DMPTool Webinar Series Brown Bag

Join us for a ~15 part webinar series on the Data Management Planning Tool, DMPTool, from the California Digital Library.  This series will introduce the tool, discuss how to use it effectively, and describe how it can be customized for institutional needs.  Librarians, staff, and information professionals interested in promoting the use of the DMPTool by researchers are encouraged to attend.

DMPTool wiki

More information on the DMPTool webinar series.

Webinar 1: Introduction to DMPTool. Recorded May 28th.  Slides also available.

Webinar 2: Learning about data management: Resources, tools, and materials you can use. Recorded June 4th.  Slides and bibliography also available.

Webinar 3:  Customizing the DMPTool for your institution. Recorded June 18th. Slides also available

Webinar 4, Tuesday, June 25, 12-1pm, 126 Memorial Library – Environmental Scan:  Identify stakeholders and partners in data management.

• How to perform an “Environmental Scan” of your campus. This will help you identify stakeholders and partners in data management.

Save the Date!

Webinar 5, Tuesday, July 9, 12-1pm, TBD – Promoting institutional services with the DMPTool; EZID as example.

Webinar 6, Tuesday, July 16, 12-1pm, TBD – Health Sciences & DMPTool – Lisa Federer, UCLA

Webinar 7, Tuesday, July 23, 12-1pm, TBD – Digital humanities and the DMPTool – Miriam Posner, UCLA

Webinar 8, Tuesday, August 13, 12-1pm, TBD – Data curation profiles and the DMPTool – Jake Carlson

Overview of VIVO

• What is VIVO with Brian Lowe, Cornell University
• Implementation with Jon Corson-Rikert, Cornell University
• Future Directions with Dean Kraft, Cornell University

Slides from the presentation are also available.

Case Studies: VIVO implementations at Colorado, Brown, Duke & Weill Cornell Medical College

• University of Colorado – Boulder implementation with Alex Viggio
• Scholars@Duke with Julia Trimmer, Duke University
• Brown University implementation with Steven McCauley
• Weill Cornell Medical College with Paul Albert

Slides from the presentation are also available.

VIVO Technical Deep Dive: A look under the hood at the VIVO ontologies, linked open data, and community processes supporting VIVO.

Slides from the presentation are also available.

About the VIVO series

A 3 part series on VIVO, an open-source research discovery tool that integrates information about researchers with additional context from their relationships to grants, publications, research facilities, projects, events, affiliations, and with other researchers.

• Webinar 1, Overview of VIVO and the VIVO community. Recorded on May 14, 2013.
• Webinar 2, Case Studies: VIVO implementations at Colorado, Brown, Duke & Weill Cornell Medical College. Recorded on June 4, 2013.
• Webinar 3,  VIVO Technical Deep Dive: A look under the hood at the VIVO ontologies, linked open data, and community processes supporting VIVO. Recorded on June 11, 2013

Or, view all of the VIVO webinar series recordings and slides at The Duraspace Community Webinar Series.

LabKey has been used in several biomedical research communities to integrate and analyze data from high throughput assays conducted in distributed labs, including the Immune Tolerance Network, the Atlas data portal for HIV Vaccine studies, and others.

LabKey is currently in use at the UW-Madison Primate Center.

Electronic Lab Notebooks (ELNs) are software counterparts to paper lab notebooks. Although the name suggests a physical notebook device, ELNs are actually just software that runs on a computer, although some ELNs have apps for tablets and phones. The ELN interface resembles a notebook page, with fields for creating text entries and for attaching and annotating data files. Most allow you to create and modify templates for frequently used protocols. Other functionalities may include inventory tools that allow you to track samples and reagents.  Some have chemistry tools for drawing and searching on chemical structures.

UW-Madison has piloted a couple of ELNs (http://academictech.doit.wisc.edu/ideas/electronic-lab-notebooks) and we are currently evaluating a few others that have recently emerged. Interest in ELNs at the UW has grown over the past 2 years from a few interested researchers at the start of the pilot to hundreds of interested researchers. In response to this interest, a campus wide effort spearheaded by the Office of the CIO, WARF, CALS, and DoIT is seeking software, funding, and infrastructure to establish an enterprise ELN service.

Are ELNs useful for data management?

In general, ELNs let you keep data and descriptive information (e.g. materials, methods, analysis, and interpretations of the data) in digital form and all in one place. (An exception may be digital data files that are too large to upload/attach to the ELN. In that case, links can be added in the ELN to the server location of these files.) For simplicity in the following discussion, we’ll refer to both data files and the descriptive information as “data,” although the descriptive information might more accurately be called metadata.

Storing data in ELNs

From a data storage perspective, ELNs come in two flavors: those that can be locally hosted and those are hosted and store data in the cloud.

Locally hosted ELNs have the advantage of keeping data on campus servers. However, they usually consist of application, file system, and database layers and can be fairly complex to install, administer, and maintain for individual labs and departments. An enterprise level ELN service could provide some economies of scale by providing a common infrastructure to provide the hardware and services needed for a locally hosted ELN.

