Summary: This manuscript introduces and describes Dugong, a Docker image based on Ubuntu 16.04, which automates installation of more than 3500 bioinformatics tools (along with their respective libraries and dependencies), in alternative computational environments. The software operates through a user-friendly XFCE4 graphic interface that allows software management and installation by users not fully familiarized with the Linux command line and provides the Jupyter Notebook to assist in the delivery and exchange of consistent and reproducible protocols and results across laboratories, assisting in the development of open science projects.
Fairly high-level entry slides presented to the members of intercollegiate graduate program in Bioinformatics and Genomics at The Pennsylvania State University.
Reproducibility, a cornerstone of research, requires defined data formats, which include the set-up and output of experiments. The Real-time PCR Data Markup Language (RDML) is a recommended standard of the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines. Despite the popularity of the RDML format for analysis of qPCR data, handling of RDML files is not yet widely supported in all PCR curve analysis softwares. Results: This study describes the open source RDML package for the statistical computing language R.RDML is compatible with RDML versions ≤ 1.2 and provides functionality to (i) import RDML data; (ii) extract sample information (e.g., targets, concentration); (iii) transform data to various formats of the R environment; (iv) generate human readable run summaries; and (v) to create RDML files from user data. In addition, RDML offers a graphical user interface to read, edit and create RDML files.
To address this critical need, the Laura and John Arnold Foundation has awarded a grant to a coalition of groups representing the international Earth and space science community, convened by the American Geophysical Union (AGU), to develop standards that will connect researchers, publishers, and data repositories in the Earth and space sciences to enable FAIR (findable, accessible, interoperable, and reusable) data – a concept first developed by Force11.org – on a large scale. This will accelerate scientific discovery and enhance the integrity, transparency, and reproducibility of this data. The resulting set of best practices will include: metadata and identifier standards; data services; common taxonomies; landing pages at repositories to expose the metadata and standard repository information; standard data citation; and standard integration into editorial peer review workflows.
This book contains a collection of 31 case studies of reproducible research workflows, written by academic researchers in the data-intensive sciences. Each case study describes how the author combined specific tools, ideas, and practices in order to complete a real-world research project. Emphasis is placed on the practical aspects of how the author organized his or her research to make it as reproducible as possible.
We present a toolchain for computational research consisting of Sacred and two supporting tools. Sacred is an open source Python framework which aims to provide basic infrastructure for running computational experiments independent of the methods and libraries used. Instead, it focuses on solving universal everyday problems, such as managing configurations, reproducing results, and bookkeeping. Moreover, it provides an extensible basis for other tools, two of which we present here: Labwatch helps with tuning hyperparameters, and Sacredboard provides a web-dashboard for organizing and analyzing runs and results.