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on page 1 showing 20 out of 131 results from 1 sources

Cite this (Adaptive Poisson-Boltzmann Solver, RRID:SCR_008387)

URL: http://www.poissonboltzmann.org/apbs/

Resource Type: Resource, software resource

APBS is a software package for modeling biomolecular solvation through solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. APBS was designed to efficiently evaluate electrostatic properties for such simulations for a wide range of length scales to enable the investigation of molecules with tens to millions of atoms. It also provides implicit solvent models of nonpolar solvation which accurately account for both repulsive and attractive solute-solvent interactions. APBS uses FEtk (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FEtk is a portable collection of finite element modeling class libraries written in an object-oriented version of C. It is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods.

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Cite this (Aggrescan: The Hot Spot Finder, RRID:SCR_008403)

URL: http://bioinf.uab.es/aggrescan/

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

Web-based tool for identifying hot spots of aggregation in polypeptides. Aggrescan uses an aggregation-propensity scale for natural amino acids derived from in vivo experiments and on the assumption that short and specific sequence stretches modulate protein aggregation. The algorithm is shown to identify a series of protein fragments involved in the aggregation of disease-related proteins and to predict the effect of genetic mutations on their deposition propensities. It also provides new insights into the differential aggregation properties displayed by globular proteins, natively unfolded polypeptides, amyloidogenic proteins and proteins found in bacterial inclusion bodies.

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Cite this (Albinism database, RRID:SCR_000632)

URL: http://www.ifpcs.org/albinism/

Resource Type: Resource, data set, service resource, data repository, storage service resource, data or information resource

Database of mutations associated with all major known forms of oculocutaneous and ocular albinism. The Albinism Database is part of the Locus Specific Mutation Databases of the Human Genome Variation Society and accepts the submission of new mutations. A link is provided for submission of new mutations. Columns in the database include: type of albinism, human locus, omim link, link to table of mutations and polymorphisms, and map of mutation locations.

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Cite this (Allen Institute for Brain Science Sleep Study, RRID:SCR_002983)

URL: http://sleep.alleninstitute.org

Resource Type: Resource, data set, atlas, data or information resource

A comprehensive collection of gene expression data in the mouse brain for five different conditions of sleep and wakefulness. Generated in collaboration with SRI International, this unique dataset is intended to help sleep researchers advance understanding of sleep deprivation and the dynamic changes underlying sleep/wake cycles. A high-throughput colorimetric in situ hybridization platform has been used to generate cellular resolution expression data for over 200 genes. In addition, microarray data for seven brain regions from the same five experimental conditions are downloadable from the web site; and difference grids are available for viewing differences between conditions in 3-D using Brain Explorer. Sleep deprivation leads to a repertoire of cognitive, attentional and emotional deficits that are seriously detrimental in occupations requiring alertness. These deficits may be associated with changes in gene expression in specific regions of the brain. The Allen Institute is in the process of generating a collection of cellular resolution data for gene expression in the mouse brain in response to sleep deprivation and sleep state. Using the Allen Institute high throughput in situ hybridization platform, gene expression has been examined under five experimental conditions in mice in collaboration with SRI International, and the images are presented online as a resource for sleep researchers. Sleep conditions include: Sleep-deprived for 6 hours; Time of day control for sleep-deprivation; Recovery sleep (4 hours) following 6 hours of sleep deprivation; Time of day control for recovery sleep; and waking. Project data is available in the following formats: Colorimetric ISH and Nissl images for 224 genes across 5 conditions, some with replicates Microarray data for 7 brain regions across 5 conditions Difference grids for viewing differences between conditions in 3-D using Brain Explorer Microarray data is available for seven brain regions collected from five experimental conditions: sleep deprivation, recovery sleep, and three time-of-day controls. The brain regions include four regions associated with sleep-wake regulation or circadian rhythm: suprachiasmatic nucleus, locus coeruleus, tuberomammillary nucleus and lateral hypothalamus in the vicinity of the hypocretin neurons. In order to assess the effect of sleep deprivation on gene expression in regions potentially involved in mood, memory, or executive function, an additional three brain regions were analyzed by microarray: orbital cortex, cortical amygdala (posteromedial), and dorsal entorhinal cortex. 140 microarray files are available for download in text, Codelink, and Rosetta Resolver file formats. Difference Grids allow the user to navigate changes in gene expression for a given gene across two experimental conditions, such as sleep deprivation compared to its time of day control. Difference grids are available for genes which have been assayed in replicate by ISH.

