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Related Concept Videos

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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...
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TACITuS: transcriptomic data collector, integrator, and selector on big data platform.

Salvatore Alaimo1, Antonio Di Maria2,3, Dennis Shasha4

  • 1Department of Clinical and Experimental Medicine, University of Catania, c/o Dipartimento di Matematica e Informatica, Viale A. Doria 6, Catania, 95125, Italy. alaimos@dmi.unict.it.

BMC Bioinformatics
|November 24, 2019
PubMed
Summary
This summary is machine-generated.

TACITuS provides a web-based system for easy access to large microarray and next-generation sequencing (NGS) data repositories. It automates data pre-processing and allows seamless import into Galaxy for user-friendly analysis.

Keywords:
Cloud storage and managementGalaxyRNA-Seq

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Public repositories like ArrayExpress and NCBI GEO contain vast amounts of microarray and RNA-seq data.
  • Accessing and manipulating this data is challenging due to large file sizes and specialized tools.
  • Inefficient data handling hinders downstream analysis of high-throughput biological data.

Purpose of the Study:

  • To develop a system for efficient querying and data extraction from public high-throughput repositories.
  • To streamline the pre-processing of microarray and next-generation sequencing (NGS) data.
  • To facilitate the integration of repository data into analysis platforms like Galaxy.

Main Methods:

  • Developed TACITuS, a web-based system with modules for managing large data files.
  • Implemented cloud storage solutions for efficient data handling.
  • Integrated data subset extraction and import functionality for analysis pipelines.

Main Results:

  • TACITuS enables rapid query access to microarray and NGS data repositories.
  • The system efficiently manages large files, extracts data subsets, and supports cloud storage.
  • Data can be seamlessly imported into the Galaxy environment for further analysis.

Conclusions:

  • TACITuS automates critical pre-processing steps for high-throughput data analysis.
  • The system simplifies the management and extraction of data from large public repositories.
  • TACITuS enhances usability by integrating with the Galaxy platform for a user-friendly analytical experience.