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Journal of Integrative Bioinformatics

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https://www.readbyqxmd.com/read/29676994/sbml-level-3-package-multistate-multicomponent-and-multicompartment-species-version-1-release-1
#1
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
https://www.readbyqxmd.com/read/29605823/synthetic-biology-open-language-sbol-version-2-2-0
#2
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
https://www.readbyqxmd.com/read/29605822/sbml-level-3-package-render-version-1-release-1
#3
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
https://www.readbyqxmd.com/read/29596055/specifications-of-standards-in-systems-and-synthetic-biology-status-and-developments-in-2017
#4
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
https://www.readbyqxmd.com/read/29550789/simulation-experiment-description-markup-language-sed-ml-level-1-version-3-l1v3
#5
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
https://www.readbyqxmd.com/read/29549707/synthetic-biology-open-language-visual-sbol-visual-version-2-0
#6
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 Novere, 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
https://www.readbyqxmd.com/read/29547394/biopydb-a-dynamic-human-cell-specific-biochemical-pathway-database-with-advanced-computational-analyses-platform
#7
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
https://www.readbyqxmd.com/read/29522419/sbml-level-3-package-flux-balance-constraints-version-2
#8
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
https://www.readbyqxmd.com/read/29522418/the-systems-biology-markup-language-sbml-language-specification-for-level-3-version-2-core
#9
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
https://www.readbyqxmd.com/read/29470175/modified-huffbit-compress-algorithm-an-application-of-r
#10
Nahida Habib, Kawsar Ahmed, Iffat Jabin, Mohammad Motiur Rahman
The databases of genomic sequences are growing at an explicative rate because of the increasing growth of living organisms. Compressing deoxyribonucleic acid (DNA) sequences is a momentous task as the databases are getting closest to its threshold. Various compression algorithms are developed for DNA sequence compression. An efficient DNA compression algorithm that works on both repetitive and non-repetitive sequences known as "HuffBit Compress" is based on the concept of Extended Binary Tree. In this paper, here is proposed and developed a modified version of "HuffBit Compress" algorithm to compress and decompress DNA sequences using the R language which will always give the Best Case of the compression ratio but it uses extra 6 bits to compress than best case of "HuffBit Compress" algorithm and can be named as the "Modified HuffBit Compress Algorithm"...
February 22, 2018: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/29236680/uv-vis-and-cielab-based-chemometric-characterization-of-manihot-esculenta-carotenoid-contents
#11
Telma Afonso, Rodolfo Moresco, Virgilio G Uarrota, Bruno Bachiega Navarro, Eduardo da C Nunes, Marcelo Maraschin, Miguel Rocha
Vitamin A deficiency is a prevalent health problem in many areas of the world, where cassava genotypes with high pro-vitamin A content have been identified as a strategy to address this issue. In this study, we found a positive correlation between the color of the root pulp and the total carotenoid contents and, importantly, showed how CIELAB color measurements can be used as a non-destructive and fast technique to quantify the amount of carotenoids in cassava root samples, as opposed to traditional methods...
December 13, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/29236679/assessing-public-metabolomics-metadata-towards-improving-quality
#12
João D Ferreira, Bruno Inácio, Reza M Salek, Francisco M Couto
Public resources need to be appropriately annotated with metadata in order to make them discoverable, reproducible and traceable, further enabling them to be interoperable or integrated with other datasets. While data-sharing policies exist to promote the annotation process by data owners, these guidelines are still largely ignored. In this manuscript, we analyse automatic measures of metadata quality, and suggest their application as a mean to encourage data owners to increase the metadata quality of their resources and submissions, thereby contributing to higher quality data, improved data sharing, and the overall accountability of scientific publications...
December 13, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/29236678/protein-protein-interaction-article-classification-using-a-convolutional-recurrent-neural-network-with-pre-trained-word-embeddings
#13
Sérgio Matos, Rui Antunes
Curation of protein interactions from scientific articles is an important task, since interaction networks are essential for the understanding of biological processes associated with disease or pharmacological action for example. However, the increase in the number of publications that potentially contain relevant information turns this into a very challenging and expensive task. In this work we used a convolutional recurrent neural network for identifying relevant articles for extracting information regarding protein interactions...
