly, we aim to be a lot of different things. We would appreciate if you could share these aims with us:

* Friendly : Respect your lab-mates. Respect their personal space and preferences. Respect their culture, religion, beliefs and sexual orientation. Everyone should feel welcome in the lab and discrimination or harassment of any kind will not be tolerated.

* Supportive: Support your lab-mates. Help them out (even if you aren’t ‘on the project’) and be a friendly ear when they need it. Science should be collaborative, not competitive. If you help others you can expect others to help you when you need it. 

* Honourable: Honesty is the best policy, especially in science. It is never ok to plagiarize, tamper with data, fabricate data, or fudge results. Null or unexpected results are normal and still important. We can do important, cool and high impact science without resorting to these practices. This cannot be emphasized enough; academic misconduct will not be tolerated. If a mistake is made admit it, correct it and move on. This may require telling collaborators if you have already shown them results or if they are working with data downstream from where an error has been discovered. *Honesty and integrity above impact.*

* Efficient: Work carefully. Rushing often leads to the wasting of resources and/or making mistakes. Mistakes happen – but they should not be because of carelessness or rushed work.

---

## Practical information for working in the lab



### Lab Meetings - Wednesdays @ 2pm

Contribute in lab meeting and come prepared – especially if you are the primary presenter!
30 minute long Lab Meetings are held once a week at 2pm on Wednesday on baillielab.net/zoom.
Lab members will take turns leading. A schedule assigning weeks is available at baillielab.net/internal.
When it is your week to present you have the options of:
* Leading the discussion of a journal article or topic of your choice.
* Getting feedback on a manuscript you are working on.
* Presenting an update on an in progress or completed project.
* Giving a practice talk for an upcoming seminar, conference presentation or interview talk.

Note: If leading the discussion of a journal article, or your own manuscript the paper should be sent to the lab email list at least 3 days before lab meeting to give adequate time for reading.

### Meetings - One-on-one and project meetings

* Show up to scheduled meetings and be on time.
* Meeting slots with Kenny are available at baillielab.net/internal
* If you need to speak to Kenny outwith these times, send an email or slack to schedule with him.


### Hours

* You are not expected to come into the lab or office on weekends or holidays. Don’t feel bad for taking time off work.
* In fact, there are no precise hours you are expected to keep. As long as you are getting your work done you can do it at whatever time of day you like. One of the benefits of academia is having flexibility in your work schedule. 
* You are welcome to work ‘off campus’ if doing 'dry' work (i.e from home, a coffee shop etc) but please come in and talk to us! There can be a temptation to work from home a lot, but some professional social interaction will benefit you mentally and also professionally! Some of the best conversations happen at lunch, or next to the Nespresso machine!
* You are expected to regularly attend the standard weekly institute events such as divisional meetings and internal seminars.

### Lab Calendar

The lab calendar is kept on a google calendar.

Kenny will update the lab calendar when he plans to be away from Roslin. Keep an eye on this as he will not email everyone.

The following should be added to the lab calendar:
* Planned absences for: holidays, conference travel, 
* Your birthday!

If you can not access the lab calendar ask Kenny or Sara to invite you. It requires a Google account.

### Leave 

#### Sick Days

Take them. If you are sick stay at home unless it is absolutely 100% necessary to come in to work (e.g. an entire experiment will be ruined because you can’t find someone to cover for you - this is a VERY unlikely event). Nobody wants your germs. Take the time to rest or if you are feeling well enough to work find something you can do at home -writing, catching up on the literature, the list is usually endless…

If you are staff, you are expected to inform Kenny and HR, as per institute policy, when you take a sick day. 

#### Holidays

Let Kenny know if you are intending to be away on holidays. Holidays > 2 consecutive weeks should be discussed – ideally before plans are made. Please enter your holidays in the lab calendar.

If you are staff apply for leave through the campus portal: https://eb.leave.mvm.ed.ac.uk/

### For 'Wet Lab' members:

* Keep the lab tidy: The lab is a common area, everyone is busy. If you see something is not working, running low or empty either do something about it yourself or find someone else to take care of it – don’t just ‘pass the buck’.  When you're in the lab you represent all of us.

