How Open Source Software Contributors Are Accelerating Biomedicine

“Each day, hundreds of thousands of scientists use open source software to advance biology and medicine, from studying cells in a microscope image to understanding how genes behave in healthy cells. Open source software underpins much of modern scientific research — providing reproducibility, transparency, and opportunities for collaboration. The impact of these tools is on par with some of the most cited papers in science in terms of reuse and adoption, yet even the most widely-used research software often lacks dedicated funding.

Our Essential Open Source Software for Science (EOSS) program was created to support these efforts — from software maintenance to growth, development, and community engagement for open source tools that are critical to science. We asked nine grantees from the first cycle of the EOSS program what drives them to create tools and how their commitment to open source moves science forward….”

Introducing the CC Search Browser Extension

This is part of a series of posts introducing the projects built by open source contributors mentored by Creative Commons during Google Summer of Code (GSoC) 2019. Mayank Nader was one of those contributors and we are grateful for his work on this project.

Creative Commons (CC) is working towards providing easy access to CC-licensed and public domain works. One significant step towards achieving that goal was the release of CC Search in 2019. Through this search and indexing tool, we’re making a plethora of CC-licensed images accessible in one place. As CC Search expands to include more than just images, CC is also developing a suite of applications and interfaces to help users across the world interact, consume, and reuse open access content.

CC Search Extension (1)

The CC Search Browser Extension is one such application. This browser extension is an open-source, lightweight plugin that can be installed and used by anyone with an updated web browser.

Why did we create this browser extension?

Browsers are the gateway to the web, and users often install browser plugins to improve productivity and overall experience. With the CC Search Browser Extension, users can now search for CC-licensed images, download them, and attribute the owner/creator without needing to head over to Flickr, Behance, Rawpixel or any other source of CC-licensed content. The other great feature? The CC Search Browser Extension works across different browsers, providing a familiar and intuitive experience for all users.

Key features of the CC Search Browser Extension: 

  • Search and filter CC-licensed content

You can use the extension filters to filter the content by the source website, types of licenses, and/or use-case.

CC Search Extension (2)

  • One-click attribution

One condition of all CC licenses is attribution. Attributing the owner/creator of CC-licensed content found using the extension is easy with one-click attribution. Both the Rich-text and HTML versions of the attribution are available.

CC Search Extension (3)

  • Download images (and attribution)

Download the image to use it in your works through the extension itself. You can also download the attribution information as a text file along with the image; this can be helpful when downloading multiple images in a single session.

  • Bookmark images

Bookmarking the images will save them in the extension. You can view and remove your bookmarks from the bookmarks section.

CC Search Extension (4)

  • Export and import bookmarks

As a user, you can easily archive and/or transfer your bookmarks. This feature makes sure that the process of archiving and transferring bookmarks is uncomplicated and straightforward.

CC Search Extension (5)

  • User-interface (UI) options available for custom settings

The extension also allows for setting default filters, etc. The “Options” page helps declutter the main popup of the extension, ensuring that it shows only the most necessary information. In the future, this “Options” page will also host additional and updated features.

CC Search Extension (6)

  • Sync your custom settings and bookmarks across devices

Chrome and Firefox have a built-in feature that syncs browser settings and preferences across your logged-in devices. The extension leverages this feature to sync your custom settings and bookmarks. This will make your experience more pleasant and familiar. 

  • Dark Mode

The extension also has a dark mode that you can toggle “on” by clicking the icon in the header. This reduces screen glare and battery consumption. You can set the dark mode as default in the “Options” page.

Future plans and development

  • Find and fix bugs
  • Add a review and feedback tab on the “Options” page
  • Integrate Vocabulary into the extension
  • Develop usability enhancements
  • Remove infinite scrolling and replace it with pagination or voluntary loading
  • Add search syntax for better specificity of results and a search syntax guide
  • Make the code more modular and add more tests
  • Port the features of the CC Search web application that are relevant in the context of the browser plugin

Installation

The latest version of the extension is available for installation via Mozilla Firefox, Google Chrome, and Opera.

Join the community

Community contribution and feedback is an essential part of the development process, so we encourage you to contact us if you have feedback or a specific suggestion. This is an open-source project, you can contribute in the form of bug reports, feature requests, or code contributions.

To install the development version of the extension, read the installation guide on Github.

