Lab Manual

Welcome to the lab! We are so thrilled to have you as part of the team. The lab manual has several key pieces of info. for getting oriented to the lab and basic lab guidelines, resources for writing here and here, as well as general resources.

Essential Reading/Onboarding Materials:

An introduction to (the art of) reading (and understanding) scientific literature.

A review (and here’s a quick guide) of best practices in molecular biology.

See the Essential Reading List in the Lab’s Github

Data curation: Science has long stressed the importance of the lab notebook, but maintaining your data files and code is just as important (if not more, depending on what type of work you are conducting!). While these efforts take more time to set up initially, the long-term benefits and payoff (for yourself and others) are well worth the time and effort! Below are a few helpful links to help with this endeavor.

Fall 2023: We are reading this book together as a lab!

New to R and Coding? Here are a few resources to get you started: intro. to programming, then here, here, and then here!

Once you have R and Rstudio downloaded, please spend some time on the following: On the importance of reproducibility, data curation, package management, and best practices for writing code/code style and data/code management.

A brief intro. to epidemiological modeling in R with a more advanced overview here.

Working with big data - linking R with cloud services.

Highly Recommend this Short Course on GtiHub: https://rfortherestofus.com/courses/git-github/

PROTOCOLS

DROSOPHILA BASICS

For in introduction and overview of culturing Drosophila

LAB BASICS

PHYSIOLOGICAL ASSAYS

BACTERIAL ASSAYS

TECHNOLOGY

IMAGER PIPELINES

  • Cytiva Imager Initial Set up and Image Saving

REPRODUCIBILITY & RESEARCH DOCUMENTATION

Lab Notebooks: All lab members should have both physical and electronic notebooks. These notebooks should include legible and interpretable details of daily research activities. Not only are these notebooks invaluable tools for your empirical toolkit, but they are also requiredd for federally-funded research. Lab notebooks cannot leave the laboratory and must be turned in at the conclusion of your tenure in the lab.

We use Benchling as a shared electronic lab notebook and central repository for all molecular biology and lab assays. Lab members will receive an invitation to join the HiteLab Benchling page. Electronic summaries of work done and data generated (gels and printouts) should be regularly annotated and recorded into your defined Benchling lab notebook project space. This means that your electronic notes should include the minimal set of notes required to repeat any molecular biology experiment that you have performed.

Your physical notebook should be ‘backed up’ in electronic form at frequent and regular intervals! Your plastic memory will be reliable the closer to the experiment/analyses so it is good practice to include the electronic notes as the final step of your experiment/assay. Benchling also has great resources for planning molecular cloning tasks and designing molecular biology reagents.

LAB SCHEDULE

Scheduling: We will use an Outlook calendar to post and keep track of lab schedules, group work sessions, lab meeting times, relevant departmental and university events, and one-on-one meeting times.

Going out of town on a cool adventure etc.? Great! Please notify me and your lab team member(s) in at least 2 weeks in advance and update those dates on the lab calendar so that other lab members are aware should anything arise (and remind us the week before since schedules are so busy).

Lab work often takes on a schedule of its own so please do not assume that a given holiday or school break means that you do not need to make arrangements for someone to maintain your assays etc. during those times. Please make sure to update the lab calendar with any pre-approved vacation days etc.

Lab GITHUB

We will use GitHub and Slack (both @ HiteLab) for basic lab organization. In case you are new to GitHub, here are some useful resources to get you started: Happy with git and Don’t be afraid to commit, and Version Control with Git on Coursera.