* Follow the 'Rule of 5' on communal aliquoted items, that is, if you take the fifth last item you are responsible for aliquoting the next lot.

* Treat equipment with respect. Don't get blood on a centrifuge and not clean it up. 

* Use booking sheets/calendars/diarys. If you don't it's your problem. Do not use a machine you haven't booked if is booked by someone else, without discussing with them first. Your 'just a ten minute spin' might throw off a whole timecourse!

* If something isn’t working let the responsible person (there will be a sign on the piece of equipment) know so we can get it fixed. 

* Make sure you have received training if you are using a piece of equipment for the first time. Even if you have used such a machine elsewhere. This is institute policy. 

### Useful resources
- Easter bush data methods club (datamethodsclub@mlist.is.ed.ac.uk) for questions about statistical analysis/ R. Also give lectures on specific topics, like introduction to R.  They are very enthusiastic! 

---
## Roles and responsibilities

### Everyone

Science is hard, but it's fun. We are a team and we all support each other. Therefore, we all have responsibilities to each other and to the lab as a whole. 

Labs naturally have a hierarchy. While there is no unimportant work in the lab (it’s all important), there is some work that requires a mature knowledge of the literature and a bird’s eye view of our international colleagues’ latest work.

No one can accomplish the work we are striving to do alone. By joining this lab, you are jumping into a big, partially-completed project, whether you realize it or not. We want your efforts flourish for this big endeavor and for your career by learning about how this one cog in the grand machinery of science operates.

### PI
#### Role
The PI is the person most likely to be able to see how all the projects in the lab relate to each other and to other contemporary research, to see opportunities for publishing individual pieces of research or combining apparently different strains of research into a single article. The PI’s ability to do this well depends on everyone’s good documentation of their work and open communication about it. Ensuring that the state of your project is always discoverable to the PI increases the chances that it can form part of an important communication, which benefits everyone involved.

#### Responsibilities
The PI, for better or worse, shoulders responsibility for the work conducted by their lab group. While everyone involved in the work will be acknowledged when work we have done is published or praised, the PI will always be primarily responsible for correcting problems when they arise, no matter who really caused them. Our work can be questioned years after it has been carried out and published, meaning the PI is the only person committed to this for long enough to realistically keep this committment.

The work we do in the lab is the PI’s life’s work. You can count on the PI to see where the projects you did that were not publishable on their own may become useful when combined with the output of other projects. Data sufficient for a research paper can take years to accumulate; in some of these cases, co-authors have completed their piece of the project many years before the paper was published. The ongoing work of the lab can help boost your work even after you have moved on, but that is only possible if the remaining lab members can fully understand and reproduce the work you did.

### Other lab members

### Roles

#### Post-docs
Post-docs have already earned their PhD, but have not yet started their own lab , or don't intend to. Post-docs are the most senior members of the lab after the PI. Depending on their mission, they might be working on their own project related to the lab’s aims, or they might be leading a project that the PI secured funding for. They have experience working in other labs, and can bring their knowledge to our procedures and help us improve them.

Roslin has a specific post-doc role called a 'Core Scentist'. While post-docs usually have specific projects/grants they work on, a core scientist will work on multiple projects as hours permit. 

There is a degree of independence to the role of post-doc and they are expected to lead projects under the guidance and supervision of the PI. 



#### Research Assistants/Lab Managers 
RAs are paid researchers carrying out designated, funded laboratory work. For most intents, RAs play similar, less independent, roles to post-docs and work on multiple projects, as hours permit.

#### PhD students
The main priority of a PhD student is completing a coherent body of research for their thesis. All of the research they undertake for that project could end up being published on its own, but pieces could also be integrated into other lab projects. This is one reason cross-project continuity is important. PhD students will usually move on to a research job elsewhere once their education is complete. At that point, research they carried out that hasn’t been published yet may not be their top priority, and the PI and post-docs can be helpful in ensuring that unfinished strands of work continue to flourish.

