Researchers at Sweden's Karolinska Institute and Royal Institute of Technology have developed a new data analysis workflow for shotgun mass spec that could help improve the technique's quantitative reproducibility. Detailed in a paper published this month in Molecular & Cellular Proteomics, the approach uses a new quality scoring system that allows for more reliable recovery of missing data points across multiple mass spec runs.
A video demonstrating noWorkflow, a non-intrusive tool that allows researchers to capture a variety of provenance information and utilize the analyses it supports, including graph-based visualization, differencing over provenance trails, and inference queries.
R is a natural fit for a reproducibility project like this: as a scripting language, the R script itself provides a reproducible documentation of every step of the process. (Revolution R Open, Microsoft's enhanced R distribution, additionally includes features to facilitate reproducibility when using R packages.) The R script used for the psychology replication project describes and executes the process for checking the results of the papers.
myExperiment is a collaborative environment where scientists can safely publish their workflows and in silico experiments, share them with groups and find those of others. Workflows, other digital objects and bundles (called Packs) can now be swapped, sorted and searched like photos and videos on the Web.
Ph.D. dissertation, Department of Computer Science, Stanford University, 2012: "By understanding the unique challenges faced during research programming, it becomes possible to apply techniques from dynamic program analysis, mixed-initiative recommendation systems, and OS-level tracing to make research programmers more productive. This dissertation characterizes the research programming process, describes typical challenges faced by research programmers, and presents five software tools that I have developed to address some key challenges."
As part of this project, in collaboration with Philippe Bonnet, we are using (and extending) our infrastructure to support the SIGMOD Repeatability effort. Below are some case studies that illustrate how authors can create provenance-rich and reproducible papers, and how reviewers can both reproduce the experiments and perform workability tests: packaging an experiment on a distributed database system (link in title).