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Found 23 result(s)

ExPASy Bioinformatics Resource Portal

SIB Bioinformatics Resource Portal

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Swiss Institute of Bioinformatics (SIB) coordinates research and education in bioinformatics throughout Switzerland and provides bioinformatics services to the national and international research community. ExPASy gives access to numerous repositories and databases of SIB. For example: array map, MetaNetX, SWISS-MODEL and World-2DPAGE, and many others see a list here http://www.expasy.org/resources

RAMEDIS

Rare Metabolic Diseases Database

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The RAMEDIS system is a platform independent, web-based information system for rare metabolic diseases based on filed case reports. It was developed in close cooperation with clinical partners to allow them to collect information on rare metabolic diseases with extensive details, e.g. about occurring symptoms, laboratory findings, therapy and molecular data.

GESDB

Genetic Epidemiology Simulation Database

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

NCBI Gene

Gene

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The Gene database provides detailed information for known and predicted genes defined by nucleotide sequence or map position. Gene supplies gene-specific connections in the nexus of map, sequence, expression, structure, function, citation, and homology data. Unique identifiers are assigned to genes with defining sequences, genes with known map positions, and genes inferred from phenotypic information. These gene identifiers are used throughout NCBI's databases and tracked through updates of annotation. Gene includes genomes represented by NCBI Reference Sequences (or RefSeqs) and is integrated for indexing and query and retrieval from NCBI's Entrez and E-Utilities systems.

NCBI Datasets

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NCBI Datasets is a continually evolving platform designed to provide easy and intuitive access to NCBI’s sequence data and metadata. NCBI Datasets is part of the NIH Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analyses for all eukaryotic organisms through an NCBI Toolkit and community collaboration.

AceView

AceView genes

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AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals’ transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated.

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.

ORegAnno

Open regulatory annotation database

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<<<!!!<<< 2017-06-02: We recently suffered a server failure and are working to bring the full ORegAnno website back online. In the meantime, you may download the complete database here: http://www.oreganno.org/dump/ ; Data are also available through UCSC Genome Browser (e.g., hg38 -> Regulation -> ORegAnno) https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=686342163_2it3aVMQVoXWn0wuCjkNOVX39wxy&c=chr1&g=oreganno >>>!!!>>> The Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. Annotation is collected from users worldwide for various biological assays and is automatically cross-referenced against PubMED, Entrez Gene, EnsEMBL, dbSNP, the eVOC: Cell type ontology, and the Taxonomy database, where appropriate, with information regarding the original experimentation performed (evidence). ORegAnno further provides an open validation process for all regulatory annotation in the public domain. Assigned validators receive notification of new records in the database and are able to cross-reference the citation to ensure record integrity. Validators have the ability to modify any record (deprecating the old record and creating a new one) if an error is found. Further, any contributor to the database can comment on any annotation by marking errors, or adding special reports into function as they see fit. These features of ORegAnno ensure that the collection is of the highest quality and uniquely provides a dynamic view of our changing understanding of gene regulation in the various genomes.

studyforrest

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This project is an open invitation to anyone and everyone to participate in a decentralized effort to explore the opportunities of open science in neuroimaging. We aim to document how much (scientific) value can be generated from a data release — from the publication of scientific findings derived from this dataset, algorithms and methods evaluated on this dataset, and/or extensions of this dataset by acquisition and incorporation of new data. The project involves the processing of acoustic stimuli. In this study, the scientists have demonstrated an audiodescription of classic "Forrest Gump" to subjects, while researchers using functional magnetic resonance imaging (fMRI) have captured the brain activity of test candidates in the processing of language, music, emotions, memories and pictorial representations.In collaboration with various labs in Magdeburg we acquired and published what is probably the most comprehensive sample of brain activation patterns of natural language processing. Volunteers listened to a two-hour audio movie version of the Hollywood feature film "Forrest Gump" in a 7T MRI scanner. High-resolution brain activation patterns and physiological measurements were recorded continuously. These data have been placed into the public domain, and are freely available to the scientific community and the general public.

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/

GenomeRNAi

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GenomeRNAi is a database containing phenotypes from RNA interference (RNAi) screens in Drosophila and Homo sapiens. In addition, the database provides an updated resource of RNAi reagents and their predicted quality.

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.

Follicular Lymphoma Genome Data at Canada's Michael Smith Genome Sciences Centre (BCGSC)

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<<<!!!<<< Genome data generated by BC Genome Sciences Centre is no longer available through this site as it is regularly deposited into controlled data repositories such as the European Genome Phenome Archive (EGA); ICGC (International Cancer Genome Consortium) and the Genome Data Commons (GDC) >>>!!!>>> Mapping, copy number analysis, sequence and gene expression data generated by the High Resolution Analysis of Follicular Lymphoma Genomes project. The data will be available for 24 patients with follicular lymphoma. All data will be made as widely and freely available as possible while safeguarding the privacy of participants, and protecting confidential and proprietary data.The data from this project will be submitted to public genomic data sources. These sources will be listed on this web site as the data becomes available in these external data sources.

