Open Access Published by De Gruyter

Volume 15 Issue 3 - Special Section: 14th International Symposium on Integrative Bioinformatics, Harpenden, UK, 2018 / Guest Editor: Keywan Hassani-Pak

September 2018

Issue of Journal of Integrative Bioinformatics

Contents
Journal Overview

Research Article

Open Access September 6, 2018

BioModelKit – An Integrative Framework for Multi-Scale Biomodel-Engineering

Mary-Ann Blätke

Article number: 20180021

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Abstract

While high-throughput technology, advanced techniques in biochemistry and molecular biology have become increasingly powerful, the coherent interpretation of experimental results in an integrative context is still a challenge. BioModelKit ( BMK ) approaches this challenge by offering an integrative and versatile framework for biomodel-engineering based on a modular modelling concept with the purpose: (i) to represent knowledge about molecular mechanisms by consistent executable sub-models (modules) given as Petri nets equipped with defined interfaces facilitating their reuse and recombination; (ii) to compose complex and integrative models from an ad hoc chosen set of modules including different omic and abstraction levels with the option to integrate spatial aspects; (iii) to promote the construction of alternative models by either the exchange of competing module versions or the algorithmic mutation of the composed model; and (iv) to offer concepts for ( omic ) data integration and integration of existing resources, and thus facilitate their reuse. BMK is accessible through a public web interface (www.biomodelkit.org), where users can interact with the modules stored in a database, and make use of the model composition features. BMK facilitates and encourages multi-scale model-driven predictions and hypotheses supporting experimental research in a multilateral exchange.

Open Access August 7, 2018

Towards FAIRer Biological Knowledge Networks Using a Hybrid Linked Data and Graph Database Approach

Marco Brandizi, Ajit Singh, Christopher Rawlings, Keywan Hassani-Pak

Article number: 20180023

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Abstract

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). We have developed a simple application ontology based on OWL/RDF with mappings to standard schemas. We are employing the ontology to power data access services like resolvable URIs, SPARQL endpoints, JSON-LD web APIs and Neo4j-based knowledge graphs. We demonstrate how the proposed ontology and graph databases considerably improve search and access to interoperable and reusable biological knowledge (i.e. the FAIRness data principles).

Open Access September 15, 2018

Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA

Christoph Brinkrolf, Nadja A. Henke, Lennart Ochel, Boas Pucker, Olaf Kruse, Petra Lutter

Article number: 20180018

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Abstract

In this work we present new concepts of VANESA, a tool for modeling and simulation in systems biology. We provide a convenient way to handle mathematical expressions and take physical units into account. Simulation and result management has been improved, and syntax and consistency checks, based on physical units, reduce modeling errors. As a proof of concept, essential components of the aerobic carbon metabolism of the green microalga Chlamydomonas reinhardtii are modeled and simulated. The modeling process is based on xHPN Petri net formalism and simulation is performed with OpenModelica, a powerful environment and compiler for Modelica. VANESA, as well as OpenModelica, is open source, free-of-charge for non-commercial use, and is available at: http://agbi.techfak.uni-bielefeld.de/vanesa.

Regular contributions

Review Article

Open Access May 10, 2018

Big Data Analytics in Medicine and Healthcare

Blagoj Ristevski, Ming Chen

Article number: 20170030

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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 security. Regarding big data characteristics, some directions of using suitable and promising open-source distributed data processing software platform are given.

Research Articles

Open Access February 22, 2018

Modified HuffBit Compress Algorithm – An Application of R

Nahida Habib, Kawsar Ahmed, Iffat Jabin, Mohammad Motiur Rahman

Article number: 20170057

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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 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”. The algorithm makes an extended binary tree based on the Huffman Codes and the maximum occurring bases (A, C, G, T). Experimenting with 6 sequences the proposed algorithm gives approximately 16.18 % improvement in compression ration over the “HuffBit Compress” algorithm and 11.12 % improvement in compression ration over the “2-Bits Encoding Method”.

