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Related Concept Videos

Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
Statistical Software for Data Analysis and Clinical Trials01:12

Statistical Software for Data Analysis and Clinical Trials

Statistical software is pivotal in data analysis and clinical trials by providing tools to analyze data, draw conclusions, and make predictions. These software packages range from simple data management applications to complex analytical platforms, supporting various statistical tests, models, and simulation techniques. Their significance lies in their ability to handle vast amounts of data with precision and efficiency, enabling researchers to validate hypotheses, identify trends, and make...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Genetic Screens02:46

Genetic Screens

Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing  genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
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Genoviz Software Development Kit: Java tool kit for building genomics visualization applications.

Gregg A Helt1, John W Nicol, Ed Erwin

  • 1Genomancer Consulting, Healdsburg, CA 95448, USA. gregghelt@gmail.com

BMC Bioinformatics
|August 27, 2009
PubMed
Summary
This summary is machine-generated.

The Genoviz Software Development Kit (SDK) enables rapid creation of genomics visualization applications. This open-source framework facilitates discovery of patterns in genomic data.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Genomic data visualization is crucial for uncovering novel biological patterns.
  • Advanced visualization tools accelerate biological science research.

Purpose of the Study:

  • Introduce the Genoviz Software Development Kit (SDK) for genomics visualization.
  • Highlight the SDK's features for building dynamic and interactive genome browsers.

Main Methods:

  • Developed an open-source, Java-based framework (Genoviz SDK).
  • Incorporated adaptive, dynamic zooming capabilities.
  • Enabled automated layout of genomic features and user interaction with graphical elements (Glyphs).

Main Results:

  • The Genoviz SDK supports diverse graphical representations and adaptive semantic zooming.
  • Demonstration applications, including the Integrated Genome Browser, showcase the SDK's potential.
  • The framework allows easy integration with existing applications and third-party data models.

Conclusions:

  • The Genoviz SDK simplifies the development of custom genomics visualization tools.
  • Separation of graphics components and data models enhances flexibility for developers.
  • Source code, documentation, and tutorials are publicly available for the Genoviz SDK.