Our PeerJ manuscript submitted Nov26 is out with open peer reviews: Composable languages for bioinformatics: the NYoSh experiment See https://peerj.com/articles/241
Here’s hoping this paper quick starts the use of Language Workbenches in Bioinformatics. It’s a complete paradigm change for information management and real life software projects that need to handle several types of abstractions.
Yes, the manuscript was published in a little more than a month with Thanksgiving and Christmas in the range. I think this is the fastest peer-review I have experienced. Here’s a detailed timeline of this submission:
We will definitely be submitting to PeerJ again.
We have posted a new tutorial to demonstrate how to write a GobyWeb Task plugin with NYoSh. See NYoSh Documentation for a complete list of tutorials.
We have released build 4 of the NYoSh workbench. This version compiles and deploys plugin scripts directly into the GobyWeb plugin directory associated with the script. We have also started adding documentation. You can find a step by step Getting Started tutorial, as well as an introductory tutorial video.
Our lab started working on language engineering over the summer. Experimenting with the MPS language workbench, we built a set of languages that work together to provide a modern scripting language. We called this scripting language NYoSh, short for “Not Your ordinary Shell” (available at http://nyosh.campagnelab.org).
MPS makes it possible to package languages in a standalone Integrated Development Environment, so we built one for NYoSh. The NYoSh Workbench is the result and now available for download (Early Access Program). In this first release, we are focusing on GobyWeb plugin scripts. The workbench makes it possible to develop scripts for the GobyWeb resources and aligner plugins.
We will add documentation to the web site in the coming weeks and some videos to illustrate the advantages of developing plugins with NYoSh.
We have pushed version 2.2.1 of the GobyWeb plugins to GitHub. The following changes are included in this release: