This may be your first time working on a scientific project, and maybe even your first time producing a scientific document (your project dissertation). The guide below is intended to help you understand what to expect, and should be read in conjunction with the project student learning agreement (MyPlace ).
Please read through these expectations and guidelines and bring any questions or concerns that you would like to discuss with Dr. Pritchard and Dr. Feeney to our first meeting.
1 Conducting Your Project
1.1 Science
- Maintain a detailed record of your work (i.e. a lab notebook), either on paper or electronically.
- All the projects run by our group are computational. You will probably find it easiest to maintain an electronic record.
- Keeping a lab notebook to document your project
- Back up your work frequently and in more than one place - you do not want to lose all of your data!
- It’s a common view in computation biology that, if there are not three copies of your data/work (ideally in two physical locations), it might as well not exist.
- At the end of the project, we expect you to provide us with the raw data files, and the outputs, from your work. For example:
- For a phylogenetic tree, we would expect: the
.fastafile containing the unaligned sequences; the multiple sequence alignment used to construct the tree (.fasta,.msa, etc.); and the.newick(or.nex) file for the tree. This is required so that projects can be continued and built upon in future years. - You may find it most convenient to manage your project using standard computational biology tools, such as version control (e.g.
gitand GitHub). We would also find that convenient and strongly recommend it.
- For a phylogenetic tree, we would expect: the
1.2 Teamwork and collegiality
We expect you to help each other. In particular, some of you may have more experience than others in the group, when using computational and bioinformatics tools. You are all doing different projects, but you are using similar tools and techniques. We expect you to share knowledge and understanding kindly with one another.
- Science is a team effort and it benefits from people working together in groups. We can accomplish more together than one person working alone can.
- Listen respectfully to each other, learn from each other, and contribute as you can.
- Be respectful of others’ different life experiences. Learn from them when appropriate, and contribute when appropriate. Do not insult or put down people who share their experiences.
If you find that you have made a mistake: listen, offer a genuine apology, and commit to learning and doing better.
1.3 Kindness
- Be kind to yourself. Be mindful of your limits, and aware of the fact that this is a world in crisis, with a myriad challenges.
- Give yourself credit for the hard work that you’re doing every day.
- Be kind to others. Give them the benefit of the doubt when needed; remember that online communication often misses nuance or meaning.
- Remember that everyone is struggling right now and may not be able to be their best selves.
- Be patient. Science can be hard work. Things take longer to accomplish when you are first learning a technique. You may need to repeat experiments or start over with a new dataset. This is all part of the process, and to be expected.
- Be assured that you are making progress, even though it may not feel that way at the time.
1.4 Good Communication
- How to ask for feedback
- How to ask good questions
- Be clear, open, and honest in your communication
I cannot help if you don’t let me know that there’s a problem.
- We will meet at least once a week in person or via Zoom (individual and/or group meetings).
- Zoom etiquette: turning your camera, microphone on/off is completely up to you, no pressure either way.
- Between meetings, We’re available by email to answer questions or you can schedule a drop-in Zoom or 1:1 meeting (depending on our schedules).
- Don’t be afraid to ask for help. You have many resources to call on, including:
- Dr Pritchard or Dr Feeney (…this is literally our job!)
- Each other. Please do talk to and help each other! - we call this “Peer Learning” and it’s deliberately part of the project. It’s not cheating or plagiarism.
- Anyone else in the SIPBS CompBiol Group
- The Microbiology group
- Ask questions in your lectures/open office sessions
- Stack Overflow, Bioinformatics Stack Exchange and other specialist sites
- Social Media (it can be a great place to crowdsource science questions, but it can also be a cesspool, so tread carefully)
- Take ownership of your project. We are here to help and to guide you, but this is not my thesis (We have already done more than one!)
- Come to meetings prepared.
- Think independently and critically
- Read broadly
Sites like Stack Overflow and Stack Exchange, while extremely useful and valuable for the community, can sometimes contain some robust communication and opinion from strong-minded people.
All of the above contributes to your project performance mark
- Don’t be afraid to tell us (anyone!) that you think we’re (they’re) wrong. We’re scientists. We’re probably wrong at least half the time - that’s how things are.
- Your data may contradict our hypotheses or ideas. That’s also how science works.
- You will probably find something in the literature that we were not aware of. We’ll be interested to hear about it.
- You may well have insights and clever thoughts that we won’t have. You are closer to your project than we are, and that will generate insight for you which is inaccessible to us. Trust yourself.
- Doing science can involve challenges to accepted dogma, and the Scientific Method requires us to prove ideas (usually our own ideas!) wrong. Be bold.
2 What you should expect from us
- Kindness, team-work, and collegiality
- Advice and guidance on planning and carrying out your experiments
- Guidance on how to write a scientific document
- Feedback on drafts and practice presentation
- Good communication
- Email responses within a working day (We will do our absolute best)
- Feedback on project performance
- References
If you want to name either of us as a reference there’s no need to ask for permission, butwe do appreciate as much notice as possible. We want to encourage an employer to hire you/a course to take you on so, if you can send us your CV and a couple of points you’d like to be highlighted, so much the better!
- Take care of yourself (a healthy mind requires a healthy body)
- Stay organized: set yourself deadlines (but be flexible when you need to be)
- Don’t feel the need to write your draft in one go – it’s much better to work on it a little bit every day (it’s a marathon, not a sprint)
- Break it down into small tasks
- Get into the habit of writing at least a few sentences daily
- Take breaks and let your mind rest/process ideas (take a walk, wash the dishes, drink some tea).
- Take breaks from the screen.
- When you read papers, and go to seminars/journal clubs: pay attention to the way that other people explain their science (what works? what doesn’t?)