#### Undergraduate researchers (UGRs)
Most UGRs are involved for less than a year, and therefore must be integrated into a larger project. UGRs learn basic research skills working in the lab, and if involved in a self-contained project (like a UG dissertation), they also take responsibility for interim communications about the work they carried out. Because their time in the lab is so limited, it is very important that UG research is well-documented so that the lab can efficiently carry it forward.

### Responsibilties
The responsibilities of lab members are detailed in the section 'Your work' below.

---
## Your work

### Reproducibility and Data Management

In order to have confidence in our work, it is important that others are able to reproduce our results. Reproducible research is an essential component of science and an expectation for all projects coming out of the lab.

#### Dry lab work

To ensure reproducibility your analysis pipeline should be well organized and well documented. 

You will be provided with an institute lab book and it is institute policy to record you project progression in this.

It is important to take extensive notes for each step of your analysis pipeline – this includes indicating any pre-processing of the data. 

It is also important to keep detailed notes on your experimental design. 

Your code should be clearly commented and in way that would be interpretable to someone else.

All data, code and samples must be archived.

All code should have tests.

The lab has a Github Team (https://github.com/baillielab). Ask Kenny to invite you to this.

Repositories should be kept clean and up to date. 

__Remember__: It might make sense to you now, but it won't in 6 months, 1 month....5 minutes?


#### Wet lab work

__Keep a record of everything in your lab book.__ This is institute policy. Ensure you use the content pages and ensure your lab book is regularly signed off by your lab book partner.

Duplicates are _*necessary*_. One robust result is better than three unconvincing results.

Templates for plate layouts, PCR mixtures, Plaque assay calculations are available in the lab Dropbox.

Design experiments with someone else, do not trust your experimental design until it has been verified. 


##### Organisation in the lab

It is vitally important you keep a good record of your specialised reagents, especially expensive ones, and anything you create.
For this reason in 2021 we are implementing a systematic way of recording EVERYTHING.

###### Freezers

- Freezers are cold dark bottomless pits. Remember this.
- Every lab member has a -20 C freezer drawer. It is your responsibility to keep your drawer organised and to know what is in there.
- We also have a communal freezer, Unicorn. This freezer contains shared frozen reagents, 


### Deadlines and Feedback

If something is important and has a firm deadline it is crucial to tell your collaborators and people, whose help you need. 
You should tell the relevant people the deadline as soon as you know when it is, preferably in writing, and make sure to remind them as the date approaches. 

This also means you shouldn’t be afraid to ‘bug’ someone about it.

* Give Kenny at least one weeks’ notice to do something with a hard deadline that doesn’t require a lot of time (e.g. reading a conference abstract, filling out paperwork).
* Give Kenny at least two weeks’ notice for something that will take a moderate amount of time (e.g. letter of recommendation, award nomination).
* If you want feedback on something that will require multiple back-and-forth interactions between you and Kenny it would be best to start this process at least three weeks before the submission deadline.
* For manuscript submission and revisions (i.e. when there is no hard deadline) send drafts to Kenny as soon as you have them and bug him to give you feedback if two weeks have passed.

Nagging is a useful skill. Deploy only when required for maximum efficiency.

### Communication - practical

You can't work alone. Science is by nature collaboative. Please answer emails and keep in contact with lab members, especially those you're directly working with!!

* Slack - this is the main mode of communication in the lab. The #general channel is reserved for announcements and chat. Specific dedicated channels are available for projects and you will be added to those relevant to you (if you think there's a channel you should join speak with Kenny!)

Most lab members will be part of multiple Slack groups and notifications can get a bit much at busy times. Please DM specific people with private (work based) chat and information to prevent overwhelming the channels.

* Email - usually slower than Slack and can even be less reliable given the volume of emails some lab members receive. Please use email responsibly and send a Slack DM if your message is short! 

* Telephone - If you have an emergency the phone numbers of specific lab members are available in the Dropbox. Whatsapp and text messaging are not recommended for work related chat as they are harder to escape from...but emergencies might necessitate this.

### Money

Grants are usually held by specific people.

