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on page 1 showing 20 out of 273 results

    HOMER

Cite this (HOMER, RRID:SCR_010881)

URL: http://homer.ucsd.edu/

Resource Type: Resource, software resource, software application, sequence analysis software, data analysis software, data processing software

Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.

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Cite this (Knowledge Engineering from Experimental Design, RRID:SCR_001238)

URL: https://wiki.birncommunity.org/display/NEWBIRNCC/Knowledge+Engineering+from+Experimental+Design+%28%27KEfED%27%29

Resource Type: Resource, software resource, software application

Knowledge engineering software for reasoning with scientific observations and interpretations. The software has three parts: (a) the KEfED model editor - a design editor for creating KEfED models by drawing a flow diagram of an experimental protocol; (b) the KEfED data interface - a spreadsheet-like tool that permits users to enter experimental data pertaining to a specific model; (c) a "neural connection matrix" interface that presents neural connectivity as a table of ordinal connection strengths representing the interpretations of tract-tracing data. This tool also allows the user to view experimental evidence pertaining to a specific connection. The KEfED model is designed to provide a lightweight representation for scientific knowledge that is (a) generalizable, (b) a suitable target for text-mining approaches, (c) relatively semantically simple, and (d) is based on the way that scientist plan experiments and should therefore be intuitively understandable to non-computational bench scientists. The basic idea of the KEfED model is that scientific observations tend to have a common design: there is a significant difference between measurements of some dependent variable under conditions specified by two (or more) values of some independent variable.

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Cite this (Open Clinical Report Repository, RRID:SCR_013585)

URL: http://www.dbmi.pitt.edu/nlpfront

Resource Type: Resource, data or information resource

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. Repository of de-identified clinical reports available for NLP researchers has been designed. Work with the AMIA NLP working group in designing annotation schemas and obtaining annotations, design a repository for shareable annotations, help design and execute a shared task in IE from clinical reports. The University of Pittsburgh NLP Repository contains clinical reports that are available to the community for NLP research purposes and comprises: # Report Repository - one month of de-identified clinical reports from multiple hospitals and # Annotation Repository - annotations performed on reports from the Report Repository. Anyone performing annotations on reports from the NLP Repository is required to deposit their annotations. The Repository contains reports of the following types generated from multiple hospitals during a single month: * History and Physicals * Progress Notes * Consultation Reports * Radiology Reports * Surgical Pathology Reports * Emergency Department Reports * Discharge Summaries * Operative Reports * Cardiology Reports

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Cite this (Bioscholar, RRID:SCR_001380)

URL: http://www.isi.edu/projects/bioscholar/overview

Resource Type: Resource, software resource, software application, source code

Knowledge management and engineering system software for experimental biomedical scientists permitting a single scientific worker (at the level of a graduate student or postdoctoral worker) to design, construct and manage a shared knowledge repository for a research group derived on a local store of PDF files. Usability is especially emphasized within a laboratory so that this software could provide support to experimental scientists attempting to construct a personalized representation of their own knowledge on a medium scale. The BioScholar system uses a graphical interface to create experimental designs based on the experimental variables in the system. The design is then analyzed to construct a tabular input form based on the data flow. They call this methodology "Knowledge Engineering from Experimental Design" or "KEfED". The approach is domain-independent but domain-specific modules reasoning can be constructed to generate interpretations from the observational data represented in the KEfED model. The application is available for download as platform-specific installers including Linux, Unix, Mac OS, and Windows. The installer will install an application that will run the BioScholar server. This server uses Jetty as its integrated web server.

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Cite this (Laboratory for Fluorescence Dynamics, RRID:SCR_001437)

URL: http://www.lfd.uci.edu/

Resource Type: Resource, biomedical technology research center, service resource, access service resource, training resource

Biomedical technology research center and training resource that develops novel fluorescence technologies, including instrumentation, methods and software applicable to cellular imaging and the elucidation of dynamic processes in cells. The LFD's main activities are: * Services and Resources: the LFD provides a state-of-the-art laboratory for fluorescence measurements, microscopy and spectroscopy, with technical assistance to visiting scientists. * Research and Development: the LFD designs, tests, and implements advances in the technology of hardware, software, and biomedical applications. * Training and Dissemination: the LFD disseminates knowledge of fluorescence spectroscopic principles, instrumentation, and applications to the scientific community.

