Open Access Published by De Gruyter

Volume 16 Issue 3 - Special Section: History and Future of Integrated Bioinformatics / Guest Editors: Ming Chen, Ralf Hofestädt, Jan Taubert

September 2019

Issue of Journal of Integrative Bioinformatics

Contents
Journal Overview

Editorial

Open Access September 13, 2019

Integrative Bioinformatics: History and Future

Ming Chen, Ralf Hofestädt, Jan Taubert

Article number: 20192001

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Research Article

Open Access June 14, 2019

Mental-Map Preserving Visualisation of Partitioned Networks in Vanted

Dimitar Garkov, Karsten Klein, Christian Klukas, Falk Schreiber

Article number: 20190026

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Abstract

Biological networks can be large and complex, often consisting of different sub-networks or parts. Separation of networks into parts, network partitioning and layouts of overview and sub-graphs are of importance for understandable visualisations of those networks. This article presents NetPartVis to visualise non-overlapping clusters or partitions of graphs in the Vanted framework based on a method for laying out overview graph and several sub-graphs (partitions) in a coordinated, mental-map preserving way.

Review Article

Open Access July 13, 2019

Non-Coding RNAs and their Integrated Networks

Peijing Zhang, Wenyi Wu, Qi Chen, Ming Chen

Article number: 20190027

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Abstract

Eukaryotic genomes are pervasively transcribed. Besides protein-coding RNAs, there are different types of non-coding RNAs that modulate complex molecular and cellular processes. RNA sequencing technologies and bioinformatics methods greatly promoted the study of ncRNAs, which revealed ncRNAs’ essential roles in diverse aspects of biological functions. As important key players in gene regulatory networks, ncRNAs work with other biomolecules, including coding and non-coding RNAs, DNAs and proteins. In this review, we discuss the distinct types of ncRNAs, including housekeeping ncRNAs and regulatory ncRNAs, their versatile functions and interactions, transcription, translation, and modification. Moreover, we summarize the integrated networks of ncRNA interactions, providing a comprehensive landscape of ncRNAs regulatory roles.

Research Articles

Open Access September 27, 2019

The CELLmicrocosmos Tools: A Small History of Java-Based Cell and Membrane Modelling Open Source Software Development

Bjorn Sommer

Article number: 20190057

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Abstract

For more than one decade, CELLmicrocosmos tools are being developed. Here, we discus some of the technical and administrative hurdles to keep a software suite running so many years. The tools were being developed during a number of student projects and theses, whereas main developers refactored and maintained the code over the years. The focus of this publication is laid on two Java-based Open Source Software frameworks. Firstly, the CellExplorer with the PathwayIntegration combines the mesoscopic and the functional level by mapping biological networks onto cell components using database integration. Secondly, the MembraneEditor enables users to generate membranes of different lipid and protein compositions using the PDB format. Technicalities will be discussed as well as the historical development of these tools with a special focus on group-based development. In this way, university-associated developers of Integrative Bioinformatics applications should be inspired to go similar ways. All tools discussed in this publication can be downloaded and installed from https://www.CELLmicrocosmos.org.

Open Access May 30, 2019

History and Future of KALIS: Towards Computer-assisted Decision Making in Prescriptive Medicine

Marcel Friedrichs, Alban Shoshi

Article number: 20190011

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Abstract

With an increasing older population in Germany and the need for polypharmacy to treat multimorbid patients computer-assisted decision making on an individual level is increasingly important to reduce prescription errors and adverse drug reactions. While current systems focus on guidelines and prescribing information, molecular information is equally important for explanation and discovery of drug-related problems. Based on the existing KALIS system and newer projects like PIMBase, a new concept for the KALIS-2 system is presented. Improvements to the modularisation of components enable future extension and greater maintainability. Interoperability with available electronic health records standards and protocols allows the integration and communication with existing workflows for healthcare professionals. Finally, new visualisation modes empower the user to explore and analyze the patient situation in an individual patient subgraph. For offline use and dialogue between patient and general practitioner, the results can be printed out using a new reporting tool. The adherence to findings from previous decision support systems and reasons for their failed adoption is an important task in the development of KALIS-2.