Finally, come and tell us about your experience on the Creative Commons Slack via the slack channel: #cc-dev-browser-extension.

The post Introducing the CC Search Browser Extension appeared first on Creative Commons.

Introducing the CC Search Browser Extension

This is part of a series of posts introducing the projects built by open source contributors mentored by Creative Commons during Google Summer of Code (GSoC) 2019. Mayank Nader was one of those contributors and we are grateful for his work on this project.

Creative Commons (CC) is working towards providing easy access to CC-licensed and public domain works. One significant step towards achieving that goal was the release of CC Search in 2019. Through this search and indexing tool, we’re making a plethora of CC-licensed images accessible in one place. As CC Search expands to include more than just images, CC is also developing a suite of applications and interfaces to help users across the world interact, consume, and reuse open access content.

CC Search Extension (1)

The CC Search Browser Extension is one such application. This browser extension is an open-source, lightweight plugin that can be installed and used by anyone with an updated web browser.

Why did we create this browser extension?

Browsers are the gateway to the web, and users often install browser plugins to improve productivity and overall experience. With the CC Search Browser Extension, users can now search for CC-licensed images, download them, and attribute the owner/creator without needing to head over to Flickr, Behance, Rawpixel or any other source of CC-licensed content. The other great feature? The CC Search Browser Extension works across different browsers, providing a familiar and intuitive experience for all users.

Key features of the CC Search Browser Extension: 

  • Search and filter CC-licensed content

You can use the extension filters to filter the content by the source website, types of licenses, and/or use-case.

CC Search Extension (2)

  • One-click attribution

One condition of all CC licenses is attribution. Attributing the owner/creator of CC-licensed content found using the extension is easy with one-click attribution. Both the Rich-text and HTML versions of the attribution are available.

CC Search Extension (3)

  • Download images (and attribution)

Download the image to use it in your works through the extension itself. You can also download the attribution information as a text file along with the image; this can be helpful when downloading multiple images in a single session.

  • Bookmark images

Bookmarking the images will save them in the extension. You can view and remove your bookmarks from the bookmarks section.

CC Search Extension (4)

  • Export and import bookmarks

As a user, you can easily archive and/or transfer your bookmarks. This feature makes sure that the process of archiving and transferring bookmarks is uncomplicated and straightforward.

CC Search Extension (5)

  • User-interface (UI) options available for custom settings

The extension also allows for setting default filters, etc. The “Options” page helps declutter the main popup of the extension, ensuring that it shows only the most necessary information. In the future, this “Options” page will also host additional and updated features.

CC Search Extension (6)

  • Sync your custom settings and bookmarks across devices

Chrome and Firefox have a built-in feature that syncs browser settings and preferences across your logged-in devices. The extension leverages this feature to sync your custom settings and bookmarks. This will make your experience more pleasant and familiar. 

  • Dark Mode

The extension also has a dark mode that you can toggle “on” by clicking the icon in the header. This reduces screen glare and battery consumption. You can set the dark mode as default in the “Options” page.

Future plans and development

  • Find and fix bugs
  • Add a review and feedback tab on the “Options” page
  • Integrate Vocabulary into the extension
  • Develop usability enhancements
  • Remove infinite scrolling and replace it with pagination or voluntary loading
  • Add search syntax for better specificity of results and a search syntax guide
  • Make the code more modular and add more tests
  • Port the features of the CC Search web application that are relevant in the context of the browser plugin

Installation

The latest version of the extension is available for installation via Mozilla Firefox, Google Chrome, and Opera.

Join the community

Community contribution and feedback is an essential part of the development process, so we encourage you to contact us if you have feedback or a specific suggestion. This is an open-source project, you can contribute in the form of bug reports, feature requests, or code contributions.

To install the development version of the extension, read the installation guide on Github.

Finally, come and tell us about your experience on the Creative Commons Slack via the slack channel: #cc-dev-browser-extension.

The post Introducing the CC Search Browser Extension appeared first on Creative Commons.

