The joint NETTAB/Integrative Bioinformatics 2015 Meeting: aims, topics and outcomes

Romano P, Hofestädt R, Lange M, D'Elia D. The joint NETTAB/Integrative Bioinformatics 2015 Meeting: aims, topics and outcomes. BMC BIOINFORMATICS. 2017;18(S5): 101.The 15th International NETTAB workshop and the 11th Integrative Bioinformatics Symposium were held together in Bari, on October 14-16, 2016, as Joint NETTAB/IB 2015 Meeting. A special topic for the meeting was "Bioinformatics for ncRNA", but the traditional topics of both meetings series were also included in the event. About 60 scientific contributions were presented, including six keynote lectures, one special guest lecture, and many oral communications and posters. A " Two-Day Hands-on Tutorial" event was organised before the workshop. Selected full papers from some of the best works presented in Bari were submitted either to the Journal of Integrative Bioinformatics or to a purpose Call for a Supplement of BMC Bioinformatics. Here, we provide an overview of meeting aims and scope. We also shortly introduce selected papers that have been either accepted for publication in this Supplement or published in the Journal of Integrative Bioinformatics, for a more complete presentation of the outcomes of the meeting

Cancernet: a database for decoding multilevel molecular interactions across diverse cancer types

Meng X, Wang J, Yuan C, et al. Cancernet: a database for decoding multilevel molecular interactions across diverse cancer types. Oncogenesis. 2015;4(12): e177.Protein-protein interactions (PPIs) and microRNA (miRNA)-target interactions are important for deciphering the mechanisms of tumorigenesis. However, current PPI databases do not support cancer-specific analysis. Also, no available databases can be used to retrieve cancer-associated miRNA-target interactions. As the pathogenesis of human cancers is affected by several miRNAs rather than a single miRNA, it is needed to uncover miRNA synergism in a systems level. Here for each cancer type, we constructed a miRNA-miRNA functionally synergistic network based on the functions of miRNA targets and their topological features in that cancer PPI network. And for the first time, we report the cancer-specific database CancerNet (http://bis.zju.edu.cn/CancerNet), which contains information about PPIs, miRNA-target interactions and functionally synergistic miRNA-miRNA pairs across 33 human cancer types. In addition, PPI information across 33 main normal tissues and cell types are included. Flexible query methods are allowed to retrieve cancer molecular interactions. Network viewer can be used to visualize interactions that users are interested in. Enrichment analysis tool was designed to detect significantly overrepresented Gene Ontology categories of miRNA targets. Thus, CancerNet serves as a comprehensive platform for assessing the roles of proteins and miRNAs, as well as their interactions across human cancers

JIB.tools 2.0 – A Bioinformatics Registry for Journal Published Tools with Interoperability to bio.tools

JIB.tools 2.0 is a new approach to more closely embed the curation process in the publication process. This website hosts the tools, software applications, databases and workflow systems published in the Journal of Integrative Bioinformatics (JIB). As soon as a new tool-related publication is published in JIB, the tool is posted to JIB.tools and can afterwards be easily transferred to bio.tools, a large information repository of software tools, databases and services for bioinformatics and the life sciences. In this way, an easily-accessible list of tools is provided which were published in JIB a well as status information regarding the underlying service. With newer registries like bio.tools providing these information on a bigger scale, JIB.tools 2.0 closes the gap between journal publications and registry publication. (Reference: https://jib.tools)

Can a quark shell model lead to nucleon clusters?

The six-quark deutron system is examined within the framework of the Bonn quark shell model to see whether this model can lead to a quark density distribution indicative of two spatially separated three-quark clusters. The deuteron ground state always leads to a quark density distribution with a central maximum. The configuration mixing of the model does not furnish the needed strong spatial correlation into three-quark clusters.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/27680/1/0000063.pd

GraphSAW: A web-based system for graphical analysis of drug interactions and side effects using pharmaceutical and molecular data

