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Journal of Integrative Bioinformatics

Marco Brandizi, Ajit Singh, Christopher Rawlings, Keywan Hassani-Pak
The speed and accuracy of new scientific discoveries - be it by humans or artificial intelligence - depends on the quality of the underlying data and on the technology to connect, search and share the data efficiently. In recent years, we have seen the rise of graph databases and semi-formal data models such as knowledge graphs to facilitate software approaches to scientific discovery. These approaches extend work based on formalised models, such as the Semantic Web. In this paper, we present our developments to connect, search and share data about genome-scale knowledge networks (GSKN)...
August 7, 2018: Journal of Integrative Bioinformatics
Mirko Busato, Rosario Distefano, Ferdia Bates, Kal Karim, Alessandra Maria Bossi, José Manuel López Vilariño, Sergey Piletsky, Nicola Bombieri, Alejandro Giorgetti
Molecularly imprinted polymers (MIPs) are high affinity robust synthetic receptors, which can be optimally synthesized and manufactured more economically than their biological equivalents (i.e. antibody). In MIPs production, rational design based on molecular modeling is a commonly employed technique. This mostly aids in (i) virtual screening of functional monomers (FMs), (ii) optimization of monomer-template ratio, and (iii) selectivity analysis. We present MIRATE, an integrated science gateway for the intelligent design of MIPs...
June 13, 2018: Journal of Integrative Bioinformatics
Alexander Platzer, Julia Polzin, Klaus Rembart, Ping Penny Han, Denise Rauer, Thomas Nussbaumer
Metagenomics provides quantitative measurements for microbial species over time. To obtain a global overview of an experiment and to explore the full potential of a given dataset, intuitive and interactive visualization tools are needed. Therefore, we established BioSankey to visualize microbial species in microbiome studies over time as a Sankey diagram. These diagrams are embedded into a project-specific webpage which depends only on JavaScript and Google API to allow searches of interesting species without requiring a web server or connection to a database...
June 13, 2018: Journal of Integrative Bioinformatics
Niklas Biere, Mehmood Ghaffar, Anja Doebbe, Daniel Jäger, Nils Rothe, Benjamin M Friedrich, Ralf Hofestädt, Falk Schreiber, Olaf Kruse, Björn Sommer
The structural modeling and representation of cells is a complex task as different microscopic, spectroscopic and other information resources have to be combined to achieve a three-dimensional representation with high accuracy. Moreover, to provide an appropriate spatial representation of the cell, a stereoscopic 3D (S3D) visualization is favorable. In this work, a structural cell model is created by combining information from various light microscopic and electron microscopic images as well as from publication-related data...
July 11, 2018: Journal of Integrative Bioinformatics
Björn Sommer, Marc Baaden, Michael Krone, Andrew Woods
Bioinformatics-related research produces huge heterogeneous amounts of data. This wealth of information includes data describing metabolic mechanisms and pathways, proteomics, transcriptomics, and metabolomics. Often, the visualization and exploration of related structural - usually molecular - data plays an important role in the aforementioned contexts. For decades, virtual reality (VR)-related technologies were developed and applied to Bioinformatics problems. Often, these approaches provide "just" visual support of the analysis, e...
July 9, 2018: Journal of Integrative Bioinformatics
Mikael Trellet, Nicolas Férey, Jakub Flotyński, Marc Baaden, Patrick Bourdot
The advances made in recent years in the field of structural biology significantly increased the throughput and complexity of data that scientists have to deal with. Combining and analyzing such heterogeneous amounts of data became a crucial time consumer in the daily tasks of scientists. However, only few efforts have been made to offer scientists an alternative to the standard compartmentalized tools they use to explore their data and that involve a regular back and forth between them. We propose here an integrated pipeline especially designed for immersive environments, promoting direct interactions on semantically linked 2D and 3D heterogeneous data, displayed in a common working space...
July 9, 2018: Journal of Integrative Bioinformatics
Michael Wiebrands, Chris J Malajczuk, Andrew J Woods, Andrew L Rohl, Ricardo L Mancera
Molecular graphics systems are visualization tools which, upon integration into a 3D immersive environment, provide a unique virtual reality experience for research and teaching of biomolecular structure, function and interactions. We have developed a molecular structure and dynamics application, the Molecular Dynamics Visualization tool, that uses the Unity game engine combined with large scale, multi-user, stereoscopic visualization systems to deliver an immersive display experience, particularly with a large cylindrical projection display...
