Semantics for an Integrative and Immersive Pipeline Combining Visualization and Analysis of Molecular Data.
Authors: Trellet M, Férey N, FlotyƄski J, Baaden M, Bourdot P Abstract 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 ...
Source: Journal of integrative bioinformatics - July 11, 2018 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

From Virtual Reality to Immersive Analytics in Bioinformatics.
Authors: Sommer B, Baaden M, Krone M, Woods A Abstract 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.g. in the case of...
Source: Journal of integrative bioinformatics - July 11, 2018 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis.
Authors: Maes A, Martinez X, Druart K, Laurent B, Guégan S, Marchand CH, Lemaire SD, Baaden M Abstract 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) r...
Source: Journal of integrative bioinformatics - June 22, 2018 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Molecular Dynamics Visualization (MDV): Stereoscopic 3D Display of Biomolecular Structure and Interactions Using the Unity Game Engine.
Authors: Wiebrands M, Malajczuk CJ, Woods AJ, Rohl AL, Mancera RL Abstract 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...
Source: Journal of integrative bioinformatics - June 22, 2018 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

BioSankey: Visualization of Microbial Communities Over Time.
Authors: Platzer A, Polzin J, Rembart K, Han PP, Rauer D, Nussbaumer T Abstract 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 c...
Source: Journal of integrative bioinformatics - June 15, 2018 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

MIRATE: MIps RATional dEsign Science Gateway.
We present MIRATE, an integrated science gateway for the intelligent design of MIPs. By combining and adapting multiple state-of-the-art bioinformatics tools into automated and innovative pipelines, MIRATE guides the user through the entire process of MIPs' design. The platform allows the user to fully customize each stage involved in the MIPs' design, with the main goal to support the synthesis in the wet-laboratory. AVAILABILITY: MIRATE is freely accessible with no login requirement at http://mirate.di.univr.it/. All major browsers are supported. PMID: 29897885 [PubMed - as supplied by publisher] (Source: Journal...
Source: Journal of integrative bioinformatics - June 15, 2018 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Interactive Molecular Graphics for Augmented Reality Using HoloLens.
Authors: Müller C, Krone M, Huber M, Biener V, Herr D, Koch S, Reina G, Weiskopf D, Ertl T Abstract 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 weig...
Source: Journal of integrative bioinformatics - June 15, 2018 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Mesoscopic Rigid Body Modelling of the Extracellular Matrix Self-Assembly.
Authors: Wong H, Prévoteau-Jonquet J, Baud S, Dauchez M, Belloy N Abstract 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 observab...
Source: Journal of integrative bioinformatics - June 11, 2018 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Big Data Analytics in Medicine and Healthcare.
Authors: Ristevski B, Chen M Abstract 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. We underline the challenging issues about big data privacy and secur...
Source: Journal of integrative bioinformatics - May 12, 2018 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

SBML Level 3 package: Multistate, Multicomponent and Multicompartment Species, Version 1, Release 1.
Authors: Zhang F, Meier-Schellersheim M Abstract 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 prov...
Source: Journal of integrative bioinformatics - April 22, 2018 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

