(r4) LabNotebooks < Lab

---+!! Lab Notebook Best Practices

%TOC%

---++ Notebook Setup

*Preferred Platform:* [[https://benchling.com/][Benchling]] Electronic Notebooks

Have an administrator add you to the Barrick Lab organization on Benchling.

Create your main Benchling project folder that will contain everything you work on in the Barrick Lab. Name it “[First Name] [Last Name] (Barrick Lab Projects)”. For example, "Jeffrey Barrick (Barrick Lab Projects)".

Right-click on the project and change the settings:
   * Make the Barrick Lab organization the owner
   * Set the privileges so that Barrick Lab members only have read access.

---++ Notebook Organization

---+++ Folders

Most researchers choose to have one folder per project inside their main folder. Then, they create several separate notebook files within each of these project folders, with each notebook covering a subproject or a series of related experiments. If your notebooks are getting large for a subproject, it can be helpful to divide them up by numbering them consecutively or with the date interval each one covers. If there are many of them, then you can also consider adding another subfolder level to keep them organized.

---+++ Content

It's good practice to write a sentence describing the purpose of each experiment at the beginning and a short summary of the results at the end. Benchling allows you to insert dates – including into the future – so you can also write out *what you plan to do* beforehand and check it off as you get to it for multi-day procedures.

What data works well in a lab notebook versus in other places?
   * Benchling - tracks history, but storage is limited and is not meant for large files.
      * Plasmid designs
      * Sanger sequencing reads
      * Assembled full-plasmid sequencing, reading
   * UT Box - much more storage for large files
      * Raw high-throughput sequencing reads (Illumina, Nanopore, etc.)
      * Spreadsheets of data compiled across many experiments
      * Plate reader output
      * Flow cytometry raw data files
      * Large microscopy images
   * GitHub - tracks commit history and can be used to share code/data. Not meant for large files.
      * Code and scripts
      * Example input data
      * Don't store large data files in GitHub repositories!
      * Create a Zenodo archive to accompany a publication
   * NCBI - data used in published studies.
      * SRA - genome/plasmid sequencing reads
      * GEO - gene expression data (RNA-seq)

---+++ Experiment IDs

Many researchers have found that giving each experiment within a project a number or other systematic unique identifier is helpful. It makes it easy to unambiguously reference a prior experiment, particularly when you have many similar experiments or repeated the same experiment multiple times on different days. If you share this identifier with a collaborator, it also makes it easy for them to find the correct notebook entry or find the data set that was used in a publication.

Some examples of unique identifer formats:
   * YEAR-INITIALS-# 
   * TOPIC-#; 
   * Project/DATE

---+++ Protocols

For experimental procedures that you use regularly, it is well worth your time to set up a folder that contains templates for these procedures. You can copy them into notebook files or attach them. If you do the same procedure many times, you can also set up a template file and use it when you create a new notebook entry.

---+++ Summary

Here’s what a folder layout might look like in Benchling:

Jeffrey Barrick’s Barrick Lab Projects
   * Protocols
   * Templates
   * Plasmids
   * Oligos
   * Project 1
      * Subproject / experiment series A notebook
      * Subproject / experiment series B notebook
      * Subproject / experiment series C notebook
      * ...
   * Project 2
   * Project 3
   * ...

---++ Notebook Backup

Lab notebooks are the record of all your hard work and amazing results. They must be carefully preserved while you are using them and especially after you leave! Benchling — or any other digital platform — could change in the future in ways that make your notebooks inaccessible, or worse it could experience failures and lose user data. For this reason, you should periodically export all of the notebook files and data that you store in Benchling. This can be accomplished by clicking on the gear next to the project name and choosing “Export project.” It may take a while, but you’ll eventually download s ZIP archive. Copy it to UT Box for long-term storage for the lab and to your hard drive or another cloud storage location so that there are multiple backup copies. *Lab clean-up days are a good time to take care of “maintenance” tasks like this and/or put a recurring reminder in your calendar every 3-6 months!*
Barrick Lab > ProtocolList > LabNotebooks
Topic revision: r4 - 2024-01-25 - 12:52:18 - Main.IsaacGifford