Tutorials1 Introduction

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1. Introduction
BiologicalNetworks has been designed to model whole cell biochemical pathways and gene regulatory networks. BiologicalNetworks uses a specialized graph visualization engine to represent biological pathways, gene regulation networks and protein-protein interaction maps for intuitive exploration and prediction. The software can handle a variety of tasks, including graphic drawing and layout optimization, data filtering and pathway expansion, and classification and prioritization of proteins.

BiologicalNetworks uses a proprietary file format (BNX or BiologicalNetworks model XML format) that stores information pertaining to the model and the corresponding simulation environment in BiologicalNetworks. BiologicalNetworks supports import and export of models from the System Biology Mark-up Language (SBML), SIF and GML file formats.

The following is a summary of the functionality of BiologicalNetworks:

    • Distribution
      BiologicalNetworks is a freely distributed Java-based web application. BiologicalNetworks network annotation is stored in an XML-based file. Users can run and obtain the software in three ways:1. Run the online BiologicalNetworks Applet Save the XML files in secure online workspace, share with other users.2. Run the full BiologicalNetworks Java Web-Start Application. Includes ability to save and read XML files on local machine, read network files. (Requires Java Web-Start.)3. Download & Install BiologicalNetworks application. Requires internet connection to retrieve ontology and database interactions from server, but can load and view XML files in offline mode.
    • Multi-platform
      BiologicalNetworks is a multi-platform software that has been developed in Java. It has been tested on Windows, Linux/Unix and Macintosh platforms.
    • Biologist-friendly User Interface (UI)
      The user interface has been designed to be as friendly as possible for the biologist. The UI provides adequate tools for cell model building while abstracting certain underlying mechanism from the users.
    • Database Integration
      The BiologicalNetworks platform is integrated with PathSys pathway database system compiled from over 20 databases and ontological data sources.
    • Database Querying
      The BiologicalNetworks platform provides extended querying functionalities to specify and retrieve biologically meaningful networks.
    • Network Analysis
      BiologicalNetworks is able to provide users the network statistics for the models, which are being loaded. In addition, finding conserved pathways between pathways is another main function in analysis.
    • Microarray Data Analysis
      BiologicalNetworks provides an integrated environment to work with gene expression data in context of biological pathways and gene regulatory networks. It provides extended functionalities for clustering, sorting, normalization and querying Microarray data.
    • SQL-like querying language
      The system is equipped with novel query engine with built in SQL-like querying language, allowing paths, trees, graphs operations.

This tutorial will guide the users through BiologicalNetworks by introducing various features and functions in greater details.

Chapter 2 describes how to download and install BiologicalNetworks. The existing BiologicalNetworks users may skip to Chapter 3 directly.

Chapter 4 highlights all details with regards to the GUI and introduces users to various functionality of BiologicalNetworks.

In Chapter 5 biologically relevant examples are presented, which provides step-by-step guide to construction of models using BiologicalNetworks.

Lastly Chapter 6 that explains Data Management of BiologicalNetworks.

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Tutorials

1. Introduction

BiologicalNetworks is a program developed by SDSC at UCSD which introduces a research environment for inferring cellular molecular mechanisms and elucidation of factors making interrelated impact on different levels of organism including genes, biomolecules, cells, and cell systems.

The program uses over 100 public databases of thousands of eukaryotic, prokaryotic and viral genomes integrated in the IntegromeDB which is a back-end database to BiologicalNetworks.

BiologicalNetworks provides a “one stop shop” experience for researchers by providing them with information needed to decipher gene regulatory networks, sequence andexperimental data, functional annotation, orthology relations, and transcriptional regulatory regions analysis.

The program is developed through multiple driving projects, about 10 of which are embedded into the program and even more are available on the BiologicalNetworks website. Driving Projects are research projects that are selected for their scientific merit in answering important biological questions and that represent a broad range of research endeavors, advancing their disciplines. Driving Projects stimulate the BiologicalNetworks project to improve its technologies and provide feedback on our work.How to become a Driving Project.

The sophisticated querying capabilities of BiologicalNetworks allow users to formulate queries with virtually any combination of properties (name/synonym, function, sequence, expression, etc.) and to condition any combination of entities (gene/protein, promoter, COG, pathway, etc.) and/or relations (interactions, co-expression, co-citations, etc.). This can be combined with the build-pathways infrastructure for molecular interactions, relationships and modules discovery from high-throughput experiments.

Integrated Genome Viewer allows the user to search and analyze gene regulatory regions, transcription factor binding sites and their conservation in multiple species in conjunction with molecular pathways/networks, experimental data and functional annotations.

BiologicalNetworks uses a specialized graph visualization engine to exemplify biological pathways, gene regulation networks and protein-protein interaction maps for intuitive exploration and prediction. The software can handle a multitude of different tasks, including graphic drawing and layout optimization, data filtering and pathway expansion, and classification and prioritization of proteins, etc.

The new software uses a proprietary file format (BNX or BiologicalNetworks model XML format) which stores information pertaining to the model and the corresponding simulation environment in BiologicalNetworks. It also allows the user to import and export of models from the System Biology Mark-up Language (SBML), SIF and GML file formats.

The following is a summary of the functionality of BiologicalNetworks:

  • Distribution
    BiologicalNetworks is a freely distributed Java web-based application.
  • Multi-platform
    BiologicalNetworks is a multi-platform software that has been developed in Java. It has been tested on Windows and Macintosh platforms.
  • Biologist-friendly User Interface (UI)
    The user interface has been designed to be as friendly as possible for the biologist. The UI provides adequate tools for cell model building while abstracting certain underlying mechanism from the users.
  • Database Integration
    The BiologicalNetworks platform is integrated with IntegromeDB integrated database system compiled from over 100 databases and ontological data sources.
  • Database Querying
    The BiologicalNetworks platform provides extended querying functionalities to specify and retrieve biologically meaningful networks.
  • Network Analysis
    BiologicalNetworks is able to provide users the network statistics for the models, which are being loaded. In addition, finding conserved pathways between pathways is another main function in analysis.
  • Genomic Sequences Analysis
    BiologicalNetworks provides an integrated environment to work with genomic sequences and regulatory regions in context of biological pathways and gene regulatory networks. It provides extended functionalities for searching regulatory regions and other sequences and comparative genomics analysis.
  • 3D protein structure Analysis
    BiologicalNetworks provides an integrated environment to work with 3D protein structure data in context of biological pathways and gene regulatory networks.
  • SQL-like querying language
    The system is equipped with novel query engine with built in SQL-like querying language, allowing paths, trees, graphs operations.

This tutorial will guide the users through BiologicalNetworks by introducing various features and functions in greater details.

Chapter 2 describes how to download and install BiologicalNetworks. The existing BiologicalNetworks users may skip to Chapter 3 directly.

Chapter 3 summarizes the accessibility of multiple features included in BiologicalNetworks.

Chapter 4 highlights all details with regards to the GUI and introduces users to various functionality of BiologicalNetworks.

In Chapter 5 biologically relevant examples are presented, which provides step-by-step guide to construction of models using BiologicalNetworks.

Chapter 6 explains Data Management of BiologicalNetworks.

Chapter 7 then provides more detail on working with Microarray data.

Finally, Chapter 8 demonstrates how to work with Gene interactions and relationships.

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