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Found 33 result(s)

INTREPID bioinformatics

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!!! >>> intrepidbio.com expired <<< !!!! Intrepid Bioinformatics serves as a community for genetic researchers and scientific programmers who need to achieve meaningful use of their genetic research data – but can’t spend tremendous amounts of time or money in the process. The Intrepid Bioinformatics system automates time consuming manual processes, shortens workflow, and eliminates the threat of lost data in a faster, cheaper, and better environment than existing solutions. The system also provides the functionality and community features needed to analyze the large volumes of Next Generation Sequencing and Single Nucleotide Polymorphism data, which is generated for a wide range of purposes from disease tracking and animal breeding to medical diagnosis and treatment.

Avibase

the world bird database

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Avibase is an extensive database information system about all birds of the world, containing over 60 million records about 10,000 species and 22,000 subspecies of birds, including distribution information, taxonomy, synonyms in several languages and more. This site is managed by Denis Lepage and hosted by Bird Studies Canada, the Canadian copartner of Birdlife International. Avibase has been a work in progress since 1992 and I am now pleased to offer it as a service to the bird-watching and scientific community.

The Monarch Initiative

Monarch Initiative

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As with most biomedical databases, the first step is to identify relevant data from the research community. The Monarch Initiative is focused primarily on phenotype-related resources. We bring in data associated with those phenotypes so that our users can begin to make connections among other biological entities of interest. We import data from a variety of data sources. With many resources integrated into a single database, we can join across the various data sources to produce integrated views. We have started with the big players including ClinVar and OMIM, but are equally interested in boutique databases. You can learn more about the sources of data that populate our system from our data sources page https://monarchinitiative.org/about/sources.

Human protein-protein interaction network database search

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<<<!!!<<< This repository is no longer available. >>>!!!>>> A human interactome map. The sequencing of the human genome has provided a surprisingly small number of genes, indicating that the complex organization of life is not reflected in the gene number but, rather, in the gene products – that is, in the proteins. These macromolecules regulate the vast majority of cellular processes by their ability to communicate with each other and to assemble into larger functional units. Therefore, the systematic analysis of protein-protein interactions is fundamental for the understanding of protein function, cellular processes and, ultimately, the complexity of life. Moreover, interactome maps are particularly needed to link new proteins to disease pathways and the identification of novel drug targets.

Natural History Museum, Data Portal

Explore and download the Natural History Museum’s research and collections data

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The Museum is committed to open access and open science, and has launched the Data Portal to make its research and collections datasets available online. It allows anyone to explore, download and reuse the data for their own research. Our natural history collection is one of the most important in the world, documenting 4.5 billion years of life, the Earth and the solar system. Almost all animal, plant, mineral and fossil groups are represented. These datasets will increase exponentially. Under the Museum's ambitious digital collections programme we aim to have 20 million specimens digitised in the next five years.

SilkDB 3.0

Silkworm Genome Database

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SilkDB is a database of the integrated genome resource for the silkworm, Bombyx mori. This database provides access to not only genomic data including functional annotation of genes, gene products and chromosomal mapping, but also extensive biological information such as microarray expression data, ESTs and corresponding references. SilkDB will be useful for the silkworm research community as well as comparative genomics

GeneCards

The Human Gene Database

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GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. It automatically integrates gene-centric data from ~125 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information.

GENCODE

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GENCODE is a scientific project in genome research and part of the ENCODE (ENCyclopedia Of DNA Elements) scale-up project. The GENCODE consortium was initially formed as part of the pilot phase of the ENCODE project to identify and map all protein-coding genes within the ENCODE regions (approx. 1% of Human genome). Given the initial success of the project, GENCODE now aims to build an “Encyclopedia of genes and genes variants” by identifying all gene features in the human and mouse genome using a combination of computational analysis, manual annotation, and experimental validation, and annotating all evidence-based gene features in the entire human genome at a high accuracy.

Project Achilles

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Project Achilles is a systematic effort aimed at identifying and cataloging genetic vulnerabilities across hundreds of genomically characterized cancer cell lines. The project uses genome-wide genetic perturbation reagents (shRNAs or Cas9/sgRNAs) to silence or knock-out individual genes and identify those genes that affect cell survival. Large-scale functional screening of cancer cell lines provides a complementary approach to those studies that aim to characterize the molecular alterations (e.g. mutations, copy number alterations) of primary tumors, such as The Cancer Genome Atlas (TCGA). The overall goal of the project is to identify cancer genetic dependencies and link them to molecular characteristics in order to prioritize targets for therapeutic development and identify the patient population that might benefit from such targets. Project Achilles data is hosted on the Cancer Dependency Map Portal (DepMap) where it has been harmonized with our genomics and cellular models data. You can access the latest and all past datasets here: https://depmap.org/portal/download/all/

Fungal Mitochondrial Genome Project

FMGP

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The goals of FMGP are to: (i) sequence complete mitochondrial genomes from all major fungal lineages, (ii) infer a robust fungal phylogeny, (iii) define the origin of the fungi, their protistan ancestors, and their specific phylogenetic link to the animals, (iv) investigate mitochondrial gene expression, introns, RNAse P RNA structures, mobile elements.