Opinion Papers

Open Access May 30, 2019

Towards an Internet of Science

Jens Allmer

Article number: 20190024

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Abstract

Big data and complex analysis workflows (pipelines) are common issues in data driven science such as bioinformatics. Large amounts of computational tools are available for data analysis. Additionally, many workflow management systems to piece together such tools into data analysis pipelines have been developed. For example, more than 50 computational tools for read mapping are available representing a large amount of duplicated effort. Furthermore, it is unclear whether these tools are correct and only a few have a user base large enough to have encountered and reported most of the potential problems. Bringing together many largely untested tools in a computational pipeline must lead to unpredictable results. Yet, this is the current state. While presently data analysis is performed on personal computers/workstations/clusters, the future will see development and analysis shift to the cloud. None of the workflow management systems is ready for this transition. This presents the opportunity to build a new system, which will overcome current duplications of effort, introduce proper testing, allow for development and analysis in public and private clouds, and include reporting features leading to interactive documents.

Open Access May 30, 2019

Integrating Molecular Biology and Bioinformatics Education

Boas Pucker, Hanna Marie Schilbert, Sina Franziska Schumacher

Article number: 20190005

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Abstract

Combined awareness about the power and limitations of bioinformatics and molecular biology enables advanced research based on high-throughput data. Despite an increasing demand of scientists with a combined background in both fields, the education of dry and wet lab subjects are often still separated. This work describes an example of integrated education with a focus on genomics and transcriptomics. Participants learned computational and molecular biology methods in the same practical course. Peer-review was applied as a teaching method to foster cooperative learning of students with heterogeneous backgrounds. The positive evaluation results indicate that this approach was accepted by the participants and would likely be suitable for wider scale application.

Regular Contributions

Research Articles

Open Access July 13, 2019

Geno2proteo, a Tool for Batch Retrieval of DNA and Protein Sequences from Any Genomic or Protein Regions

Yaoyong Li, Elisa Aguilar-Martinez, Andrew D. Sharrocks

Article number: 20180090

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Abstract

The interconversion of sequences that constitute the genome and the proteome is becoming increasingly important due to the generation of large amounts of DNA sequence data. Following mapping of DNA segments to the genome, one fundamentally important task is to find the amino acid sequences which are coded within a list of genomic sections. Conversely, given a series of protein segments, an important task is to find the genomic loci which code for a list of protein regions. To perform these tasks on a region by region basis is extremely laborious when a large number of regions are being studied. We have therefore implemented an R package geno2proteo which performs the two mapping tasks and subsequent sequence retrieval in a batch fashion. In order to make the tool more accessible to users, we have created a web interface of the R package which allows the users to perform the mapping tasks by going to the web page http://sharrocksresources.manchester.ac.uk/tofigaps and using the web service.

Open Access May 28, 2019

Gene Expression Studies to Identify Significant Genes in AR, MTOR, MAPK Pathways and their Overlapping Regulatory Role in Prostate Cancer

Nimisha Asati, Abhinav Mishra, Ankita Shukla, Tiratha Raj Singh

Article number: 20180080

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Abstract

Gene expression studies revealed a large degree of variability in gene expression patterns particularly in tissues even in genetically identical individuals. It helps to reveal the components majorly fluctuating during the disease condition. With the advent of gene expression studies many microarray studies have been conducted in prostate cancer, but the results have varied across different studies. To better understand the genetic and biological regulatory mechanisms of prostate cancer, we conducted a meta-analysis of three major pathways i.e. androgen receptor (AR), mechanistic target of rapamycin (mTOR) and Mitogen-Activated Protein Kinase (MAPK) on prostate cancer. Meta-analysis has been performed for the gene expression data for the human species that are exposed to prostate cancer. Twelve datasets comprising AR, mTOR, and MAPK pathways were taken for analysis, out of which thirteen potential biomarkers were identified through meta-analysis. These findings were compiled based upon the quantitative data analysis by using different tools. Also, various interconnections were found amongst the pathways in study. Our study suggests that the microarray analysis of the gene expression data and their pathway level connections allows detection of the potential predictors that can prove to be putative therapeutic targets with biological and functional significance in progression of prostate cancer.

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).