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Cite this (Allen Institute Mouse Diversity Study, RRID:SCR_008009)

URL: http://mousediversity.alleninstitute.org/

Resource Type: Resource, atlas, expression atlas, data or information resource, database

A database, and associated atlas, that characterizes gene expression across genetic backgrounds and sex, expanding beyond the adult male C57BL/6J reference brain comprising the Allen Mouse Brain Atlas to include seven strains of male mice and female C57BL/6J mice. Gene expression was detected using colorimetric RNA in situ hybridization (ISH) that provides cellular level anatomic resolution. ISH data are searchable and organized by gene, strain, or sex.

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Cite this (Annozilla (Annotea on Mozilla), RRID:SCR_007549)

URL: http://annozilla.mozdev.org/

Resource Type: Resource, data set, data or information resource

The Annozilla project was designed to view and create annotations associated with a web page, as defined by the W3C Annotea project. Annotations are stored as RDF on a server, using XPointer (or at least XPointer-like constructs) to identify the region of the document being annotated. Additionally, the Annozilla source code is available. The intention of Annozilla is to use Mozilla''''s native facilities to manipulate annotation data - its built-in RDF handling to parse the annotations, and nsIXmlHttpRequest to submit data when creating annotations. To use Annozilla, you will need to install the packages, get set up with a user account with an annotation server (e.g., the W3C test server), and then you should be ready to start using the extension.

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Cite this (ApiDB CryptoDB, RRID:SCR_013455)

URL: http://cryptodb.org/cryptodb/

Resource Type: Resource, data or information resource, database

An integrated genomic and functional genomic database for the parasite Cryptosporidium. CryptoDB integrates whole genome sequence and annotation along with experimental data and environmental isolate sequences provided by community researchers. The database includes supplemental bioinformatics analyses and a web interface for data-mining. Organisms included in CryptoDB are Cryptosporidium parvum, Cryptosporidium hominis, Cryptosporidium muris and environmental isolate sequences from numerous species. CryptoDB is allied with the databases PlasmoDB and ToxoDB via ApiDB, an NIH/NIAID-funded Bioinformatics Resource Center. Tools include: * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Cryptosporidium Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * CryptoCyc: Explore Automatically Defined Metabolic Pathways * Searches via Web Services: Web service access to our data

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Cite this (Arabidopsis Reactome, RRID:SCR_002063)

URL: http://www.arabidopsisreactome.org

Resource Type: Resource, data or information resource, database

Curated database of core pathways and reactions in plant biology that covers biological pathways ranging from the basic processes of metabolism to high-level processes such as cell cycle regulation. While it is targeted at Arabidopsis pathways, it also includes many biological events from other plant species. This makes the database relevant to the large number of researchers who work on other plants. Arabidopsis Reactome currently contains both in-house curated pathways as well as imported pathways from AraCyc and KEGG databases. All the curated information is backed up by its provenance: either a literature citation or an electronic inference based on sequence similarity. Their ontology ensures that the various events are linked in an appropriate spatial and temporal context.

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    AraCyc

Cite this (AraCyc, RRID:SCR_008109)

URL: http://www.plantcyc.org

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Tool for visualizing biochemical pathways of Arabidopsis thaliana, the database contains a mix of information: extracted from peer-reviewed literature and computationally predicted. Users are strongly encouraged to share their pathway knowledge to help in the constant task of improving data content (see the Data Submission page). The manual curation of the database, which includes correcting pathways and adding missing pathways, is on-going. AraCyc is released on a semi-annual basis with a summary of the DataBase Content and PathoLogic Software Report with each release. The OMICS Viewer allows the overlay of data from gene expression, proteomic, or metabolomic experiments on a metabolic map. Other tools for mining the data in AraCyc are provided including the Comparative Analysis tool and an Advanced Query Page. Users can download the AraCyc database files from the Plant Metabolic Network website, by FTP, or programmatically.

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Cite this (Artificial Selected Proteins/Peptides Database, RRID:SCR_007557)

URL: http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/

Resource Type: Resource, data or information resource, database

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 04, 2014. Curated database on selected from randomized pools proteins and peptides designed for accumulation of experimental data on protein functionality obtained by in vitro directed evolution methods (phage display, ribosome display, SIP etc.) ASPD is integrated by means of hyperlinks with different databases (SWISS-PROT, PDB, PROSITE, etc). The database also contains modules for pairwise correlation analysis and BLAST search.

