Some Friday Zen as Highlighter markers are made, and a classic trip to the crayon factory is revisited.
Why is the latest internet craze so difficult? An engineer explains…
The post The Physics of the Milk Crate Challenge (and Why You Will Fall) appeared first on The Scholarly Kitchen.
What do we really know about the linkages between good metadata and positive, productive user experiences with scholarly journals?
The post The Experience of Good Metadata: Linking Metadata to Research Impacts appeared first on The Scholarly Kitchen.
Joe Esposito revisits his 2012 post on the unstated theory of the e-book, which assumes that a book consists only of its text and can be manipulated without regard to the nature and circumstances of its creation. This is only one theory of many, but it is now the prevailing one.
Turns out, digital transformation is actually more human than technical. Learn more in these case studies from Emerald and De Gruyter.
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A look at BioASQ — an annual competition to develop AI systems to help drive medical progress.
The post Guest Post — BioASQ for the Win: Inside the Healthiest Competition You’ve Never Heard Of appeared first on The Scholarly Kitchen.
The Journal of Open Source Software was designed from scratch using the principles of open source and software design practices. This has both advantages and disadvantages, particularly with respect to elements of the traditional scholarly publishing ecosystem.
How big is the universe? How small is the quantum realm? The answer lies in a sheet of A4 paper…
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Reproducibility continues to be one of the major challenges facing computational biologists today. Complicated experiments, massive data sets, scantily described protocols, and constantly evolving code can make experimental documentation and replication very difficult. In addition, the need for specialized knowledge and access to large computational resources can create barriers when trying to design and model macromolecules.
Every year, the Rosetta developer community meets to discuss these challenges and advancements via Rosetta, a software suite that models and helps design macromolecules. In 2010, PLOS announced the RosettaCon2010 Collection, which made the latest research on protocols used to create macromolecular models available to all. Now, the PLOS ONE RosettaCon 2012 Collection continues to tackle issues related to use, reproducibility and documentation by highlighting new scientific developments within the Rosetta community.
The RosettaCon 2012 Collection comprises 14 articles detailing the scientific advancements made by developers that use Rosetta. In order to address reproducibility and documentation challenges, each article within this Collection includes an archive containing links to the exact version of the code used in the paper, all input data, links to external tools and example scripts.
This year’s Collection marks the tenth anniversary of RosettaCon and focuses on three long-term goals of the community: increase the usability of Rosetta, improve its current methods, and introduce completely new protocols.
Increasing the usability of Rosetta – Rosetta still requires specialized knowledge and large computational resources, but this collection features two articles describing advancements that make it easier for non-experts to use its applications. These articles introduce the Rosetta Online Server that Includes Everyone (ROSIE) workflow, which allows for rapid conversion of Rosetta applications into public web servers, and PyRosetta, a new graphical user interface (GUI) which allows users to run standard Rosetta design tasks.
Improving current prediction methods – Several articles describe improvements to Rosetta’s structure prediction capabilities and design methodologies. Some examples include improvements to loop conformational sampling, and a recently developed ray-casting (DARC) method for small molecule docking now enables virtual screening of large compound libraries.
Introducing new protocols – A number of articles featuring new procedures and applications that debuted at the conference are introduced in the Collection. Highlights include new methods for dealing with ligand docking, advancements to pre-refine scaffold proteins prior to computational design of functional sites, and new protocols to drive Rosetta de novo modeling.
The RosettaCon 2012 Collection continues to help serve the Rosetta community in an effort to ensure that newly developed protocols are as usable as more established workflows, are transparent, and are accurately documented even in an active development environment.
This post has been adapted from “The RosettaCon 2012 Special Collection: Code Writ on Water, Documentation Writ in Stone” which serves as a more in-depth overview of the new collection. To read all that this Collection has to offer, click here.