Lab values and expectations

Scientific goals

Our goal is to use population genomics and statistical methods to study the epidemiology and evolution of bacterial pathogens of human and animal populations, including addressing the pressing public health threat of antimicrobial resistance. The lab employs computational tools using microbial whole genome sequencing data to reconstruct pathogen transmission, investigate adaptation during infection and transmission, and inform the development of novel diagnostics and interventions.

We also aim to train scientists who work both independently and collaboratively to study the impact of pathogen ecology and evolution on public health using microbial genomic data. Trainees are encouraged to devise projects aligned with their career goals and establish collaborations both inside and outside the lab.

Diversity, equity, and inclusion

In the Mortimer Lab, we are committed to fostering a diverse scientific workforce through our research, mentorship, and teaching activities within the lab, across the university, and in the community. Lab members agree to the following actions:

  • Regularly reflect on the impact of our research on our community. The burden of infectious diseases disproportionately impacts minoritized communities in the United States and under resourced settings globally. In our lab meetings, we discuss scientific literature related to diversity, equity, and inclusion (DEI). Reproducible research and equitable access to results is also a lab value, and we commit to posting preprints, publishing in open access journals, and sharing data and code for published manuscripts.

  • Increase exposure to and representation in microbiology and computational biology. Graduate student and postdoctoral trainees are expected to participate in mentorship of other lab members. As a lab, we will engage in at least one volunteer or outreach activity in the Athens-Clarke County area yearly. Lab members are also encouraged to participate in community outreach activities individually. Some activities we recommend include Letters to a Pre-Scientist and Skype a Scientist.

  • Recruit and retain lab members from underrepresented backgrounds. The unspoken rules of academia are often barriers to first generation and minoritized students. This lab handbook includes information to help trainees in the lab, prospective lab members, and the UGA research community. To ensure that the opportunity to work in our lab is equitable, we do not have volunteer positions. If you are an undergraduate at University of Georgia, our lab policy is that undergraduate students who work in the lab will either receive undergraduate course credit or be paid hourly. We also participate in summer internship programs for undergraduates like NSURP.

Reproducible research

Our goal is to make all research from the lab reproducible, meaning given the raw data and our code someone else could rerun the analyses from start to finish and get the same results. Additionally, we need to keep a record of when and why code is written or changed.

Making your workflow reproducible from the start provides several benefits. Well documented data, pipelines, and scripts make writing the methods section of your manuscript and complying with academic journal and funding agency requirements for data sharing straightforward. Additionally, the scripts and pipelines written for one project may be easily adapted for your next project. Lastly, when you inevitably have to rerun most of your analyses because of an update in the data or a change in one piece of the code, you will be thankful that your past self made this simple!

When we have agreement from any outside collaborators, all manuscripts in the lab will be posted first as a preprint and then published in an open access journal after peer review. If you do not have access to a published article from the lab, please email to get a PDF.

Wellness

In addition to the stress that comes with academic training, your wellness and productivity may be impacted by health, home, and family matters. We are committed to supporting all trainees throughout their time in the lab, including encouraging healthy work life balance, mental health, and pointing you to wellness resources available here at UGA.

General expectations

  1. Treat other lab members and collaborators with respect
  2. Let me know if you are not being treated with respect or something about the lab environment is not working for you
  3. Conduct research responsibly, reproducibly, and rigorously
  4. Thoroughly document and share your work
  5. Ask for feedback from me, collaborators, and other lab members in a timely manner
  6. Contribute to the lab environment: share your expertise with others, participate in lab meetings, and offer feedback on experimental design, code, figures, and drafts

Lab day to day

Work hours and time off

Hours and remote work

One of the perks of working in a primarily computational lab is the ability to work when and where is best for you, and I won’t be keeping tabs on exactly when you are in the lab as long as you are making progress on your work. However, there are many benefits to socializing with and learning from other members of the lab and department, so I would encourage everyone to physically be in the lab at least three days per week during normal working hours (overlapping 11am-3pm). To that end, if there are ways I can make the lab a more comfortable space for you to work, please let me know. I expect that hourly employees will accurately report their time.

The above does not apply to undergraduate students who need to work around their class schedules, may not work more than 20 hours per week, and should only be in lab during normal work hours. Students doing research for credit should plan to work at least 45 hours per credit hour in a given semester. Undergrads should discuss their planned schedule and work hours with me at the beginning of the semester.

Vacation

I will not be in the lab on official UGA paid holidays, and I hope that everyone will take this time off as well. If you observe holidays that are not on UGA’s holiday calendar and will need time off, please let me know.

UGA benefits eligible employees and postdoctoral researchers accrue vacation hours at a rate of 10 hours per month. While graduate students do not officially accrue any leave, I also encourage graduate students to take time off, and you should feel free to take 15 days off in addition to UGA holidays. I do not need to approve the dates of your vacation in advance, but I would appreciate it if you let me and the rest of the lab know when you plan to be on vacation. When you are on vacation, I do not expect you to respond to lab-related communications. Work or career-related travel (like attending conferences) is work, and it does not count as vacation.

UGA policies on annual leave for benefits-eligible employees

Postdoctoral Researcher specific policies

Sick time

Please do not come to lab if you are sick and take the time you need to rest and recover! If you are feeling well enough to work but may still be contagious, please work remotely.

UGA policy on sick leave for benefits-eligible employees

Lab communication

The lab primarily communicates via a slack workspace. If you have a question for me or another lab member, please first consider if it can be posted in a public channel. It’s likely that someone else has the same question now (or in the future) and that multiple lab members will be able to help you with your problem. Posting in a channel, rather than a direct message, will allow the discussion to be searchable in the future.

If my office door is open, please feel free to come in. If I’m out of office or my office door is closed, it is best to send me a message on slack. I expect that everyone checks in on the lab slack a few times a day on days you are working. You do not need to respond to messages at night, on the weekend, or on vacation even if other lab members are working during those times.

The lab also has a shared calendar. If you do not have access to the lab calendar, please ask Tatum to share it with you. Everyone should feel free to add or update events on the calendar that may be of interest to the lab, including lab meetings, seminars, and conference abstract deadlines. I will also keep the calendar up to date with days that I will be traveling for work or on vacation.

If you would like to share your planned vacations on the lab calendar or update your slack status when you are away or sick, you are welcome to do so. However, I want to emphasize that this is not a requirement, and while you should let me know when you will be away from the lab, you do not have to share your specific schedule or reasons for being out with the whole lab.

Meetings

Individual meetings

For junior trainees, we will have weekly one-on-one meetings; after one year in the lab, we can reduce the frequency of meetings to every other week (or keep meeting weekly!). Prior to our meetings please make an agenda for the meeting and share it with me on slack or in your lab notebook. This time is yours to use as you like, but I suggest including an update on what you accomplished in the last week and a plan for the next week’s work. It can also be helpful to share slides with data you’d like to discuss.

Yearly individual goals meeting

In the spring, we will use one of our individual meetings to complete any required yearly evaluations and discuss your long-term research and career goals. If you do not have a required written evaluation as part of your training program, I would suggest using an individual development plan. Unless your program has a different timeline for yearly evaluations, please plan to have this meeting during our first individual meeting after UGA’s spring break.

Lab meeting

We have a weekly, one hour lab meeting. We will use this the first 10-15 minutes for general lab updates, and we will use the remaining time for research presentations, practice talks or poster review, discussion of journal articles, tutorials on computational or other scientific skills, or discussion of broader topics which put our work in context with our community, including outreach, advocacy, and DEI. At the beginning of the fall, spring, and summer, we will reschedule our weekly lab meetings to best accommodate everyone’s schedules. The schedule for lab meeting can be found in the OneDrive.

Yearly lab goals meeting

In the fall, we will schedule a half day lab meeting to discuss our projects and goals as a lab. During this time, I will also give a ‘state of the lab’ update on lab achievements, funding, and lab directions for the next year. We will also use this time to review this handbook to make sure it is up-to-date, useful, and reflects our shared values and expectations.

Yearly lab organization and cleaning

We will have a day dedicated to lab organization and cleaning scheduled during the last week of classes in the spring semester on our normal lab meeting day. All lab members are expected to participate during the time you would normally be in the lab. Our goals for the day include:

  • Ensuring your lab notebook is organized and up-to-date and creating a compressed back-up to send to me
  • Organizing and documenting your data and code for ongoing projects
  • Reviewing lab inventory in LabSuit and our sample inventory spreadsheets
  • Cleaning and organizing the wet lab and dry lab spaces
  • Double checking that we are complying with all lab safety requirements

We will also have a lab lunch on me!

Seminars

Department of Microbiology Seminars

Schedule

Resources

Lab space

The main lab space is located in the Poultry Diagnostic and Research Center Building (953 College Station Rd) in Room 121, which can be accessed from the main lobby. My office is within Room 121. It is on the left right before you go up the stairs to the breakroom/kitchen. There is a pink sign with 121 on it in the lobby, and our doors have a “Mortimer Lab” sign. The wet lab space is also in PDRC in Room 150.

Computers

The lab will provide a computer, monitor, external hard drive, and workspace for anyone working full-time in the lab (staff, graduate students, postdocs). If you are an undergraduate or rotation student in the lab who does not have a usable laptop for your work, please come talk to me; we will find a way to get you a computer with either lab or university resources.

Slack

The lab’s slack workspace is the main method of lab communication. You will be automatically added to several channels when you join, but please also check out the channel browser and join any other public channels related to your work.

Calendar

We have a shared lab Outlook calendar. Please request access if you have not been added to the calendar.

GitHub

We share all project related code through the lab GitHub organization.

OneDrive

UGA provides up to 5TB of storage through Microsoft OneDrive. We have a shared lab folder, and I would also encourage you to use your individual account for automatic back up of your work-related files.

Adobe Creative Cloud

UGA faculty and staff have free access to Adobe Creative Cloud. For more information, see the CVM intranet article here.

UGA students have access to a 4 week, renewable license. Request access to a license here.

GACRC Sapelo2 Cluster

The majority of your work will take place on UGA’s research cluster Sapelo2. Once your training progresses to work on the cluster, please request an account. Depending on your prior experience working on clusters, you may be required to attend one or more trainings before being given access.

Please regularly review best practices for working on Sapelo2.

Academic journal access

For some academic journals, you may need to access articles through UGA’s subscriptions. I find that the easiest way to get access to an article through UGA is to go to the library homepage and use the Google Scholar search option from there.

Wellness resources

Joining and leaving the lab

Lab Onboarding

  1. Complete new hire checklists provided by PDRC
  2. Complete required training available through PEP
  3. Make sure you have access to the lab resources above. If I’ve forgotten to give you access to one of them, please remind me!
  4. Send me a short bio and a picture of yourself for the lab website

Optional onboarding for beginners in bioinformatics:

  1. Complete tutorials in unix, git, and python.
  2. Try to complete as many problems as you can through Rosalind. During our first few weekly meetings, we can discuss where you got stuck, what you think the problem is, and work through a solution together. Feel free to discuss the problems with other lab members as well!

Before you go

  1. Make sure that all published and unpublished data is available according to the data storage and sharing section below
  2. Double check that you have all the data you need from lab-owned computers and contact IT to have them reset for a future lab member’s use
  3. Clean your workspace
  4. Schedule a meeting with me and anyone who will be working on your projects going forward to make sure we know where everything stands
  5. Share your contact information, so we can stay in touch!

Data storage and sharing

Lab Notebooks

Electronic lab notebooks

In this lab, we use Obsidian as an electronic lab notebook. Please create an Obsidian vault in your OneDrive account and share the folder with me. To save your Obsidian vault in OneDrive, you will need the desktop app available here. Also, check out the numerous plugins available for Obsidian. This beginner’s guide is a helpful resource for getting started with Obsidian.

For each project, please create a folder in your notebook which contains the following: an up-to-date note listing locations for raw data, analyses, results, presentations, and manuscripts related to your project; a note outlining research related tasks that are in progress, still to do, or done; and any other project related notes. Ideally, all analyses should be 100% reproducible, so code, commands, and data should primarily reside on the cluster and changes should be tracked using version control with git and pushed to the lab’s GitHub regularly. If you receive data from a collaborator, please take detailed notes about who sent you the data, when you received the data, and what they had to say about the data.