SBML Level 3 package: Render, Version 1, Release 1.
Authors: Bergmann FT, Keating SM, Gauges R, Sahle S, Wengler K Abstract 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 elem...
Source: Journal of integrative bioinformatics - April 2, 2018 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Synthetic Biology Open Language (SBOL) Version 2.2.0.
Authors: Cox RS, Madsen C, McLaughlin JA, Nguyen T, Roehner N, Bartley B, Beal J, Bissell M, Choi K, Clancy K, Grünberg R, Macklin C, Misirli G, Oberortner E, Pocock M, Samineni M, Zhang M, Zhang Z, Zundel Z, Gennari JH, Myers C, Sauro H, Wipat A Abstract 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 wou...
Source: Journal of integrative bioinformatics - April 2, 2018 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017.
Authors: Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, Novère NL, Myers C, Nickerson D, Sommer B, Waltemath D Abstract 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 prese...
Source: Journal of integrative bioinformatics - March 30, 2018 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0.
Authors: Cox RS, Madsen C, McLaughlin J, Nguyen T, Roehner N, Bartley B, Bhatia S, Bissell M, Clancy K, Gorochowski T, Grünberg R, Luna A, Le Novere N, Pocock M, Sauro H, Sexton JT, Stan GB, Tabor JJ, Voigt CA, Zundel Z, Myers C, Beal J, Wipat A Abstract 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 Synthet...
Source: Journal of integrative bioinformatics - March 20, 2018 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3).
Authors: Bergmann FT, Cooper J, König M, Moraru I, Nickerson D, Novère NL, Olivier BG, Sahle S, Smith L, Waltemath D Abstract 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 ...
Source: Journal of integrative bioinformatics - March 20, 2018 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform.
Authors: Chowdhury S, Sinha N, Ganguli P, Bhowmick R, Singh V, Nandi S, Sarkar RR Abstract BIOPYDB: 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 ...
Source: Journal of integrative bioinformatics - March 18, 2018 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.
Authors: Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Novère NL, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ Abstract 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...
Source: Journal of integrative bioinformatics - March 10, 2018 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

SBML Level 3 Package: Flux Balance Constraints version 2.
Authors: Olivier BG, Bergmann FT Abstract 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 b...
Source: Journal of integrative bioinformatics - March 10, 2018 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Modified HuffBit Compress Algorithm - An Application of R.
Authors: Habib N, Ahmed K, Jabin I, Rahman MM Abstract 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 v...
Source: Journal of integrative bioinformatics - February 24, 2018 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Selected Extended Papers of the 11th International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB).
Authors: Fdez-Riverola F, Rocha M PMID: 29236675 [PubMed - in process] (Source: Journal of integrative bioinformatics)
Source: Journal of integrative bioinformatics - December 15, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Supervised Learning and Knowledge-Based Approaches Applied to Biomedical Word Sense Disambiguation.
Authors: Antunes R, Matos S Abstract 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 datab...
Source: Journal of integrative bioinformatics - December 15, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

A Chemometrics Approach for Nuclear Magnetic Resonance Data to Characterize the Partial Metabolome Banana Peels from Southern Brazil.
Authors: Cardoso S, Maraschin M, Peruch LAM, Rocha M, Pereira A Abstract 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 process...
Source: Journal of integrative bioinformatics - December 15, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Protein-Protein Interaction Article Classification Using a Convolutional Recurrent Neural Network with Pre-trained Word Embeddings.
Authors: Matos S, Antunes R Abstract 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. Using the BioCreative III Article Classificatio...
Source: Journal of integrative bioinformatics - December 15, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Assessing Public Metabolomics Metadata, Towards Improving Quality.
Authors: Ferreira JD, Inácio B, Salek RM, Couto FM Abstract 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 contrib...
Source: Journal of integrative bioinformatics - December 15, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

UV-Vis and CIELAB Based Chemometric Characterization of Manihot esculenta Carotenoid Contents.
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. We trained several machine learning models using UV-visible spectrophotometry data, CIELAB data and a low-level data fusion of the two. Best performance models were obtained for the total carotenoids contents calculated using the UV-visible dataset as input, with R2 values above 90 %. Using CIELAB and fusion...
Source: Journal of integrative bioinformatics - December 15, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

A Machine Learning Approach for MicroRNA Precursor Prediction in Retro-transcribing Virus Genomes.
In this study we analyzed 5 human retro virus genomes; Human endogenous retrovirus K113, Hepatitis B virus (strain ayw), Human T lymphotropic virus 1, Human T lymphotropic virus 2, Human immunodeficiency virus 2, and Human immunodeficiency virus 1. We then predicted pre-miRNAs by using the information from known virus and human pre-miRNAs. Our results indicate that these viruses produce novel unknown miRNA precursors which warrant further experimental validation. PMID: 29216001 [PubMed - in process] (Source: Journal of integrative bioinformatics)
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