Open PHACTS

Open Pharmacological Space

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<<<!!!<<< The Open PHACTS Linked Data API and associated infrastructure was closed down in March 2019 to allow the team to focus on the next phase. http://www.openphactsfoundation.org/open-phacts-platform-update-march-2019/ >>>!!!>>>

ClinicalCodes.org

ClinicalCodes repository

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The ClinicalCodes repository aims to hold code lists for all published electronic medical record studies, irrespective of code type (e.g. Read, ICD9-10, SNOMED) and database (CPRD, QResearch, THIN etc.). Once deposited, code lists will be freely available, with no login needed to download codes.

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.

PhysioBank Archive

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PhysioBank is a large and growing archive of well-characterized digital recordings of physiologic signals and related data for use by the biomedical research community.

EUROCAT

European Surveillance of Congenital Anomalies

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A European network of population-based registries for the epidemiologic surveillance of congenital anomalies.

University Hospital Medical Information Network Individual Case Data Repository

UMIN-CTR

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The UMIN case data repository system was implemented by adding a function to the UMIN Clinical Trials Registry System. The aim of this system is to keep anonymized case data from clinical research conducted by individual researchers at the UMIN center, and to guarantee the content of the data to third parties. This system enables other researchers to inspect case data or to repeat statistical analyses

European Zebrafish Resource Center

EZRC

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The EZRC at KIT houses the largest experimental fish facility in Europe with a capacity of more than 300,000 fish. Zebrafish stocks are maintained mostly as frozen sperm. Frequently requested lines are also kept alive as well as a selection of wildtype strains. Several thousand mutations in protein coding genes generated by TILLING in the Stemple lab of the Sanger Centre, Hinxton, UK and lines generated by ENU mutagenesis by the Nüsslein-Volhard lab in addition to transgenic lines and mutants generated by KIT groups or brought in through collaborations. We also accept submissions on an individual basis and ship fish upon request to PIs in Europe and elsewhere. EZRC also provides screening services and technologies such as imaging and high-throughput sequencing. Key areas include automation of embryo handling and automated image acquisition and processing. Our platform also involves the development of novel microscopy techniques (e.g. SPIM, DSLM, robotic macroscope) to permit high-resolution, real-time imaging in 4D. By association with the ComPlat platform, we can support also chemical screens and offer libraries with up to 20,000 compounds in total for external users. As another service to the community the EZRC provides plasmids (cDNAs, transgenes, Talen, Crispr/cas9) maintained by the Helmholtz repository of Bioparts (HERBI) to the scientific community. In addition the fish facility keeps a range of medaka stocks, maintained by the Loosli group.

Biomedical Informatics Research Network

BIRN

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>>>!!!<<< As stated 2017-05-16 The BIRN project was finished a few years ago. The web portal is no longer live.>>>!!!<<< BIRN is a national initiative to advance biomedical research through data sharing and online collaboration. It supports multi-site, and/or multi-institutional, teams by enabling researchers to share significant quantities of data across geographic distance and/or incompatible computing systems. BIRN offers a library of data-sharing software tools specific to biomedical research, best practice references, expert advice and other resources.

PATRIC

Pathosystems Resource Integration Center

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<<<!!!<<< This repository is no longer available. >>>!!!>>> PATRIC will go offline by mid-December2022. Here is what you need to know. As announced previously, PATRIC, the bacterial BRC, and IRD / ViPR, the viral BRCs, are being merged into the new Bacterial and Viral Bioinformatics Resource Center (BV-BRC). BV-BRC combines the data, tools, and technologies from these BRCs to provide an integrated resource for bacterial and viral genomics-based infectious disease research.

ALEXA

ALEXA-A

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ALEXA is a microarray design platform for 'alternative expression analysis'. This platform facilitates the design of expression arrays for analysis of mRNA isoforms generated from a single locus by the use of alternative transcription initiation, splicing and polyadenylation sites. We use the term 'ALEXA' to describe a collection of novel genomic methods for 'alternative expression' analysis. 'Alternative expression' refers to the identification and quantification of alternative mRNA transcripts produced by alternative transcript initiation, alternative splicing and alternative polyadenylation. This website provides supplementary materials, source code and other downloads for recent publications describing our studies of alternative expression (AE). Most recently we have developed a method, 'ALEXA-Seq' and associated resources for alternative expression analysis by massively parallel RNA sequencing.