#### Your own grant
Spend your grant responsibly. You will be free to spend without approval up to a specific pre-defined amount. It's the repsonsibility of the grant holder to keep track of what is left and ensure the grant is managed appropriately.

#### Project grants
We have a responsibility to funders to spend grants appropriately. Do not spend grant money from project A on project B!

We have shared grant with other labs for consumables, historically named the 'Maclab communal budget'. What this can be spent on is tightly controlled and the expenditure is audited yearly.

#### Central lab grants
These will be accessible to all lab members and will be used to support core lab activitues, both day-to-day and long term. If you think something should go on a central grant, check with Sara.

#### When a grant is ending
Normally, any money not used in  agrant will be taken back by the funder.

If you are coming to the end of a grant work on a 3 month deadline:
-Month e-3 = Determine what you will need after your grant end date, plan and contact reps to detrmine shipping dates for laregr items.
-Month e-2 = Order what you need. Try not to order *after* e-2.
-Month e-1 = Your invoices for last month will now come in. Everything will come out of the remianing grant balance before it ends and finance is not angry with you.
e = end of grant. Stop using the grant code - it will casue you a bigger headache in a month. Trust me.

### Work Life Balance
You have a responsibility to yourself, to be happy and healthy, and to the lab, to be the best you can reasonably be. This means taking a break.

While there may be a period of time where you enjoy spending all of your time working (or feel like you must to meet a deadline), it is important to offset these periods with other relaxing and/or fulfilling endeavours. 

Unless there's something going on that you feel you *need* to be present for (last minute grant, paper for example), turn off notifications from email and Slack outside your normal working hours. 


---



## What non-lab/non-bioinformatic skills should you cultivate?

### Independent learning
When you don't understand something you are responsible for asking someone to explain it to you or researching it. There is no cirriculum!
You are ultimately responsible for what you read and what you learn. You are expected to gather knowledge of your field outwith lab meetings and the specific reading you need to do for your project. 

If you find this challenging or don't know where to start, start small. Find a review on a topic, preferably from a good journal, and read it in chunks. Then choose papers from that review and follow them up. If you need accountability ask someone in the lab! 

If you are still stuck, ask. Use lab meetings as a time to pose questions to the group.

Reading scientific papers can be daunting. Some are excessively long, others are jargon-filled gobbledygook. Here are some resources to help you devise your own method for ingesting the literature:

https://www.sciencemag.org/careers/2016/03/how-seriously-read-scientific-paper
https://www.elsevier.com/connect/infographic-how-to-read-a-scientific-paper
https://www.huffpost.com/entry/how-to-read-and-understand-a-scientific-paper_b_5501628?guccounter=1&guce_referrer=aHR0cHM6Ly93d3cuZ29vZ2xlLmNvbS8&guce_referrer_sig=AQAAADka9u7nTeb1BORYAIdK9-KRJoJcMv1TZIeh4CR5Pzwf2ZEjQfgESYwPGs9NQ50ygRONNAtQyK8vQlIkaq3muN3ERM5jrKmUliXBrC3oy5Ju0dBS1ADxWWzfDFKRJyf7LG_yuFZgue4LU-xhQUG2tpa7srEEbnwKnY_4MO1h4J_o

### Critical appraisal of the literature

(as requested by Sara 20 Nov 2020 following journal club)

Some ideas for systematically reviewing a paper - these come from appraisal of an RCT (randomised clinical trial, or 'human experiment') but perhaps some of the points are valid for any experiment.


Validity: is the strength of our conclusions. In short, are the conclusions correct or believable?
- Internal Validity 	
    - Is the study conducted well? 
    - Do you believe the results? 
    - Are there sources of bias?
- External Validity
    - Can the results of this trial be used to guide treatment your patients?
    - or would the experiment work outside of that lab, is it generalisable?