Additionally, your Obsidian vault can be a useful place to keep notes on literature, our individual meetings, ideas for future projects and fellowship applications, and things like tricky software installations. If you have notes that you think would benefit the whole lab, feel free to share them through OneDrive, or we can make the information available in this handbook.

Paper lab notebooks

If you are working on sample collection or sequencing in the wet lab, you can keep records in a traditional, paper lab notebook if you prefer. Please periodically scan your notebook and save in Obsidian.

Sapelo2 Cluster

Information on GACRC storage can be found here.

Home directory

  • Path: /home/{user_name}
  • Space: 200 GB
  • Back up: backed up
  • What to store here: user specific configuration files and software installation

Scratch directory

  • Path: /scratch/{user_name}
  • Space: no quota
  • Back up: not backed up, 30 day purge
  • What to store here: active data analysis

Work directory

  • Path: /work/tdmlab
  • Space: 500 GB/10,000 files
  • Back up: not backed up, no purge
  • What to store here: shared, often used resources (e.g. shared software installation, copies of shared datasets actively being analyzed)

Project directory

  • Path: /project/tdmlab
  • Space: 1 TB
  • Back up: backed up, however only attached to transfer nodes
  • What to store here:
    • in a user specific directory: data and code for unpublished projects or published projects with ongoing follow up
    • shared wgs datasets with the following structure: 
      /project/tdmlab/genus_species/
assemblies/
annotations/
vcfs/
pseudogenomes/
clustering/
trees/
pangenomes/

GitHub

  • Private repository containing collected metadata for publicly available and Mortimer lab whole genome sequencing data
  • Public repositories for general assembly/analysis pipelines
  • Private repositories for unpublished, ongoing projects
  • Public repositories for published projects (including preprints)
  • Lab handbook and website

OneDrive

Information on OneDrive resources provided by UGA can be found here: OneDrive at UGA

Lab shared folder

  • Code and results for published projects
  • Successful fellowship applications
  • Sharing manuscript drafts, grant applications, abstracts, lab meeting slides (fine to use google drive here if preferred; however, only 3GB available)

Individual folder

  • Lab notebooks (shared with me)
  • Ideally used as a backup for all your UGA related files

For published projects

  • Raw data should be uploaded to appropriate databases (e.g. SRA for WGS reads)
  • Code and data (analysis results < 50MB) should be in a public repository on GitHub
  • Code and all analysis results (not raw data if it’s been uploaded to a database) should be in lab OneDrive
  • Both GitHub and OneDrive directories should have a detailed README

External Hard Drive

In addition to using OneDrive to automatically sync your files, please regularly back up your computer to an external hard drive. The lab will provide a hard drive for this purpose.

Data organization best practices

Project organization

I suggest making an individual directory and git repository for each project you are working on that contains the data and scripts associated with the project, including a README.txt file describing the contents of the folder and a license text file (see https://choosealicense.com/). You should also use a workflow manager (Snakemake, Nextflow) or notebook (Jupyter, R Markdown) to document your analyses.

Here’s an example directory structure for a project using Snakemake for workflow management and conda for software installation.

conda_envs/
data/
   raw_data/
   analysis1/
   analysis2/
   analysis3/
figures/
LICENSE.txt
scripts/
Snakefile
README.txt

File names

Please follow these rules for file names:

  • Please don’t use spaces, instead use underscores or hyphens
  • Use descriptive names (not figure1.txt or draft.docx)
  • Use dates when it makes sense. If you start your files with YYMMDD or YYYY-MM-DD, they will automatically be sorted in date order. Pick one and be consistent. Use a date rather than writing “final_FINAL-final” in your file names.

Tables and spreadsheets

If you are creating a new dataset in a table or spreadsheet, please consider these guidelines from Karl Broman and Kara Woo and the Data tidying chapter from R for Data Science .

Training

Introductory Reading

Computational Skills

In the Mortimer Lab, we regularly use the Unix command line and slurm to interact with the cluster, git and GitHub for version control, Python for sequencing data analyses, R for statistical analyses, and Snakemake to create data analysis pipelines.

Offered by UGA

GACRC offers extensive Unix and slurm training in order to set up a new account on the Sapelo2 cluster.

In addition to cluster training, GACRC offers additional training on topics like Python and R. Check out the most up to date training information here.

Training is also available through Carpentries@UGA.

