Category Archives: Tools for Data

Ensuring access to critical research data

For the last two months, UC3 have been working with the teams at Data.gov, Data Refuge, Internet Archive, and Code For Science (creators of the Dat Project) to aggregate the government data.

Data that spans the globe

There are currently volunteers across the country working to discover and preserve publicly funded research, especially climate data, from being deleted or lost from the public record. The largest initiative is called Data Refuge and is led by librarians and scientists. They are holding events across the UC campuses and the US that you should attend and help out in person, and are organizing the library community to band together to curate the data and ensure it’s preserved and accessible.

Our initiative builds on this and is looking to build a corpus of government data and corresponding metadata.  We are focusing on public research data, especially those at risk of disappearing. The initiative was nicknamed “Svalbard” by Max Ogden of the Dat project, after the Svalbard Global Seed Vault in the Arctic.  As of today, our friends at Code for Science have released 38GB of metadata, over 30 million hashes and URLs of research data files.

The Svalbard Global Seed Vault in the Arctic

To aid in this effort

We have assembled the following metadata as part of the Code for Science’s Svalbard v1:

  • 2.7 million SHA-256 hashes for all downloadable resources linked from Data.gov, representing around 40TB of data
  • 29 million SHA-1 hashes of files archived by the Internet Archive and the Archive Team from federal websites and FTP servers, representing over 120TB of data
  • All metadata from Data.gov, about 2.1 million datasets
  • A list of ~750 .gov and .mil FTP servers

There are additional sources such as Archivers.Space, EDGI, Climate Mirror, Azimuth Data Backup that we are working adding metadata for in future releases.

Following the principles set forth by the librarians behind Data Refuge, we believe it’s important to establish a clear and trustworthy chain of custody for research datasets so that mirror copies can be trusted. With this project, we are working to curate metadata that includes strong cryptographic hashes of data files in addition to metadata that can be used to reproduce a download procedure from the originating host.

We are hoping the community can use this data in the following ways:

  • To independently verify that the mirroring processes that produced these hashes can be reproduced
  • To aid in developing new forms of redundant dataset distribution (such as peer to peer networks)
  • To seed additional web crawls or scraping efforts with additional dataset source URLs
  • To encourage other archiving efforts to publish their metadata in an easily accessible format
  • To cross reference data across archives, for deduplication or verification purposes

What about the data?

The metadata is great, but the initial release of 30 million hashes and urls is just part of our project. The actual content (how the hashes were derived) have also been downloaded.  They are stored at either the Internet Archive or on our California Digital Library servers.

The Dat Project carried out a Data.gov HTTP mirror (~40TB) and uploaded it to our servers at California Digital Library. We are working with them to access ~160TB of data in the future and have partnered with UC Riverside to offer longer term storage .

Download

You can download the metadata here using Dat Desktop or Dat CLI tool.  We are using the Dat Protocol for distribution so that we can publish new metadata releases efficiently while still keeping the old versions around. Dat provides a secure cryptographic ledger, similar in concept to a blockchain, that can verify integrity of updates.

Feedback

If you want to learn more about how CDL and the UC3 team is involved, contact us at uc3@ucop.edu or @UC3CDL. If you have suggestions or questions, you can join the Code for Science Community Chat.  And, if you are a technical user you can report issues or get involved at the Svalbard GitHub.

This is crossposted here: https://medium.com/@maxogden/project-svalbard-a-metadata-vault-for-research-data-7088239177ab#.f933mmts8

csv conf is back in 2017!

csv,conf,v3 is happening!csv

This time the community-run conference will be in Portland, Oregon, USA on 2nd and 3rd of May 2017. It will feature stories about data sharing and data analysis from science, journalism, government, and open source. We want to bring together data makers/doers/hackers from backgrounds like science, journalism, open go
vernment and the wider software industry to share knowledge and stories.

csv,conf is a non-profit community conference run by people who love data and sharing knowledge. This isn’t just a conference about spreadsheets. CSV Conference is a conference about data sharing and data tools. We are curating content about advancing the art of data collaboration, from putting your data on GitHub to producing meaningful insight by running large scale distributed processing on a cluster.

Submit a Talk!  Talk proposals for csv,conf close Feb 15, so don’t delay, submit today! The deadline is fast approaching and we want to hear from a diverse range of voices from the data community.

Talks are 20 minutes long and can be about any data-related concept that you think is interesting. There are no rules for our talks, we just want you to propose a topic you are passionate about and think a room full of data nerds will also find interesting. You can check out some of the past talks from csv,conf,v1 and csv,conf,v2 to get an idea of what has been pitched before.