UCSD Signaling gateway

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<<<!!!<<< This repository is no longer available. >>>!!!>>>

National Marine Mammal Data Portal

NMMDB

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The Australian Marine Mammal Centre has developed database applications to support marine mammal conservation and policy initiatives.

Animal Genome Size Database

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Welcome to the Animal Genome Size Database, Release 2.0, a comprehensive catalogue of animal genome size data.

Harvard Medical School, Library of Integrated Network-Based Cellular Signatures Database

HMS, LINCS database

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The Database contains all publicly available HMS LINCS datasets and information for each dataset about experimental reagents (small molecule perturbagens, cells, antibodies, and proteins) and experimental and data analysis protocols.

German Federation for Biological Data

GFBio

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The project brings together national key players providing environmentally related biological data and services to develop the ‘German Federation for Biological Data' (GFBio). The overall goal is to provide a sustainable, service oriented, national data infrastructure facilitating data sharing and stimulating data intensive science in the fields of biological and environmental research.

Human Intermediate Filament Database

HIFD

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The Intermediate Filament Database will function as a continuously updated review of the intermediate filament field and it is hoped that users will contribute to the development and expansion of the database on a regular basis. Contributions may include novel variants, new patients with previously discovered sequence and allelic variants. Suggestions on ways to improve the database are also welcome.

PlasmoDB

Plasmodium Genomics Resource

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PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria.

Cancer Cell Line Encyclopedia

CCLE

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The Cancer Cell Line Encyclopedia project is a collaboration between the Broad Institute, and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE provides public access to genomic data, analysis and visualization for about 1000 cell lines.

LifeMap Discovery

Embryonic development & stem cell Compendium

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LifeMap Discovery® is a compendium of embryonic development for stem cell research and regenerative medicine, constructed by integrating extensive molecular, cellular, anatomical and medical data curated from scientific literature and high-throughput data sources.

Australian Drosophila Ecology and Evolution Resource

ADEER

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The Australian Drosophila Ecology and Evolution Resource (ADEER) from the Hoffmann lab and other contributors is a nationally significant life science collection. The Drosophila Clinal Data Collection contains data on populations along the eastern coast of Australia. It remains an excellent resource for understanding past and future evolutionary responses to climate change. The Drosophila Genomic Data Collection hosts Drosophila genomes sequenced as part of the Genomic Basis for Adaptation to Climate Change Project. 23 genomes have been sequenced as part of this project. Currently assemblies and annotations are available for Drosophila birchii, D. bunnanda, D. hydei, and D. repleta. The Drosophila Species Distribution Data Collection contains distribution data of nine drosophilid species that have been collected in Australia by the Hoffmann lab and other research groups between 1924 and 2005. More than 300 drosophilid species have been identified in the tropical and temperate forests located on the east coast of Australia. Many species are restricted to the tropics, a few are temperate specialists, and some have broad distributions across climatic regions. Their varied distribution along the tropical - temperate cline provide a powerful tool for studying climate adaptation and species distribution limits.

Drosophila Genetic Reference Panel 2

DGRP2

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The Drosophila Genetic Reference Panel (DGRP) is a population consisting of more than 200 inbred lines derived from the Raleigh, USA population. The DGRP is a living library of common polymorphisms affecting complex traits, and a community resource for whole genome association mapping of quantitative trait loci.

DEPOD

DEPhOsphorylation Database

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DEPOD - the human DEPhOsphorylation Database (version 1.1) is a manually curated database collecting human active phosphatases, their experimentally verified protein and non-protein substrates and dephosphorylation site information, and pathways in which they are involved. It also provides links to popular kinase databases and protein-protein interaction databases for these phosphatases and substrates. DEPOD aims to be a valuable resource for studying human phosphatases and their substrate specificities and molecular mechanisms; phosphatase-targeted drug discovery and development; connecting phosphatases with kinases through their common substrates; completing the human phosphorylation/dephosphorylation network.

Pain Genes Database

PainGenesdb

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<<<!!!<<< The data are no longer accessible. Message: Adobe Flash Player is no longer supported >>>!!!>>>

FlyCircuit

A Database of Drosophila Brain Neurons

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FlyCircuit is a public database for online archiving, cell type inventory, browsing, searching, analysis and 3D visualization of individual neurons in the Drosophila brain. The FlyCircuit Database currently contains about 30,000 high resolution 3D brain neural images of the drosophila fruit fly brain that are combined into a neural circuitry network that researchers can use as a blueprint to further explore how the brain of a fruit fly processes external sensory signals (i.e. how vision, hearing, and smell are transmitted to the central nerve system).

PhenoGen Informatics

PhenoGen

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The PhenoGen website shares experimental data with a worldwide community of investigators and provides a flexible, integrated, multi-resolution repository of neuroscience transcriptomic genetic data for collaborative research on genomic disorders. The main development focus is on providing Hybrid Rat Diversity Panel transcriptomic data (sequencing, genome coverage, reconstructed totalRNA/smallRNA transcriptomes, quanification of the transcriptome, eQTLs, and WGCNA) and integrating additional tools to provide platform for visualization and analysis of HRDP transcriptome data.