Core Scientific Dataset Model: A lightweight and portable model and file format for multi-dimensional scientific data

Abstract:  The Core Scientific Dataset (CSD) model with JavaScript Object Notation (JSON) serialization is presented as a lightweight, portable, and versatile standard for intra- and interdisciplinary scientific data exchange. This model supports datasets with a p-component dependent variable, {U0, …, Uq, …, Up?1}, discretely sampled at M unique points in a d-dimensional independent variable (X0, …, Xk, …, Xd?1) space. Moreover, this sampling is over an orthogonal grid, regular or rectilinear, where the principal coordinate axes of the grid are the independent variables. It can also hold correlated datasets assuming the different physical quantities (dependent variables) are sampled on the same orthogonal grid of independent variables. The model encapsulates the dependent variables’ sampled data values and the minimum metadata needed to accurately represent this data in an appropriate coordinate system of independent variables. The CSD model can serve as a re-usable building block in the development of more sophisticated portable scientific dataset file standards.

Researchers develop new open-source system to manage and share complex datasets

“But often, sharing that data with other scientists—or with peer-reviewed journal editors, or funders—is difficult. The software might be proprietary, and prohibitively expensive to purchase. It might take years of training for a person to be able to manage and understand the software. Or the company that created the software might have gone out of business.

A research team has developed an open-source data-management system that the scientists hope will solve all of those problems. The researchers outlined their system today in the journal PLOS ONE….”

Copyright Guide for Scientific Software | Zenodo

Abstract:  Today, science involves software. And although many scientists understand that their work stands on the shoulders of others, they may not know how copyright affects their rights to use others’ software, or how they can publish their software tools so others can use or cite it. The Copyright Guide to Scientific Software, a joint project of the Harvard Cyberlaw Clinic and the Center for Astrophysics, in association with the Software Preservation Network, aims to fill that gap, by providing clear, easy-to-read answers to common questions about how scientific software and copyright interact. 

 

The Open Book Project is designing a non-proprietary eReader – Liliputing

“There’s no shortage of devices designed for reading eBooks. But whether you’re using a Kindle, Kobo, or Nook device or something else entirely, you’re probably running proprietary software on proprietary hardware.

The Open Book Project is an effort to build… something more open. It’s still a work in progress, but the design files are shared at github which means that not only can anyone try to build their own, but you can also modify the designs to add or remove features….”

A community-maintained standard library of population genetic models | bioRxiv

Abstract:  The explosion in population genomic data demands ever more complex modes of analysis, and increasingly these analyses depend on sophisticated simulations. Recent advances in population genetic simulation have made it possible to simulate large and complex models, but specifying such models for a particular simulation engine remains a difficult and error-prone task. Computational genetics researchers currently re-implement simulation models independently, leading to duplication of effort and the possibility for error. Population genetics, as a field, also lacks standard benchmarks by which new tools for inference might be measured. Here we describe a new resource, stdpopsim, that attempts to rectify this situation. Stdpopsim is a community-driven open source project, which provides easy access to a standard catalog of published simulation models from a wide range of organisms and supports multiple simulation engine backends. We share some examples demonstrating how stdpopsim can be used to systematically compare demographic inference methods, and we encourage an even broader community of developers to contribute to this growing resource.

 

 

The importance and challenges of sharing research software Tickets, Wed 5 Feb 2020 at 18:00 | Eventbrite

“Research software is increasingly being recognised as an important research output which also has a role in supporting the transparency and reproducibility of papers and associated experimental results. Funders such as Wellcome now include software in their data sharing policies, while more journals are supporting open sharing of software. The Research Software Engineering movement, which has developed over the last few years to support the people who build research software, is also developing awareness and understanding of the importance of research software….”

Open Science Prize goes to software tool for tracking viral outbreaks | Livingston Ledger

“After three rounds of competition—one of which involved a public vote—a software tool developed by researchers at Fred Hutchinson Cancer Research Center and the University of Basel to track Zika, Ebola and other viral disease outbreaks in real time has won the first-ever international Open Science Prize.

Fred Hutch evolutionary biologist Dr. Trevor Bedford and physicist and computational biologist Dr. Richard Neher of the Biozentum Center for Molecular Life Studies in Basel, Switzerland, designed a prototype called nextstrain to analyze and track genetic mutations during the Ebola and Zika outbreaks. Using the platform Bedford and Neher built, anyone can download the source code from the public-access code-sharing site GitHub, run genetic sequencing data for the outbreak they are following through the pipeline and build a web page showing a phylogenetic tree, or genetic history of the outbreak, in a few minutes, Bedford said….”