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Cite this (ATID: Alternative Translational Initiation Database, RRID:SCR_009432)

URL: http://bioinfo.au.tsinghua.edu.cn/atie/

Resource Type: Resource, data or information resource, database

A database of publicly available genes, alternatively translational isoforms and their detailed annotation. Alternative translational initiation is one of mechanisms to increase the complexity level of an organism by alternative gene expression pathways. The use of alternative translation initiation codons in a singe mRNA contributes to the generation of protein diversity. The genes produce two or more versions of the encoded proteins, and the shorter version, initiated from a downstream in-frame start codon, lacks the N-terminal amino acids fragment of the full-length isoform version. Since the first discovery of alternative translation initiation, a small, yet growing, number of mRNAs initiating translation from alternative start codons have been reported. Various studies began to emerge focusing on this new field in gene expression and revealed the biological significance of the use of alternative initiation. In response to the need for systematic studies on genes involving alternative translational initiation, Alternative Translational Initiation Database(ATID) is established to provide data of publicly available genes, alternatively translational isoforms and their detailed annotation.

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Cite this (Bacterial Genomes, RRID:SCR_008141)

URL: http://www.sanger.ac.uk/Projects/Microbes/

Resource Type: Resource, data analysis software, data processing software, database, software application, software resource, data or information resource

This website includes a list of projects that the Sanger Institute is currently working on or completed. All projects consist of the genomic sequencing of different bacteria. Each description of the bacteria includes its classification, a description, and the types of diseases that the bacteria is likely to cause. The Sanger Institute bacterial sequencing effort is concentrated on pathogens and model organisms. Data is accessible in a number of ways; for each organism there is a BLAST server, allowing users to search the sequences with their own query and retrieve the matching contigs. Sequences can also be downloaded directly by FTP. Data is accessible in a number of ways; for each organism there is a BLAST server, allowing you to search the sequences with your own query and retrieve the matching contigs. Sequences can also be downloaded directly by FTP. The primary sequence viewer and annotation tool, Artemis is available for download. This is a portable Java program which is used extensively within the Microbial Genomes group for the analysis and annotation of sequence data from cosmids to whole genomes. The Artemis Comparison Tool (ACT) is also useful for interactive viewing of the comparisons between large and small sequences.

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    BARD

Cite this (BARD, RRID:SCR_006283)

URL: http://bard.nih.gov/

Resource Type: Resource, data or information resource, database

Database that allows scientists without specialized training to effectively utilize Molecular Libraries Program (MLP) data. It allows the research community to utilize and develop new chemical probes to explore biological functions by building a central, permanently accessible link to all aspects of chemical biology data and analyses. The project is split into two basic segments, the first segment delivering functionality for a data dictionary, as well as assay protocol and data entry tools. The second builds a data warehouse for analysis and visualization, accessible through a public RESTful API. They will initially deploy two clients that will use this API - a web-based interface and a desktop application. Advanced access to data and the platforms will also be available to support plug-in development and the repackaging of data by others. Initially the project will focus on small molecule assays. Features: * allow scientists to annotate assay data using a common, shared language * provide facile access to data, integrating existing chemical biology and computational resources * enable meaningful analysis and interpretation of discovery data by the research community * support hypothesis generation for iterative probe- and drug-discovery projects * inform the entire small molecule discovery and development process

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Cite this (BarleyBase, RRID:SCR_001946)

URL: http://www.barleybase.org/

Resource Type: Resource, data or information resource, database

A MIAME/Plant-compliant and plant ontology enhanced expression database for Barley microarray data. It contains data from two Affymetrix genome arrays, Barley1 and Arabidopsis ATH1. Users can search based on experiment type, experimental factors, array design, or experimenter. They can also choose to browse lists of available data.

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Cite this (BGI-RISe - Beijing Genomics Institute Rice Information System, RRID:SCR_013446)

URL: http://rise.genomics.org.cn/

Resource Type: Resource, data or information resource, database

Integrated information resource for rice genomes as well as a workbench for comparative genomic analysis among cereal crops. Sequence contigs of Beijing indica and Syngenta japonica have been further assembled and anchored onto the rice chromosomes. The rice genomes have been annotated for gene content, repetitive elements, and SNPs. Sequence polymorphisms between different rice subspecies have also been identified. Designed as a basic platform for rice study, the sequenced genomes and related information is presented in systematic and graphical ways for the convenience of in-depth comparative studies. In addition to the comprehensive data of Oryza sativa L. ssp. indica sequenced, BGI-RIS will host carefully curated genome information of Oryza sativa L. ssp. japonica.

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Cite this (BiGG Database, RRID:SCR_005809)

URL: http://bigg.ucsd.edu/

Resource Type: Resource, data or information resource, database

A knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest.

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Cite this (Biochemical Pathways database, RRID:SCR_008111)

URL: http://www.mol-net.de/databases/biopath.html

Resource Type: Resource, data or information resource, database

A database of biochemical pathways that provides access to metabolic transformations and cellular regulations derived from the Roche Applied Science Biochemical Pathways wall chart.