miRquant 2.0: an Expanded Tool for Accurate Annotation and Quantification of MicroRNAs and their isomiRs from Small RNA-Sequencing Data.
Authors: Kanke M, Baran-Gale J, Villanueva J, Sethupathy P Abstract Small non-coding RNAs, in particular microRNAs, are critical for normal physiology and are candidate biomarkers, regulators, and therapeutic targets for a wide variety of diseases. There is an ever-growing interest in the comprehensive and accurate annotation of microRNAs across diverse cell types, conditions, species, and disease states. Highthroughput sequencing technology has emerged as the method of choice for profiling microRNAs. Specialized bioinformatic strategies are required to mine as much meaningful information as possible from the seque...
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Computational miRNomics.
Authors: Allmer J, Yousef M Abstract Editorial The term MicroRNA or its contraction miRNA currently appears in 21,215 titles of abstracts, published between 1997 and now, available on Pubmed (2016-21-22:12:59 EET). 4,108 of these were published in 2016 alone which signifies the importance of miRNA-related research. MicroRNAs can be detected experimentally using various techniques like directional cloning of endogenous small RNAs but they are time consuming [1]. Additionally, it is necessary for the miRNA and its mRNA target(s) to be co-expressed to infer a functional relationship which is difficult, if not impossib...
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Current Progress of High-Throughput MicroRNA Differential Expression Analysis and Random Forest Gene Selection for Model and Non-Model Systems: an R Implementation.
Authors: Zhang J, Hadj-Moussa H, Storey KB Abstract MicroRNAs are short non-coding RNA transcripts that act as master cellular regulators with roles in orchestrating virtually all biological functions. The recent affordability and widespread use of high-throughput microRNA profiling technologies has grown along with the advancement of bioinformatics tools available for analysis of the mounting data flow. While there are many computational resources available for the management of data from genomesequenced animals, researchers are often faced with the challenge of identifying the biological implications of the daunt...
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Ensemble Clustering Classification Applied to Competing SVM and One-Class Classifiers Exemplified by Plant MicroRNAs Data.
In conclusion, this study shows that the chosen classifier shows high performance when the distance metric is carefully chosen. PMID: 29216005 [PubMed - in process] (Source: Journal of integrative bioinformatics)
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Differential Expression of Hyperhydricity Responsive Peach MicroRNAs.
This study went one step further to advance understanding of molecular miRNA-based regulatory mechanisms regarding responses to hyperhydricity in peach. PMID: 29216006 [PubMed - in process] (Source: Journal of integrative bioinformatics)
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Dynamics of miRNA biogenesis and nuclear transport.
Authors: Kotipalli A, Gutti R, Mitra CK Abstract MicroRNAs (miRNAs) are short noncoding RNA sequences ~22 nucleotides in length that play an important role in gene regulation-transcription and translation. The processing of these miRNAs takes place in both the nucleus and the cytoplasm while the final maturation occurs in the cytoplasm. Some mature miRNAs with nuclear localisation signals (NLS) are transported back to the nucleus and some remain in the cytoplasm. The functional roles of these miRNAs are seen in both the nucleus and the cytoplasm. In the nucleus, miRNAs regulate gene expression by binding to the tar...
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

UV-visible scanning spectrophotometry and chemometric analysis as tools for carotenoids analysis in cassava genotypes (Manihot esculenta Crantz).
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. The data set was used for the construction of a descriptive model by chemometric analysis. The...
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Integrating data from heterogeneous DNA microarray platforms.
Authors: Valente E, Rocha M Abstract 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 ...
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Genomic Islands: an overview of current software tools and future improvements.
Authors: Soares SC, Oliveira LC, Jaiswal AK, Azevedo V Abstract Microbes are highly diverse and widely distributed organisms. They account for ~60% of Earth's biomass and new predictions point for the existence of 1011 to 1012 species, which are constantly sharing genes through several different mechanisms. Genomic Islands (GI) are critical in this context, as they are large regions acquired through horizontal gene transfer. Also, they present common features like genomic signature deviation, transposase genes, flanking tRNAs and insertion sequences. GIs carry large numbers of genes related to specific lifestyle an...
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

