KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database

<p>Abstract</p> <p>Background</p> <p>The KEGG Pathway database is a valuable collection of metabolic pathway maps. Nevertheless, the production of simulation capable metabolic networks from KEGG Pathway data is a challenging complicated work, regardless the already developed tools for this scope. Originally used for illustration purposes, KEGG Pathways through KGML (KEGG Markup Language) files, can provide complete reaction sets and introduce species versioning, which offers advantages for the scope of cellular metabolism simulation modelling. In this project, KEGGconverter is described, implemented also as a web-based application, which uses as source KGML files, in order to construct integrated pathway SBML models fully functional for simulation purposes.</p> <p>Results</p> <p>A case study of the integration of six human metabolic pathways from KEGG depicts the ability of KEGGconverter to automatically produce merged and converted to SBML fully functional pathway models, enhanced with default kinetics. The suitability of the developed tool is demonstrated through a comparison with other state-of-the art relevant software tools for the same data fusion and conversion tasks, thus illustrating the problems and the relevant workflows. Moreover, KEGGconverter permits the inclusion of additional reactions in the resulting model which represent flux cross-talk with neighbouring pathways, providing in this way improved simulative accuracy. These additional reactions are introduced by exploiting relevant semantic information for the elements of the KEGG Pathways database. The architecture and functionalities of the web-based application are presented.</p> <p>Conclusion</p> <p>KEGGconverter is capable of producing integrated analogues of metabolic pathways appropriate for simulation tasks, by inputting only KGML files. The web application acts as a user friendly shell which transparently enables the automated biochemically correct pathway merging, conversion to SBML format, proper renaming of the species, and insertion of default kinetic properties for the pertaining reactions. The tool is available at: <url>http://www.grissom.gr/keggconverter</url></p

Webpage Genre Identification Using Variable-length Character n-grams

An important factor for discriminating between webpages is their genre (e.g., blogs, personal homepages, e-shops, online newspapers, etc). Webpage genre identification has a great potential in information retrieval since users of search engines can combine genre-based and traditional topic-based queries to improve the quality of the results. So far, various features have been proposed to quantify the style of webpages including word and html-tag frequencies. In this paper, we propose a low-level representation for this problem based on character n-grams. Using an existing approach, we produce feature sets of variable-length character n-grams and combine this representation with information about the most frequent html-tags. Based on two benchmark corpora, we present webpage genre identification experiments and improve the best reported results in both cases. 1

Packaging and Optimization of a Capacitive Biosensor and Its Readout Circuit

In pipeline production, there is a considerable distance between the moment when the operation principle of a biosensor will be verified in the laboratory until the moment when it can be used in real conditions. This distance is often covered by an optimization and packaging process. This article described the packaging and optimization of a SARS-CoV-2 biosensor, as well as the packaging of its electronic readout circuit. The biosensor was packed with a photosensitive tape, which forms a protective layer and is patterned in a way to form a well in the sensing area. The well is meant to limit the liquid diffusion, thereby reducing the measurement error. Subsequently, a connector between the biosensor and its readout circuit was designed and 3D-printed, ensuring the continuous and easy reading of the biosensor. In the last step, a three-dimensional case was designed and printed, thus protecting the circuit from any damage, and allowing its operation in real conditions