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Cite this (Ascidian Stock Center (ASC), RRID:SCR_014949)

URL: http://www.ascidiancenter.ucsb.edu/index.html

Resource Type: Resource, biomaterial supply resource, material resource, organism supplier

Supplier of Ciona (C. robusta and C. savignyi) adults and stable transgenic animals expressing tissue-specific fluorescent proteins for research laboratories. This ascidian culturing facility is located at the marine laboratory of the University of California at Santa Barbara (UCSB).

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Cite this (TFmodeller, RRID:SCR_015715)

URL: http://www.ccg.unam.mx/tfmodeller

Resource Type: Resource, data analysis software, data processing software, software application, sequence analysis software, web application, data visualization software, software resource

Web application that scans a library of protein-DNA complexes and builds comparative models of proteins bound to DNA. Its results include complex coordinates, schematic interface diagrams, interface alignments and DNA motifs.

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Cite this (UCSF ChimeraX, RRID:SCR_015872)

URL: https://www.cgl.ucsf.edu/chimerax/

Resource Type: Resource, data processing software, software application, data visualization software, 3d visualization software, 4d visualization software, software resource

Software for 3D/4D image reconstruction. UCSF ChimeraX is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera.

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Cite this (StringTie , RRID:SCR_016323)

URL: https://ccb.jhu.edu/software/stringtie/

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ .

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Cite this (PMI-Byonic, RRID:SCR_016735)

URL: https://www.proteinmetrics.com/products/byonic/

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software package for advanced peptide and protein identification by tandem mass spectrometry. Allows to define unlimited number of variable modification type and allows the user to set a separate limit on the number of occurrences of each modification type.

  • From Current Category

Cite this (CCPN Data Model, RRID:SCR_016982)

URL: https://www.ccpn.ac.uk/v2-software/software/extras/datamodelfolder

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

Model to cover data for macromolecular NMR spectroscopy from the initial experimental data to the final validation. Used for the large scale data deposition, data mining and program interoperability. Enables movement from one software package to another without difficulties with data conversion or loss of information. Works with CcpNmr Analysis software for analysis and interactive display, CcpNmr FormatConverter for allowing transfer of data from programs used in NMR to and from the Data Model, and the CLOUDS software for automated structure calculation and assignment. Used within the CCPN software suite for NMR spectroscopy and at the BioMagResBank for converting existing deposited restraint lists to a standard IUPAC nomenclature.

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    RSRef

Cite this (RSRef, RRID:SCR_017211)

URL: https://biochem.missouri.edu/chapman/software.htm

Resource Type: Resource, software resource, software application, data processing software

Software for fitting of atomic models into density maps derived from x-ray crystallography or electron microscopy.

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    BEAST2

Cite this (BEAST2, RRID:SCR_017307)

URL: https://www.beast2.org/

Resource Type: Resource, data analysis software, data processing software, software application, sequence analysis software, software resource, software toolkit

Software package for advanced Bayesian evolutionary analysis by sampling trees. Used for phylogenetics, population genetics and phylodynamics. Program for Bayesian phylogenetic analysis of molecular sequences. Estimates rooted, time measured phylogenies using strict or relaxed molecular clock models. Framework can be extended by third parties. Comprised of standalone programs including BEAUti, BEAST, MASTER, RBS, SNAPP, MultiTypeTree, BDSKY, LogAnalyser, LogCombiner, TreeAnnotator, DensiTree and package manager.

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Cite this (Aptamer Database - The Ellington Lab, RRID:SCR_001781)

URL: https://sites.google.com/site/friaptamerstream/

Resource Type: Resource, data or information resource, database

The Aptamer Database is a comprehensive, annotated repository for information about aptamers and in vitro selection. This resource is provided to collect, organize and distribute all the known information regarding aptamer selection. Aptamers are DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules. Aptamers have been selected which bind nucleic acid, proteins, small organic compounds, and even entire organisms.

