Duke LabArchives Frequently Asked Questions

Information presented is based on Duke specific resources and the following ERN websites: LabArchives Knowledgebase, Columbia University, University of Pittsburgh, University of Pennsylvania, and University of Wisconsin.

 

What is LabArchives?

Duke University supports a LabArchives Electronic Research Notebook (ERN) institutional license for the Duke research community. It is a web-based application designed for scientists to create, store, share and manage their research data. A LabArchives Notebook may be shared among any number of Duke users; access rights are controlled by the Notebook Owner/Administrator and can be easily modified to suit the individual needs of each researcher or contributor. The platform is flexible and can be customized to support multiple different research workflows.

What are the benefits of an ERN System like LabArchives?

Duke University has an interest in adopting a centrally-support ERN system in support of improved data management practices. The LabArchives ERN system has the following benefits:

  • Access your research notebook entries anywhere
  • Data are searchable
  • Saves space by reducing/eliminating paper notebooks
  • Unlimited data storage (up to 15GB max per individual file uploaded)
  • Secure storage of research data in a central location
  • Support collaboration within research groups, including external (non-Duke) collaborators
  • Flexibility in setting user roles and customized permissions for research notebook viewing and editing
  • Able to customize templates, protocols and processes for different research workflows
  • Integrates with multiple programs including Microsoft Office, Duke Box, Duke shibboleth log-in, Google docs, ChemDoodle, PubMed, FlowJo, GraphPad Prism, and SnapGene.
    • If you identify other programs you would like to connect with LabArchives, please contact ASIST@duke.edu.
  • Able to store a variety of file types, including images, video, spreadsheets, etc.
  • Allows signing, file versioning, and activity tracking in support of data provenance
  • Supported Duke University service with security and legal protections in place

Can I enter Protected Health Information (PHI) or other sensitive data into LabArchives?

No Protected Health Information (PHI) or other sensitive data may be entered or stored into LabArchives.  Protected Health Information is defined by the Health Insurance Portability and Accountability Act (HIPAA) as:

Individually identifiable health information, including demographic data, that relates to:

  • the individual’s past, present or future physical or mental health or condition,
  • the provision of health care to the individual, or
  • the past, present, or future payment for the provision of health care to the individual

Examples of PHI include a patient’s name, date of birth, date of visit for treatment, age, address, and any other information that could directly or indirectly lead to identification.

De-identified data and information may be stored in LabArchives.  De-identified data has separated the data from the identifiers such that the data cannot be linked back to the individual.

Duke’s IT Security Office recommends different storage guidelines depending on the classification of the data from Sensitive-high, to Restrictive-medium, to Public-low. No Sensitive-high data should be stored in the LabArchives notebook.  Duke recommends the use of REDCap for input of data with PHI and OnCore for managing clinical research studies.  Additionally, PACE is another tool that may be used for analyzing data with PHI. Duke IT Services provides options for storing sensitive data in a secure manner and the PRDN (Protected Research Data Network- Social Science Research Institute) also provides consultation to researchers working with sensitive data to ensure they meet the associated data management requirements. 

What are the storage limitations?

Duke University users have unlimited storage and can create as many notebooks as they want. The maximum file size that can be uploaded is 15GB for an individual file.

Files Less than 250MB

  • Saved on secure cloud storage in your LabArchives notebook
  • Content fully searchable (if the document is editable in LabArchives)
  • Will get pulled in via Folder Monitor

Files Between 250MB-15GB

  • Saved in your LabArchives notebook in a unique DukeBox account (this is separate from your individual Duke Box account)
  • Searching within the content is not available; only file name is searchable
  • Cannot be previewed, edited, or annotated within LabArchives; download the file to edit
  • Will NOT get pulled in via Folder Monitor
  • Will NOT be exported in PDF or HTML versions of notebooks (only name of large files will be available in these offline copies)

Files Greater than 15GB

  • CANNOT be saved directly in LabArchives notebooks
  • Recommend storage on a Duke secure network drive or server and embed a link to that external drive/server location within your notebook page (see LabArchives knowledgebase link)
  • Searchability will be confined to the descriptive text written in the notebook page next to the hyperlink and text within the hyperlink. Descriptive text might include information about the server location and file names.
  • Will NOT get pulled in via Folder Monitor

Are there version controls?

All data entered into LabArchives is date and time stamped with the user who completed the action recorded as well. The timestamp is generated by National Institute of Standards and Technology (NIST) standard time. Each action (e.g., addition, deletion or revision) has a unique timestamp, and previous versions can be viewed. No data or notebook entries may be permanently deleted from Duke LabArchives notebooks (i.e. data and entries may be edited and moved into the notebook’s “trashcan”, but they can always be restored). This ensures full data traceability and supports intellectual property rights by documenting who did what and when they did it.  LabArchives also offers a “page signing” feature which permanently freezes a specific version of a notebook page (i.e. no further edits can be made to the page or the data on it).  

