The challenge in bioinformatics is not integration by itself, which could be achieved with ad-hoc scripting, but to do so in a manner that is repeatable, customisable, and enables powerful queries and visualisations. Here we present a case study which should provide some valuable insights. We set out to integrate public datasets from Drosophila melanogaster, including pathway data from BioCyc a...

...........................................................................................................iv CHAPTER 1. INTRODUCTION ................................................................................... 1 1.1 Background ......................................................................................................... 1 1.2 Network Diagram...................................

MOTIVATION The identification of functional modules from protein-protein interaction (PPI) networks is an important step toward understanding the biological features of PPI networks. The detection of functional modules in PPI networks is often performed by identifying internally densely connected subnetworks, and often produces modules with "core" and "peripheral" proteins. The core proteins ar...

Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graph...

Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interac...

Alzheimer's disease (AD) is an age-associated progressive neurodegenerative disorder which is of clinical concern. The association between the nervous and immune system is defined as an neuroimmunological theory that supports a model of pathology or treatment for AD. Interleukin (IL)-1β has a pro-inflammatory function in AD; however, the mechanism of its dysregulation in AD remains unknown. It ...

Integrating expression data with gene interactions in a network is essential for understanding the functional organization of the cells. Consequently, knowledge of interaction types in biological networks is important for data interpretation. Signing of Regulatory Networks (SIREN) plugin for Cytoscape is an open-source Java tool for discrimination of interaction type (activatory or inhibitory) ...

SUMMARY Protein-protein interaction detection methods are applied on a daily basis by molecular biologists worldwide. After generating a set of potential interactions, biologists face the problem of highlighting the ones that are novel and collecting evidence with respect to literature and annotation. This task can be as tedious as searching for every predicted interaction in several interactio...

UNLABELLED BiNoM (Biological Network Manager) is a new bioinformatics software that significantly facilitates the usage and the analysis of biological networks in standard systems biology formats (SBML, SBGN, BioPAX). BiNoM implements a full-featured BioPAX editor and a method of 'interfaces' for accessing BioPAX content. BiNoM is able to work with huge BioPAX files such as whole pathway databa...

UNLABELLED The propagation of perturbations in protein concentration through a protein interaction network (PIN) can shed light on network dynamics and function. In order to facilitate this type of study, PerturbationAnalyzer, which is an open source plugin for Cytoscape, has been developed. PerturbationAnalyzer can be used in manual mode for simulating user-defined perturbations, as well as in...