containerit packages R script/session/workspace and all dependencies as a Docker container by automagically generating a suitable Dockerfile. The package’s website is https://o2r.info/containerit/.
Background:The complex nature of biological data has driven the development of specialized software tools. Scientificworkflow management systems simplify the assembly of such tools into pipelines, assist with job automation, and aidreproducibility of analyses. Many contemporary workflow tools are specialized or not designed for highly complexworkflows, such as with nested loops, dynamic scheduling, and parametrization, which is common in, e.g., machinelearning.Findings:SciPipe is a workflow programming library implemented in the programming language Go, for managingcomplex and dynamic pipelines in bioinformatics, cheminformatics, and other fields. SciPipe helps in particular withworkflow constructs common in machine learning, such as extensive branching, parameter sweeps, and dynamicscheduling and parametrization of downstream tasks. SciPipe builds on flow-based programming principles to supportagile development of workflows based on a library of self-contained, reusable components. It supports running subsets ofworkflows for improved iterative development and provides a data-centric audit logging feature that saves a full audit tracefor every output file of a workflow, which can be converted to other formats such as HTML, TeX, and PDF on demand. Theutility of SciPipe is demonstrated with a machine learning pipeline, a genomics, and a transcriptomics pipeline.Conclusions:SciPipe provides a solution for agile development of complex and dynamic pipelines, especially in machinelearning, through a flexible application programming interface suitable for scientists used to programming or scripting.
Among the top challenges of reproducible computational science are the following: 1) creation, curation, usage, and publication of research software; 2) acceptance, adoption, and standardization of open-science practices; and 3) misalignment with academic incentive structures and institutional processes for career progression. I will mainly address the first two here, proposing a praxis of reproducible computational science.
Neuroscience has been carried into the domain of big data and high performance computing (HPC) on the backs of initiatives in data collection and an increasingly compute-intensive tools. While managing HPC experiments requires considerable technical acumen, platforms and standards have been developed to ease this burden on scientists. While web-portals make resources widely accessible, data organizations such as the Brain Imaging Data Structure and tool description languages such as Boutiques provide researchers with a foothold to tackle these problems using their own datasets, pipelines, and environments. While these standards lower the barrier to adoption of HPC and cloud systems for neuroscience applications, they still require the consolidation of disparate domain-specific knowledge. We present Clowdr, a lightweight tool to launch experiments on HPC systems and clouds, record rich execution records, and enable the accessible sharing of experimental summaries and results. Clowdr uniquely sits between web platforms and bare-metal applications for experiment management by preserving the flexibility of do-it-yourself solutions while providing a low barrier for developing, deploying and disseminating neuroscientific analysis.
Scientific reproducibility is key to the advancement of science as researchers can build on sound and validated results to design new research studies. However, recent studies in biomedical research have highlighted key challenges in scientific reproducibility as more than 70% of researchers in a survey of more than 1500 participants were not able to reproduce results from other groups and 50% of researchers were not able to reproduce their own experiments. Provenance metadata is a key component of scientific reproducibility and as part of the Provenance for Clinical and Health Research (ProvCaRe) project, we have: (1) identified and modeled important provenance terms associated with a biomedical research study in the S3 model (formalized in the ProvCaRe ontology); (2) developed a new natural language processing (NLP) workflow to identify and extract provenance metadata from published articles describing biomedical research studies; and (3) developed the ProvCaRe knowledge repository to enable users to query and explore provenance of research studies using the S3 model. However, a key challenge in this project is the automated classification of provenance metadata extracted by the NLP workflow according to the S3 model and its subsequent querying in the ProvCaRe knowledge repository. In this paper, we describe the development and comparative evaluation of deep learning techniques for multi-class classification of structured provenance metadata extracted from biomedical literature using 12 different categories of provenance terms represented in the S3 model. We describe the application of the Long Term Short Memory (LSTM) network, which has the highest classification accuracy of 86% in our evaluation, to classify more than 48 million provenance triples in the ProvCaRe knowledge repository (available at: https://provcare.case.edu/).
The results of a scientific experiment have to be reproduced to be valid. The scientific method is well known in experimental sciences but it is not always the case for computer scientists. Recent publications and studies has shown that there is a significant reproducibility crisis in Biology and Medicine. This problem has also been demonstrated for hundreds of publications in computer science where only a limited set of publication results could be reproduced. In this paper we present the reproducibility challenge and we examine the reproducibility of a Parallel Discrete Event System Specification (PDEVS) model with two different execution frameworks.