OneNote
This case study focuses on one of the most universal solutions for an electronic notebook – Microsoft OneNote. This has been the notebook of choice for over a decade for one Professor’s research group based in Physics. Currently the group numbers about 30 people, including technicians and other research staff, who all use OneNote for their personal and collaborative notebooks.
Notebook
The group primarily generate data from optical spectroscopic techniques, such as ramen spectroscopy data. Their notebooks are used in a number of different ways during the course of the research. The health of the instruments used is tracked in shared notebooks to monitor any abrupt changes or gradual reduction in performance. Researchers also use personal notebooks to keep track of their experiments, including the design, results (sometimes in the form of screenshots), observations and summary of conclusions. Group meetings are recorded in shared notebooks with everyone able to contribute to the notes. Notes are mostly typed but pens are occasionally used to draw things during meetings and other media are incorporated using links or embedding images such as png or jpeg files. During experiments they are working on computers and so can type directly into the notebook.
The group have found the notebook easy to use and intuitive, although they admit they are not doing very complicated things. They have not had to seek any support or training as it is similar to Word. It is easy to find information in the notebook because the in-build search function is very fast and thorough, for example it will even recognise handwriting when searching. The results are shown in sections explaining their relation to the search term, such as: “recent”, “in title”, or “on page”.
On collaborative pages, it is possible to tell who has authored what contribution and when, although there doesn’t appear to be a built-in versioning mechanism for this (although it is acknowledged this feature may exist). This has caused a few issues but not many. The data is held on a server in the department and links to the data are added in the notebook.
Within the group they share links to the right part of the notebook. For external collaborators they make a pdf of the relevant part and send this over via email. Group notebooks highlight text that has been changed, making it easy to see when something has been updated and also highlights the page in the navigation menu so you can see which pages have changes. This function is useful and intuitive.
The group shares quite openly so access controls in the notebook are not important to them, but there are controls on the data folders on the server so that only the data originator can edit or delete the files.
The group is using a local version of OneNote that they access via the University network (or VPN). It is held on a local server. This negates any worries about third party infrastructure or data security that the group might have. There is an option to back up the notebook to Sharepoint should the group want to create additional back-ups.
The notebook can be saved offline as a OneNote file but this is a proprietary format. Part of the reason the PI chose OneNote was because Microsoft are well established and although it is proprietary it is unlikely to suddenly be unsupported in the future. It is possible to export the notebook or pages as pdf or docx files. One potential issue is that any hyperlinks used in the notebook to files or websites might not work in the exported file (whereas URLs would work).
RDM
It should be noted that the PI has been using this notebook system for over a decade with his group and so must have an exit strategy for group members.
- Shared notebooks are organised in a standardised way but individuals can organise their personal notebooks in a way that suits them. This approach has been taken as experiments vary a lot within the group.
- The group meeting notebook is set up systematically with sections divided into years and months with a new page for each meeting. The researcher interviewed for this study uses this system in their personal notebook and finds it works well but some members in the group prefer to organise their notes by experiment.
- The postdoc I spoke to thought they would probably replicate this system if they start their own group or as a personal notebook if they left the group – if you find a good way to organise your work, then stick with it!
Return to Electronic Notebook Guidance
Read more case studies: Hivebench, LabArchives and Benchling
Hivebench
This case study focuses on Hivebench, an electronic lab notebook product from Elsevier, and how it is being used by a group conducting cancer research at the University. The group is sizeable, with around 20 researchers plus around the same number of support staff. The group originally started using Hivebench a few years ago as part of a pilot that Elsevier were running and therefore have seen features change overtime as the product has been developed. Hivebench no longer offer the set-up that this group use and so their experience will be very different to other Hivebench users.
Notebook
The group collects a range of different data types, from numerical data, sequencing data (collected as large text files) to very large, high resolution microscopy images. Experiment plans are written up in the electronic notebook and some resulting data is imported in, for example, Excel files of numerical data. However, this group have not had a good experience of using Hivebench for large files, such as the images that are produced, and these are saved elsewhere with their location copied into the Hivebench notebook along with metadata information.
Hivebench provides an app so the notebook can be used at the lab bench; however, the researcher I spoke to prefers to print out the experiment designs and take notes by hand as he finds this quicker. The important information is typed up into Hivebench but this may mean some of the thought process is not captured in the electronic notebook.
The instance of Hivebench that is being used by the group was set up locally so that they could save all the data onto their own servers. This is because the group works with NHS data and must be very careful about where it is saved to. Regular snapshots are taken of the data and the biggest data loss the group have had to cope with is four hours when their server crashed. Hivebench stopped supporting local set ups like the one piloted by this group and now only offers a cloud version. This has left the group with problems with the app not working and Hivebench taking a different direction with their product.
