Ensembl genome database project is a scientific project at the European Bioinformatics Institute, which provides a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other vertebrates and model organisms. Ensembl is one of several well known genome browsers for the retrieval of genomic information.
The Rat Genome Database (RGD) is a database of rat genomics, genetics, physiology and functional data, as well as data for comparative genomics between rat, human and mouse. RGD is responsible for attaching biological information to the rat genome via structured vocabulary, or ontology, annotations assigned to genes and quantitative trait loci (QTL), and for consolidating rat strain data and making it available to the research community. They are also developing a suite of tools for mining and analyzing genomic, physiologic and functional data for the rat, and comparative data for rat, mouse, human, and five other species.
Metabolic network modelling, also known as metabolic network reconstruction or metabolic pathway analysis, allows for an in-depth insight into the molecular mechanisms of a particular organism. In particular, these models correlate the genome with molecular physiology. A reconstruction breaks down metabolic pathways into their respective reactions and enzymes, and analyzes them within the perspective of the entire network. In simplified terms, a reconstruction collects all of the relevant metabolic information of an organism and compiles it in a mathematical model. Validation and analysis of reconstructions can allow identification of key features of metabolism such as growth yield, resource distribution, network robustness, and gene essentiality. This knowledge can then be applied to create novel biotechnology.
The completion of the human genome sequencing in the early 2000s was a turning point in genomics research. Scientists have conducted series of research into the activities of genes and the genome as a whole. The human genome contains around 3 billion base pairs nucleotide, and the huge quantity of data created necessitates the development of an accessible tool to explore and interpret this information in order to investigate the genetic basis of disease, evolution, and biological processes. The field of genomics has continued to grow, with new sequencing technologies and computational tool making it easier to study the genome.
GenePattern is a freely available computational biology open-source software package originally created and developed at the Broad Institute for the analysis of genomic data. Designed to enable researchers to develop, capture, and reproduce genomic analysis methodologies, GenePattern was first released in 2004. GenePattern is currently developed at the University of California, San Diego.
GenMAPP is a free, open-source bioinformatics software tool designed to visualize and analyze genomic data in the context of pathways, connecting gene-level datasets to biological processes and disease. First created in 2000, GenMAPP is developed by an open-source team based in an academic research laboratory. GenMAPP maintains databases of gene identifiers and collections of pathway maps in addition to visualization and analysis tools. Together with other public resources, GenMAPP aims to provide the research community with tools to gain insight into biology through the integration of data types ranging from genes to proteins to pathways to disease.
Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming or systems administration experience. Although it was initially developed for genomics research, it is largely domain agnostic and is now used as a general bioinformatics workflow management system.
MicrobesOnline is a publicly and freely accessible website that hosts multiple comparative genomic tools for comparing microbial species at the genomic, transcriptomic and functional levels. MicrobesOnline was developed by the Virtual Institute for Microbial Stress and Survival, which is based at the Lawrence Berkeley National Laboratory in Berkeley, California. The site was launched in 2005, with regular updates until 2011.
The UCSC Genome Browser is an online and downloadable genome browser hosted by the University of California, Santa Cruz (UCSC). It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. The Browser is a graphical viewer optimized to support fast interactive performance and is an open-source, web-based tool suite built on top of a MySQL database for rapid visualization, examination, and querying of the data at many levels. The Genome Browser Database, browsing tools, downloadable data files, and documentation can all be found on the UCSC Genome Bioinformatics website.
FAIRE-Seq is a method in molecular biology used for determining the sequences of DNA regions in the genome associated with regulatory activity. The technique was developed in the laboratory of Jason D. Lieb at the University of North Carolina, Chapel Hill. In contrast to DNase-Seq, the FAIRE-Seq protocol doesn't require the permeabilization of cells or isolation of nuclei, and can analyse any cell type. In a study of seven diverse human cell types, DNase-seq and FAIRE-seq produced strong cross-validation, with each cell type having 1-2% of the human genome as open chromatin.
BioMart is a community-driven project to provide a single point of access to distributed research data. The BioMart project contributes open source software and data services to the international scientific community. Although the BioMart software is primarily used by the biomedical research community, it is designed in such a way that any type of data can be incorporated into the BioMart framework. The BioMart project originated at the European Bioinformatics Institute as a data management solution for the Human Genome Project. Since then, BioMart has grown to become a multi-institute collaboration involving various database projects on five continents.
In silico PCR refers to computational tools used to calculate theoretical polymerase chain reaction (PCR) results using a given set of primers (probes) to amplify DNA sequences from a sequenced genome or transcriptome.
A bioinformatics workflow management system is a specialized form of workflow management system designed specifically to compose and execute a series of computational or data manipulation steps, or a workflow, that relate to bioinformatics.
geWorkbench is an open-source software platform for integrated genomic data analysis. It is a desktop application written in the programming language Java. geWorkbench uses a component architecture. As of 2016, there are more than 70 plug-ins available, providing for the visualization and analysis of gene expression, sequence, and structure data.
MG-RAST is an open-source web application server that suggests automatic phylogenetic and functional analysis of metagenomes. It is also one of the biggest repositories for metagenomic data. The name is an abbreviation of Metagenomic Rapid Annotations using Subsystems Technology. The pipeline automatically produces functional assignments to the sequences that belong to the metagenome by performing sequence comparisons to databases in both nucleotide and amino-acid levels. The applications supply phylogenetic and functional assignments of the metagenome being analysed, as well as tools for comparing different metagenomes. It also provides a RESTful API for programmatic access.
Gene set enrichment analysis (GSEA) (also called functional enrichment analysis or pathway enrichment analysis) is a method to identify classes of genes or proteins that are over-represented in a large set of genes or proteins, and may have an association with different phenotypes (e.g. different organism growth patterns or diseases). The method uses statistical approaches to identify significantly enriched or depleted groups of genes. Transcriptomics technologies and proteomics results often identify thousands of genes, which are used for the analysis.
DisGeNET is a discovery platform designed to address a variety of questions concerning the genetic underpinning of human diseases. DisGeNET is one of the largest and comprehensive repositories of human gene-disease associations (GDAs) currently available. It also offers a set of bioinformatic tools to facilitate the analysis of these data by different user profiles. It is maintained by the Integrative Biomedical Informatics (IBI) Group, of the (GRIB)-IMIM/UPF, based at the Barcelona Biomedical Research Park (PRBB), Barcelona, Spain.
Metascape is a free gene annotation and analysis resource that helps biologists make sense of one or multiple gene lists. Metascape provides automated meta-analysis tools to understand either common or unique pathways and protein networks within a group of orthogonal target-discovery studies.
