journal
MENU ▼
Read by QxMD icon Read
search

Journal of Integrative Bioinformatics

journal
https://www.readbyqxmd.com/read/27402693/petriscape-a-plugin-for-discrete-petri-net-simulations-in-cytoscape
#1
Diogo Almeida, Vasco Azevedo, Artur Silva, Jan Baumbach
Systems biology plays a central role for biological network analysis in the post-genomic era. Cytoscape is the standard bioinformatics tool offering the community an extensible platform for computational analysis of the emerging cellular network together with experimental omics data sets. However, only few apps/plugins/tools are available for simulating network dynamics in Cytoscape 3. Many approaches of varying complexity exist but none of them have been integrated into Cytoscape as app/plugin yet. Here, we introduce PetriScape, the first Petri net simulator for Cytoscape...
2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/26673933/extracting-kinetic-information-from-literature-with-kineticre
#2
Ana Alão Freitas, Hugo Costa, Miguel Rocha, Isabel Rocha
To better understand the dynamic behavior of metabolic networks in a wide variety of conditions, the field of Systems Biology has increased its interest in the use of kinetic models. The different databases, available these days, do not contain enough data regarding this topic. Given that a significant part of the relevant information for the development of such models is still wide spread in the literature, it becomes essential to develop specific and powerful text mining tools to collect these data. In this context, this work has as main objective the development of a text mining tool to extract, from scientific literature, kinetic parameters, their respective values and their relations with enzymes and metabolites...
2015: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/26673932/integrating-data-from-heterogeneous-dna-microarray-platforms
#3
Eduardo Valente, Miguel Rocha
DNA microarrays are one of the most used technologies for gene expression measurement. However, there are several distinct microarray platforms, from different manufacturers, each with its own measurement protocol, resulting in data that can hardly be compared or directly integrated. Data integration from multiple sources aims to improve the assertiveness of statistical tests, reducing the data dimensionality problem. The integration of heterogeneous DNA microarray platforms comprehends a set of tasks that range from the re-annotation of the features used on gene expression, to data normalization and batch effect elimination...
2015: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/26673931/uv-visible-scanning-spectrophotometry-and-chemometric-analysis-as-tools-for-carotenoids-analysis-in-cassava-genotypes-manihot-esculenta-crantz
#4
Rodolfo Moresco, Virgílio Gavicho Uarrota, Aline Pereira, Maíra Maciel Tomazzoli, Eduardo da C Nunes, Luiz Augusto Martins Peruch, Jussara Gazzola, Christopher Costa, Miguel Rocha, Marcelo Maraschin
In this study, the metabolomics characterization focusing on the carotenoid composition of ten cassava (Manihot esculenta) genotypes cultivated in southern Brazil by UV-visible scanning spectrophotometry and reverse phase-high performance liquid chromatography was performed. Cassava roots rich in β-carotene are an important staple food for populations with risk of vitamin A deficiency. Cassava genotypes with high pro-vitamin A activity have been identified as a strategy to reduce the prevalence of deficiency of this vitamin...
2015: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/26673930/discrimination-of-brazilian-propolis-according-to-the-seasoning-using-chemometrics-and-machine-learning-based-on-uv-vis-scanning-data
#5
Maíra Maciel Tomazzoli, Remi Dal Pai Neto, Rodolfo Moresco, Larissa Westphal, Amélia Regina Somensi Zeggio, Leandro Specht, Christopher Costa, Miguel Rocha, Marcelo Maraschin
Propolis is a chemically complex biomass produced by honeybees (Apis mellifera) from plant resins added of salivary enzymes, beeswax, and pollen. The biological activities described for propolis were also identified for donor plant's resin, but a big challenge for the standardization of the chemical composition and biological effects of propolis remains on a better understanding of the influence of seasonality on the chemical constituents of that raw material. Since propolis quality depends, among other variables, on the local flora which is strongly influenced by (a)biotic factors over the seasons, to unravel the harvest season effect on the propolis' chemical profile is an issue of recognized importance...