If you are passionate about data and the many applications it has in society, then join us in Portland!

csv-pic

Speaker perks:

  • Free pass to the conference
  • Limited number of travel awards available for those unable to pay
  • Did we mention it’s in Portland in the Spring????

Submit a talk proposal today at csvconf.com

Early bird tickets are now on sale here.

If you have colleagues or friends who you think would be a great addition to the conference, please forward this invitation along to them! csv,conf,v3 is committed to bringing a diverse group together to discuss data topics. 

– UC3 and the entire csv,conf,v3 team

For questions, please email csv-conf-coord@googlegroups.com, DM @csvconference or join the csv,conf public slack channel.

This was cross-posted from the Open Knowledge International Blog: http://blog.okfn.org/2017/01/12/csvconf-is-back-in-2017-submit-talk-proposals-on-the-art-of-data-analysis-and-collaboration/

Dispatches from PIDapalooza

Last month, California Digital Library, ORCID, Crossref, and Datacite brought together the brightest minds in scholarly infrastructure to do the impossible: make a conference on persistent identifiers fun!

screen-shot-2016-09-22-at-11-53-28-am

Usually discussions about persistent identifiers (PIDs) and networked research are dry and hard to get through or we find ourselves discussing the basics and never getting to the meat.

We designed PIDapalooza to attract kindred spirits who are passionate about improving interoperability and the overall quality of our scholarly infrastructure. We knew if we built it, they would come!

The results were fantastic and there was a great showing from the University of California community:

All PIDapalooza presentations are being archived on Figshare: https:/pidapalooza.figshare.com

Take a look and make sure you are following @pidapalooza for word on future PID fun!

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There’s a new Dash!

Dash: an open source, community approach to data publication

We have great news! Last week we refreshed our Dash data publication service.  For those of you who don’t know, Dash is an open source, community driven project that takes a unique approach to data publication and digital preservation.

Dash focuses on search, presentation, and discovery and delegates the responsibility for the data preservation function to the underlying repository with which it is integrated. It is a project based at the University of California Curation Center (UC3), a program at California Digital Library (CDL) that aims to develop interdisciplinary research data infrastructure.

Dash employs a multi-tenancy user interface; providing partners with extensive opportunities for local branding and customization, use of existing campus login credentials, and, importantly, offering the Dash service under a tenant-specific URL, an important consideration helping to drive adoption. We welcome collaborations with other organizations wishing to provide a simple, intuitive data publication service on top of more cumbersome legacy systems.

There are currently seven live instances of Dash: – UC BerkeleyUC IrvineUC MercedUC Office of the PresidentUC RiversideUC Santa CruzUC San FranciscoONEshare (in partnership with DataONE)

Architecture and Implementation

Dash is completely open source. Our code is made publicly available on GitHub (http://cdluc3.github.io/dash/). Dash is based on an underlying Ruby-on-Rails data publication platform called Stash. Stash encompasses three main functional components: Store, Harvest, and Share.

  • Store: The Store component is responsible for the selection of datasets; their description in terms of configurable metadata schemas, including specification of ORCID and Fundref identifiers for researcher and funder disambiguation; the assignment of DOIs for stable citation and retrieval; designation of an optional limited time embargo; and packaging and submission to the integrated repository
  • Harvest: The Harvest component is responsible for retrieval of descriptive metadata from that repository for inclusion into a Solr search index
  • Share: The Share component, based on GeoBlacklight, is responsible for the faceted search and browse interface

Dash Architecture Diagram

Individual dataset landing pages are formatted as an online version of a data paper, presenting all appropriate descriptive and administrative metadata in a form that can be downloaded as an individual PDF file, or as part of the complete dataset download package, incorporating all data files for all versions.

To facilitate flexible configuration and future enhancement, all support for the various external service providers and repository protocols are fully encapsulated into pluggable modules. Metadata modules are available for the DataCite and Dublin Core metadata schemas. Protocol modules are available for the SWORD 2.0 deposit protocol and the OAI-PMH and ResourceSync harvesting protocols. Authentication modules are available for InCommon/Shibboleth and Google/OAuth19 identity providers (IdPs). We welcome collaborations to develop additional modules for additional metadata schemas and repository protocols. Please email UC3 (uc3 at ucop dot edu) or visit GitHub (http://cdluc3.github.io/dash/) for more information.