How are the electronic data and notebooks in LabArchives backed-up?

Once a research notebook is created in LabArchives at Duke, it cannot be deleted. Data saved on LabArchives will be stored using Amazon Web Services.  Both primary and secondary Amazon data centers for storage are located in the US. If desired, individual research groups may create locally stored copies of their LabArchives notebooks by exporting the notebooks in either PDF or HTML formats.

***NOTE: The Duke Libraries Research Data Repository provides support for long-term data archiving and public sharing . If you are thinking about how to best archive your data and whether there are existing repositories that might work well for your research data, contact askdata@duke.edu to learn more about repository options.

What data entry formats are supported?

Rich text data, tables, images, sketches, as well as annotations of images are supported. Any file (less than 15GB per individual file) can be uploaded, but not all files can be edited within LabArchives. For files that exceed this 15GB limit, you can link to files or folders from another server by adding a URL or a server address.  

What external software applications are directly integrated?

LabArchives integrates with a variety of programs including Microsoft Office, Duke Box, Duke shibboleth log-in, Google docs, ChemDoodle, PubMed, FlowJo, GraphPad Prism, and SnapGene. Some integrated features requires downloading a plugin from the LabArchives website, such as Microsoft Office.

LabArchives knowledgebase link for Microsoft plugin -- Windows users

LabArchives knowledgebase link for Microsoft plugin -- Mac users

***NOTE:  Mac users may need to follow additional manual steps listed in the knowledgebase (see “install shortcuts manually” sections) to save directly to LabArchives notebooks from the desktop Word, Excel and PowerPoint programs

***NOTE:  Duke LabArchives users login through a Single Sign on System and will need to create a password token in order to use the partner applications.

Widgets are available for additional flexibility and process sheets (e.g., freezer storage widget), and custom widgets can be made. If you identify other programs you would like to connect with LabArchives please contact ASIST@duke.edu.

What browser and operating systems are supported?

LabArchives can be used by Windows, Mac, Android and Linux operating systems. LabArchives provides a free mobile app for both iOS (Mac) and Android devices. 

LabArchives should be used with the following browsers:

  • Chrome  
  • Firefox ESR 
  • Firefox  
  • Safari  
  • Edge  

NOTE: Internet Explorer is not recommended, and it is no longer supported by Microsoft.

Who can access my research data?

No one can view your research notebook without your permission and/or knowledge. To share your notebook (either full notebook or sections) with team members or collaborators follow this LabArchives link. You can provide read-only or edit access to collaborators.

How will I access my notebooks if there is an outage or loss of connectivity?

The LabArchives service is in use at multiple US academic research institutions and has a record of high availability. However, your access to LabArchives, like other web-based services, is dependent on internet connectivity. If you are offline, or if the LabArchives service is down, you will not be able to edit or access the most recent version of your notebooks. LabArchives notebooks are backed up in triplicate through Amazon Web Services, so when the internet activity is restored, all notebooks and data will be restored and accessible. 

If desired, individual research groups may create locally stored copies of their LabArchives notebooks by exporting the notebooks in either PDF or HTML formats.  This backup strategy can be helpful, but care must be taken to keep track of multiple copies of exported versions. 

Does LabArchives offer electronic signatures?

Yes, and once signed, those pages are no longer editable (LabArchives knowledgebase on page signing). LabArchives also offers a “witness” feature, which means that the page must be reviewed by a specified member of the research team before the version is officially considered signed and frozen as the final version.  The witness feature helps to ensure that there is additional review and oversight of the page’s contents before it is signed and frozen (LabArchives knowledgebase on witnessing a signed page).

Where will my data be stored?

LabArchives hosts all of its software and customer data at Amazon data centers located in two regions: the primary is US East (Virginia) and their failover is US West (Oregon). Data are always stored within the United States and does not travel outside of US borders.

How secure is my LabArchives data?

LabArchives utilizes Amazon Web Services for its application, database, storage, and backup servers.  Amazon Web Services Compliance. Key security controls in the Duke’s LabArchives service include:

  • Encryption of data in transit and at rest
  • Firewalls and other security devices on all servers
  • Monitoring of all network traffic for suspicious activity
  • Regular testing, upgrades, and patching for vulnerabilities
  • Regular third party security audits

Can I use LabArchives to store my computer code for our research team’s analyses?