Other ELNs are cloud services that store data in the cloud, external to UW servers.  However, there are a lot of questions about security, protection of intellectual property and other issues when research data is moved to the cloud.  An advantage of an exploring an enterprise cloud ELN would be that the university could negotiate for favorable terms with vendors to secure agreements about the geographic location of cloud servers, segmentation of the our data from that of other institutions, encryption and advanced security provisions, etc., through a purchasing exercise.

Organizing and Tracking Versions of Files

When it comes to keeping an audit trail and preserving versioning information for entries and attached data, ELNs have a lot going for them. ELNs log time, date, user names and actions, and track version information. In many ELNs, these audit trails are designed to meet Federal government requirements for electronic records: the Code of Federal Regulations Title 21, Part II Electronic Records; Electronic Signatures.

Sharing and Collaborating
Similar to collaborative tools such as Google Drive, ELNs let you tag, comment, define workgroups, and share entries, files, folders, and templates with specified groups and individuals. In addition, a few labs on campus have been showing data recorded in their ELN at lab meetings and find that generally works out well.

Most ELNs also have features that allow electronic signing and witnessing of entries, enabling a level of legal documentation needed for research leading to patents.

Exporting and Archiving
Most ELNs let you export (and print) entries as PDF files and data files that are attached in their native formats. Some have xml and/or html export formats. However, there are no standards for exports which would make it easier to move records from one vendor’s ELN to another. We’d like to see that happen.

One of the strongest arguments for using an ELN system is its promise as a solution for data stewardship. Since the campus data stewardship policy specifies data be retained for at least 7 years (longer for some types of research), an enterprise ELN service would need to have a backend archival system. This would allow older data in the ELN to be moved to cheaper storage but would still allow search and retrieval from the archive with the appropriate access permissions in place. Researchers can also save ELN entries in PDF format and retain both print outs and electronic versions of these files.

Publishing
ELNs also offer the potential for publishing data. For example, one ELN provides a permanent digital object identifier (DOI) for each entry, which have been used in a publication.

Cost: Free, premium, and enterprise accounts available. The pricing for storage is better compared to Dropbox; $10/month gets you 100GB at SpiderOak vs. 50GB from Dropbox. SpiderOak also has no maximum storage limit. Additionally, it offers a 50% educational discount to anyone with a valid .edu email address.

Ease of Use: SpiderOak’s forte is security, not interface design. The web and mobile interfaces are fairly plain and not nearly as user-friendly as Dropbox’s interfaces. Additionally, while Dropbox has a very simple set-up–everything goes in the Dropbox folder and syncs to all your devices unless you tell it not to–SpiderOak’s set up is a bit more involved. First, you need to set up a back-up. You can choose multiple folders and even specific types of files. After you’ve done this, you can sync the folders across your devices. Finally, access from the web and mobile interfaces is read-only. You can only upload files from the desktop client.

Sharing and Collaboration: SpiderOak provides ShareRooms which allow you to selectively share folders (with anyone; not limited to other SpiderOak users), but the files are read-only. It also allows sharing of a single file, but this is read-only as well. The sharing is more secure: the ShareRoom is access through a unique URL and a RoomKey (password) must be entered, but there is no mechanism for collaborative editing.

Organizing: Other than the traditional hierarchical file system structure, SpiderOak does not have any built-in organizational features.

Exporting: Files can easily be exported. Simply de-select the folders or files in question from the syncing and back-up.

Backups and Versioning: This is one area where SpiderOak does well. It says all historical versions of a file, and does extensive de-duplication, so only the parts that are different are saved, not the entire file.

Security: SpiderOak is, as Ars Technica puts it, “Dropbox for the security obsessive.” Its main selling point is not that’s cloud storage, but that it is secure cloud storage. Unlike the other major cloud storage services, SpiderOak employees cannot access your files. Both Dropbox and SpiderOak encrypt their data, but SO also encrypts the decryption key. The downside to SpiderOak’s superior security is that if you forget your password, your files are gone.

The authors of the new review were able to obtain the original data and found a number of problems in the analysis, which are well summarized in this blog post. This episode stands as a cautionary tale about proper data management and open access; these issues are finally being recognized as critical to the integrity of science.

Project needs:
The research project, Learning in the Making: Studying and Designing Makerspaces, is funded by the National Science Foundation.  Breanne and her advisor are collaborating with co-investigators from George Mason University and the Children’s Museum Pittsburgh.  Box appealed to them as a tool for file storage, sharing, and collaboration because it was free and supported cross-institutional collaboration.
The group is conducting ethnographic research at makerspaces in Madison, Detroit, and along the east coast, with the goal of designing activities for the Makeshop in Pittsburgh.  They are conducting interviews and generating video and large audio files, as well as meeting notes, and other documentation related to the research.  They also do brainstorming and initial analysis in Box.  There are eight individuals working on this project, including undergraduate students, so another requirement for their data management tool was the ability to grant differential access privileges.  They organize files using Box’s folder system and have a main folder, a public folder, a private folder in which their sensitive data is stored, and each research site has its own folder.