Features of the newly refreshed Dash service

What are the new features on our refresh of the Dash services?  Take a look.

Feature Tech-focused User-focused Description
Open Source X All components open source, MIT licensed code (http://cdluc3.github.io/dash/)
Standards compliant X Dash integrates with any SWORD/OAI-PMH-compliant repository
Pluggable Framework X Inherent extensibility for supporting additional protocols and metadata schemas
Flexible metadata schemas X Support Datacite metadata schema out-of-the-box, but can be configured to support any schema
Innovation X Our modular framework will make new feature development easier and quicker
Mobile/responsive design X X Built mobile-first, from the ground up, for better user experience
Geolocation – Metadata X X For applicable research outputs, we have an easy to use way to capture location of your datasets
Persistent Identifers – ORCID X X Dash allows researchers to attach their ORCID, allowing them to track and get credit for their work
Persistent Identifers – DOIs X X Dash issues DOIs for all datasets, allowing researchers to track and get credit for their work
Persistent Identifers – Fundref X X Dash tracks funder information using FundRef, allowing researchers and funders to track their reasearch outputs
Login – Shibboleth /OAuth2 X X We offer easy single-sign with your campus credentials or Google account
Versioning X X Datasets can change. Dash offers a quick way for you to upload new versions of your datasets and offer a simple process for tracking updates
Accessibility X X The technology, design, and user workflows have all been built with accessibility in mind
Better user experience X Self-depositing made easy. Simple workflow, drag-and-drop upload, simple navigation, clean data publication pages, user dashboards
Geolocation – Search X With GeoBlacklight, we can offer search by location
Robust Search X Search by subject, filetype, keywords, campus, location, etc.
Discoverability X Indexing by search engines for Google, Bing, etc.
Build Relationships X Many datasets are related to publications or other data. Dash offers a quick way to describe these relationships
Supports Best Practices X Data publication can be confusing. But with Dash, you can trust Dash is following best practices
Data Metrics X See the reach of your datasets through usage and download metrics
Data Citations X Quick access to a well-formed citiation reference (with DOI) to every data publication. Easy for your peers to quickly grab
Open License X Dash supports open Creative Commons licensing for all data deposits; can be configured for other licenses
Lower Barrier to Entry X For those in a hurry, Dash offers a quick interface to self-deposit. Only three steps and few required fields
Support Data Reuse X Focus researchers on describing methods and explaining ways to reuse their datasets
Satisfies Data Availability Requirements X Many publishers and funders require researchers to make their data available. Dash is an readily accepted and easy way to comply

A little Dash history

The Dash project began as DataShare, a collaboration among UC3, the University of California San Francisco Library and Center for Knowledge Management, and the UCSF Clinical and Translational Science Institute (CTSI). CTSI is part of the Clinical and Translational Science Award program funded by the National Center for Advancing Translational Sciences at the National Institutes of Health. Dash version 2 developed by UC3 and partners with funding from the Alfred P. Sloan Foundation (our funded proposal). Read more about the code, the project, and contributing to development on the Dash GitHub site.

A little Dash future

We will continue the development of the new Dash platform and will keep you posted. Next up: support for timed deposits and embargoes.  Stay tuned!

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An RDM Model for Researchers: What we’ve learned

Thanks to everyone who gave feedback on our previous blog post describing our data management tool for researchers. We received a great deal of input related to our guide’s use of the term “data sharing” and our guide’s position in relation to other RDM tools as well as quite a few questions about what our guide will include as we develop it further.

As stated in our initial post, we’re building a tool to enable individual researchers to assess the maturity of their data management practices within an institutional or organizational context. To do this, we’ve taken the concept of RDM maturity from in existing tools like the Five Organizational Stages of Digital Preservation, the Scientific Data Management Capability Model, and the Capability Maturity Guide and placed it within a framework familiar to researchers, the research data lifecycle.

researchercmm_090916

A visualization of our guide as presented in our last blog post. An updated version, including changed made in response to reader feedback, is presented later in this post.

Data Sharing

The most immediate feedback we received was about the term “Data Sharing”. Several commenters pointed out the ambiguity of this term in the context of the research data life cycle. In the last iteration of our guide, we intended “Data Sharing” as a shorthand to describe activities related to the communication of data. Such activities may range from describing data in a traditional scholarly publication to depositing a dataset in a public repository or publishing a data paper. Because existing data sharing policies (e.g. PLOS, The Gates Foundation, and The Moore Foundation) refer specifically to the latter over the former, the term is clearly too imprecise for our guide.

