6,096 research outputs found
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
Reproducibility and Replicability in Unmanned Aircraft Systems and Geographic Information Science
Multiple scientific disciplines face a so-called crisis of reproducibility and replicability (R&R) in which the validity of methodologies is questioned due to an inability to confirm experimental results. Trust in information technology (IT)-intensive workflows within geographic information science (GIScience), remote sensing, and photogrammetry depends on solutions to R&R challenges affecting multiple computationally driven disciplines. To date, there have only been very limited efforts to overcome R&R-related issues in remote sensing workflows in general, let alone those tied to disruptive technologies such as unmanned aircraft systems (UAS) and machine learning (ML). To accelerate an understanding of this crisis, a review was conducted to identify the issues preventing R&R in GIScience. Key barriers included: (1) awareness of time and resource requirements, (2) accessibility of provenance, metadata, and version control, (3) conceptualization of geographic problems, and (4) geographic variability between study areas. As a case study, a replication of a GIScience workflow utilizing Yolov3 algorithms to identify objects in UAS imagery was attempted. Despite the ability to access source data and workflow steps, it was discovered that the lack of accessibility to provenance and metadata of each small step of the work prohibited the ability to successfully replicate the work. Finally, a novel method for provenance generation was proposed to address these issues. It was found that artificial intelligence (AI) could be used to quickly create robust provenance records for workflows that do not exceed time and resource constraints and provide the information needed to replicate work. Such information can bolster trust in scientific results and provide access to cutting edge technology that can improve everyday life
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