Favorite features:
Storage and sharing – The group creates Word documents and Google Docs right in Box and appreciates the ability to lock open files to prevent conflicting copies.  This feature is also available on the mobile app.  The previews for documents, audio, and photos are “fantastic”, and the folder system for organization, tagging capability, and search feature are helpful.  Breanne expressed the opinion that the 50 GB of free storage that UW affiliates have access to will be a huge draw for graduate students.
Security – Box makes it easy to comply with IRB requirements regarding access to sensitive information.  In fact, the biggest attraction of Box was that it meets NSF and IRB standards for secure data management.  The ability to create, open, edit, and save directly to Box and not on your machine adds to this security.
Permissions – It’s simple to manage permissions of each individual file, unlike other project management tools the group looked into, which required users to go through an administrator.
Collaboration – Comments, tasks, and discussion features facilitate cross-institution, cross-country collaboration, making it easy to communicate while minimizing the need to email.  The group also found it easy to control email notifications to avoid being overwhelmed, compared to other project management tools.  The ability to link directly to files and folders is very convenient, as is the ability to track changes and revert to previous versions.
Overall, Breanne felt that it was easy to get started with Box.  There’s a low barrier to entry: one can use it without exploiting its total functionality and start getting things done without being overwhelmed.  In contrast, other tools the group considered require too many decisions to set up, as well as requiring meetings with an administrator.  Box offers collaborative teams autonomy, flexibility, and adaptability.
She’s found it to be a great tool for project and data management and collaboration and described it as “Facebook, Dropbox, and a project management tool in one!”  She feels that it does data management, as well as day-to-day project management, better than other tools.

What it is

Box is a cloud-based file storage, synchronization, and collaboration service.  It can be used by groups for storing, creating, editing, and sharing data files, documents, and other digital objects.

Cost

A personal account offers 5 GB of storage and a 100 MB file size limit for free; you can pay for more storage and larger file limits.  Business and enterprise accounts are also available for a fee.  UW-Madison affiliates can participate in the Box pilot, which includes 50 GB of storage.

Sharing and collaboration

Users can share folders with other users, share files with individuals without Box accounts, and embed files in websites.  In addition to sharing and editing files, users can post comments and discussions and assign tasks.  You can also lock files while you are editing them.  Email notifications keep you updated about edits, comments, tasks, and uploads.  In addition to the web interface, there are desktop clients for Windows and Mac as well as Windows, Android, and Apple phones and tablets.

If you are the owner of a Box account used for collaboration, keep any private files you also store there separate from the files the group sees. One way to do this is to set up separate folders for shared and private at the top level of your folder structure and ensure that files always go in the appropriate area.

Organizing

You can’t readily make links between documents in Box like you can on a wiki or website; putting related documents together in folders is the most straightforward way to associate them in Box. Before your group starts adding documents to Box, collaborators should agree on a folder hierarchy structure so that all parties know where everything goes and related files/docs can be tied together by their folder location.

Exporting

To export files in bulk from Box, download the folders that contain them. It will be more convenient to do this if you have a well-organized hierarchy of nested folders rather than multiple folders at the top of your hierarchy. If you have installed Box Synch on your computer, you can also duplicate the files in your Box Documents folder and save them in another location on your computer.

Box does not give you options for exporting your documents in new formats. If you need to convert a file to a different format, you will need to do this in an application that can open and read the file.

If you have important information about what was done to create different versions of files that you need to preserve, there are currently only a couple of options for getting this information out of Box:

• Take screenshots of screens in Box that display the comments, version information, discussions, etc.
• Copy and paste the text from these items into a “read me” file.

Be sure to give the files you create using either of these methods meaningful names so you know which files they are describing. Save them alongside those files in the same folders.

Archiving

It is always a good idea to keep multiple copies of your data in several secure places and in formats that will be usable over a long period. You can download folders in Box and save them in other locations. But, will this preserve everything you need?

Backups and Versioning

Box keeps a record of file versions, and users can restore a previous version.

Security

Box is a member of the Cloud Security Alliance, and has provided safeguards to help ensure  HIPAA compliance.

The book–which uses R code to illustrate examples–begins with a clear definition of Data Science:Data Science refers to an emerging area of work concerned with the collection, preparation, analysis, visualization, management and preservation of large collections of information.

Recently, a workshop was held in Germany to expand the scope of DDI and make it simpler to use. To those ends, DDI plans to adopt a model-based specification that can be expressed in XML, RDF/OWL technology, relational database schema, and other languages.  To broaden its appeal beyond a programmer and software developer audience, it was decided that DDI needs to avoid jargon and use terminology that is familiar to social science researchers and data librarians. Please contact RDS if you are interested in applying DDI to your research project.