Like “Data Sharing”, “Data Publication” is a popular term for describing activities surrounding the communication of data. Even more than “Sharing”, “Publication” relays our desire to advance practices that treat data as a first class research product. Unfortunately the term is simultaneously too precise and too ambiguous it to be useful in our guide. On one hand, the term “Data Publication” can refer specifically to a peer reviewed document that presents a dataset without offering any analysis or conclusion. While data papers may be a straightforward way of inserting datasets into the existing scholarly communication ecosystem, they represent a single point on the continuum of data management maturity. On the other hand, there is currently no clear consensus between researchers about what it means to “publish” data.

For now, we’ve given that portion of our guide the preliminary label of “Data Output”. As the development process proceeds, this row will include a full range of activities- from description of data in traditional scholarly publications (that may or may not include a data availability statement) to depositing data into public repositories and the publication of data papers.

Other Models and Guides

While we correctly identified that there are are range of rubrics, tools, and capability models with similar aims as our guide, we overstated that ours uniquely allows researchers to assess where they are and where they want to be in regards to data management. Several of the tools we cited in our initial post can be applied by researchers to measure the maturity of data management practices within a project or institutional context.

Below we’ve profiled four such tools and indicated how we believe our guide differs from each. In differentiating our guide, we do not mean to position it strictly as an alternative. Rather, we believe that our guide could be used in concert with these other tools.

Collaborative Assessment of Research Data Infrastructure and Objectives (CARDIO)

CARDIO is a benchmarking tool designed to be used by researchers, service providers, and coordinators for collaborative data management strategy development. Designed to be applied at a variety of levels, from entire institutions down to individual research projects, CARDIO enables its users to collaboratively assess data management requirements, activities, and capacities using an online interface. Users of CARDIO rate their data management infrastructure relative to a series of statements concerning their organization, technology, and resources. After completing CARDIO, users are given a comprehensive set of quantitative capability ratings as well as a series of practical recommendations for improvement.

Unlike CARDIO, our guide does not necessarily assume its users are in contact with data-related service providers at their institution. As we stated in our initial blog post, we intend to guide researchers to specialist knowledge without necessarily turning them into specialists. Therefore, we would consider a researcher making contact with their local data management, research IT, or library service providers for the first time as a positive application of our guide.

Community Capability Model Framework (CCMF)

The Community Capability Model Framework is designed to evaluate a community’s readiness to perform data intensive research. Intended to be used by researchers, institutions, and funders to assess current capabilities, identify areas requiring investment, and develop roadmaps for achieving a target state of readiness, the CCMF encompasses eight “capability factors” including openness, skills and training, research culture, and technical infrastructure. When used alongside the Capability Profile Template, the CCMF provides its users with a scorecard containing multiple quantitative scores related to each capability factor.   

Unlike the CCMF, our guide does not necessarily assume that its users should all be striving towards the same level of data management maturity. We recognize that data management practices may vary significantly between institutions or research areas and that what works for one researcher may not necessarily work for another. Therefore, we would consider researchers understanding the maturity of their data management practices within their local contexts to be a positive application of our guide.

Data Curation Profiles (DCP) and DMVitals

The Data Curation Profile toolkit is intended to address the needs of an individual researcher or research group with regards to the “primary” data used for a particular project. Taking the form of a structured interview between an information professional and a researcher, a DCP can allow an individual research group to consider their long-term data needs, enable an institution to coordinate their data management services, or facilitate research into broader topics in digital curation and preservation.

DMVitals is a tool designed to take information from a source like a Data Curation Profile and use it to systematically assess a researcher’s data management practices in direct comparison to institutional and domain standards. Using the DMVitals, a consultant matches a list of evaluated data management practices with responses from an interview and ranks the researcher’s current practices by their level of data management “sustainability.” The tool then generates customized and actionable recommendations, which a consultant then provides to the researcher as guidance to improve his or her data management practices.  

Unlike DMVitals, our guide does not calculate a quantitative rating to describe the maturity of data management practices. From a measurement perspective, the range of practice maturity may differ between the four stages of our guide (e.g. the “Project Planning” stage could have greater or fewer steps than the “Data Collection” stage), which would significantly complicate the interpretation of any quantitative ratings derived from our guide. We also recognize that data management practices are constantly evolving and likely dependent on disciplinary and institutional context. On the other hand, we also recognize the utility of quantitative ratings for benchmarking. Therefore, if, after assessing the maturity of their data management practices with our guide, a researcher chooses to apply a tool like DMVitals, we would consider that a positive application of our guide.

