Tips for getting started with LabArchives
LabArchives is a flexible platform with endless possibilities for customization to match your research workflow. LabArchives allows you to securely store, search, and share your research data. With LabArchives, you can organize your data and use the access management tools to work with your research team as well as external collaborators.
Tip #1: Create Notebook Policies and Procedures
It’s important to discuss with your team how you would like to use LabArchives. Creating consistent strategies and methodologies will increase efficiency and promote better communication throughout the team.
You may want to periodically review and discuss notebook policies. Keep in mind these policies can be modified anytime in the future as you find what works best for your teams.
Here are items to consider:
- Do we have any funding agency, company, client, government, or institution policies that we need to consider?
- Should we organize data by project, client, application, date, user, or piece of equipment?
- Do we currently have, or do we need to create standardized metadata or naming conventions for files, folders, sub-folders and pages?
- Should we create standardized formatting and structure or use templates?
- Should we use page signing or witnessing to indicate the final version of a page?
- Should we change the way we are formatting or storing data?
- Do we need to create a standardized list of tags to be used in the notebook?
- Do we need a standardized naming convention for files or pages?
- How should we handle large files or data that is stored in another location?
- Do we have current data and files that need to be migrated? See LabArchives Folder Monitor for more details on data migration assistance?
- How do we handle preexisting data that will continue to be stored externally?
- Do we need additional devices to access LabArchives?
Tip #2: Share Your Notebooks
One of the most helpful features of LabArchives is its ability to share data. You can share data with individuals in your research group or with collaborators. You can set up custom permissions for each notebook, folder, page or entry and you can change an individual’s access rights at any time. An individual can have Can Edit, Can View, or No access to different parts of a notebook and they can have a different User Role in each notebook.
You can manage access to the data with User Management, Group Management, Account Manager, and you can share portions of a notebook.
In most labs or research teams, the PI, Department Manager, Lab Manager, or Senior team member, owns all the notebooks. Each member of the lab has User or Administrator (Account or Notebook) rights to the appropriate notebooks.
Some things to consider when planning notebook access:
- Who should own notebooks?
- Who should be able to share data with others?
- Should we share data with external collaborators or make data publicly accessible?
- Should everyone have access to all data or should we set up custom permissions based on project or user?
Tip #3: Organize Your Data
LabArchives allows you to create multiple Notebooks, each of which is a completely separate entity. Each Notebook is divided into Folders, sub-Folders, Pages and Entries, much as the file system on your computer. You can rename or move data in the folder structure. Overall, the organization of your Notebook should be tailored to your needs.
Project or Grant-based Notebook
Some teams will organize notebooks based on projects. All data associated with that project would be stored in this notebook and everyone associated with the project would have access.
Shared Resource Notebook
Most teams create a notebook that is shared with everyone. This notebook could contain lab protocols, safety information, weekly meeting notes, or policies in the lab. This is a great way to quickly share data with everyone on the team.
Individual Notebook
Many teams will create one notebook for each member of the team. You can create a standard notebook for each person.
Instrument-based Notebook
You may want to create a notebook for a shared piece of equipment in the lab. With LabArchives Folder Monitor, files generated on a piece of equipment could be automatically uploaded to LabArchives.
Date-based Notebook
You may want to organize your notebook by date. You can create folders for each month or year and add pages for each day or week. This can be a great way to document things like equipment calibration information.
Template Notebook
To standardize a notebook or procedure across your team, you may want to create templates. Templates can help you maintain consistency and reproducibility across all members of the team.
Some teams build a standard folder structure and use the Clone or Copy from Another Notebook feature to create multiple notebooks with the same structure.
You can create template pages using several preformatted entries. Each user can select Copy existing page to use that template.
Some teams build custom Widgets in LabArchives. Widgets are simple HTML forms that can be used by the entire team in all notebooks.
Tip #4: Add Protocols, Safety Information, and Data
Anyone with edit access to a notebook can add new entries to a page or edit existing entries. You can add Rich Text entries, Headings, and Attachments of any file type. Your notebooks could contain lab protocols, safety information, manuscripts, important files, photos, and any other data that you want to record.
Add Text to Your Notebook
You can add text to your lab notebook using a Rich Text entry, Heading or Plain Text entry.
- Rich Text entries support text formatting like highlighting, font size, and you can add tables, images, and even videos to the entry.
- A Heading can be used to quickly break up a page.
- A Plain Text entry can be used to display code like markdown in your notebook.
Add Attachments to Your Notebook
You can add attachments of any file type to your notebook. You will see a thumbnail for any file saved and there are viewers for Office documents, PDF’s, and Images.
- Microsoft Office Documents: You can edit your Microsoft Office documents by using Office Online. Your edits will be saved automatically. You can also open files on the desktop version of Office using the Microsoft Office Plugin.
- Images: You can annotate images in your notebook using the Image annotator.
- SnapGene: You can view molecular biology files like .dna, .seq, etc using the SnapGene Viewer.
Build Custom Forms with Widgets
Widgets are customizable, interactive HTML forms or applications. Widgets can be tailored for your specific experiment and contain interactive text boxes, buttons, drop-down menus, and more. With LabArchives, you can use built-in widgets, manage tables through a database or freezer box widget, or create your own widget with The Widget Manager.
Manage an Inventory and Materials
You can use LabArchives Inventory to track materials like plasmids, cell lines, chemicals, and other lab consumables. Within LabArchives Notebook, you can add an Inventory List entry to the notebook. This allows you to add details about an item directly to the page and it will link back to the item details in LabArchives Inventory.
Tip #5: Promote Data Provenance and Reproducibility
It’s becoming increasingly difficult to find the original source for some data. Funding agencies, government organizations, and research institutions across the world are adding policies to encourage data integrity. You should be able to prove where your data came from, who produced this data, and how it was produced.
LabArchives has several tools to promote data provenance with your team. It’s also important to discuss the principles of reproducible data as you develop notebook policies and workflows.
Version Control
LabArchives maintains a complete revision history for every entry and page. Each revision is stored with a timestamp. You can always revert to a previous version of your data or undelete an entry.
Search Your Notebook
You can search across all notebooks in your account or you can search through a specific folder. You can enter Boolean (i.e. "AND", "OR", and "NOT") logic, literal phrases, and much more. You may want to develop a standardized file naming convention or use Tags to improve the search results.
Link to Other Data
You may want to connect data stored in another location to your notebook. You can link to data stored in LabArchives, to a web address and to a local file. Many teams will add Entry links to connect data with a specific version of a protocol. Some teams will add a Share URL to connect data stored in another location to a specific page or entry in the notebook. If working with large files or data stored outside of LabArchives, you can provide file paths, instructions, or links to the data.
Manage Activities in the Notebook
Your team can easily see recent changes to the notebook using the Activity Feed. This provides you with a chronological view of all logins, edits, and deletions. You can also find all entries created or edited by a specific user or all entries made in the last day, week or month using the Notebook Dashboard.
Communicate with your Lab Members
You can communicate directly with members of your lab using Comments. To alert a specific individual, use @ mentions. Comments can be added to any entry and you can receive email notifications or Activity Feed notifications about comments made in the notebook.
Additional Help and Support
Find help through the help center, view Video tutorials, or submit a question directly to our Support team.