June 21, 2018: Journal of Integrative Bioinformatics
Alexandre Maes, Xavier Martinez, Karen Druart, Benoist Laurent, Sean Guégan, Christophe H Marchand, Stéphane D Lemaire, Marc Baaden
Proteomic and transcriptomic technologies resulted in massive biological datasets, their interpretation requiring sophisticated computational strategies. Efficient and intuitive real-time analysis remains challenging. We use proteomic data on 1417 proteins of the green microalga Chlamydomonas reinhardtii to investigate physicochemical parameters governing selectivity of three cysteine-based redox post translational modifications (PTM): glutathionylation (SSG), nitrosylation (SNO) and disulphide bonds (SS) reduced by thioredoxins...
June 21, 2018: Journal of Integrative Bioinformatics
Christoph Müller, Michael Krone, Markus Huber, Verena Biener, Dominik Herr, Steffen Koch, Guido Reina, Daniel Weiskopf, Thomas Ertl
Immersive technologies like stereo rendering, virtual reality, or augmented reality (AR) are often used in the field of molecular visualisation. Modern, comparably lightweight and affordable AR headsets like Microsoft's HoloLens open up new possibilities for immersive analytics in molecular visualisation. A crucial factor for a comprehensive analysis of molecular data in AR is the rendering speed. HoloLens, however, has limited hardware capabilities due to requirements like battery life, fanless cooling and weight...
June 13, 2018: Journal of Integrative Bioinformatics
Hua Wong, Jessica Prévoteau-Jonquet, Stéphanie Baud, Manuel Dauchez, Nicolas Belloy
The extracellular matrix (ECM) plays an important role in supporting tissues and organs. It even has a functional role in morphogenesis and differentiation by acting as a source of active molecules (matrikines). Many diseases are linked to dysfunction of ECM components and fragments or changes in their structures. As such it is a prime target for drugs. Because of technological limitations for observations at mesoscopic scales, the precise structural organisation of the ECM is not well-known, with sparse or fuzzy experimental observables...
June 11, 2018: Journal of Integrative Bioinformatics
Blagoj Ristevski, Ming Chen
This paper surveys big data with highlighting the big data analytics in medicine and healthcare. Big data characteristics: value, volume, velocity, variety, veracity and variability are described. Big data analytics in medicine and healthcare covers integration and analysis of large amount of complex heterogeneous data such as various - omics data (genomics, epigenomics, transcriptomics, proteomics, metabolomics, interactomics, pharmacogenomics, diseasomics), biomedical data and electronic health records data...
May 10, 2018: Journal of Integrative Bioinformatics
Fengkai Zhang, Martin Meier-Schellersheim
Rule-based modeling is an approach that permits constructing reaction networks based on the specification of rules for molecular interactions and transformations. These rules can encompass details such as the interacting sub-molecular domains (components) and the states such as phosphorylation and binding status of the involved components. Fine-grained spatial information such as the locations of the molecular components relative to a membrane (e.g. whether a modeled molecular domain is embedded into the inner leaflet of the cellular plasma membrane) can also be provided...
April 20, 2018: Journal of Integrative Bioinformatics
Robert Sidney Cox, Curtis Madsen, James Alastair McLaughlin, Tramy Nguyen, Nicholas Roehner, Bryan Bartley, Jacob Beal, Michael Bissell, Kiri Choi, Kevin Clancy, Raik Grünberg, Chris Macklin, Goksel Misirli, Ernst Oberortner, Matthew Pocock, Meher Samineni, Michael Zhang, Zhen Zhang, Zach Zundel, John H Gennari, Chris Myers, Herbert Sauro, Anil Wipat
Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards...