Online Articles, Tutorials, and Textbooks

Unix

Git

Python

R

Snakemake

Bioinformatics and Microbial Genomics

Statistics

Books Available in the Lab

  • Statistical Rethinking
  • Evolutionary Dynamics
  • Microbiology: an evolving science
  • A Biologist’s Guide to Mathematical Modeling in Ecology and Evolution
  • Modeling Evolution
  • The Practice of Programming
  • Bioinformatics Data Skills
  • The C Programming Language
  • The Academic Job Search Handbook
  • The Professor is In
  • NextGen PhD

Lab Safety

First Aid Kits

There are first aid kits in both the dry lab space and wet lab space. In the dry lab (Room 121), the first aid kit is located on the bottom shelf of the bookshelf. In the wet lab (Room 150), the first aid kit is located on the wall next to the door.

Severe Weather

The severe weather and tornado gathering space is in the admin hallway of PDRC.

Laboratory and Chemical Safety

If you will be working at the bench, please complete the safety training available through UGA’s PEP:

Biosafety

Our lab is a BSL-2 laboratory. You must complete the Proficiency in Standard and Special Microbiological Practices form after training. If you will be working at the bench, please complete the safety training available through UGA’s PEP:

  • UGA Right to Know: Bloodborne Pathogens Training (annual)
  • BSL-2 Training Curriculum

Our biosafety manual can be found in the lab OneDrive.

Professional Development

Resources at UGA

Online Resources

Conferences

Graduate students and postdocs can expect to attend at least one conference per year funded by the lab. Trainees are expected to submit an abstract to present at conferences they plan to attend, and you should plan to apply for any travel awards provided by the conference or university if you are eligible. A final draft of the abstract must be sent to all co-authors at least one week before the submission deadline for feedback. Please have a draft to me at least two weeks in advance, so that we have time for edits before sending to co-authors.

The following are conferences that you might consider attending:

Microbiology

Microbial Genomics

Antimicrobial Resistance

Sexually Transmitted Infections

Evolution

Funding Opportunities

Successful funding applications can be found in the lab OneDrive if an example would be helpful to work from! Please do not share these applications outside of the lab unless you have the permission of the original author.

Postdoctoral

Graduate

Undergraduate

Job Boards

Science job boards

Microbiology or infectious diseases job boards

Ecology and evolution job boards

I need help with…

Computing on Windows

Windows Subsystem for Linux

The easiest way to get a unix terminal on Windows is to install Windows Subsystem for Linux.

Choosing a text editor or IDE

When you are working on a cluster system or in the unix shell, it can be helpful to know how to use a text editor since you may frequently need to edit files like job submission scripts without transferring back and forth from your own computer. People have strong opinions on which text editor is best, but you should use whichever you are most comfortable with.

Text editors available on Sapelo2

Vim

Vim is the text editor that I use, so it is the one I will be able to help you with if you choose to use it.

Vim resources and plugins

emacs

Emacs is another popular text editor.

emacs resources

nano

Nano is a basic text editor. It is probably more intuitive than vim or emacs, but it is also less powerful.

nano resources

Open OnDemand text editor

You can also edit files in the browser using through Open OnDemand. This text editor has options for both vim and emacs key bindings.

Text editors for your personal computer

You can also use vim, emacs, or nano on your personal computer if you are working in the Windows Subsystem for Linux, Linux, or Mac Terminal. Additionally, you could use a text editor with a graphical user interface, like these:

Integrated Development Environments (IDEs) and Notebooks

IDEs and notebooks allow you to interactively edit and test your code within the same software.

RStudio

If you regularly work in R, you might enjoy using RStudio. RStudio is available for Windows, MacOS, and Linux. It is also available on Sapelo2 through Open OnDemand. RStudio also recently added support for Python.

RStudio resources

Jupyter

Jupyter is another popular notebook-based IDE, which you can use on your computer or Sapelo2. You can use Jupyter for Python, R, or Julia.

Jupyter resources

Computing on Sapelo2

Logging in to Sapelo2

If you are trying to connect to Sapelo2 off campus, you must be logged in to the VPN. Your UGA MyID and password are used to connect to Sapelo2. In the command line, you can type ssh UGAmyID@sapelo2.gacrc.uga.edu, enter your password, and accept the push notification through Duo.

