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Found 38 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.

GESDB

Genetic Epidemiology Simulation Database

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

Signature Bank

Banque Signature

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One of the world’s largest banks of biological, psychosocial and clinical data on people suffering from mental health problems. The Signature center systematically collects biological, psychosocial and clinical indicators from patients admitted to the psychiatric emergency and at four points throughout their journey in the hospital: upon arrival to the emergency room (state of crisis), at the end of their hospital stay, as well as at the beginning and the end of outpatient treatment. For all hospital clients who agree to participate, blood specimens are collected for the purpose of measuring metabolic, genetic, toxic and infectious biomarkers, while saliva samples are collected to measure sex hormones and hair samples are collected to measure stress hormones. Questionnaire has been selected to cover important dimensional aspects of mental illness such as Behaviour and Cognition (Psychosis, Depression, Anxiety, Impulsiveness, Aggression, Suicide, Addiction, Sleep),Socio-demographic Profile (Spiritual beliefs, Social functioning, Childhood experiences, Demographic, Family background) and Medical Data (Medication, Diagnosis, Long-term health, RAMQ data). On 2016, May there are more than 1150 participants and 400 for the longitudinal Follow-Up

Health and Retirement Study

HRS

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The Health and Retirement Study (HRS) is a longitudinal panel study that surveys a representative sample of more than 26,000 Americans over the age of 50 every two years. The study has collected information about income, work, assets, pension plans, health insurance, disability, physical health and functioning, cognitive functioning, genetic information and health care expenditures.

Cell Centered Database

CCDB

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>>> !!!!! The Cell Centered Database is no longer on serice. It has been merged with "Cell image library": https://www.re3data.org/repository/r3d100000023 !!!!! <<<<

Cancer GenomeAtlas Data Portal

Cancer Genome Atlas Data Portal

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The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The Data Coordinating Center (DCC) is the central provider of TCGA data. The DCC standardizes data formats and validates submitted data.

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/

Genomic Data Commons

GDC

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The NCI's Genomic Data Commons (GDC) provides the cancer research community with a unified data repository that enables data sharing across cancer genomic studies in support of precision medicine. The GDC obtains validated datasets from NCI programs in which the strategies for tissue collection couples quantity with high quality. Tools are provided to guide data submissions by researchers and institutions.

Viral Bioinformatics Resource Center

VBRC

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Databases of viral genomic information (genes, gene families, and genomes), and software to perform comparative genomics analyses

GeneCorner Plasmid Collection

BCCM/GeneCorner Plasmid Collection

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The BCCM/GeneCorner Plasmid Collection accepts plasmids from and distributes plasmids to researchers worldwide. Funding by the Belgian Science Policy (Belspo) allowed BCCM/GeneCorner to evolve into a unique plasmid repository in Europe.

Bacterial and Viral Bioinformatics Resource Center

BV-BRC

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The Bacterial and Viral Bioinformatics Resource Center (BV-BRC) is an information system designed to support research on bacterial and viral infectious diseases. BV-BRC combines two long-running BRCs: PATRIC, the bacterial system, and IRD/ViPR, the viral systems.

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.

Gemma

Tools and database for meta-analysis of functional genomics data

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Gemma is a database for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles. Gemma contains data from thousands of public studies, referencing thousands of published papers. Users can search, access and visualize co-expression and differential expression results.

NCBI dbGaP

DataBase of Genotypes And Phenotypes

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The NCBI database of Genotypes and Phenotypes archives and distributes the results of studies that have investigated the interaction of genotype and phenotype, including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits. The database provides summaries of studies, the contents of measured variables, and original study document text. dbGaP provides two types of access for users, open and controlled. Through the controlled access, users may access individual-level data such as phenotypic data tables and genotypes.

Future of Families and Child Wellbeing Study

FFCWS

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The Fragile Families and Child Wellbeing Study changed its name to The Future of Families and Child Wellbeing Study (FFCWS). Note that all documentation issued prior to January 2023 contains the study’s former name. Any further reference to FFCWS should kindly observe this name change. The Fragile Families & Child Wellbeing Study is following a cohort of nearly 5,000 children born in large U.S. cities between 1998 and 2000 (roughly three-quarters of whom were born to unmarried parents). We refer to unmarried parents and their children as “fragile families” to underscore that they are families and that they are at greater risk of breaking up and living in poverty than more traditional families. The core Study was originally designed to primarily address four questions of great interest to researchers and policy makers: (1) What are the conditions and capabilities of unmarried parents, especially fathers?; (2) What is the nature of the relationships between unmarried parents?; (3) How do children born into these families fare?; and (4) How do policies and environmental conditions affect families and children?

