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InterMine
InterMine is an open source data warehouse system, licensed under the LGPL 2.1. InterMine is used to create databases of biological data accessed by sophisticated web query tools. InterMine can be used to create databases from a single data set or can integrate multiple sources of data. Support is provided for several common biological formats and there is a framework for adding other data. InterMine includes a user-friendly web interface that works 'out of the box' and can be easily customised. InterMine makes it easy to integrate multiple data sources into a single data warehouse. It has a core data model based on the sequence ontology and supports several biological data formats, allowing sysadmins to configure which organisms or data files are required. It is easy to extend the data model and integrate other data, with a web service API, clients in seven different languages, and an XML format to help import custom data. As an active open source project, InterMine maintains d ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Generic Model Organism Database
The Generic Model Organism Database (GMOD) project provides biological research communities with a toolkit of open-source software components for visualizing, annotating, managing, and storing biological data. The GMOD project is funded by the United States National Institutes of Health, National Science Foundation and the USDA Agricultural Research Service. History The GMOD project was started in the early 2000s as a collaboration between several model organism databases (MODs) who shared a need to create similar software tools for processing data from sequencing projects. MODs, or organism-specific databases, describe genome and other information about important experimental organisms in the life sciences and capture the large volumes of data and information being generated by modern biology. Rather than each group designing their own software, four major MODs--FlyBase, Saccharomyces Genome Database, Mouse Genome Database, and WormBase—worked together to create applications ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Structure Initiative
The Protein Structure Initiative (PSI) was a USA based project that aimed at accelerating discovery in structural genomics and contribute to understanding biological function. Funded by the U.S. National Institute of General Medical Sciences (NIGMS) between 2000 and 2015, its aim was to reduce the cost and time required to determine three-dimensional protein structures and to develop techniques for solving challenging problems in structural biology, including membrane proteins. Over a dozen research centers have been supported by the PSI for work in building and maintaining high-throughput structural genomics pipelines, developing computational protein structure prediction methods, organizing and disseminating information generated by the PSI, and applying high-throughput structure determination to study a broad range of important biological and biomedical problems. The project has been organized into three separate phases. The first phase of the Protein Structure Initiative (PSI- ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Genetics In The United Kingdom
Genetics is the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) It is an important branch in biology because heredity is vital to organisms' evolution. Gregor Mendel, a Moravian Augustinian friar working in the 19th century in Brno, was the first to study genetics scientifically. Mendel studied "trait inheritance", patterns in the way traits are handed down from parents to offspring over time. He observed that organisms (pea plants) inherit traits by way of discrete "units of inheritance". This term, still used today, is a somewhat ambiguous definition of what is referred to as a gene. Trait inheritance and molecular inheritance mechanisms of genes are still primary principles of genetics in the 21st century, but modern genetics has expanded to study the function and behavior of genes. Gene structure and function, variation, and distribution are studied within the context of the cell, the organism (e.g. dominance), and within the context ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Data Warehousing Products
In the pursuit of knowledge, data (; ) is a collection of discrete values that convey information, describing quantity, quality, fact, statistics, other basic units of meaning, or simply sequences of symbols that may be further interpreted. A datum is an individual value in a collection of data. Data is usually organized into structures such as tables that provide additional context and meaning, and which may themselves be used as data in larger structures. Data may be used as variables in a computational process. Data may represent abstract ideas or concrete measurements. Data is commonly used in scientific research, economics, and in virtually every other form of human organizational activity. Examples of data sets include price indices (such as consumer price index), unemployment rates, literacy rates, and census data. In this context, data represents the raw facts and figures which can be used in such a manner in order to capture the useful information out of it. Dat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Biological Databases
Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics. Information contained in biological databases includes gene function, structure, localization (both cellular and chromosomal), clinical effects of mutations as well as similarities of biological sequences and structures. Biological databases can be classified by the kind of data they collect (see below). Broadly, there are molecular databases (for sequences, molecules, etc.), functional databases (for physiology, enzyme activities, phenotypes, ecology etc), taxonomic databases (for species and other taxonomic ranks), images and other media, or specimens (for museum collections etc.) Databases are important tools in assisting scientists to analyze and explain ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics Software
The list of bioinformatics software tools can be split up according to the license used: *List of proprietary bioinformatics software *List of open-source bioinformatics software Alternatively, here is a categorization according to the respective bioinformatics subfield specialized on: *Sequence analysis software **List of sequence alignment software ** List of alignment visualization software **Alignment-free sequence analysis **De novo sequence assemblers **List of gene prediction software ** List of disorder prediction software ** List of Protein subcellular localization prediction tools **List of phylogenetics software **List of phylogenetic tree visualization software ** :Metagenomics_software *Structural biology software **List of molecular graphics systems **List of protein-ligand docking software **List of RNA structure prediction software **List of software for protein model error verification **List of protein secondary structure prediction programs **List of protein struct ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ensembl
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. Similar databases and browsers are found at NCBI and the University of California, Santa Cruz (UCSC). History The human genome consists of three billion base pairs, which code for approximately 20,000–25,000 genes. However the genome alone is of little use, unless the locations and relationships of individual genes can be identified. One option is manual annotation, whereby a team of scientists tries to locate genes using experimental data from scientific journals and public databases. However this is a slow, painstaking task. The alternative, known as automated annotation, is to use the power of computers ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gene Ontology
The Gene Ontology (GO) is a major bioinformatics initiative to unify the representation of gene and gene product attributes across all species. More specifically, the project aims to: 1) maintain and develop its controlled vocabulary of gene and gene product attributes; 2) annotate genes and gene products, and assimilate and disseminate annotation data; and 3) provide tools for easy access to all aspects of the data provided by the project, and to enable functional interpretation of experimental data using the GO, for example via enrichment analysis. GO is part of a larger classification effort, the Open Biomedical Ontologies, being one of the Initial Candidate Members of the OBO Foundry. Whereas gene nomenclature focuses on gene and gene products, the Gene Ontology focuses on the function of the genes and gene products. The GO also extends the effort by using markup language to make the data (not only of the genes and their products but also of curated attributes) machine read ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
UniProt
UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. It is maintained by the UniProt consortium, which consists of several European bioinformatics organisations and a foundation from Washington, DC, United States. The UniProt consortium The UniProt consortium comprises the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB), and the Protein Information Resource (PIR). EBI, located at the Wellcome Trust Genome Campus in Hinxton, UK, hosts a large resource of bioinformatics databases and services. SIB, located in Geneva, Switzerland, maintains the ExPASy (Expert Protein Analysis System) servers that are a central resource for proteomics tools and databases. PIR, hosted by the National Biomedical Research Foundation (NBRF) at the Geor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Open-source License
An open-source license is a type of license for computer software and other products that allows the source code, blueprint or design to be used, modified and/or shared under defined terms and conditions. This allows end users and commercial companies to review and modify the source code, blueprint or design for their own customization, curiosity or troubleshooting needs. Open-source licensed software is mostly available free of charge, though this does not necessarily have to be the case. Licenses which only permit non-commercial redistribution or modification of the source code for personal use only are generally not considered as open-source licenses. However, open-source licenses may have some restrictions, particularly regarding the expression of respect to the origin of software, such as a requirement to preserve the name of the authors and a copyright statement within the code, or a requirement to redistribute the licensed software only under the same license (as in a copy ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