Our Model (Redux)

Perhaps the biggest takeaway from the response to our  last blog post is that it is very difficult to give detailed feedback on a guide that is mostly whitespace. Below is an updated mock-up, which describes a set of RDM practices along the continuum of data management maturity. At present, we are not aiming to illustrate a full range of data management practices. More simply, this mock-up is intended to show the types of practices that could be described by our guide once it is complete.

screen-shot-2016-11-08-at-11-37-35-am

An updated visualization of our guide based on reader feedback. At this stage, the example RDM practices are intended to be representative not comprehensive.

Project Planning

The “Project Planning” stage describes practices that occur prior to the start of data collection. Our examples are all centered around data management plans (DMPs), but other considerations at this stage could include training in data literacy, engagement with local RDM services, inclusion of “sharing” in project documentation (e.g. consent forms), and project pre-registration.

Data Collection

The “Data Collection” stage describes practices related to the acquisition, accumulation, measurement, or simulation of data. Our examples relate mostly to standards around file naming and structuring, but other considerations at this stage could include the protection of sensitive or restricted data, validation of data integrity, and specification of linked data.

Data Analysis

The “Data Analysis” stage describes practices that involve the inspection, modeling, cleaning, or transformation of data. Our examples mostly relate to documenting the analysis workflow, but other considerations at this stage could include the generation and annotation of code and the packaging of data within sharable files or formats.

Data Output

The “Data Output” stage describes practices that involve the communication of either the data itself of conclusions drawn from the data. Our examples are mostly related to the communication of data linked to scholarly publications, but other considerations at this stage could include journal and funder mandates around data sharing, the publication of data papers, and the long term preservation of data.

Next Steps

Now that we’ve solicited a round of feedback from the community that works on issues around research support, data management, and digital curation, our next step is to broaden our scope to include researchers.

Specifically we are looking for help with the following:

  • Do you find the divisions within our model useful? We’ve used the research data lifecycle as a framework because we believe it makes our tool user-friendly for researchers. At the same time, we also acknowledge that the lines separating planning, collection, analysis, and output can be quite blurry. We would be grateful to know if researchers or data management service providers find these divisions useful or overly constrained.
  • Should there be more discrete “steps” within our framework? Because we view data management maturity as a continuum, we have shied away from creating discrete steps within each division. We would be grateful to know how researchers or data management service providers view this approach, especially when compared to the more quantitative approach employed by CARDIO, the Capability Profile Template, and DMVitals.
  • What else should we put into our model? Researchers are faced with changing expectations and obligations in regards to data management. We want our model to reflect that. We also want our model to reflect the relationship between research data management and broader issues like openness and reproducibility. With that in mind, what other practices and considerations should or model include?
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Building a user-friendly RDM maturity model

UC3 is developing a guide to help researchers assess and progress the maturity of their data management practices.

What are we doing?

Researchers are increasingly faced with new expectations and obligations in regards to data management. To help researchers navigate this changing landscape and to complement existing instruments that enable librarians and other data managers to assess the maturity of data management practices at an institutional or organizational level, we’re developing a guide that will enable researchers to assess the maturity of their individual practices within an institutional or organizational context.

Our aim is to be descriptive rather than prescriptive. We do not assume every researcher will want or need to achieve the same level of maturity for all their data management practices. Rather, we aim to provide researchers with a guide to specialist knowledge without necessarily turning researchers into specialists. We want to help researchers understand where they are and, where appropriate, how to get to where they want or need to be.

Existing Models

As a first step in building our own guide, we’ve researched the range of related tools, rubrics, and capability models. Many, including the Five Organizational Stages of Digital Preservation, the Scientific Data Management Capability Model, and the Capability Maturity Guide developed by the Australian National Data Service, draw heavily from the SEI Capability Maturity Model and are intended to assist librarians, repository managers, and other data management service providers in benchmarking the policies, infrastructure, and services of their organization or institution.  Others, including the Collaborative Assessment of Research Data Infrastructure and Objectives (CARDIO), DMVitals, and the Community Capability Framework, incorporate feedback from researchers and are intended to assist in benchmarking a broad set of data management-related topics for a broad set of stockholders – from organizations and institutions down to individual research groups.

