By Jan Cheetham, Research and Instructional Technologies Consultant, DoIT
LabArchives is an ELN (Electronic Lab Notebook) that provides data storage, data documentation, collaboration, and export features. Like traditional paper lab notebooks, an ELN can serve as a continuous and complete record of the research process.
Collaboration and Sharing
LabArchives provides flexible permissions and roles for lab members and their collaborators. It is recommended that PI’s assume the Owner role in all their lab’s notebooks, in alignment with UW-Madison’s Policy on Data Stewardship, Access, and Retention and to ensure that no data is lost when lab members graduate or leave the university.
There are several approaches for organizing notebooks and managing edit/read rights of individuals. Permissions can be set at the level of the notebook, page, or entry. It also possible for individuals in the Owner or Admin role to share notebooks, pages, and entries with collaborators outside the university. Although LabArchives has a method for creating Digital Object Identifiers (DOIs) for notebooks, this requires making the notebook publicly available. The UW-Madison LabArchives site currently has the public sharing feature turned off as a security measure to prevent inadvertent sharing of notebooks.
The ELN provides a timestamp and record of every user action, creating an electronic record of who added or edited an entry and when. In addition, nothing can be permanently deleted from the ELN. ( LabArchives allows you to move a notebook, page, or entry to a Delete Bin; however, these items are not actually deleted and can be recovered at any time.)
Organizing and Documenting
The ability to blend digital data with the human readable narrative of the research process is one of the main advantages of an ELN over other file sharing/storage services or hybrid paper/electronic systems. LabArchives has a number of different entry types for entering data and recording the narratives. Below are a few suggestions that will help ensure that the information you enter in LabArchives can be readily retrieved.
LabArchives currently does not offer a way to browse through folders or pages chronologically. Therefore, you may want to use file-naming conventions for pages (and possibly, folders). Names should contain a project name, date, experiment identifier, etc. For more specific suggestions, see naming conventions in an ELN. It is also a good idea to use similar naming conventions for files you attach or link to in the ELN to make it easier to trace through versions and locate those with transformations.
Documenting attached files
In LabArchives, you upload and attach a single data file to an attachment entry on a page. The file can be of any type and up to 250 MB in size. The entry will display the name of the attached file and you can also enter a description with detailed information (metadata) about the file. When you upload a new version of the file to the same entry, LabArchives retains all prior versions and lets you revert back to older versions through the entry’s revision history. However, as noted below, only the most recent version is included in HTML export. Therefore, to ensure that all data files that you or someone else would need to reproduce your findings are archived both inside the ELN and in HTML exports, be sure to create a separate attachment entry for each essential file that needs to be retained in its original, unaltered form. Then, new versions of the data file (in which the original data are cleaned, transformed, analyzed, visualized, etc.) should be added to the ELN as one or more new entries.
Documenting linked files
When data files are too big (>250 MB) or too numerous to attach to the ELN, you can create links to them from within a rich text entry. However, LabArchives does not check links or verify locations, so you will need to ensure the files are in a secure and permanent location. It is also a good practice to record the name of the file and its location directly in the rich text entry since the URL you add when you create a link is not directly visible in the entry.
Exporting and Archiving
LabArchives has two export formats, PDF and HTML. The PDF version is similar to a scanned paper notebook page. The HTML version lacks some of the appearance of the notebook but contains more complete information, including attached files. As with any digital platform you use for your research data, you will want to have a backup and archival plan. This should take into account how often you make changes to the notebook and include methods for retaining duplicate copies of important data files in alternate locations.
PDFs can be created for a single entry or page or entire notebook. PDFs include: text entries, thumbnails of images and widgets, annotations and descriptions of attachments, user name and time/date stamps. They do not include: attached files, version history of attachments, or comments. URLs of links in rich text entries may be retrievable, depending on the application you use to read the PDF.
The HTML option exports an entire notebook. Each page in the notebook is a separate HTML file and the most recent version of each attached file is also included. This export option also does not include version history of attachments or comments. Again, URLs that you add to create links in rich text entries may be retrievable, depending on the browser you use to read the HTML pages.
Do you have additional questions or concerns about electronic lab notebooks? Contact us.