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    ASAP

Cite this (ASAP, RRID:SCR_001849)

URL: https://omictools.com/asap-3-tool

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

Database and web interface developed to store, update and distribute genome sequence data and gene expression data. ASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments. Use of some of this preliminary data is conditional, and it is the users responsibility to read the data release policy and to verify that any use of specific data obtained through ASAP is consistent with this policy. There are four main routes to viewing the information in ASAP: # a summary page, # a form to query the genome annotations, # a form to query strain collections, and # a form to query the experimental data. Navigational buttons appear on every page allowing users to jump to any of these four points.

  • From Current Category

Cite this (Pathway Commons, RRID:SCR_002103)

URL: http://www.pathwaycommons.org/pc

Resource Type: Resource, web service, software resource, data or information resource, data access protocol, database

Database of publicly available pathways from multiple organisms and multiple sources represented in a common language. Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes. Pathways were downloaded directly from source databases. Each source pathway database has been created differently, some by manual extraction of pathway information from the literature and some by computational prediction. Pathway Commons provides a filtering mechanism to allow the user to view only chosen subsets of information, such as only the manually curated subset. The quality of Pathway Commons pathways is dependent on the quality of the pathways from source databases. Pathway Commons aims to collect and integrate all public pathway data available in standard formats. It currently contains data from nine databases with over 1,668 pathways, 442,182 interactions,414 organisms and will be continually expanded and updated. (April 2013)

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    Seg3D

Cite this (Seg3D, RRID:SCR_002552)

URL: http://www.seg3d.org

Resource Type: Resource, segmentation software, image analysis software, data processing software, software application, data visualization software, software resource, image processing software, rendering software

A free volume processing segmenting tool that combines a flexible manual interface with powerful image processing and segmentation algorithms. Users can explore and label image volumes using slice windows and 3D volume rendering.

  • From Current Category

Cite this (SuperTarget, RRID:SCR_002696)

URL: http://bioinf-apache.charite.de/supertarget_v2/

Resource Type: Resource, data or information resource, database

Database for analyzing drug-target interactions, it integrates drug-related information associated with medical indications, adverse drug effects, drug metabolism, pathways and Gene Ontology (GO) terms for target proteins. At present (May 2013), the updated database contains >6000 target proteins, which are annotated with >330 000 relations to 196 000 compounds (including approved drugs); the vast majority of interactions include binding affinities and pointers to the respective literature sources. The user interface provides tools for drug screening and target similarity inclusion. A query interface enables the user to pose complex queries, for example, to find drugs that target a certain pathway, interacting drugs that are metabolized by the same cytochrome P450 or drugs that target proteins within a certain affinity range.

  • From Current Category

Cite this (Diseasome, RRID:SCR_002792)

URL: http://diseasome.eu

Resource Type: Resource, narrative resource, map, image, data set, book, service resource, data or information resource

A disease / disorder relationships explorer and a sample of a map-oriented scientific work. It uses the Human Disease Network dataset and allows intuitive knowledge discovery by mapping its complexity. The Human Disease Network (official) dataset, a poster of the data and related book (Biology - The digital era, ISBN: 978-2-271-06779-1) are available. This kind of data has a network-like organization, and relations between elements are at least as important as the elements themselves. More data could be integrated to this prototype and could eventually bring closer phenotype and genotype. Results should be visual, but also printable. Creating posters can enhance collaborative work. It facilitates discussion and sharing of ideas about the data. This website initiative is an invitation to think about the benefits of networks exploration but above all it tries to outline future designs of scientific information systems.

  • From Current Category

    BioPerl

Cite this (BioPerl, RRID:SCR_002989)

URL: http://www.bioperl.org

Resource Type: Resource, wiki, source code, narrative resource, software repository, software resource, software toolkit, data or information resource

BioPerl is a community effort to produce Perl code which is useful in biology. This toolkit of perl modules is useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules in our repository. The BioPerl toolkit provides a library of hundreds of routines for processing sequence, annotation, alignment, and sequence analysis reports. It often serves as a bridge between different computational biology applications assisting the user to construct analysis pipelines. This chapter illustrates how BioPerl facilitates tasks such as writing scripts summarizing information from BLAST reports or extracting key annotation details from a GenBank sequence record. BioPerl includes modules written by Sohel Merchant of the GO Consortium for parsing and manipulating OBO ontologies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

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