Software Incubator Workshop: A Synthesis

Sebastian P. Benthall • February 25, 2019

Thanks for comments from: Dan Katz, Suresh Marru, Abby Cabunoc Mayes, Micaela S. Parker, Danielle Robinson, and Nic Weber. Research software is software created by scholarly researchers. Often researchers produce source code that is ‘open’, in alignment with scientific norms. But this code and the research it supports is not always “sustainable”, because it does not have a viable community of developers and users working with it in an ongoing way.

The Molecular Sciences Software Institute: The Time is Ripe for Change

T. Daniel Crawford and Daniel G. A. Smith • February 6, 2019

We are witnessing the early stages of a revolution in the computational molecular sciences. Numerous community codes in quantum chemistry, biomolecular simulation, and computational materials science are beginning to adopt modern, collaborative software engineering practices and tools, to the benefit of the broader field. Over their long history, the computational molecular sciences have emerged as an essential partner with experiment in elucidating the structures and mechanisms that control chemical processes, and, in fact, often precede experiment in the knowledge-based design of new systems.

Revisiting authorship, and JOSS software publications

C. Titus Brown, University of California, Davis • January 17, 2019

(reposted from Titus’s blog) We are slowly working towards a v2.0 release of sourmash, our software for MinHash and modulo hash analysis of genomic data, and the question of proper authorship is once again on my mind! The question du jour: how should authorship on software papers be decided? Some background - our previous take on authorship Those of you with long memories may recall a hullabaloo in 2015 over this occasioned by the khmer v2.

Why Research Software Sustainability Won't Be Fixed by Containers

Henry Neeman, University of Oklahoma • December 21, 2018

Containers, such as Singularity and Docker, are an amazing advance in software sustainability. By allowing software developers to package not only application software but also other components of the software stack, including software dependencies, that the application needs, and with which the application is well tested, containers make the porting of applications to new platforms much more straightforward, convenient and efficient. In the large scale research computing world, containers are a miracle in the near-term, but a looming challenge in the medium- to long-term.

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