PetriScape - A plugin for discrete Petri net simulations in Cytoscape.
Authors: Almeida D, Azevedo V, Silva A, Baumbach J Abstract 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 simula...
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Feature Fusion Based SVM Classifier for Protein Subcellular Localization Prediction.
Authors: Rahman J, Mondal NI, Islam KB, Hasan AM Abstract For the importance of protein subcellular localization in different branch of life science and drug discovery, researchers have focused their attentions on protein subcellular localization prediction. Effective representation of features from protein sequences plays most vital role in protein subcellular localization prediction specially in case of machine learning technique. Single feature representation like pseudo amino acid composition (PseAAC), physiochemical property model (PPM), amino acid index distribution (AAID) contains insufficient information fr...
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Integrated Automatic Workflow for Phylogenetic Tree Analysis Using Public Access and Local Web Services.
Authors: Damkliang K, Tandayya P, Sangket U, Pasomsub E Abstract At the present, coding sequence (CDS) has been discovered and larger CDS is being revealed frequently. Approaches and related tools have also been developed and upgraded concurrently, especially for phylogenetic tree analysis. This paper proposes an integrated automatic Taverna workflow for the phylogenetic tree inferring analysis using public access web services at European Bioinformatics Institute (EMBL-EBI) and Swiss Institute of Bioinformatics (SIB), and our own deployed local web services. The workflow input is a set of CDS in the Fasta format. T...
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Clustering of Biological Datasets in the Era of Big Data.
Authors: Röttger R Abstract Clustering is a long-standing problem in computer science and is applied in virtually any scientific field for exploring the inherent structure of datasets. In biomedical research, clustering tools have been utilized in manifold areas, among many others in expression analysis, disease subtyping or protein research. A plethora of different approaches have been developed but there is only little guideline what approach is the optimal in what particular situation. Furthermore, a typical cluster analysis is an entire process with several highly interconnected steps; from preprocessing, ...
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Computational Lipidomics and Lipid Bioinformatics: Filling In the Blanks.
Authors: Pauling JK, Klipp E Abstract Lipids are highly diverse metabolites of pronounced importance in health and disease. While metabolomics is a broad field under the omics umbrella that may also relate to lipids, lipidomics is an emerging field which specializes in the identification, quantification and functional interpretation of complex lipidomes. Today, it is possible to identify and distinguish lipids in a high-resolution, high-throughput manner and simultaneously with a lot of structural detail. However, doing so may produce thousands of mass spectra in a single experiment which has created a high demand ...
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Feature Learning applied to the Estimation of Tensile Strength at Break in Polymeric Material Design.
Authors: Fiorella C, Jimena MM, Gustavo V, Díaz MF, Ignacio P Abstract Several feature extraction approaches for QSPR modelling in Cheminformatics are discussed in this paper. In particular, this work is focused on the use of these strategies for predicting mechanical properties, which are relevant for the design of polymeric materials. The methodology analysed in this study employs a feature learning method that uses a quantification process of 2D structural characterization of materials with the autoencoder method. Alternative QSPR models inferred for tensile strength at break (a well-known mechanical prop...
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Estimation of biomass composition from genomic and transcriptomic information.
Authors: Santos S, Rocha I Abstract Given the great potential impact of the growing number of complete genome-scale metabolic network reconstructions of microorganisms, bioinformatics tools are needed to simplify and accelerate the course of knowledge in this field. One essential component of a genomescale metabolic model is its biomass equation, whose maximization is one of the most common objective functions used in Flux Balance Analysis formulations. Some components of biomass, such as amino acids and nucleotides, can be estimated from genome information, providing reliable data without the need of performing la...
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.
Authors: Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Novère NL, Myers C, Nickerson D, Sommer B, Waltemath D Abstract Standards are essential to the advancement of science and technology. In systems and synthetic biology, numerous standards and associated tools have been developed over the last 16 years. This special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards, as well as to provide centralised and easily citable access to them. PMID: 29215991 [PubMed - in process] (Source: Journal of integrative bioinformatics)
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Synthetic Biology Open Language (SBOL) Version 2.1.0.
Authors: Beal J, Cox RS, Grünberg R, McLaughlin J, Nguyen T, Bartley B, Bissell M, Choi K, Clancy K, Macklin C, Madsen C, Misirli G, Oberortner E, Pocock M, Roehner N, Samineni M, Zhang M, Zhang Z, Zundel Z, Gennari JH, Myers C, Sauro H, Wipat A Abstract 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 woul...
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

