Hyku Open Source Institutional Repository Development partnership awarded $1M Arcadia grant to improve open scholarship infrastructure | UVA Library News and Announcements

“The University of Virginia is pleased to announce a two-year award in the amount of $1,000,000 from Arcadia—a charitable fund of philanthropists Lisbet Rausing and Peter Baldwin—in support of the “Advancing Hyku: Open Source Institutional Repository Platform Development” project.

Through this project, the University of Virginia and its partner institutions—Ubiquity Press and the British Library—will support the growth of open access through institutional repositories. Working with the global open infrastructure community, the partners will introduce significant structural improvements and new features to the Samvera Community’s Hyku Institutional Repository platform….”

Schmidt Futures Supports Invest in Open Infrastructure | Invest in Open Infrastructure

“We are thrilled to announce that Invest in Open Infrastructure (IOI) has been generously supported with an award of 150k USD from Schmidt Futures, a philanthropic initiative founded by Eric and Wendy Schmidt. IOI is an effort to enable durable, scalable, and long lasting open scientific and scholarly infrastructure to emerge, thrive, and deliver its benefits on a global scale. We are a global coalition of projects, organizations, and initiatives actively working to build a sustainable future for open scholarly infrastructure….

With this initial support, we will be opening the search for a Director in the next few weeks. This will be a full time, remote-friendly position offered in partnership with IOI’s fiscal sponsor Code for Science & Society. Stay tuned for more details on this opportunity, and visit investinopen.org to show your support and get the latest news….”


Code for Science & Society | Jobs with CS&S and Sponsored Projects

“Are you interested in open science, open source, open scholarship, and public interest technology? Do you love helping things run smoothly? Organizing information? Managing projects? Facilitating team communication? Sorting out logistics? Then we need you! Come help a small multi-organizational, distributed team to support the future of open public interest technology in science, civic tech, new media, and beyond!…”

Code for Science & Society | Jobs with CS&S and Sponsored Projects

“Are you interested in open science, open source, open scholarship, and public interest technology? Do you love helping things run smoothly? Organizing information? Managing projects? Facilitating team communication? Sorting out logistics? Then we need you! Come help a small multi-organizational, distributed team to support the future of open public interest technology in science, civic tech, new media, and beyond!…”

1168219FP-R Software Engineer – Recruitment at the University of Southampton

“Applications are invited for a Software Engineer to work as part of an Enterprise team within the University of Southampton.

EPrints Services are part of the successful and long running enterprise activities in the School of Electronics and Computer Science. Enterprise activities are expanding and as such the team needs to grow too….

At the core is an open source repository platform that provides a flexible way to configure operations concerning data capture, structure and presentation, and a range of services that allow content to be accessed in a variety of ways.

We require applicants who can take responsibility for the development of customer focused projects for both EPrints systems and more varied engineering projects relating to Open Data, Digital Education, and systems integrations. All projects require some level of design, programming, testing, project management, and customer support….”

Workflow systems turn raw data into scientific knowledge

“Finn is head of the sequence-families team at the European Bioinformatics Institute (EBI) in Hinxton, UK; Meyer is a computer scientist at Argonne National Laboratory in Lemont, Illinois. Both run facilities that let researchers perform a computationally intensive process called metagenomic analysis, which allows microbial communities to be reconstructed from shards of DNA. It would be helpful, they realized, if they could try each other’s code. The problem was that their analytical ‘pipelines’ — the carefully choreographed computational steps required to turn raw data into scientific knowledge — were written in different languages. Meyer’s team was using an in-house system called AWE, whereas Finn was working with nearly 9,500 lines of Python code.

“It was a horrible Python code base,” says Finn — complicated, and difficult to maintain. “Bits had been bolted on in an ad hoc fashion over seven years by at least four different developers.” And it was “heavily tied to the compute infrastructure”, he says, meaning it was written for specific computational resources and a particular way of organizing files, and thus essentially unusable outside the EBI. Because the EBI wasn’t using AWE, the reverse was also true. Then Finn and Meyer learnt about the Common Workflow Language (CWL).

CWL is a way of describing analytical pipelines and computational tools — one of more than 250 systems now available, including such popular options as Snakemake, Nextflow and Galaxy. Although they speak different languages and support different features, these systems have a common aim: to make computational methods reproducible, portable, maintainable and shareable. CWL is essentially an exchange language that researchers can use to share pipelines for whichever system. For Finn, that language brought sanity to his codebase, reducing it by around 73%. Importantly, it has made it easier to test, execute and share new methods, and to run them on the cloud….”

Repository Ouroboros – Ruth Kitchin Tillman

“The library is going to adopt a new repository and you just got hired to make it happen. You may be fresh out of library school with a few metadata projects under your belt. Perhaps you did metadata work on a two-year digitization grant and are looking forward to getting out of the spreadsheet mines. Or maybe you worked in a similar job at your last institution—running a turnkey repository like DSpace, CONTENTdm, or BePress. Perhaps you’ve moved into the role at an angle, from something more traditional like cataloging….