Shoshi A, Hoppe T, Kormeier B, Ogultarhan V, Hofestädt R. GraphSAW: A web-based system for graphical analysis of drug interactions and side effects using pharmaceutical and molecular data. BMC Medical Informatics and Decision Making. 2015;15(1): 15.Background Adverse drug reactions are one of the most common causes of death in industrialized Western countries. Nowadays, empirical data from clinical studies for the approval and monitoring of drugs and molecular databases is available. Methods The integration of database information is a promising method for providing well-based knowledge to avoid adverse drug reactions. This paper presents our web-based decision support system GraphSAW which analyzes and evaluates drug interactions and side effects based on data from two commercial and two freely available molecular databases. The system is able to analyze single and combined drug-drug interactions, drug-molecule interactions as well as single and cumulative side effects. In addition, it allows exploring associative networks of drugs, molecules, metabolic pathways, and diseases in an intuitive way. The molecular medication analysis includes the capabilities of the upper features. Results A statistical evaluation of the integrated data and top 20 drugs concerning drug interactions and side effects is performed. The results of the data analysis give an overview of all theoretically possible drug interactions and side effects. The evaluation shows a mismatch between pharmaceutical and molecular databases. The concordance of drug interactions was about 12% and 9% of drug side effects. An application case with prescribed data of 11 patients is presented in order to demonstrate the functionality of the system under real conditions. For each patient at least two interactions occured in every medication and about 8% of total diseases were possibly induced by drug therapy. Conclusions GraphSAW (http://tunicata.techfak.uni-bielefeld.de/graphsaw/ webcite) is meant to be a web-based system for health professionals and researchers. GraphSAW provides comprehensive drug-related knowledge and an improved medication analysis which may support efforts to reduce the risk of medication errors and numerous drastic side effects

Evaluation and Visualization of Pathway Efficiency based on Subcellular Protein Localizations (Workshop Abstract)

Popik OV, Sommer B, Hofestädt R, Ivanisenko VA. Evaluation and Visualization of Pathway Efficiency based on Subcellular Protein Localizations (Workshop Abstract). In: Sommer B, ed. Proceedings of the CELLmicrocosmos neXt workshop. Bielefeld: Bielefeld University; 2014: 9-10

Reversibility in Chemical Reactions

open access bookIn this chapter we give an overview of techniques for the modelling and reasoning about reversibility of systems, including outof- causal-order reversibility, as it appears in chemical reactions. We consider the autoprotolysis of water reaction, and model it with the Calculus of Covalent Bonding, the Bonding Calculus, and Reversing Petri Nets. This exercise demonstrates that the formalisms, developed for expressing advanced forms of reversibility, are able to model autoprotolysis of water very accurately. Characteristics and expressiveness of the three formalisms are discussed and illustrated

KALIS – An eHealth system for biomedical risk analysis of drugs

Shoshi A, Müller U, Shoshi A, Ogultarhan V, Hofestädt R. KALIS – An eHealth system for biomedical risk analysis of drugs. In: Hayn D, Schreier G, eds. Health Informatics Meets eHealth: Digital Insight – Information-Driven Health & Care. Proceedings of the 11th eHealth2017 Conference. Studies in Health Technology and Informatics. Vol 236. Amsterdam: IOS Press; 2017: 128-135.Background: In Germany, adverse drug reactions and events cause hospitalizations, which lead to numerous thousands of deaths and several million Euros in additional health costs annually. Objectives: Approximately one in two deaths could be avoided by an appropriate system for risk analysis of drugs. Methods: The integration and storage of several data sources from life sciences are an ongoing need to address various questions with respect to drug therapy. A software architecture for data integration was implemented in order to build up a new data warehouse named KALIS-DWH, which includes pharmacological, biomolecular and patient-related data. Results: Based on this comprehensive KALIS-DWH, an eHealth system named KALIS for biomedical risk analysis of drugs was implemented. The task-specific modules of KALIS offer efficient algorithms for analyzing medication and supporting decision-making in drug therapy. Conclusion: KALIS is meant to be a web-based information system for health professionals and researchers. KALIS provides comprehensive knowledge and modules for risk analysis of drugs, which can contribute to minimizing prescribing errors

Formal Molecular Biology Done in CCS-R

AbstractWe present CCS-R, a reversible variant of Milner's CCS offering a backtracking mechanism. Formalization of biological systems satisfying a “perfect mix” assumption within CCS-R is discussed