SBML Level 3 package: Groups, Version 1 Release 1.
Authors: Hucka M, Smith LP Abstract Biological models often contain components that have relationships with each other, or that modelers want to treat as belonging to groups with common characteristics or shared metadata. The SBML Level 3 Version 1 Core specification does not provide a n explicit mechanism for expressing such relationships, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The SBML Groups package for SBML Level 3 adds the necessary features to SBML to allow grouping of model components to be expressed. Such groups do not af...
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

New insights into genotype-phenotype correlation in individuals with different level of general non-specific reactivity of an organism.
The objective of the study was to investigate the genetic basis of general non-specific reactivity of an organism. Systematic search in PubMedCentral, PDB, KEGG and SNP databases identified a set of genes and their polymorphisms that can determine pain sensitivity and therefore the level of general non-specific reactivity of the human organism. Six SNPs were selected for genotyping kit design; 230 healthy volunteers were enrolled in the study. It was revealed that very high pain threshold was associated with allele A in rs1851048 and allele C in rs6777055. High level of general non-specific reactivity of an organism was as...
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data processing.
Authors: Almeida D, Skov I, Lund J, Mohammadnejad A, Silva A, Vandin F, Tan Q, Baumbach J, Röttger R Abstract Measuring differential methylation of the DNA is the nowadays most common approach to linking epigenetic modifications to diseases (called epigenome-wide association studies, EWAS). For its low cost, its efficiency and easy handling, the Illumina HumanMethylation450 BeadChip and its successor, the Infinium MethylationEPIC BeadChip, is the by far most popular techniques for conduction EWAS in large patient cohorts. Despite the popularity of this chip technology, raw data processing and statistical analy...
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

Web-based hybrid-dimensional Visualization and Exploration of Cytological Localization Scenarios.
Authors: Kovanci G, Ghaffar M, Sommer B Abstract The CELLmicrocosmos 4.2 PathwayIntegration (CmPI) is a tool which provides hybriddimensional visualization and analysis of intracellular protein and gene localizations in the context of a virtual 3D environment. This tool is developed based on Java/Java3D/JOGL and provides a standalone application compatible to all relevant operating systems. However, it requires Java and the local installation of the software. Here we present the prototype of an alternative web-based visualization approach, using Three.js and D3.js. In this way it is possible to visualize and explor...
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

PGMiner reloaded, fully automated proteogenomic annotation tool linking genomes to proteomes.
Authors: Has C, Lashin SA, Kochetov A, Allmer J Abstract Improvements in genome sequencing technology increased the availability of full genomes and transcriptomes of many organisms. However, the major benefit of massive parallel sequencing is to better understand the organization and function of genes which then lead to understanding of phenotypes. In order to interpret genomic data with automated gene annotation studies, several tools are currently available. Even though the accuracy of computational gene annotation is increasing, a combination of multiple lines of experimental evidences should be gathered. Mass ...
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research

DaTo: an atlas of biological databases and tools.
Authors: Li Q, Zhou Y, Jiao Y, Zhang Z, Bai L, Tong L, Yang X, Sommer B, Hofestädt R, Chen M Abstract This work presents DaTo, a semi-automatically generated world atlas of biological databases and tools. It extracts raw information from all PubMed articles which contain exact URLs in their abstract section, followed by a manual curation of the abstract and the URL accessibility. DaTo features a user-friendly query interface, providing extensible URL-related annotations, such as the status, the location and the country of the URL. A graphical interaction network browser has also been integrated into the DaTo w...
Source: Journal of integrative bioinformatics - December 9, 2017 Category: Bioinformatics Tags: J Integr Bioinform Source Type: research