We intend for our guide to build on these tools but to have a different, and we think novel, focus. While we believe it could be a useful tool for data management service providers, the intended audience of our guide is research practitioners. While integration with service providers in the library, research IT, and elsewhere will be included where appropriate, the the focus will be on equipping researchers to assess and refine their individual own data management activities. While technical infrastructure will be included where appropriate, the focus will be on behaviors, “soft skills”, and training.

Our Guide

Below is a preliminary mockup of our guide. Akin to the “How Open Is It?” guide developed by SPARC, PLOS, and the OASPA, our aim is to provide a tool that is comprehensive, user-friendly, and provides tangible recommendations.  

researchercmm_090916

Obviously we still have a significant amount of work to do to refine the language and fill in the details. At the moment, we are using elements of the research data lifecycle to broadly describe research activities and very general terms to describe the continuum of practice maturity. Our next step is to fill in the blanks- to more precisely describe research activities and more clearly delineate the stages of practice maturity. From there, we will work to outline the behaviors, skills, and expertise present for each research activity at each stage.

Next Steps

Now that we’ve researched existing tools for assessing data management services and sketched out a preliminary framework for our guide, our next step is to elicit feedback from the broader community that works on issues around research support, data management, and digital curation and preservation.

Specifically we are looking for help on the following:

  • Have we missed anything? There is a range of data management-related rubrics, tools, and capability models – from the community-focused frameworks described above to frameworks focused on the preservation and curation of digital assets (e.g. the Digital Asset Framework, DRAMBORA). As far as we’re aware, there isn’t a complementary tool that allows researchers to assess where they are and where they want to be in regards to data management. Are there efforts that have already met this need? We’d be grateful for any input about the existence of frameworks with similar goals.
  • What would be the most useful divisions and steps within our framework? The “three legged stool” developed by the Digital Preservation Management workshop has been highly influential for community and data management provider-focused tools. Though examining policies, resources, and infrastructure are also important for researchers when self-assessing their data management practices, we believe it would be more useful for our guide to be more reflective of how data is generated, managed, disseminated in a research context. We’d be grateful for any insight into how we could incorporate related models – such as those depicting the research data lifecycle – into our framework.
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Who “owns” your data?

This post was originally published on the University of California Office of Scholarly Communication blog.

Which of these is true?

“The PI owns the data.”

“The university owns the data.”

“Nobody can own it; data isn’t copyrightable.”

You’ve probably heard somebody say at least one of these things — confidently. Maybe you’ve heard all of them. Maybe about the same dataset (but in that case, hopefully not from the same person). So who really owns research data? Well, the short answer is “it depends.”

A longer answer is that determining ownership (and whether there’s even anything to own) can be frustratingly complicated — and, even when obvious, ownership only determines some of what can be done with data. Other things like policies, contracts, and laws may dictate certain terms in circumstances where ownership isn’t relevant — or even augment or overrule an owner where it is. To avoid an unpleasant surprise about what you can or can’t do with your data, you’ll want to plan ahead and think beyond the simple question of ownership. Continue reading

Science Boot Camp West

Last week Stanford Libraries hosted the third annual Science Boot Camp West (SBCW 2015),

“… building on the great Science Boot Camp events held at the University of Colorado, Boulder in 2013 and at the University of Washington, Seattle in 2014. Started in Massachusetts and spreading throughout the USA, science boot camps for librarians are 2.5 day events featuring workshops and educational presentations delivered by scientists with time for discussion and information sharing among all the participants. Most of the attendees are librarians involved in supporting research in the sciences, engineering, medicine or technology although anybody with an interest in science research is welcome.”

As a former researcher and newcomer to the library and research data management (RDM) scenes, I was already familiar with many of the considerable challenges on both sides of the equation (Jake Carlson recently summarized the plight of data librarians). What made SBCW 2015 such an excellent event is that it brought researchers and librarians together to identify immediate opportunities for collaboration. It also showcased examples of Stanford libraries and librarians directly facilitating the research process, from the full-service Stanford Geospatial Center to organizing Software and Data Carpentry workshops (more on this below, and from an earlier post).

Collaboration: Not just a fancy buzzword

The mostly Stanford-based researchers were generous with their time, introducing us to high-level concerns (e.g., why electrons do what they do in condensed matter) as well as more practical matters (e.g., shopping for alternatives to Evernote—yikes—for electronic lab notebooks [ELNs]). They revealed the intimate details of their workflows and data practices (Dr. Audrey Ellerbee admitted that it felt like letting guests into her home to find dirty laundry strewn everywhere, a common anxiety among researchers that in her case was unwarranted), flagged the roadblocks, and presented a constant stream of ideas for building relationships across disciplines and between librarians and researchers.

