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….”

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….”

Pondering the arrival of the Open Publishing Awards | FORCE11

“This year, Coko’s Founder Adam Hyde organized and launched the Open Publishing Awards with a stated mission to celebrate all things open and publishing. The initial ‘launch’ of the awards via social media and a website debut was in August, and somehow the organization managed to assemble a panel of judges, solicit nominations, plan an event and deliver on a shortlist of winners, all within a few weeks. After the awards ceremony last week at FORCE 2019, it is a good time to stop and think: were the awards successful? How can we assess the success, failure, or utility of awards programs, in general? Is there room for another?

First, we can take a look at the ‘why’ behind the awards. The Open Publishing Awards website makes it clear: they aim to celebrate and raise awareness about all things open and publishing. This year, that meant open software and open content, as those were the two categories that nominations were solicited within. Is it enough to “celebrate” and announce a “shortlist” – or are we really hungry to create single category “winners” the way that other awards programs tend to?

Next, who is ordained to decide a) what is open, and/or b) how open is ‘open’? This is a semantic and ideological discussion that occurs on an ongoing basis. My open may not be open enough for you or vice versa. The category descriptions offered some help, but was it enough? …”

Openscapes

“At Openscapes, we champion open practices in environmental science to help uncover data-driven solutions faster. Regardless of research question, environmental scientists are united by the need to analyze data — and to do so in a way that is efficient, reproducible, and easily communicated. With tools specifically created to meet modern demands for collaborative data science, we help create a positive open culture to enable better science in less time….”

Open Software Means Kinder Science – Scientific American Blog Network

“As a marine ecologist, I never expected I would one day advocate that science should operate more like the tech industry.

This is not about “moving fast and breaking things.” For me, it is about openness. 

Open software, both a driver and a result of Silicon Valley’s success, has been game-changing for me as a scientist. Its transformative power has improved my ability to analyze data and collaborate with other scientists….

My own transformation from scientist to open science champion has emboldened me to help enable others, and to help bring the kindness of the open software community to science. That is the whole idea behind the Openscapes, an organization I founded to advocate for open practices in environmental science. The idea is to empower early career scientists with existing open tools and communities, focusing on the research group, the campus and beyond….”

Insights into the Economy of Open Scholarship: A look into OpenEdition with Pierre Mounier, deputy director

“OpenEdition is supported financially by the four founding institutions (CNRS [French National Centre for Scientific Research], Aix-Marseille University, EHESS [School for Advanced Studies in the Social Sciences], Avignon University), which provide the platform with staff, infrastructure and funds to cover operating costs. They also receive support directly from the Ministry of Research (as a research infrastructure). About 50 FTE staff are permanently seconded from the four founding institutions. The staff are divided into an editorial department that manages the relationships with the content producers (blogging researchers, publishers, journal editors), an IT department that runs systems and development, a department for international development and a department dedicated to the Freemium services – ‘Freemium’ being a pricing strategy by which a digital product or service is provided free of charge, but money is charged for additional features. The other main source of revenue stems from project funding – national, regional and European. These funds are used to develop new and innovative tools and services. Recently, OpenEdition has added the Freemium model (ji.sc/2Vxjge3) to their revenue streams, but this system has not been introduced to cover operating costs or infrastructures. Rather, it serves to help the journal publishers and editors to cover their publishing and editing costs. Two-thirds of the money collected is transferred to the publishers OpenEdition works with, while the remaining third is retained to operate the commercial services that sell these Freemium services….”