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Cite this (Bioinformatics Links Directory, RRID:SCR_008018)

URL: http://bioinformatics.ca/links_directory/

Resource Type: Resource, data or information resource, database

Database of curated links to molecular resources, tools and databases selected on the basis of recommendations from bioinformatics experts in the field. This resource relies on input from its community of bioinformatics users for suggestions. Starting in 2003, it has also started listing all links contained in the NAR Webserver issue. The different types of information available in this portal: * Computer Related: This category contains links to resources relating to programming languages often used in bioinformatics. Other tools of the trade, such as web development and database resources, are also included here. * Sequence Comparison: Tools and resources for the comparison of sequences including sequence similarity searching, alignment tools, and general comparative genomics resources. * DNA: This category contains links to useful resources for DNA sequence analyses such as tools for comparative sequence analysis and sequence assembly. Links to programs for sequence manipulation, primer design, and sequence retrieval and submission are also listed here. * Education: Links to information about the techniques, materials, people, places, and events of the greater bioinformatics community. Included are current news headlines, literature sources, educational material and links to bioinformatics courses and workshops. * Expression: Links to tools for predicting the expression, alternative splicing, and regulation of a gene sequence are found here. This section also contains links to databases, methods, and analysis tools for protein expression, SAGE, EST, and microarray data. * Human Genome: This section contains links to draft annotations of the human genome in addition to resources for sequence polymorphisms and genomics. Also included are links related to ethical discussions surrounding the study of the human genome. * Literature: Links to resources related to published literature, including tools to search for articles and through literature abstracts. Additional text mining resources, open access resources, and literature goldmines are also listed. * Model Organisms: Included in this category are links to resources for various model organisms ranging from mammals to microbes. These include databases and tools for genome scale analyses. * Other Molecules: Bioinformatics tools related to molecules other than DNA, RNA, and protein. This category will include resources for the bioinformatics of small molecules as well as for other biopolymers including carbohydrates and metabolites. * Protein: This category contains links to useful resources for protein sequence and structure analyses. Resources for phylogenetic analyses, prediction of protein features, and analyses of interactions are also found here. * RNA: Resources include links to sequence retrieval programs, structure prediction and visualization tools, motif search programs, and information on various functional RNAs.

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Cite this (Bio-Job.org, RRID:SCR_000933)

URL: http://www.bio-job.org/

Resource Type: Resource, job resource

Bio-Job.org is a sister site to PROTOCOL-ONLINE.ORG and offers free job posting to not-for-profit employers such as universities, governments, research institutions/organizations. Currently industrial job listing is also free. * Employer's Services: Post a Job, Manage Jobs Posts, View Resumes * Jobseeker: Announce your availability and submit your resume to hundreds of Employers that visit this site. Employers can contact you directly as soon as a suitable position becomes available. Why is this site created: It's never been an easy job to recruit qualified people for employer or PI who runs a lab--Not only have you to pay a fee for job listing that could be as high as hundreds of dollars, you have to go through all the hassle of setting up an account, dealing with your account manager and making the payment. In an era when science is free, genome data is free, publications are free, and why is job posting not free? With this belief in mind, we created this site to allow free job posting for academia. What types of jobs can be posted here: Jobs in any scientific discipline and biotech jobs can be posted.

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Cite this (BIRD - Bio Info R and D, RRID:SCR_008010)

URL: http://www-bird.jst.go.jp/index_e.html

Resource Type: Resource, organization portal, portal, topical portal, data or information resource

BIRD''s mission is to aid the progress of bioinformatics and promote creation of new biology, which has computational, deductive, predictive, and theoretical features. (most of this site is in Japanese) To carry out its responsibilities, BIRD: * Promotes appropriate development of bioinformatics research and development, such as what kinds of databases and analysis software should be developed and what kind of computer facilities are needed for that development. * Maintains the computer environment and network and functions as a funding agency to further promotion plans. * Develops basic databases: genome sequence database, protein 3D structure database, gene expression profile database, molecular interaction database, etc. * Conducts and coordinates integration, enhancement, and standardization of the basic databases. * Develops computing tools for analyzing various kinds of biological and experimental data, data mining from databases, computer simulation of living systems and so on. * Develops ontologies necessary for data and knowledge description of databases storing biological functions and integration of the basic databases. * Conducts and coordinates research and development of innovative and creative technologies and theories which move toward understanding life as an information system, especially approaches by collaboration of computer scientists and experimental scientists. * Provides computer facilities for developing databases and software and making them publicly available. * Sets up training courses for teaching utilization of databases and tools for novices in bioinformatics and sponsors scientific meetings. * Provides community space with high performance computing facilities where innovative ideas are cultivated by free discussion and "trial and error" with the computer in order to promote development of young scientists who will create new biological discoveries based on bioinfomatics and become leaders in the field.

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