LabArchives can be used to store files of any format as long as the individual file size is less than 15GB. However, while developing and testing new coding scripts for computational analysis, the coding script files may be better stored in a different repository designed to track version control and other computational notes and requirements.  Some people have used Jupyter or RStudio for writing, editing and testing the code as it is being developed and allows for improved documentation and linkage to datasets.  And then version control can be maintained in your personal library with Git or in a web-repository through Github.  Additional version control resources include Duke GitLab and Duke Libraries is currently testing CodeOcean for improved reproducibility when archiving coding scripts.

Can I use LabArchives as a repository to make my data sets available to the public?

Duke has turned OFF all options for directly sharing LabArchives Notebooks with the public, including turning OFF the option to generate Digital Object Identifiers and turning OFF the option to generate a public url link directly to or within in a LabArchives notebook.  Users may share their notebooks or notebook entries with as many users as they would like. 

Before data are shared in a repository, they should be prepared for re-use. This includes ensuring fields and values are properly labeled, programming scripts annotated and end user documentation created.   The Duke libraries provide tools and consultative services to support data curation and can provide guidance if you are not sure which repository to use or how to prepare your datasets. The libraries also host and maintain a local research data repository for public sharing.

Who should I contact if I have questions about how to use LabArchives?

Duke research community members are encouraged to contact LabArchives with questions about how to utilize specific features within LabArchives.  LabArchives provides extensive customer support with the LabArchives Knowledgebase where users can search for informational how-to guides and video tutorials, sign-up for in-person tutorial webinars, and directly contact LabArchives expert technical support with specific questions at support@labarchives.com.

Contact ASIST (ASIST@duke.edu) for support on best practices in data management within LabArchives, how to organize notebooks, identifying other resources that may be useful for instances where LabArchives is not the best fit for your research team’s needs, additional training and consultation on using LabArchives at Duke.   ASIST is also the Duke contact for LabArchives systems updates and requests.

Duke Office of Information Technology (OIT) or Duke Health Technology Services (DHTS) can provide help with shibboleth authentication issues or internet connection issues depending on your affiliation.  To contact Duke OIT  call (919) 684-2200 or contact via live-chat on the OIT support website.  To contact DHTS, email researchservicedesk@duke.edu or call Research Support Services at (919) 684-2243, and select Option 4.

Is there a way to share or see widgets developed by Duke LabArchives users?

ASIST is working to build/utilize a platform so that the Duke research community may share useful LabArchives widgets.  We will let Duke LabArchives users know more as soon as we can develop a good process for sharing widgets. In the meantime, please contact ASIST if you have developed widgets that you think the Duke community might find useful, we can post these on the LabArchives ERN website behind shibboleth login where the Duke community may access them.

How do I set up Folder Monitor to automatically transfer files from my computer to LabArchives?

LabArchives can automatically transfer folders and files directly from a hard drive (connected to your computer or instrument) into a LabArchives notebook through Folder Monitor.   If the Folder Monitor rule is active, any updates and new files added to the local source folder will automatically be updated in your LabArchives notebooks.

***NOTE: Changes made in LabArchives will not be transmitted to the local source folder, the flow of information only works in one direction: from the local source folder to LabArchives.

Folder Monitor plugin – Windows users

Folder Monitor plugin – Mac users

***NOTE: Duke LabArchives users login through a Single Sign on System and will need to create a password token in order to use the Folder Monitor through the plugin.

I am leaving Duke, how do I transfer notebook ownership? Can I maintain access to my notebook after I leave?

As stated in Appendix P - Policies Related to Research- in the Duke Faculty Handbook, “the primary owner of research records is the University” and “in the event an investigator leaves the University for any reason, the original research records must be retained at the University and the investigator’s department and collaborators notified as to their location.”

Before leaving Duke, persons should transfer notebook ownership to the principal investigator or other designated team leaders to ensure that the data and research documentation stay at Duke.  Transferring ownership may be done at anytime and users can follow instructions in the LabArchives Knowledgebase for additional guidance.  

Before leaving Duke, persons should also speak with the principal investigator and collaborators about how and whether research records may be copied and utilized in any research that may continue as a part of the person’s next position outside of Duke.  If the person leaving Duke is a faculty member, additional consultation with the faculty member’s departmental leadership is advised.

Can I share my LabArchives notebooks or folders with non-Duke external collaborators?

Duke researchers may share a notebook or part of a notebook with an unlimited number of non-Duke collaborators.  Notebook ownership cannot be transferred to a non-Duke collaborator, but a non-Duke collaborator may be given a “guest” role with read-only privileges for as long as is needed or read-edit privileges for 60 days. Additionally, Duke’s institutional LabArchives license provides Duke notebook owners with the option to grant a limited number of non-Duke collaborators a “user” role which will remain active for as long as is needed by the notebook owner.