The group haven’t found Hivebench very easy to use and do not find it intuitive. At the time of the pilot, the knowledge base offered was quite limited for self-learning and the group was frustrated by the interface – this is something to be wary of for all new products that are still in development. On the positive side, they did like the overall design of Hivebench having separate notebook and experiment sections as well as a separate protocol area. The search function in Hivebench seems to generally work quite well although it has been more difficult to find protocols as these do not have standard naming conventions. A lack of a version history mechanism means you cannot easily see who has changed what information in the protocols. Within the group, information is shared via links to notebooks or sections of a notebook. Unfortunately, they cannot grant an external user access.
As the group have a local instance of Hivebench they are confident that they can maintain the information in the system for as long as they need. If someone leaves the group then they grant access to their work to their PI and lab manager. The real problem the group faces is if they want to export their work out of Hivebench. They can only export files as pdfs, which they wouldn’t find useful. The loss of links to other files and the structure would be a big problem for the group, which means they currently feel locked in to using the notebook.
RDM
The group works in a way that encourages good data management and these principles can be applied no matter what notebook is used.
- In order to respect academic freedom, there is no standard procotol used by the group for organising work in the electronic notebook. Everyone naturally uses project as the highest level but beyond this may sort their work by data type, conclusion or another method. The researcher I spoke to keeps a description of how his data is organised and believes that this should enable someone else to find a piece of his work should they need to.
- Files that are not saved within Hivebench are linked to by copying the file directory structure into the notebook rather than using hyperlinks. This is used because even if the data is moved from the top level active folder to an archive folder, the root underneath should remain the same and therefore the file is findable even if it takes a little bit of searching. This is much more preferrable to having a broken hyperlink.
- Searching for information is made easier by using a good file naming convention.
- It would be useful for the group to have their own protocol around sharing and granting others access as well as countersigning notebooks to ensure this is done consistently.
Return to Electronic Notebook Guidance
Read more case studies: OneNote, LabArchives and Benchling
LabArchives
LabArchives is an electronic notebook product that is being used by a life sciences group. The group number about 15 and have a lab manager who is able to organise the notebook and assist group members who are using it. The group chose to use LabArchives as it offered the easiest user interface with a format that could directly replace their paper lab notebooks. The group had previously lost work due to people leaving without leaving proper notes. The PI asking to see paper notebooks regularly would have felt distrustful and so the group turned to an electronic solution so that the PI could retain an overview of the work being done in a way that felt less intrusive to the group members. The group used a paid-for plan in order to access advanced features.
Notebook
The group is working in the area of cell biology and protein science, using data from cell lines and RNA extraction. The notebook is solely used like a journal to record what needs to be done, summaries of experiments, and notes and observations. They use templates in the notebook to ensure that the right metadata is recorded for each experiment type. Data is held on a server or on instruments with links inserted into the notebook to reference the data. Routine protocols are held on the notebook but as the versioning is not that great on LabArchives, the group prefer to keep them in their GoogleDrive. The group have installed a desktop in their tissue culture lab so that notes can be directly entered into LabArchives and the risk of contamination from lab books moving around is minimised. Otherwise notes are made on paper which is taken out of the room and then typed up.
Collaboration within the group is usually done by setting up a shared notebook, although organising access has been tricky. Otherwise individual pages can be shared easily with another user (although they don’t get a notification that it has been shared) and access can be given on a read only or editing basis. Being able to control who can access each members’ notebook(s) is important as they are worried that if they were completely open then researchers might write less in the notebook due to fears around competition. When it comes to sharing with external people, they are able to generate a DOI for a specific page, which can then be shared with the collaborator.
The group have found LabArchives incredibly easy to use. New users don’t usually need a tutorial to get started. The more complex features take a bit more time to learn and the group has been able to support each other without really consulting the online help offered by LabArchives. The search function allows you to search through just one notebook or multiple notebooks and so far there hasn’t been a problem with finding things by key word or date; however, not that many people have left the group so whether or not this freedom becomes an issue down the line remains to be seen.
The group admit to putting a lot of trust in their notebook provider but as they are paying for this service they feel that it is implicit that the data is backed up securely. LabArchives will remains a core resource to the group until a better alternative comes up. One of the biggest challenges the group faces is ensuring they have funding which they can use to pay for the account as it is not regarded as an eligible expense by all funding bodies.
RDM
The group works in a way that encourages good data management and these principles can be applied no matter what notebook is used.
- Members of the group are allowed to set up and use their notebooks however they wish – just as they would with a paper notebook. Some people use it like a diary and have their notes organised by month and day, others organise it by project. This seems to work well for the group.
- The lab manager makes links to files that are not LabArchives by inserting just the file name into the notebook. His computer can then just be searched for that file name. This requires using a good file naming convention, which may be a problem for other group members.