[After a long struggle] But you feel like a fraud. You feel so discouraged. You are sure everyone else is ahead of you. You do not yet see that you are just one more person riding the Repository Ouroboros.”

METRO | 599 | Digital Repository Developer – Metropolitan New York Library Council

“METRO is seeking a developer with experience working as a Drupal 8 site builder and theme developer. We have developed an innovative new open source repository architecture called Archipelago, and as the Digital Repository Developer, you will have a chance to contribute to this project in its infancy! Archipelago uses a modified version of Drupal 8 for the public front end and administrative interface. The first software METRO will build using this architecture will be a digital asset management solution meant for libraries, archives, and museums. Reporting to the Lead Developer, the successful candidate will work collaboratively with our team on our base repository solution, contracts building new custom repositories and new features, and they may manage a portfolio of support contracts as well….”

Development sneak preview – Editoria

Editoria’s web-based word processor is being upgraded, along with the rest of the system, in response to the community’s most recent roadmap. In the current version of Editoria, Monemvasia, we have contextually sensitive styles. This means that once a component is recognized as a frontmatter item, for example, the ‘menu’ of style options available automatically updates to display only the styles relevant within the context of a front matter component. The same is true for parts, unnumbered components and chapters.

To take styling in the web-based word processor (via the Wax editor) to the next level, Christos Kokosias, Wax lead developer, is working up functionality (suggested by friends at punctum books) that adds the ability to customize tags at the chapter level. This will help with pagination as it improves the quality of the HTML available to export tools using CSS to automatically typeset content prepared in the browser….”

Essential Open Source Software for Science – Chan Zuckerberg Science Initiative – Medium

We followed two guiding principles in creating this opportunity:

  • First, we didn’t want to limit funding to pure software development. Open source is more than just writing code. It includes improving documentation, addressing usability, managing the project, and building community. We want to provide opportunities in whatever form will help make the computational foundations of biological research more usable and robust….
  • Second, we wanted to be inclusive in defining the scope of what counts as essential software for biomedical research. The proposed work does not need to be tied to novel research. Additionally, both domain-specific software and foundational tools and infrastructure used across several domains of science will be eligible to apply, so long as they have some impact in biomedical science. Such foundational tools can range from data structures to numerical computation libraries to toolkits for workflow execution and reproducibility. These tools play a critical role, often acting as dependencies for more domain-specific tools….”

Coming Soon: Essential Open Source Software for Science – Chan Zuckerberg Initiative

The Chan Zuckerberg Initiative will soon invite applications for open source software projects that are essential to biomedical research. Applicants can request funding between $50k and $250k for one year. This RFA is the first of a series. CZI will invite applications during three distinct cycles, with rounds beginning June 18, 2019; mid-December 2019; and mid-June 2020. Read our Medium post to learn more….”

Open NetSci Hackathon

The Open NetSci Hackathon is an event sponsored by PLOS. It is part of the extended program of the 14th International School and Conference on Network Science (NetSci 2019).

The goal of the Hackathon is to promote open research practice in Network Science. For the first edition, the theme will be open code and data.

We hope to make the hackathon a perfect venue for getting together, and hacking away at fun projects in a laid-back, friendly environment….”

PubSweet Collaboration Week – May 7 – 13 : Collaborative Knowledge Foundation

About three years ago, we set out to build a framework for building publishing software with components. Take a component here, a component there, make one on your own, and, presto! you have your custom publishing platform! While the framework itself has matured significantly, we’re not there yet in terms of the available components and how they fit together.

At the same time, we started building a community around this framework, organisations and people looking to innovate within this space and looking for a way to do so. While building a community has to happen in parallel with software development, I think that if you’re doing open source development right, your community will be ahead of the software most of the time. This is certainly the case for us. We envisioned a community that openly shares their experiences and solutions and is willing to collaborate on new ideas, despite basically being competitors, and I can happily (and proudly) say that our community has already reached this ideal.

To close the loop and make PubSweet the go-to framework and component library for developing publishing software, we need to take the lessons from the three systems in production right now (Hindawi’s, EBI’s and eLife’s publishing systems) and incorporate them into PubSweet itself, for everyone to use and benefit from. If we could just get the designers and developers of these systems in the same room, get them to talk to each other, share their custom approaches and try to find commonalities between them… wouldn’t that be awesome? Luckily our community is awesome, and well-versed in that sort of thing, and that’s exactly what’s happening in our event this week!

For the inaugural PubSweet Collaboration Week, starting on May 7th, Coko, EBI, eLife and Hindawi are getting together in Cambridge to make more parts of these systems reusable and add them to PubSweet’s component library….”

Hopkins partners with Harvard and MIT to launch Public Access Submission System (PASS) and support open access – The Sheridan Libraries Blog

“Johns Hopkins University’s Sheridan Libraries, in collaboration with the Harvard University Office for Scholarly Communication, the MIT Libraries, and with inspiration from Jeff Spies, formerly of the Center for Open Science, have developed the Public Access Submission System, or PASS. The innovative web application helps researchers comply simultaneously with the open access policies of both their funders and their institutions….”