IVOA Provenance data model: hints from the CTA Provenance prototype

We present the last developments on the IVOA Provenance data model, mainly based on the W3C PROV concept. In the context of the Cherenkov astronomy, the data processing stages imply both assumptions and comparison to dedicated simulations. As a consequence, Provenance information is crucial to the end user in order to interpret the high level data products. The Cherenkov Telescope Array (CTA), currently in preparation, is thus a perfect test case for the development of an IVOA standard on Provenance information. We describe general use-cases for the computational Provenance in the CTA production pipeline and explore the proposed W3C notations like PROV-N formats, as well as Provenance access solutions.Comment: 4 pages, 3 figures, to appear in ADASS XXV proceedings, edited by N. P. F. Lorente, & K. Shortridge (San Francisco: ASP), ASP Conf. Se

BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments

Advances in sequencing techniques have led to exponential growth in biological data, demanding the development of large-scale bioinformatics experiments. Because these experiments are computation- and data-intensive, they require high-performance computing (HPC) techniques and can benefit from specialized technologies such as Scientific Workflow Management Systems (SWfMS) and databases. In this work, we present BioWorkbench, a framework for managing and analyzing bioinformatics experiments. This framework automatically collects provenance data, including both performance data from workflow execution and data from the scientific domain of the workflow application. Provenance data can be analyzed through a web application that abstracts a set of queries to the provenance database, simplifying access to provenance information. We evaluate BioWorkbench using three case studies: SwiftPhylo, a phylogenetic tree assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a RASopathy analysis workflow. We analyze each workflow from both computational and scientific domain perspectives, by using queries to a provenance and annotation database. Some of these queries are available as a pre-built feature of the BioWorkbench web application. Through the provenance data, we show that the framework is scalable and achieves high-performance, reducing up to 98% of the case studies execution time. We also show how the application of machine learning techniques can enrich the analysis process

A posteriori metadata from automated provenance tracking: Integration of AiiDA and TCOD

In order to make results of computational scientific research findable, accessible, interoperable and re-usable, it is necessary to decorate them with standardised metadata. However, there are a number of technical and practical challenges that make this process difficult to achieve in practice. Here the implementation of a protocol is presented to tag crystal structures with their computed properties, without the need of human intervention to curate the data. This protocol leverages the capabilities of AiiDA, an open-source platform to manage and automate scientific computational workflows, and TCOD, an open-access database storing computed materials properties using a well-defined and exhaustive ontology. Based on these, the complete procedure to deposit computed data in the TCOD database is automated. All relevant metadata are extracted from the full provenance information that AiiDA tracks and stores automatically while managing the calculations. Such a protocol also enables reproducibility of scientific data in the field of computational materials science. As a proof of concept, the AiiDA-TCOD interface is used to deposit 170 theoretical structures together with their computed properties and their full provenance graphs, consisting in over 4600 AiiDA nodes

Automatic vs Manual Provenance Abstractions: Mind the Gap

In recent years the need to simplify or to hide sensitive information in provenance has given way to research on provenance abstraction. In the context of scientific workflows, existing research provides techniques to semi automatically create abstractions of a given workflow description, which is in turn used as filters over the workflow's provenance traces. An alternative approach that is commonly adopted by scientists is to build workflows with abstractions embedded into the workflow's design, such as using sub-workflows. This paper reports on the comparison of manual versus semi-automated approaches in a context where result abstractions are used to filter report-worthy results of computational scientific analyses. Specifically; we take a real-world workflow containing user-created design abstractions and compare these with abstractions created by ZOOM UserViews and Workflow Summaries systems. Our comparison shows that semi-automatic and manual approaches largely overlap from a process perspective, meanwhile, there is a dramatic mismatch in terms of data artefacts retained in an abstracted account of derivation. We discuss reasons and suggest future research directions.Comment: Preprint accepted to the 2016 workshop on the Theory and Applications of Provenance, TAPP 201

When Provenance Aids and Complicates Reproducibility Judgments

It is well-established that the provenance of a scientific result is important, sometimes more important than the actual result. For computational analyses that involve visualization, this provenance information may contain the steps involved in generating visualizations from raw data. Specifically, data provenance tracks the lineage of data and process provenance tracks the steps executed. In this paper, we argue that the utility of computational provenance may not be as clear-cut as we might like. One common use case for provenance is that the information can be used to reproduce the original result. However, in visualization, the goal is often to communicate results to a user or viewer, and thus the insights obtained are ultimately most important. Viewers can miss important changes or react to unimportant ones. Here, interaction provenance, which tracks a user's actions with a visualization, or insight provenance, which tracks the decision-making process, can help capture what happened but don't remove the issues. In this paper, we present scenarios where provenance impacts reproducibility in different ways. We also explore how provenance and visualizations can be better related

A provenance-based semantic approach to support understandability, reproducibility, and reuse of scientific experiments

Understandability and reproducibility of scientific results are vital in every field of science. Several reproducibility measures are being taken to make the data used in the publications findable and accessible. However, there are many challenges faced by scientists from the beginning of an experiment to the end in particular for data management. The explosive growth of heterogeneous research data and understanding how this data has been derived is one of the research problems faced in this context. Interlinking the data, the steps and the results from the computational and non-computational processes of a scientific experiment is important for the reproducibility. We introduce the notion of end-to-end provenance management'' of scientific experiments to help scientists understand and reproduce the experimental results. The main contributions of this thesis are: (1) We propose a provenance modelREPRODUCE-ME'' to describe the scientific experiments using semantic web technologies by extending existing standards. (2) We study computational reproducibility and important aspects required to achieve it. (3) Taking into account the REPRODUCE-ME provenance model and the study on computational reproducibility, we introduce our tool, ProvBook, which is designed and developed to demonstrate computational reproducibility. It provides features to capture and store provenance of Jupyter notebooks and helps scientists to compare and track their results of different executions. (4) We provide a framework, CAESAR (CollAborative Environment for Scientific Analysis with Reproducibility) for the end-to-end provenance management. This collaborative framework allows scientists to capture, manage, query and visualize the complete path of a scientific experiment consisting of computational and non-computational steps in an interoperable way. We apply our contributions to a set of scientific experiments in microscopy research projects