From the myriad opportunities for library involvement, here are some of the highlights:

  • Facilitate community discussions of best practices, especially for RDM issues such as programming, digital archiving, and data sharing
  • Consult with researchers about available software solutions (e.g., ELNs such as Labguru and LabArchives; note: representatives from both of these companies gave presentations and demonstrations at SBCW 2015), connect them with other users on campus, and provide help with licensing
  • Provide local/basic IT support for students and researchers using commercial products such as ELNs (e.g., maintain FAQ lists to field common questions)
  • Leverage experience with searching databases to improve delivery of informatics content to researchers (e.g., chemical safety data)
  • Provide training in and access to GIS and other data visualization tools

A winning model

The final half-day was dedicated to computer science-y issues. Following a trio of presentations involving computational workflows and accompanying challenges (the most common: members of the same research group writing the same pieces of code over and over with scant documentation and zero version control), Tracy Teal (Executive Director of Data Carpentry) and Amy Hodge (Science Data Librarian at Stanford) introduced a winning model for improving everyone’s research lives.

Software Carpentry and Data Carpentry are extremely affordable 2-day workshops that present basic concepts and tools for more effective programming and data handling, respectively. Training materials are openly licensed (CC-BY) and workshops are led by practitioners for practitioners allowing them to be tailored to specific domains (genomics, geosciences, etc.). At present the demand for these (international) workshops exceeds the capacity to meet it … except at Stanford. With local, library-based coordination, Amy has brokered (and in some cases taught) five workshops for individual departments or research groups (who covered the costs themselves). This is the very thing I wished for as a graduate student—muddling through databases and programming in R on my own—and I think it should be replicated at every research institution. Better yet, workshops aren’t restricted to the sciences; Data Carpentry is developing training materials for techniques used in the digital humanities such as text mining.

Learning to live outside of the academic bubble

Another, subtler theme that ran throughout the program was the need/desire to strengthen connections between the academy and industry. Efforts along these lines stand to improve the science underlying matters of public policy (e.g., water management in California) and public health (e.g., new drug development). They also address the mounting pressure placed on researchers to turn knowledge into products. Mark Smith addressed this topic directly during his presentation on ChEM-H: a new Stanford initiative for supporting research across Chemistry, Engineering, and Medicine to understand and advance Human Health. I appreciated that Mark—a medicinal chemist with extensive experience in both sectors—and others emphasized the responsibility to prepare students for jobs in a rapidly shifting landscape with increasing demand for technical skills.

Over the course of SBCW 2015 I met engaged librarians, data managers, researchers, and product managers, including some repeat attendees who raved about the previous two SBCW events; the consensus seemed to be that the third was another smashing success. Helen Josephine (Head of the Engineering Library at Stanford who chaired the organizing committee) is already busy gathering feedback for next year.

SBCW 2015 at Stanford included researchers from:

Gladstone Institutes in San Francisco

ChEM-H Stanford’s lab for Chemistry, Engineering & Medicine for Human Health

Water in the West Institute at Stanford

NSF Engineering Research Center for Re-inventing the Nation’s Urban Water Infrastructure (ReNUWIt)

DeepDive

Special project topics on Software and Data Carpentry with Physics and BioPhysics faculty and Tracy Teal from Software Carpentry.

Many thanks to:

Helen Josephine, Suzanne Rose Bennett, and the rest of the Local Organizing Committee at Stanford. Sponsored by the National Network of Libraries of Medicine – Pacific Southwest Region, Greater Western Library Alliance, Stanford University Libraries, SPIE, IEEE, Springer Science+Business Media, Annual Reviews, Elsevier.

From Flickr by Paula Fisher (It was just like this, but indoors, with coffee, and powerpoints.)

From Flickr by Paula Fisher (It was just like this, but indoors, with coffee, and powerpoints.)

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Announcing The Dash Tool: Data Sharing Made Easy

We are pleased to announce the launch of Dash – a new self-service tool from the UC Curation Center (UC3) and partners that allows researchers to describe, upload, and share their research data. Dash helps researchers perform the following tasks:

  • Prepare data for curation by reviewing best practice guidance for the creation or acquisition of digital research data.
  • Select data for curation through local file browse or drag-and-drop operation.
  • Describe data in terms of the DataCite metadata schema.
  • Identify data with a persistent digital object identifier (DOI) for permanent citation and discovery.
  • Preserve, manage, and share data by uploading to a public Merritt repository collection.
  • Discover and retrieve data through faceted search and browse.