- The lab manager does admit to being cautious though and creating his own back ups by exporting his notes as pdfs every month or so and backing these up elsewhere.
- When someone leaves the group their paper notebook would be left behind so it is essentially the same with their electronic notebook – the user account is closed but all the data remains with the group and the lab manager can give access to those notes to whoever needs it.
- The group thought about an exit strategy before they started using the notebook. If they needed to extract all their work, they could export everything as pdfs. Whilst they acknowledged that this isn’t the most useful form for the information, it wouldn’t be any worse than having the information in a paper notebook.
Return to Electronic Notebook Guidance
Read more case studies: OneNote, Hivebench and Benchling
Benchling
This case study explores the use of Benchling for academics by a research group in the School of Biological Sciences working on plant genetics. The core of the group is small – about six researchers and technicians – but also works with undergraduates and summer placement students who are expected to use the notebook. The group has a lab manager who also ensures the notebook is used properly and manages the admin side of the notebook on behalf of the group. Benchling is a notebook specifically designed for molecular biology research. This case study shows how they are currently using Benchling and the good data management principles they employ to make their use even more successful.
Further information about how this group and how they use Benchling has been published in the blog Generating FAIR — Findable, Accessible, Interoperable, Reusable — Resources with Marchantia, a Prototype for Plant Synthetic Biology on benchling.com.
Notebook
The group works with molecular biology data, primarily DNA assembly and sanger sequencing data and all the associated data around designing and analysing transformation experiments. They use the notebook for designing experiments and plasmids they want to build using the tools in the notebook. These tools help them keep track of how the experiment has been designed, the provenance of design elements and the author or editor of the design. Once the physical experiment has taken place the resulting sequence can be imported into the notebook and checked against the design. Metadata is added to the notebooks using registries and schemas set up by the lab manager.
Observations are also added to the notebook in the form of text or images, such as screenshots, and paper notebooks are still used at the bench with the resulting information typed up into the notebooks.
Benchling handily records information about who creates and adds experiments in the notebook section as well as in the inventory they keep, which is useful for knowing who has been working on what, especially if someone has subsequently left the research group. Some date information is added by the lab manager using a feature of the notebook. Whilst this is very useful, it does need to be used properly in order to be effective. Data can be exported out of the notebook as a csv and the group frequently do this to work on data analysis in R.
The notebook is very intuitive and new users only need a basic tutorial from the lab manager before they can get going on the group instance of Benchling. When they started using it, the lab manager used the tutorials created by Benchling and found these very useful. The support has also been very responsive and willing to help with any of the group’s queries. The group hasn’t needed any help from the department or University IT in order to use Benchling. Searching the notebook for information is generally very straightforward if you know what you are looking for, but it might perhaps be more difficult to find something in the notebook section if you are searching for a term or phrase.
If the group wants to share something with an external collaborator, they simply ask them to sign up to Benchling. The lab manager can set the permissions of anyone using their group instance so that they have control over who can read, write and edit entries. Failing that, the data can be exported in various formats and are small enough to share via email. The group isn’t aware of any notification systems that will inform a current user that a page has been updated, although the version history will list who edited the page last and when but it doesn’t detail the changes made.
Benchling for Academia takes snapshots of the data in such a way that allows data to be restored on the level of minutes. Weekly back ups are also made and stored for at least a year. It uses AWS technology and stores the data securely in the cloud.
The group knows that they could get all their data out of Benchling if they wanted to. Plasmids, metadata and notebooks can all be exported in file types that work for the type of information, and although it might be a bit of a hassle exporting it all, it would all be reusable.
RDM
The group works in a way that encourages good data management and these principles can be applied no matter what notebook is used.
- They use controlled vocabularies to ensure there is consistency and standardisation across the work of the whole group.
- Because they use a common naming system for their files it is easy to find corresponding data or images that they need for analysis, whether that data is kept in the notebook itself or elsewhere, as is the case for the images they create.
- The group uses an end of project process to ensure that useful plasmids are registered and physical copies are left in the lab. The lab manager has a list of the minimum information needed when someone leaves, which helps them to ensure that work is not lost or unintelligible to the next person.
- When someone leaves or their project comes to an end, the lab manager ensures any remaining researchers or technicians have access to the project if they need it. Otherwise, the project is archived.
- Group members are free to organise their personal notebooks how they wish and usually choose to order it by data and then experiment type. This respects the researchers’ freedom to choose their own organisation strategies.
The biggest worry the group has is what happens if the lab manager leaves. The rigorous use of standards and naming conventions is one of the reasons why Benchling is proving to be such a successful tool for the group. If the lab manager was not there to ensure it was being used consistently then finding information might become more difficult, metadata might not be recorded and key information might be lost when someone leaves the group.
Return to Electronic Notebook Guidance
Read more case studies: OneNote, Hivebench and LabArchives