Blog topic: Open source

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Protocols.io Premium Edition Now Available for Stanford Users

September 3, 2019
by Amy E. Hodge

The Premium version of protocols.io -- a collaborative platform and preprint server for methods and protocols -- is now available free to all Stanford users! Funded by the Dean of Research and supported by Stanford Libraries, protocols.io allows you to create step-by-step detailed, interactive and dynamic protocols that can be run on mobile or web. This platform is useful for researchers in any discipline that uses a step-by-step methodology, including life sciences, engineering, chemistry, data science, and computational social sciences.

  • Creating Protocols: Protocols can be made from scratch or uploaded and converted from an existing Word or PDF document quickly and easily. In addition, if you have a particularly complex protocol, the staff at protocols.io will import a protocol for you.
  • DOIs & Publishing: Using the Premium version of protocols.io, you can share your protocols privately with labmates and collaborators, or publish them publicly with a Digitial Object Identifier (DOI) via protocol.io's open access repository. Getting a DOI for your protocol will make it easier for others to find and cite your protocols and give you credit for your work. And when you link from articles you publish to one of your own published protocols, you make your research articles more reproducible.
  • ORCID Connection: You can also connect your protocols.io account with your ORCID iD, which will allow protocols.io to automatically post information about your published protocols onto the Works section of your ORCID record.

Keep reading to find out how to get started!

Announcing the ArcLight Phase II work cycle kickoff

August 19, 2019
by Mark A. Matienzo

Last week, contributors from five institutions – Stanford University, Duke University, Indiana University, University of Michigan, and Princeton University – kicked off a collaborative nine-week work cycle for ArcLight. The work cycle, which runs from August 13 to October 11, 2019, will build on the ArcLight MVP implementation from 2017, and focuses on refining ArcLight’s usability and accessibility, addressing strategic needs in a community-based project. Major areas for this work cycle include:

  • Usability and accessibility refinements, including potential design changes
  • Revamping the tools used for indexing archival description into ArcLight’s Solr index
  • Analysis and implementation supporting better integration with request management systems, digital object viewers, and more

You can follow our work on the #arclight channel on the Code4Lib Slack team or the GitHub project board for the current work cycle. We expect to release public demo videos on YouTube, and will share them on Slack as well as the arclight-community Google Group to report on our progress. The work cycle’s conclusion coincides with the 2019 Blacklight Summit, to be held in Durham, North Carolina from October 9-11.

Call for feedback and contributions to forthcoming ArcLight work cycle

June 12, 2019
by Mark A. Matienzo

Stanford Libraries is organizing a work cycle later this year for ArcLight, a Rails engine supporting discovery of archival material. The work cycle is expected to run from August 12 to October 11, 2019, with planned contributions in terms of staff and development time from Stanford University, University of Michigan, Indiana University, and Princeton University. This work expands upon the work undertaken between April to June 2017 to develop a minimum viable product, and focuses on adding features, fixing bugs, and ensuring it is better suited as a product for future adoption and development. 

As a part of planning for this work cycle, Stanford, Michigan, Indiana, and Princeton have begun developing a collaborative roadmap to help us scope candidate areas of development. Following the process undertaken recently by the Spotlight community, we are now looking for contributions to and feedback on the roadmap to inform our work. If you’ve previously shared evaluations of ArcLight internal to your organization, we welcome you incorporating your ideas for features and improvements to this document. Our first deadline for contributions to the ArcLight work cycle roadmap is June 28, 2019.

ArcLight MVP work cycle completed

June 23, 2017
by Mark A. Matienzo

The ArcLight MVP project team has completed our eight-week work cycle to develop a minimum viable product to support discovery and delivery of archival materials using Blacklight, and have released ArcLight 0.1. More details, including a demo video and list of implemented features, follow below. The code for ArcLight, as well as documentation on how to get started can be found on GitHub.

Introducing Mirador 3: The next generation image comparison viewer

We are proud to announce the completion of the first phase of development of Mirador 3.  For fourteen weeks between January and April, a team consisting of contributors from four institutions across the US and Europe rebuilt Mirador anew.  Following a comprehensive year-long design process led by Jennifer Vine and Gary Geisler, a dedicated team of engineers from Stanford University, Universität Leipzig, Princeton University and Harvard University followed an agile software development process and produced a feature-rich alpha version that is ready for testing and ongoing development.  

students attending the workshop

Learners give high marks to coding skills workshop

January 28, 2019
by Amy E. Hodge

Last week, Stanford Libraries hosted our 10th two-day Carpentries workshop (I think -- I'm starting to lose count!). These workshops are designed to teach foundational coding and data science skills to graduate students, post-docs, research staff -- really, anyone on Stanford's campus who is doing research and needs to develop computational skills to help them get their tasks done more efficiently and less painfully. 

This workshop focused on the open source tools of shell, Git, and R, and focused on tasks like automation, version control, and modular programming. We had a fabulous all-female instructor team that included the Libraries' Claudia Engel, Mary-Ellen Petrich from LOCKSS, and Melissa Ko, lecturer in the Thinking Matters program. Our instructors were assisted by helpers John Borghi, Max Czapanskiy, Edgar Vivanco, and Amy Hodge.

The Carpentries (and the Libraries, for that matter) are very interested in assessment so that we can check how good a job we're doing. Fourteen of the nineteen attendees at our workshop filled out our survey at the end of the event, and here's what they had to say:

Improvements to SearchWorks in Summer and Fall 2018

During a four-month span between August and November of 2018, an interdepartmental team from the Stanford Libraries worked diligently to make a series of improvements to SearchWorks, Stanford’s world-class online catalog and discovery system.  The improvements are wide-ranging and diverse, and touch nearly every aspect of SearchWorks, which is an essential tool for Stanford faculty and students in support of research and instruction.  The work described below is the result of over four months of hard work by a world-class team of experts drawn

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