Open Access July 3, 2018

Identification of Missing Carbon Fixation Enzymes as Potential Drug Targets in Mycobacterium Tuberculosis

Amit Katiyar, Harpreet Singh, Krishna Kant Azad

Article number: 20170041

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Abstract

Metabolic adaptation to the host environment has been recognized as an essential mechanism of pathogenicity and the growth of Mycobacterium tuberculosis ( Mtb ) in the lungs for decades. The Mtb uses CO 2 as a source of carbon during the dormant or non-replicative state. However, there is a lack of biochemical knowledge of its metabolic networks. In this study, we investigated the CO 2 fixation pathways (such as ko00710 and ko00720) most likely involved in the energy production and conversion of CO 2 in Mtb . Extensive pathway evaluation of 23 completely sequenced strains of Mtb confirmed the existence of a complete list of genes encoding the relevant enzymes of the reductive tricarboxylic acid (rTCA) cycle. This provides the evidence that an rTCA cycle may function to fix CO 2 in this bacterium. We also proposed that as CO 2 is plentiful in the lungs, inhibition of CO 2 fixation pathways (by targeting the relevant CO 2 fixation enzymes) could be used in the expansion of new drugs against the dormant Mtb . In support of the suggested hypothesis, the CO 2 fixation enzymes were confirmed as a potential drug target by analyzing a number of attributes necessary to be a good bacterial target.

Open Access March 16, 2018

BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform

Saikat Chowdhury, Noopur Sinha, Piyali Ganguli, Rupa Bhowmick, Vidhi Singh, Sutanu Nandi, Ram Rup Sarkar

Article number: 20170072

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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 Topological, Logical and Dynamic analyses, BIOPYDB offers both the experimental and computational biologists to acquire a comprehensive understanding of signaling cascades in the cells. Automated pathway image reconstruction, cross referencing of pathway molecules and interactions with other databases and literature sources, complex search operations to extract information from other similar resources, integrated platform for pathway data sharing and computation, etc. are the novel and useful features included in this database to make it more acceptable and attractive to the users of pathway research communities. The RESTful API service is also made available to the advanced users and developers for accessing this database more conveniently through their own computer programmes.

About this journal

Objective
Journal of Integrative Bioinformatics (JIB) is an international open access journal publishing original peer-reviewed research articles in all aspects of integrative bioinformatics.

Molecular biology produces huge amounts of data in the post-genomic era. This includes data describing metabolic mechanisms and pathways, structural genomic organization, patterns of regulatory regions; proteomics, transcriptomics, and metabolomics. On the one hand, analysis of this data uses essentially the methods and concepts of computer science; on the other hand, the range of biological tasks solved by researchers determines the range and scope of the data. Currently, there are about 1,000 database systems and various analytical tools available via the Internet which are directed at solving various biological tasks.

The challenge we have is to integrate these list-parts and relationships from genomics and proteomics at novel levels of understanding. Integrative Bioinformatics is a new area of research using the tools of computer science and electronic infrastructure applied to Biotechnology. These tools will also represent the backbone of the concept of a virtual cell.

Topics

Software applications/tools and databases covering the following topics:

Molecular Databases, Information Systems and Data Warehouses
Integration of Data, Methods and Tools
Metabolic and Regulatory Network Modeling and Simulation
Signal Pathways and Cell Control
Network Analysis
Medical Informatics, Biomedicine and Biotechnology
Integrative Approaches for Drug Design
Integrative Data and Text Mining Approaches
Integrative, whole cell and molecular modeling
Visualization and animation

Review papers are also welcome with regard to JIB.tools.

Article formats
Research articles, Review papers, Workshop contributions (if peer-reviewed)

Article processing charges (APCs)
Each unsolicited article, which is accepted for publication in the Journal of Integrative Bioinformatics is subject to an Article Processing Charge of 1,000€.
The Open Access publication of invited articles for Special Issues is sponsored by the editors.

Inquiries concerning APCs should be addressed to the Editorial Office at De Gruyter (see contact details below).