Senja Pollak had an invited lecture on the University of Edinburgh entitled "Bisociative knowledge discovery for cross-domain literature mining". The invited lecture, where we presented the bisociative methods for knowledge discovery from medical and biological terms, was organized on December 10th, 2018 within the CMI seminars (Seminar Series of Centre For Medical Informatics, University of Edinburgh). The lecture was attended by 30 participants and it was also available to the external visitors through online streaming.
B.04 Guest lecture
COBISS.SI-ID: 31960615In this study, we aimed to use network modeling to better understand immune signaling in potato (Solanum tuberosum). For this, we first built on a reliable Arabidopsis (Arabidopsis thaliana) immune signaling model, extending it with the information from diverse publicly available resources. Next, we translated the resulting prior knowledge network (20,012 nodes and 70,091 connections) to potato and superimposed it with an ensemble network inferred from time-resolved transcriptomics data for potato. We used different network modeling approaches to generate specific hypotheses of potato immune signaling mechanisms. An interesting finding was the identification of a string of molecular events illuminating the ethylene pathway modulation of the salicylic acid pathway through Nonexpressor of PR Genes1 gene expression. Functional validations confirmed this modulation, thus supporting the potential of our integrative network modeling approach for unraveling molecular mechanisms in complex systems. In addition, this approach can ultimately result in improved breeding strategies for potato and other sensitive crops.
F.02 Acquisition of new scientific knowledge
COBISS.SI-ID: 32031015The paper presents a platform for distributed computing, developed using the latest software technologies and computing paradigms to enable big data mining. The platform, called ClowdFlows, is implemented as a cloud-based web application with a graphical user interface which supports the construction and execution of data mining workflows, including web services used as workflow components. The constructed workflows can be declared either as private or public, which enables sharing the developed solutions, data and results on the web and in scientific publications. From a developer’s perspective the platform is easy to extend and supports distributed development with packages. The paper focuses on big data processing in the batch and real-time processing mode. Big data analytics is provided through several algorithms, including novel ensemble techniques, implemented using the map-reduce paradigm and a special stream mining module for continuous parallel workflow execution. The ability of ClowdFlows to handle big data sets and its nearly perfect linear speedup is demonstrated.
F.02 Acquisition of new scientific knowledge
COBISS.SI-ID: 29851943Virus-induced gene silencing (VIGS) is an optimal tool for functional analysis of genes in plants, as the viral vector spreads throughout the plant and causes reduced expression of selected gene over the whole plant. Potato (Solanum tuberosum) is one of the most important food crops, therefore studies performing functional analysis of its genes are very important. However, the majority of potato cultivars used in laboratory experimental setups are not well amenable to available VIGS systems, thus other model plants from Solanaceae family are used (usually Nicotiana benthamiana). Wild potato relatives can be a better choice for potato model, but their potential in this field was yet not fully explored. This manuscript presents the set-up of VIGS, based on Tobacco rattle virus (TRV) in wild potato relatives for functional studies in potato–virus interactions.
F.02 Acquisition of new scientific knowledge
COBISS.SI-ID: 3877967This paper describes the development of TextFlows, a visual programming platform for text mining that supports construction, execution and sharing of text mining workflows. The usability and utility of the TextFlows platform is illustrated on a number of use cases: complex workflows for document acquisition and preprocessing, document classification using various stemming, lemmatization and part-of-speech methods, and the detection of outliers in text corpora.
F.02 Acquisition of new scientific knowledge
COBISS.SI-ID: 29549095