5 min read
Keeping a Lab Notebook
Nov 23, 2019 1:16:38 PM
Jean Peccoud has experienced first hand the challenges of managing research programs that combine experimental and computational elements. He is passionate about increasing the productivity of his own research and hopes to help other groups by blogging about his experience. Jean is also the founder of GenoFAB. Nov 23, 2019 1:16:38 PM
Is keeping a lab notebook challenging? Does it feel like a waste of time? Do you even have a lab journal? GenoFAB can provide you and your team with the notebook solution and support it needs to increase the speed of your next project. Contact us to discuss how better record keeping can increase accelerate your project and decrease its cost.
The lab notebook bad rep
Keeping a lab notebook may be one of the most challenging aspects a scientific research. It's fair to say that the lab notebook has a bad reputation. It's often perceived as a waste of valuable time that would be better spent collecting more data. This perception is the direct consequence of the limitations of paper notebooks used until the lab notebooks started turning digital about 20 years ago.
The linear format of paper notebooks was not very suitable to keep track of multiple experiments conducted in parallel. For instance, someone could be working on assembling a plasmid while at the same time preparing a cell culture that will be transformed with the plasmid. A project may require working with mice and cell cultures at the same time. One solution to this challenge was to dedicate different notebooks to different aspects of a project or, to different projects. However, there is so far this approach can go.
Papers notebooks are notoriously difficult to search. Flipping pages after pages of poorly handwritten notes trying to remember the details of an experiment could be very frustrating. This limitation of paper records challenges the value of keeping a notebook. What's the point of spending time documenting experiments if it proves virtually impossible to retrieve critical information when you need to?
The personal nature of paper notebooks make collaborations difficult. For legal reasons, notebooks were assigned to a person, not to a group. Collaborative projects that require experiments performed by different persons become extremely difficult to track because records are scattered across multiple notebooks belonging to different collaborators.
Finally, keeping paper notebooks is very time consuming because the same protocols have to be written over and over. After a while, it becomes tedious to recopy the same transformation protocol every week. This prompts people to take shortcuts, take increasingly spotty notes, until they reach a point where the notes captured in a paper notebook are essentially useless.
Advantages of electronic lab notebooks
CambridgeSoft E-Notebook (now part of Perkin-Elmer) was probably one of the first commercially available Electronic Laboratory Notebook (ELN). There are now many ELN available on the market. They all address the main limitations of paper notebooks.
Their digital content is easily searchable. They are easier to read than handwritten notebooks. They have search features that make it easier to retrieve information.
They have a hierarchical structure that makes it possible to work on as many projects as needed simultaneously.
They are collaborative as they make it easy to share notebooks or even entries within a notebook. This makes it possible for multiple people to write entries together. It is also easier for third parties to get access to a notebook. For instance, a manager may be interested in keeping an eye on a project progress by reading the corresponding lab notebook entries.
Procedures, experiments, etc...
And most importantly, ELNs make it much faster to keep a good records as long as the team adopts the right strategy that captures the hierarchical nature of laboratory activities.
Procedures are like family recipes
Just like there are many recipes to make brownies, there are many ways to perform routine procedures like plasmid mini preps or bacterial transformations. It is often the responsibility of the lab manager to develop a collection of preferred protocols used by the entire group just like some families would have their preferred brownie recipe in the family cookbook. Having a preferred protocol will reduce material and supply expenses as everybody will use the same kits. It helps standardize training and troubleshooting. More importantly, it increases the reproducibility of experiments and reduces failure rate.
Many labs still have a binder of preferred protocols somewhere on a shelf. Others have moved this in a shared drive. These collection of protocols are like the lab family cookbook.
Experiments are like a six-course meal
Performing an experiment requires the execution of a series of protocols. Just like a chef preparing a six course meal will execute the recipes of six courses included in the menu, someone assembling a plasmid will perform a ligation, a transformation, a mini prep, a restriction digest, and prepare plasmids for sequencing.
Standardizing experiments can be a little challenging. An experienced laboratory manager will recognize sequences of procedures used by most projects in a group. The ligation, transformation, miniprep sequence is very common. Other sequences of protocols may be more project-specific. For example, experiments aiming at collecting data to test the behavior of a gene circuit will be specific to this project.
When planning to document upcoming experiments, it is beneficials to identify the workflows that will generate the bulk of the data as this will improve reproducibility, efficiency, and data quality. One of the challenges of this exercise is to set the limit between two experiments. Does an experiment correspond to a series of lab operations that will take a year or two to perform or should it correspond to a smaller unit of work?
We suggest breaking down a project workflow into experiments corresponding to the sequences of operations between decision points. For instance, a project may require making a plasmid, transforming the plasmid into a cell line, and performing different tests on that cell lines. Each of steps would correspond to experiments.
Studies lead to figures and projects to articles
How should experiments be organized? It is practical to group experiment into studies, and studies into projects.
Practically, a study may correspond to the experiments producing the data that will be summarized in the figures of an article. For instance, a study will include a series of experiments performed on a library of samples to collect data that will be summarized in chart.
Organizing studies into projects may be the most difficult choice. Is a project a line of work that will extend over multiple years or is it a series of studies that will lead to a paper? We suggest to keep projects small enough that it is possible to archive them on a regularly basis. It is necessary to bring projects to a term to prevent them from getting so big that navigating them would become overwhelming. So, associating projects with a body of work leading to one publication or one patent application seems to make sense for most groups.
Start keeping a lab notebook
In a follow-up post, we will explain how this planning effort dramatically increases the efficiency of record keeping.
How does your lab document its operations? Has your group ever lost data? Is it more challenging than it should to retrieve data when filing a patent or preparing a manuscript? Is there too much variability of basic laboratory operations? Does it feel like everyone in your team is working differently? Do you wish to adopt an ELN but are unsure of which one to choose and how to deploy it?
Let's talk. GenoFAB can provide your team with the ELN and support it needs to increase the speed of your next project.
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