Kerfuffle: a web tool for multi-species gene colocalization analysis

The evolutionary pressures that underlie the large-scale functional organization of the genome are not well understood in eukaryotes. Recent evidence suggests that functionally similar genes may colocalize (cluster) in the eukaryotic genome, suggesting the role of chromatin-level gene regulation in shaping the physical distribution of coordinated genes. However, few of the bioinformatic tools currently available allow for a systematic study of gene colocalization across several, evolutionarily distant species. Kerfuffle is a web tool designed to help discover, visualize, and quantify the physical organization of genomes by identifying significant gene colocalization and conservation across the assembled genomes of available species (currently up to 47, from humans to worms). Kerfuffle only requires the user to specify a list of human genes and the names of other species of interest. Without further input from the user, the software queries the e!Ensembl BioMart server to obtain positional information and discovers homology relations in all genes and species specified. Using this information, Kerfuffle performs a multi-species clustering analysis, presents downloadable lists of clustered genes, performs Monte Carlo statistical significance calculations, estimates how conserved gene clusters are across species, plots histograms and interactive graphs, allows users to save their queries, and generates a downloadable visualization of the clusters using the Circos software. These analyses may be used to further explore the functional roles of gene clusters by interrogating the enriched molecular pathways associated with each cluster.Comment: BMC Bioinformatics, In pres

Web tool railway museum

Treball desenvolupat dins el marc del programa 'European Project Semester' i l'"International Design Project Semester".This project is a product of collaboration between the EPS students at EPSEVG and Catalonia Railway Museum. The goal was to create a web tool, test it and launch it. The aim of the web tool is to facilitate the communication between railway museums on a global level. A need for such a tool is present because at the moment there is no existing platform for a fast, private and simple communication between railway museums. The web tool functions like a forum, the message board will enable the possibility to have discussions, group chats and other functions that can be expected in a forum. AngularJS, as the backend framework, and Lumen, for the backend, were used to develop the web tool. The code is documented well, to make sure that next developers have an easy start and are able to implement new features quickly. Since this is a forum that will be used by colleagues on an international level the main language will be English, with a possibility to translate it to any other language. The web tool gets translated by the Google translate widget, owned and powered by Google. Before the launching of the web tool a user survey was complete. The test persons included museum personnel, students, usability professors, family and friends. After a mostly positive feedback, few corrections were made before the web tool, with the name "Elephorum", was launched

Improving the Power Electronics Laboratory teaching/learning process: an interactive web tool

European Higher Education Area; Power Electronics Laboratory; educational methods Resumen: The forthcoming European Higher Education Area implies an important change in the teaching/learning process: it is necessary to get students more involved as well as to promote their independence and active participation. To achieve this objective, the new teaching methodologies aimed at more effective and appropriate learning for professional practice involve the use of audiovisual, computer and multimedia tools on the part of lecturers. Therefore, a web tool, based on a content management system, has been developed for the teaching in Power Electronics Laboratory. Moreover, the use of these multimedia tools makes possible to promote the students independence. Finally, the use of this web tool results in a very significant increase in the motivation students.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