Who can use Dash?

There are multiple instances of the Dash tool that all have similar functions, look, and feel.  We took this approach because our UC campus partners were interested in their Dash tool having local branding (read more). It also allows us to create new Dash instances for projects or partnerships outside of the UC (e.g., DataONE Dash and our Site Descriptors project).

Researchers at UC Merced, UCLA, UC Irvine, UC Berkeley, or UCOP can use their campus-specific Dash instance:

Other researchers can use DataONE Dash (oneshare.cdlib.org). This instance is available to anyone, free of charge. Use your Google credentials to deposit data.

Note: Data deposited into any Dash instance is visible throughout all of Dash. For example, if you are a UC Merced researcher and use dash.ucmerced.edu to deposit data, your dataset will appear in search results for individuals looking for data via any of the Dash instances, regardless of campus affiliation.

See the Users Guide to get started using Dash.

Stay connected to the Dash project:

Dash Origins

The Dash project began as DataShare, a collaboration among UC3, the University of California San Francisco Library and Center for Knowledge Management, and the UCSF Clinical and Translational Science Institute (CTSI). CTSI is part of the Clinical and Translational Science Award program funded by the National Center for Advancing Translational Sciences at the National Institutes of Health (Grant Number UL1 TR000004).

Fontana del Nettuno

Sound the horns! Dash is live! “Fontana del Nettuno” by Sorin P. from Flickr.

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Dash Project Receives Funding!

We are happy to announce the Alfred P. Sloan Foundation has funded our project to improve the user interface and functionality of our Dash tool! You can read the full grant text at http://escholarship.org/uc/item/2mw6v93b.

More about Dash

Dash is a University of California project to create a platform that allows researchers to easily describe, deposit and share their research data publicly. Currently the Dash platform is connected to the UC3 Merritt Digital Repository; however, we have plans to make the platform compatible with other repositories using protocols during our Sloan-funded work. The Dash project is open-source; read more on our GitHub site. We encourage community discussion and contribution via GitHub Issues.

Currently there are five instances of the Dash tool available:

We plan to launch the new DataONE Dash instance in two weeks; this tool will replace the existing DataUp tool and allow anyone to deposit data into the DataONE infrastructure via the ONEShare repository using their Google credentials. Along with the release of DataONE Dash, we will release Dash 1.1 for the live sites listed above. There will be improvements to the user interface and experience.

The Newly Funded Sloan Project

Problem Statement

Researchers are not archiving and sharing their data in sustainable ways. Often data sharing involves using commercially owned solutions, posting data on personal websites, or submitting data alongside articles as supplemental material. A better option for data archiving is community repositories, which are owned and operated by trusted organizations (i.e., institutional or disciplinary repositories). Although disciplinary repositories are often known and used by researchers in the relevant field, institutional repositories are less well known as a place to archive and share data.

Why aren’t researchers using institutional repositories?

First, the repositories are often not set up for self-service operation by individual researchers who wish to deposit a single dataset without assistance. Second, many (or perhaps most) institutional repositories were created with publications in mind, rather than datasets, which may in part account for their less-than-ideal functionality. Third, user interfaces for the repositories are often poorly designed and do not take into account the user’s experience (or inexperience) and expectations. Because more of our activities are conducted on the Internet, we are exposed to many high-quality, commercial-grade user interfaces in the course of a workday. Correspondingly, researchers have expectations for clean, simple interfaces that can be learned quickly, with minimal need for contacting repository administrators.

Our Solution

We propose to address the three issues above with Dash, a well-designed, user friendly data curation platform that can be layered on top of existing community repositories. Rather than creating a new repository or rebuilding community repositories from the ground up, Dash will provide a way for organizations to allow self-service deposit of datasets via a simple, intuitive interface that is designed with individual researchers in mind. Researchers will be able to document, preserve, and publicly share their own data with minimal support required from repository staff, as well as be able to find, retrieve, and reuse data made available by others.

Three Phases of Work

  1. Requirements gathering: Before the design process begins, we will build requirements for researchers via interviews and surveys
  2. Design work: Based on surveys and interviews with researchers (Phase 1), we will develop requirements for a researcher-focused user interface that is visually appealing and easy to use.
  3. Technical work: Dash will be an added-value data sharing platform that integrates with any repository that supports community protocols (e.g., SWORD (Simple Web-service Offering Repository Deposit).

The dash is a critical component of any good ascii art. By reddit user Haleljacob

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