Motivation Systems biology faces two key challenges when dealing with large amounts of disparate data produced by different experiments: the integration of results across different experiments, and the extraction of meaningful information from the data produced by these experiments. An ongoing challenge is to provide better tools that can mine data patterns that could not have been discovered through simple visualization. Such mining capabilities also need to be coupled with intuitive visualization to portray those findings. We introduce a software toolbox entitled BioNetApp to mine these patterns and visualize them across all experiments. Results BioNetApp is an interactive visual data mining software for analyzing high-volume molecular expression data obtained from multiple ‘omics experiments. By integrating visualization, statistical methods, and data mining techniques, BioNetApp can perform interactive correlative and comparative analysis along time-course studies of molecular expression data. Correlation analysis provides several visualization features such as Kamada-Kawai, Fruchterman-Reingold Spring embedding network layouts, in addition to single circle, multiple circle and heatmap layouts, whereas comparative analysis presents expression-data distributions across samples, groups, and time points with boxplot display, outlier detection, and data curve fitting. BioNetApp also provides data clustering based on molecular concentrations using Self Organizing Maps (SOM), K-Means, K-Medoids, and Farthest First algorithms. Conclusion BioNetApp has been utilized in a metabolomics study to investigate the metabolite abundance changes in alcohol induced fatty liver, where pair-wise analyses of metabolome concentration revealed correlation networks and interesting patterns in the metabolomics dataset. This study case demonstrates the effectiveness of the BioNetApp software as an interactive visual analysis tool for molecular expression data in systems biology. The BioNetApp software is freely available under GNU GPL license and can be downloaded (including the case-study data and user-manual) at: https://doi.org/10.5281/zenodo.2563129 .
The vast number of published medical documents is considered a vital source for relationship discovery. This paper presents a statistical unsupervised system, called BioNoculars, for extracting protein-protein interactions from biomedical text. BioNoculars uses graph-based mutual reinforcement to make use of redundancy in data to construct extraction patterns in a domain independent fashion. The system was tested using MED-LINE abstract for which the protein-protein interactions that they contain are listed in the database of interacting proteins and proteinprotein interactions (DIPPPI). The system reports an F-Measure of 0.55 on test MED-LINE abstracts.
The widespread use of location-aware devices together with the increased popularity of micro-blogging applications (e.g., Twitter) led to the creation of large streams of spatio-textual data. In order to serve real-time applications, the processing of these large-scale spatio-textual streams needs to be distributed. However, existing distributed stream processing systems (e.g., Spark and Storm) are not optimized for spatial/textual content. In this demonstration, we introduce Tornado, a distributed in-memory spatio-textual stream processing server that extends Storm. To efficiently process spatio-textual streams, Tornado introduces a spatio-textual indexing layer to the architecture of Storm. The indexing layer is adaptive, i.e., dynamically re-distributes the processing across the system according to changes in the data distribution and/or query workload. In addition to keywords, higher-level textual concepts are identified and are semantically matched against spatio-textual queries. Tornado provides data deduplication and fusion to eliminate redundant textual data. We demonstrate a prototype of Tornado running against real Twitter streams, where the users can register continuous or snapshot spatio-textual queries using a map-assisted query-interface.
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