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.
Focusing on bioinformatics workflows, the WEP @cite_24 tool enables the modularization of the workflow, allowing the user to execute the entire experiment or just the necessary activities. In addition, WEP also allows access to intermediate files and final results through the web interface. It does not provide detailed computational profiling or parallel and distributed execution features as does BioWorkbench. ADAM @cite_34 is a scalable API for genome processing workflows that uses Spark @cite_0 , a framework for managing Big Data. Both tools allow for running experiments in HPC environments, but they implement parallelism at a lower level, within the activities. ADAM requires the API functions to be implemented according to Spark's model of computation, using distributed datasets and applying actions and transformations, such as map and reduce, to these. BioWorkbench allows for the parallel composition of workflow activities that may be implemented using different models of computation. Therefore, BioWorkbench is more flexible in incorporating existing and legacy bioinformatics tools into its workflows.
@cite_24 @cite_34 @cite_0
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We introduce a dataset for facilitating audio-visual analysis of music performances. The dataset comprises 44 simple multi-instrument classical music pieces assembled from coordinated but separately recorded performances of individual tracks. For each piece, we provide the musical score in MIDI format, the audio recordings of the individual tracks, the audio and video recording of the assembled mixture, and ground-truth annotation files including frame-level and note-level transcriptions. We describe our methodology for the creation of the dataset, particularly highlighting our approaches to address the challenges involved in maintaining synchronization and expressiveness. We demonstrate the high quality of synchronization achieved with our proposed approach by comparing the dataset with existing widely used music audio datasets. We anticipate that the dataset will be useful for the development and evaluation of existing music information retrieval (MIR) tasks, as well as for novel multimodal tasks. We benchmark two existing MIR tasks (multipitch analysis and score-informed source separation) on the dataset and compare them with other existing music audio datasets. In addition, we consider two novel multimodal MIR tasks (visually informed multipitch analysis and polyphonic vibrato analysis) enabled by the dataset and provide evaluation measurements and baseline systems for future comparisons (from our recent work). Finally, we propose several emerging research directions that the dataset enables. We describe a system for extracting complex events among genes and proteins from biomedical literature, developed in context of the BioNLP'09 Shared Task on Event Extraction. For each event, its text trigger, class, and arguments are extracted. In contrast to the prevailing approaches in the domain, events can be arguments of other events, resulting in a nested structure that better captures the underlying biological statements. We divide the task into independent steps which we approach as machine learning problems. We define a wide array of features and in particular make extensive use of dependency parse graphs. A rule-based post-processing step is used to refine the output in accordance with the restrictions of the extraction task. In the shared task evaluation, the system achieved an F-score of 51.95 on the primary task, the best performance among the participants. Abstract Vast amounts of data are generated every day, constituting a volume that is challenging to analyze. Techniques such as feature selection are advisable when tackling large datasets. Among the tools that provide this functionality, Weka is one of the most popular ones, although the implementations it provides struggle when processing large datasets, requiring excessive times to be practical. Parallel processing can help alleviate this problem, effectively allowing users to work with Big Data. The computational power of multicore machines can be harnessed by using multithreading and distributed programming, effectively helping to tackle larger problems. Both these techniques can dramatically speed up the feature selection process allowing users to work with larger datasets. The reimplementation of four popular feature selection algorithms included in Weka is the focus of this work. Multithreaded implementations previously not included in Weka as well as parallel Spark implementations were developed for each algorithm. Experimental results obtained from tests on real-world datasets show that the new versions offer significant reductions in processing times. We seek to enable efficient large-scale parallel execution of applications in which a shared filesystem abstraction is used to couple many tasks. Such parallel scripting (many-task computing, MTC) applications suffer poor performance and utilization on large parallel computers because of the volume of filesystem I O and a lack of appropriate optimizations in the shared filesystem. Thus, we design and implement a scalable MTC data management system that uses aggregated compute node local storage for more efficient data movement strategies. We co-design the data management system with the data-aware scheduler to enable dataflow pattern identification and automatic optimization. The framework reduces the time to solution of parallel stages of an astronomy data analysis application, Montage, by 83.2 on 512 cores; decreases the time to solution of a seismology application, CyberShake, by 7.9 on 2,048 cores; and delivers BLAST performance better than mpiBLAST at various scales up to 32,768 cores, while preserving the flexibility of the original BLAST application.