OPEN SOURCE WEB TOOL FOR TRACKING IN A LOWCOST MOBILE MAPPING SYSTEM

During the last decade several Mobile Mapping Systems (MMSs), i.e. systems able to acquire efficiently three dimensional data using moving sensors (Guarnieri et al., 2008, Schwarz and El-Sheimy, 2004), have been developed. Research and commercial products have been implemented on terrestrial, aerial and marine platforms, and even on human-carried equipment, e.g. backpack (Lo et al., 2015, Nex and Remondino, 2014, Ellum and El-Sheimy, 2002, Leica Pegasus backpack, 2016, Masiero et al., 2017, Fissore et al., 2018).<br><br> Such systems are composed of an integrated array of time-synchronised navigation sensors and imaging sensors mounted on a mobile platform (Puente et al., 2013, Tao and Li, 2007). Usually the MMS implies integration of different types of sensors, such as GNSS, IMU, video camera and/or laser scanners that allow accurate and quick mapping (Li, 1997, Petrie, 2010, Tao, 2000). The typical requirement of high-accuracy 3D georeferenced reconstruction often makes such systems quite expensive. Indeed, at time of writing most of the terrestrial MMSs on the market have a cost usually greater than 50000, which might be expensive for certain applications (Ellum and El-Sheimy, 2002, Piras et al., 2008). In order to allow best performance sensors have to be properly calibrated (Dong et al., 2007, Ellum and El-Sheimy, 2002).<br><br> Sensors in MMSs are usually integrated and managed through a dedicated software, which is developed ad hoc for the devices mounted on the mobile platform and hence tailored for the specific used sensors. Despite the fact that commercial solutions are complete, very specific and particularly related to the typology of survey, their price is a factor that restricts the number of users and the possible interested sectors.<br><br> This paper describes a (relatively low cost) terrestrial Mobile Mapping System developed at the University of Padua (TESAF, Department of Land Environment Agriculture and Forestry) by the research team in CIRGEO, in order to test an alternative solution to other more expensive MMSs. The first objective of this paper is to report on the development of a prototype of MMS for the collection of geospatial data based on the assembly of low cost sensors managed through a web interface developed using open source libraries. The main goal is to provide a system accessible by any type of user, and flexible to any type of upgrade or introduction of new models of sensors or versions thereof. After a presentation of the hardware components used in our system, a more detailed description of the software developed for the management of the MMS will be provided, which is the part of the innovation of the project. According to the worldwide request for having big data available through the web from everywhere in the world (Pirotti et al., 2011), the proposed solution allows to retrieve data from a web interface Figure 4. Actually, this is part of a project for the development of a new web infrastructure in the University of Padua (but it will be available for external users as well), in order to ease collaboration between researchers from different areas.<br><br> Finally, strengths, weaknesses and future developments of the low cost MMS are discussed

PhysBinder : improving the prediction of transcription factor binding sites by flexible inclusion of biophysical properties

The most important mechanism in the regulation of transcription is the binding of a transcription factor (TF) to a DNA sequence called the TF binding site (TFBS). Most binding sites are short and degenerate, which makes predictions based on their primary sequence alone somewhat unreliable. We present a new web tool that implements a flexible and extensible algorithm for predicting TFBS. The algorithm makes use of both direct (the sequence) and several indirect readout features of protein-DNA complexes (biophysical properties such as bendability or the solvent-excluded surface of the DNA). This algorithm significantly outperforms state-of-the-art approaches for in silico identification of TFBS. Users can submit FASTA sequences for analysis in the PhysBinder integrative algorithm and choose from >60 different TF-binding models. The results of this analysis can be used to plan and steer wet-lab experiments. The PhysBinder web tool is freely available at http://bioit.dmbr.ugent.be/physbinder/index.php

Reverse engineering of biochar

This study underpins quantitative relationships that account for the combined effects that starting biomass and peak pyrolysis temperature have on physico-chemical properties of biochar. Meta-data was assembled from published data of diverse biochar samples (n = 102) to (i) obtain networks of intercorrelated properties and (ii) derive models that predict biochar properties. Assembled correlation networks provide a qualitative overview of the combinations of biochar properties likely to occur in a sample. Generalized Linear Models are constructed to account for situations of varying complexity, including: dependence of biochar properties on single or multiple predictor variables, where dependence on multiple variables can have additive and/or interactive effects; non-linear relation between the response and predictors; and non-Gaussian data distributions. The web-tool Biochar Engineering implements the derived models to maximize their utility and distribution. Provided examples illustrate the practical use of the networks, models and web-tool to engineer biochars with prescribed properties desirable for hypothetical scenarios

TICAL - a web-tool for multivariate image clustering and data topology preserving visualization

In life science research bioimaging is often used to study two kinds of features in a sample simultaneously: morphology and co-location of molecular components. While bioimaging technology is rapidly proposing and improving new multidimensional imaging platforms, bioimage informatics has to keep pace in order to develop algorithmic approaches to support biology experts in the complex task of data analysis. One particular problem is the availability and applicability of sophisticated image analysis algorithms via the web so different users can apply the same algorithms to their data (sometimes even to the same data to get the same results) and independently from her/his whereabouts and from the technical features of her/his computer. In this paper we describe TICAL, a visual data mining approach to multivariate microscopy analysis which can be applied fully through the web.We describe the algorithmic approach, the software concept and present results obtained for different example images