December 13, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/29236677/a-chemometrics-approach-for-nuclear-magnetic-resonance-data-to-characterize-the-partial-metabolome-banana-peels-from-southern-brazil
#14
Sara Cardoso, Marcelo Maraschin, Luiz Augusto Martins Peruch, Miguel Rocha, Aline Pereira
Banana peels are well recognized as a source of important bioactive compounds, such as phenolics, carotenoids, biogenic amines, among others. As such, they have recently started to be used for industrial purposes. However, its composition seems to be strongly affected by biotic or abiotic ecological factors. Thus, this study aimed to investigate banana peels chemical composition, not only to get insights on eventual metabolic changes caused by the seasons, in southern Brazil, but also to identify the most relevant metabolites for these processes...
December 13, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/29236676/supervised-learning-and-knowledge-based-approaches-applied-to-biomedical-word-sense-disambiguation
#15
Rui Antunes, Sérgio Matos
Word sense disambiguation (WSD) is an important step in biomedical text mining, which is responsible for assigning an unequivocal concept to an ambiguous term, improving the accuracy of biomedical information extraction systems. In this work we followed supervised and knowledge-based disambiguation approaches, with the best results obtained by supervised means. In the supervised method we used bag-of-words as local features, and word embeddings as global features. In the knowledge-based method we combined word embeddings, concept textual definitions extracted from the UMLS database, and concept association values calculated from the MeSH co-occurrence counts from MEDLINE articles...
December 13, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/29236675/selected-extended-papers-of-the-11th-international-conference-on-practical-applications-of-computational-biology-and-bioinformatics-pacbb
#16
EDITORIAL
Florentino Fdez-Riverola, Miguel Rocha
No abstract text is available yet for this article.
December 13, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28941356/computational-approaches-to-identify-genetic-interactions-for-cancer-therapeutics
#17
Graeme Benstead-Hume, Sarah K Wooller, Frances M G Pearl
The development of improved cancer therapies is frequently cited as an urgent unmet medical need. Here we describe how genetic interactions are being therapeutically exploited to identify novel targeted treatments for cancer. We discuss the current methodologies that use 'omics data to identify genetic interactions, in particular focusing on synthetic sickness lethality (SSL) and synthetic dosage lethality (SDL). We describe the experimental and computational approaches undertaken both in humans and model organisms to identify these interactions...
September 23, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28941355/a-novel-method-to-detect-bias-in-short-read-ngs-data
#18
Jamie Alnasir, Hugh P Shanahan
Detecting sources of bias in transcriptomic data is essential to determine signals of Biological significance. We outline a novel method to detect sequence specific bias in short read Next Generation Sequencing data. This is based on determining intra-exon correlations between specific motifs. This requires a mild assumption that short reads sampled from specific regions from the same exon will be correlated with each other. This has been implemented on Apache Spark and used to analyse two D. melanogaster eye-antennal disc data sets generated at the same laboratory...
September 23, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28918420/computer-analysis-of-glioma-transcriptome-profiling-alternative-splicing-events
#19
Vladimir N Babenko, Natalya V Gubanova, Anatoly O Bragin, Irina V Chadaeva, Gennady V Vasiliev, Irina V Medvedeva, Alexey S Gaytan, Alexey L Krivoshapkin, Yuriy L Orlov
Here we present the analysis of alternative splicing events on an example of glioblastoma cell culture samples using a set of computer tools in combination with database integration. The gene expression profiles of glioblastoma were obtained from cell culture samples of primary glioblastoma which were isolated and processed for RNA extraction. Transcriptome profiling of normal brain samples and glioblastoma were done by Illumina sequencing. The significant differentially expressed exon-level probes and their corresponding genes were identified using a combination of the splicing index method...
September 18, 2017: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28902625/biological-big-bytes-integrative-analysis-of-large-biological-datasets
#20
EDITORIAL
Ming Chen, Andrew Harrison, Hugh Shanahan, Yuriy Orlov
No abstract text is available yet for this article.
September 13, 2017: Journal of Integrative Bioinformatics
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