Are there sources of Chance, Error, Bias , Confounding?
- Chance: is it adequately powered?
- Error:  measurements are always open to error
- Bias:  can be thought of as error which affects one group more than another
- Confounding:  “variables capable of producing spurious associations between treatment and outcome, not attributable to their causative dependence”

System to critically appraise a paper
1) summarise it simply
2) check quality and validity
   a)  Internal Validity:  Is the study well conducted?
    b) External Validity:  Are the results clinically useful?
3) Present the results in a user friendly way


### Concise, understandable writing.
Writing takes practice, just look at all the typos Sara managed to make in this document. 
During your scientific career there are two things you will not be able to avoid writing:
- Your thesis
- A scientific paper
And if you choose to continue in academia, good luck avoiding grant applications.
Each document will have its own structure and layout but all will require clear and concise writing. Practice as often as you can and improve by getting feedback. 

One of the most important things to remember about writing is that it is difficult. And that's ok. Scientific writing is a particular style of writing. In Sara's PhD supervisor's words "This is not a Guardian article". It is short sentences, it is jargon while trying to sound clear, it is no split infinitives. 

Here are some resources to help you get started with writing:
https://www.nature.com/articles/d41586-018-02404-4
https://www.sciencemag.org/careers/2012/03/how-write-scientist

Here are some resources for common grammar mistakes:
https://www.grammarly.com/blog/30-grammar-mistakes-writers-should-avoid/
https://www.grammarly.com/blog/affect-vs-effect/#:~:text=Here's%20the%20short%20version%20of,the%20result%20of%20a%20change.



### Creating a presentation
A presentation is telling a story. Having a beginning a middle and an end is a necessity. 

#### Beginning 'Here's what I'm going to talk about'
- Frame the question you are answering
- Give some background - remember your audience might not be familiar with your subject.
- State your question

#### Middle 'This is me talking about it'
- Introduce your methods
- Results should be framed as part of a whole
- Explain how a result answers a question or subquestion
- Conclusions should lead to the next question

#### End 'This is what I said'
- Explain how your results have answered, or don't answer, or partially answer your question
- Describe limitations and advantages of your approach or results
- What will you do next
- Summary slides do not have to be bullet points, but it's definitely convenient
- Acknowledge everyone! (or as many people as you can!)


When you give a presentation, especially at a conference or seminar, you expect that everyone in the room is looking at you. But they're not. They're thinking about lunch. They're staring at their phone. Or they're purposefully forming a question specifically crafted to throw you off your game (I doubt anyone actually sets out to do this...).  Because of this, you need to make understanding your slides an impossibly easy task for them. 

Designing a slide is an art. There are some guidelines you can follow that can help make it easier for you:

- Put the conclusion in the title. That way if someone doesn't listen to you, your point is right there on the top of the slide.
- Less is more, particularly with text. No one is reading a wall of text. A few words should be sufficient to communicate your conclusion.
- Pictures tell 1000 words. Use pictures where you can to communicate ideas. Not only will creating the pictures help you solidify your ideas but they are easier for your audience to digest when they look up from facebook.
- Keep animations to a minimum. Animations should be used to slowly introduce ideas and guide your audience.
- Keep slides consistent. Choose a style and stick to it.
- Make it colour blind friendly. It's just polite.

Resources welcome.









---

## When things aren't going well

Self awareness is something everyone struggles with. There's whole schools of philosophical thought centred around developing it. With this in mind, try to keep an objective view of your progress but remember that this may not always be possible.
![](https://i.imgur.com/L1bKHvH.png)





### It's ok not to be ok - tell someone
* If you are struggling tell someone. Science is hard and your health and happiness are important! We are here to help, please don’t suffer alone. Everyone finds things difficult at some times.

* If you feel you are not progressing please speak to someone. There's a really good chance you're over-estimating what is expected of you.

* If you make a mistake, telling someone sooner rather than later is always the best strategy. We will have regular meetings to discuss such occurences, but these are to review not report. 

### When relationships are strained

* If there is tension, conflict or hostility in the lab it needs to be resolved as soon as possible. If you don’t feel comfortable confronting the person in question or if the situation is escalating, tell Kenny or Sara.
* If you have a problem with Kenny and are comfortable telling him about it, please do so. If you aren’t comfortable then tell another lab member or another member of the institute (for more serious issues). 