April 2, 2018: Journal of Integrative Bioinformatics
Frank T Bergmann, Sarah M Keating, Ralph Gauges, Sven Sahle, Katja Wengler
Many software tools provide facilities for depicting reaction network diagrams in a visual form. Two aspects of such a visual diagram can be distinguished: the layout (i.e.: the positioning and connections) of the elements in the diagram, and the graphical form of the elements (for example, the glyphs used for symbols, the properties of the lines connecting them, and so on). This document describes the SBML Level 3 Render package that complements the SBML Level 3 Layout package and provides a means of capturing the precise rendering of the elements in a diagram...
April 2, 2018: Journal of Integrative Bioinformatics
Falk Schreiber, Gary D Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M Keating, Nicolas Le Novère, Chris Myers, David Nickerson, Björn Sommer, Dagmar Waltemath
Standards are essential to the advancement of Systems and Synthetic Biology. COMBINE provides a formal body and a centralised platform to help develop and disseminate relevant standards and related resources. The regular special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards by providing unified, easily citable access. This paper provides an overview of existing COMBINE standards and presents developments of the last year.
March 29, 2018: Journal of Integrative Bioinformatics
Frank T Bergmann, Jonathan Cooper, Matthias König, Ion Moraru, David Nickerson, Nicolas Le Novère, Brett G Olivier, Sven Sahle, Lucian Smith, Dagmar Waltemath
The creation of computational simulation experiments to inform modern biological research poses challenges to reproduce, annotate, archive, and share such experiments. Efforts such as SBML or CellML standardize the formal representation of computational models in various areas of biology. The Simulation Experiment Description Markup Language (SED-ML) describes what procedures the models are subjected to, and the details of those procedures. These standards, together with further COMBINE standards, describe models sufficiently well for the reproduction of simulation studies among users and software tools...
March 19, 2018: Journal of Integrative Bioinformatics
Robert Sidney Cox, Curtis Madsen, James McLaughlin, Tramy Nguyen, Nicholas Roehner, Bryan Bartley, Swapnil Bhatia, Mike Bissell, Kevin Clancy, Thomas Gorochowski, Raik Grünberg, Augustin Luna, Nicolas Le Novère, Matthew Pocock, Herbert Sauro, John T Sexton, Guy-Bart Stan, Jeffrey J Tabor, Christopher A Voigt, Zach Zundel, Chris Myers, Jacob Beal, Anil Wipat
People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard for organizing and systematizing such conventions in order to produce a coherent language for expressing the structure and function of genetic designs...
March 19, 2018: Journal of Integrative Bioinformatics
Saikat Chowdhury, Noopur Sinha, Piyali Ganguli, Rupa Bhowmick, Vidhi Singh, Sutanu Nandi, Ram Rup Sarkar
BIOchemical PathwaY DataBase is developed as a manually curated, readily updatable, dynamic resource of human cell specific pathway information along with integrated computational platform to perform various pathway analyses. Presently, it comprises of 46 pathways, 3189 molecules, 5742 reactions and 6897 different types of diseases linked with pathway proteins, which are referred by 520 literatures and 17 other pathway databases. With its repertoire of biochemical pathway data, and computational tools for performing Topological, Logical and Dynamic analyses, BIOPYDB offers both the experimental and computational biologists to acquire a comprehensive understanding of signaling cascades in the cells...
March 16, 2018: Journal of Integrative Bioinformatics
Brett G Olivier, Frank T Bergmann
Constraint-based modeling is a well established modeling methodology used to analyze and study biological networks on both a medium and genome scale. Due to their large size and complexity such steady-state flux models are, typically, analyzed using constraint-based optimization techniques, for example, flux balance analysis (FBA). The Flux balance constraints (FBC) Package extends SBML Level 3 and provides a standardized format for the encoding, exchange and annotation of constraint-based models. It includes support for modeling concepts such as objective functions, flux bounds and model component annotation that facilitates reaction balancing...
March 9, 2018: Journal of Integrative Bioinformatics
Michael Hucka, Frank T Bergmann, Andreas Dräger, Stefan Hoops, Sarah M Keating, Nicolas Le Novère, Chris J Myers, Brett G Olivier, Sven Sahle, James C Schaff, Lucian P Smith, Dagmar Waltemath, Darren J Wilkinson
Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations...
March 9, 2018: Journal of Integrative Bioinformatics
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