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See detailOnTheFly: a tool for automated document-based text annotation, data linking and network generation
Pavlopoulos, Georgios A.; Pafilis, Evangelos; Kuhn, M. et al

in Bioinformatics (2009), 25(7), 977-978

OnTheFly is a web-based application that applies biological named entity recognition to enrich Microsoft Office, PDF and plain text documents. The input files are converted into the HTML format and then ... [more ▼]

OnTheFly is a web-based application that applies biological named entity recognition to enrich Microsoft Office, PDF and plain text documents. The input files are converted into the HTML format and then sent to the Reflect tagging server, which highlights biological entity names like genes, proteins and chemicals, and attaches to them JavaScript code to invoke a summary pop-up window. The window provides an overview of relevant information about the entity, such as a protein description, the domain composition, a link to the 3D structure and links to other relevant online resources. OnTheFly is also able to extract the bioentities mentioned in a set of files and to produce a graphical representation of the networks of the known and predicted associations of these entities by retrieving the information from the STITCH database. [less ▲]

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See detailjClust: a clustering and visualization toolbox
Pavlopoulos, Georgios A.; Moschopoulos, Charalampos N.; Hooper, Sean D. et al

in Bioinformatics (2009), 25(15), 1994-1996

jClust is a user-friendly application which provides access to a set of widely used clustering and clique finding algorithms. The toolbox allows a range of filtering procedures to be applied and is ... [more ▼]

jClust is a user-friendly application which provides access to a set of widely used clustering and clique finding algorithms. The toolbox allows a range of filtering procedures to be applied and is combined with an advanced implementation of the Medusa interactive visualization module. These implemented algorithms are k-Means, Affinity propagation, Bron-Kerbosch, MULIC, Restricted neighborhood search cluster algorithm, Markov clustering and Spectral clustering, while the supported filtering procedures are haircut, outside-inside, best neighbors and density control operations. The combination of a simple input. le format, a set of clustering and filtering algorithms linked together with the visualization tool provides a powerful tool for data analysis and information extraction. [less ▲]

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