2015: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/26673929/multi-agent-system-for-obtaining-relevant-genes-in-expression-analysis-between-young-and-older-women-with-triple-negative-breast-cancer
#6
Alfonso González-Briones, Juan Ramos, Juan Francisco De Paz, Juan Manuel Corchado
Triple negative breast cancer is an aggressive form of breast cancer. Despite treatment with chemotherapy, relapses are frequent and response to these treatments is not the same in younger women as in older women. Therefore, the identification of genes that cause this difference is required. The identification of therapeutic targets is one of the sought after goals to develop new drugs. Within the range of different hybridization techniques, the developed system uses expression array analysis to measure the expression of the signal levels of thousands of genes in a given sample...
2015: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/26673793/managing-and-documenting-legacy-scientific-workflows
#7
Ruben Acuña, Jacques Chomilier, Zoé Lacroix
Scientific legacy workflows are often developed over many years, poorly documented and implemented with scripting languages. In the context of our cross-disciplinary projects we face the problem of maintaining such scientific workflows. This paper presents the Workflow Instrumentation for Structure Extraction (WISE) method used to process several ad-hoc legacy workflows written in Python and automatically produce their workflow structural skeleton. Unlike many existing methods, WISE does not assume input workflows to be preprocessed in a known workflow formalism...
2015: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/26673792/machine-learning-approach-to-discriminate-saccharomyces-cerevisiae-yeast-cells-using-sophisticated-image-features
#8
Mohamed S Tleis, Fons J Verbeek
In biological research, Saccharomyces cerevisiae yeast cells are used to study the behaviour of proteins. This is a time consuming and not completely objective process. Hence, Image analysis platforms are developed to address these problems and to offer analysis per cell as well. The robust segmentation algorithms implemented in such platforms enables us to apply a machine learning approach on the measured cells. Such approach is based on a set of relevant individual cell features extracted from the microscope images of the yeast cells...
2015: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/26673791/retromine-or-how-to-provide-in-depth-retrospective-studies-from-medline-in-a-glance-the-hepcidin-use-case
#9
Bertrand Ameline de Cadeville, Olivier Loréal, Fouzia Moussouni-Marzolf
The rapid expansion of biomedical literature has provoked an increased development of advanced text mining tools to rapidly extract relevant events from the continuously increasing amount of knowledge published periodically in PubMed. However, bioinvestigators are still reluctant to use these tools for two reasons: i) a large volume of events is often extracted upon a query, and this volume is hard to manage, and ii) background events dominate search results and overshadow more pertinent published information, especially for domain experts...
2015: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/26673790/openlabnotes-an-electronic-laboratory-notebook-extension-for-openlabframework
#10
Markus List, Michael Franz, Qihua Tan, Jan Mollenhauer, Jan Baumbach
Electronic laboratory notebooks (ELNs) are more accessible and reliable than their paper based alternatives and thus find widespread adoption. While a large number of commercial products is available, small- to mid-sized laboratories can often not afford the costs or are concerned about the longevity of the providers. Turning towards free alternatives, however, raises questions about data protection, which are not sufficiently addressed by available solutions. To serve as legal documents, ELNs must prevent scientific fraud through technical means such as digital signatures...
2015: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/26673789/taxonomic-and-functional-metagenomic-analysis-of-anodic-communities-in-two-pilot-scale-microbial-fuel-cells-treating-different-industrial-wastewaters
#11
Larisa Kiseleva, Sofya K Garushyants, Hongwu Ma, David J W Simpson, Viatcheslav Fedorovich, Michael F Cohen, Igor Goryanin
The combined processes of microbial biodegradation accompanied by extracellular electron transfer make microbial fuel cells (MFCs) a promising new technology for cost-effective and sustainable wastewater treatment. Although a number of microbial species that build biofilms on the anode surfaces of operating MFCs have been identified, studies on the metagenomics of entire electrogenic communities are limited. Here we present the results of whole-genome metagenomic analysis of electrochemically active robust anodic microbial communities, and their anaerobic digester (AD) sludge inocula, from two pilot-scale MFC bioreactors fed with different distillery wastewaters operated under ambient conditions in distinct climatic zones...