You can also use a config file (.ssh/config) to save the Sapelo2 host information, so that you don’t need to type it every time. For example, with the following config file, you can log in with the command ssh sapelo2.

Host sapelo2
	HostName sapelo2.gacrc.uga.edu
	User myID

GACRC Documentation: Connecting to Sapelo2

Software on Sapelo2

Centrally Installed Software

GACRC centrally installs software packages on Sapelo2 through software modules or singularity containers.

GACRC Documentation: Software

Conda and Mamba

If the software you would like to use is not already installed on Sapelo2, consider using conda (or mamba, a faster version of conda) to install the software in a dedicated environment.

Steps to install conda and mamba (run in command line):

  1. Download miniforge: wget https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
  2. Run the installation script: bash Miniforge3-Linux-x86_64.sh
  3. Mambaforge will be installed in your home directory
  4. Choose yes when asked if you would like the installer to initialize Mambaforge
  5. Exit and reconnect to the cluster

Steps to install specific software:

  1. Create a new conda environment: mamba create -n name_of_environment
  2. Activate the environment: mamba activate name_of_environment
  3. Install software: mamba install name_of_software

Steps to export a conda environment to a file (helpful for snakemake configuration):

  1. Activate the environment: mamba activate name_of_environment
  2. Export the environment to a file: mamba env export > name_of_environment.yml

Transferring files between Sapelo2 and your computer

GACRC Documentation: Transferring Files

You can transfer files to and from Sapelo2 using scp or rsync. Here is an example of a command that will transfer a file in your current working directory to Sapelo2:

scp filename MyID@xfer.gacrd.uga.edu:/full/path/to/where/you/want/the/file/

Reading and citing the scientific literature

Finding relevant articles

Primary research articles and review articles

Primary research articles describe original research, and you should aim to stay up to date on published primary literature in your field. However, review articles can be a helpful place to start to get an overview of a new field and find citations to relevant primary literature.

Databases and Alerts

Popular databases:

Many databases also have the option to create citation alerts for particular search terms, which will send a digest of relevant literature via email. UGA has instructions on creating alerts for various databases here.

Peer-reviewed articles and preprints

What is a preprint?

A preprint is a version of an article that has been shared publicly but has not yet been peer reviewed. Popular preprint servers in biology include bioRxiv and medRxiv. In the Mortimer Lab, we aim to publish all articles as preprints prior to or at the time of submission to a peer-reviewed journal.

What is peer review?

In peer-reviewed journals, articles are sent out for review to a few experts in the field before publication. Most reviews are single-blind peer review where reviewers know the identity of the authors, but reviewers remain anonymous and reviews are not published alongside the article. However, journals are experimenting with other peer review mechanisms, including double blind peer review (both authors and reviewers are unknown to one another), signed peer review (where reviewers have the option to reveal their identity to authors), and publication of reviewer names and comments alongside the article.

There are also venues for post-publication peer review like PubPeer, which facilitates anonymous comments on published articles.

If you have been asked to review an article, here is some advice on performing peer review:

Open access vs. subscription journals

Journal articles are either published open access, meaning they are available to anyone at no cost, or through a subscription to the journal. Some journals are fully open access (e.g. journals in the PLOS family, mBio), and some journals have the option to publish open access for an extra fee paid by authors. In the Mortimer Lab, we aim to publish all articles open access.

UGA has several options to access the full text of journals requiring a subscription online. Articles presenting work funded by NIH are also required to be available through PubMed Central within 12 months of publication. If you cannot get access to the article through any available databases, you can try emailing the corresponding author of the article for a copy.

Reference managers

To keep track of papers you’ve read and cite them in your own work, it can be helpful to use a reference manager. A good reference manager will have browser plugins to easily save citation information and PDFs, the ability to organize your citations, and functions or plugins to export citations or insert them into your document in the correct format.

Zotero is a free, open source citation manager with browser, Microsoft Word, and Google Doc integration. We have a shared lab Zotero library. Mendeley is another free citation manager. Here at University of Georgia, we also have access to Refworks and EndNote. You can find out how to access these tools through UGA University Libraries.

How to read a scientific article