Fungal Genetics Stock Center

FGSC

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The Fungal Genetics Stock Center has preserved and distributed strains of genetically characterized fungi since 1960. The collection includes over 20,000 accessioned strains of classical and genetically engineered mutants of key model, human, and plant pathogenic fungi. These materials are distributed as living stocks to researchers around the world.

Cancer Genomics Hub

CGHub

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>>>>!!!!<<<< The Cancer Genomics Hub mission is now completed. The Cancer Genomics Hub was established in August 2011 to provide a repository to The Cancer Genome Atlas, the childhood cancer initiative Therapeutically Applicable Research to Generate Effective Treatments and the Cancer Genome Characterization Initiative. CGHub rapidly grew to be the largest database of cancer genomes in the world, storing more than 2.5 petabytes of data and serving downloads of nearly 3 petabytes per month. As the central repository for the foundational genome files, CGHub streamlined team science efforts as data became as easy to obtain as downloading from a hard drive. The convenient access to Big Data, and the collaborations that CGHub made possible, are now essential to cancer research. That work continues at the NCI's Genomic Data Commons. All files previously stored at CGHub can be found there. The Website for the Genomic Data Commons is here: https://gdc.nci.nih.gov/ >>>>!!!!<<<< The Cancer Genomics Hub (CGHub) is a secure repository for storing, cataloging, and accessing cancer genome sequences, alignments, and mutation information from the Cancer Genome Atlas (TCGA) consortium and related projects. Access to CGHub Data: All researchers using CGHub must meet the access and use criteria established by the National Institutes of Health (NIH) to ensure the privacy, security, and integrity of participant data. CGHub also hosts some publicly available data, in particular data from the Cancer Cell Line Encyclopedia. All metadata is publicly available and the catalog of metadata and associated BAMs can be explored using the CGHub Data Browser.

Cancer Genome Anatomy Project

CGAP

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>>>!!!<<< Noticed 26.08.2020: The NCI CBIIT instance of the CGAP no longer exist on this website. The Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer has a new home at the NCI-funded Institute for Systems Biology Cancer Genomics Cloud available at the following location: https://mitelmandatabase.isb-cgc.org >>>!!!<<<

Addgene

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Addgene archives and distributes plasmids for researchers around the globe. They are working with thousands of laboratories to assemble a high-quality library of published plasmids for use in research and discovery. By linking plasmids with articles, scientists can always find data related to the materials they request.

Data and Specimen Hub

DASH

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The Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) Data and Specimen Hub (DASH) is a centralized resource that allows researchers to share and access de-identified data from studies funded by NICHD. DASH also serves as a portal for requesting biospecimens from selected DASH studies.

HumanCyc

Encyclopedia of Human Genes and Metabolism

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HumanCyc provides an encyclopedic reference on human metabolic pathways. It provides a zoomable human metabolic map diagram, and it has been used to generate a steady-state quantitative model of human metabolism. 2016: Subscriptions are now required to access HumanCyc. For more information on obtaining a subscription, click here: http://www.phoenixbioinformatics.org/biocyc#product-biocyc-subscription

Stemformatics

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Stemformatics is a collaboration between the stem cell and bioinformatics community. We were motivated by the plethora of exciting cell models in the public and private domains, and the realisation that for many biologists these were mostly inaccessible. We wanted a fast way to find and visualise interesting genes in these exemplar stem cell datasets. We'd like you to explore. You'll find data from leading stem cell laboratories in a format that is easy to search, easy to visualise and easy to export.

Clinical Proteomic Tumor Analysis Consortium Data Portal

CPTAC Data Portal

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The CPTAC Data Portal is the centralized repository for the dissemination of proteomic data collected by the Proteome Characterization Centers (PCCs) for the CPTAC program. The portal also hosts analyses of the mass spectrometry data (mapping of spectra to peptide sequences and protein identification) from the PCCs and from a CPTAC-sponsored common data analysis pipeline (CDAP).

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.