2015: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/26528570/synthetic-biology-open-language-sbol-version-2-0-0
#12
Bryan Bartley, Jacob Beal, Kevin Clancy, Goksel Misirli, Nicholas Roehner, Ernst Oberortner, Matthew Pocock, Michael Bissell, Curtis Madsen, Tramy Nguyen, Zhen Zhang, John H Gennari, Chris Myers, Anil Wipat, Herbert Sauro
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...
2015: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/26528569/systems-biology-markup-language-sbml-level-2-version-5-structures-and-facilities-for-model-definitions
#13
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 function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. 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...
2015: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/26528568/the-systems-biology-markup-language-sbml-level-3-package-qualitative-models-version-1-release-1
#14
Claudine Chaouiya, Sarah M Keating, Duncan Berenguier, Aurélien Naldi, Denis Thieffry, Martijn P van Iersel, Nicolas Le Novère, Tomáš Helikar
Quantitative methods for modelling biological networks require an in-depth knowledge of the biochemical reactions and their stoichiometric and kinetic parameters. In many practical cases, this knowledge is missing. This has led to the development of several qualitative modelling methods using information such as, for example, gene expression data coming from functional genomic experiments. The SBML Level 3 Version 1 Core specification does not provide a mechanism for explicitly encoding qualitative models, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs...
2015: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/26528567/the-systems-biology-markup-language-sbml-level-3-package-flux-balance-constraints
#15
Brett G Olivier, Frank T Bergmann
Constraint-based modeling is a well established modelling methodology used to analyze and study biological networks on both a medium and genome scale. Due to their large size, genome scale models are typically analysed using constraint-based optimization techniques. One widely used method is Flux Balance Analysis (FBA) which, for example, requires a modelling description to include: the definition of a stoichiometric matrix, an objective function and bounds on the values that fluxes can obtain at steady state...
2015: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/26528566/sbml-level-3-package-hierarchical-model-composition-version-1-release-3
#16
Lucian Paul Smith, Michael Hucka, Stefan Hoops, Andrew Finney, Martin Ginkel, Chris J Myers, Ion Moraru, Wolfram Liebermeister
Constructing a model in a hierarchical fashion is a natural approach to managing model complexity, and offers additional opportunities such as the potential to re-use model components. The SBML Level 3 Version 1 Core specification does not directly provide a mechanism for defining hierarchical models, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The SBML Hierarchical Model Composition package for SBML Level 3 adds the necessary features to SBML to support hierarchical modeling...
2015: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/26528565/the-systems-biology-markup-language-sbml-level-3-package-layout-version-1-core
#17
Ralph Gauges, Ursula Rost, Sven Sahle, Katja Wengler, Frank Thomas Bergmann
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). For software tools that also read and write models in SBML (Systems Biology Markup Language) format, a common need is to store the network diagram together with the SBML representation of the model...
2015: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/26528564/the-systems-biology-markup-language-sbml-language-specification-for-level-3-version-1-core
#18
Michael Hucka, Frank T Bergmann, Stefan Hoops, Sarah M Keating, Sven Sahle, James C Schaff, Lucian P Smith, Darren J Wilkinson
Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. 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...
2015: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/26528563/systems-biology-graphical-notation-activity-flow-language-level-1-version-1-2
#19
Huaiyu Mi, Falk Schreiber, Stuart Moodie, Tobias Czauderna, Emek Demir, Robin Haw, Augustin Luna, Nicolas Le Novère, Anatoly Sorokin, Alice Villéger
The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail...
2015: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/26528562/systems-biology-graphical-notation-entity-relationship-language-level-1-version-2
#20
Anatoly Sorokin, Nicolas Le Novère, Augustin Luna, Tobias Czauderna, Emek Demir, Robin Haw, Huaiyu Mi, Stuart Moodie, Falk Schreiber, Alice Villéger
The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail...
2015: Journal of Integrative Bioinformatics
journal
journal
42323
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"