Curator Dashboard

Database containing a set of DNA sequences that have been collected to analyse the evolutionary relatedness of a population. The population could originate from different members of the same species, or from organisms from different species. Users may submit a Popset using Sequin.

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• SciCrunch
• 13 years ago - by Anonymous

Our Investigational Pharmacy team is responsible for dispensing both inpatient and outpatient investigational medication for industry-sponsored, grant-funded and investigator-initiated protocols. We provide pharmacy services customized to each research protocol conducted at Cincinnati Children�s.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Public archive providing a comprehensive record of the world''''s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. All submitted data, once public, will be exchanged with the NCBI and DDBJ as part of the INSDC data exchange agreement. The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources including submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centers and routine and comprehensive exchange with their partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature. ENA is made up of a number of distinct databases that includes the EMBL Nucleotide Sequence Database (Embl-Bank), the newly established Sequence Read Archive (SRA) and the Trace Archive. The main tool for downloading ENA data is the ENA Browser, which is available through REST URLs for easy programmatic use. All ENA data are available through the ENA Browser. Note: EMBL Nucleotide Sequence Database (EMBL-Bank) is entirely included within this resource.

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• SciCrunch
• 14 years ago - by Anonymous

Preclinical ultrasound imaging. Provided instruments include Vevo 3100, Vevo 3100 LAZR-X, Perkin Elmer Vega.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Database of the U.S. National Archives and Records Administration that allows users to search by keyword or category. Specific topics in personal history, private sectors, places, wars or time periods can be chosen to help filter your research findings of the 85 million electronic records that have been made available.

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• SciCrunch
• 13 years ago - by Anonymous

Software R package for multivariate microbiome analysis. Statistical methods for analysing multivariate abundance data.

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• RRID
• 4 years ago - by Anonymous

A software toolbox that provides a method for generating Region of Interest (ROI) masks based on the Talairach Daemon database. The atlases include Brodmann area, Lobar, Hemisphere, Anatomic Label (gyral anatomy), and Tissue type. The atlases have been extended to the vertex in MNI space, and corrected for the precentral gyrus anomaly. Additional atlases (including non-human atlases) can be added without difficulty., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

Core provides designing studies and developing statistical analysis plans in clinical trials, clinical and community based intervention studies, laboratory experiments, and observational studies.Provides expertise in traditional and modern statistical methods.Can help with trial design and analysis, epidemiologic analysis, sample size and power, high dimensional data analysis, risk prediction, complex survey analysis, time-to-event and longitudinal models, and statistical simulation,data management and wrangling, analytic variable coding and data set creation, research database design, data visualization, manuscript preparation, statistical programming, and much more.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

R software package providing a Graphical User Interface for analysis of Affymetrix microarray data, using the limma package (Linear Models for MicroArray data). While not as powerful as limma to the expert user, it offers a simple point-and-click interface to many of the commonly-used limma and affy functions. You need to have R 1.9.0 or later, Tcl/Tk 8.3 or later (ActiveTcl for Windows, Tcl/Tk Source for Linux/Unix, or X11 Tcl/Tk for MacOSX) and the limma, affylmGUI, and tkrplot R packages. It has been succesfully tested on Windows 2000, Windows XP, RedHat/Fedora Linux, and on Mac OSX with X11.

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• SciCrunch
• 13 years ago - by Anonymous

Open source software provides GUI tool for spectra processing from 1D NMR metabolomics data, based on interactive interface for spectra visualization, that helps spectra processing.

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• RRID
• 4 years ago - submitted by Daniel Jacob

Freely available corpus of manually annotated brain region mentions created to facilitate text mining of neuroscience literature. The corpus contains 1,377 abstracts with 18,242 brain region annotations. Interannotator agreement was evaluated for a subset of the documents, and was 90.7% and 96.7% for strict and lenient matching respectively. We observed a large vocabulary of over 6,000 unique brain region terms and 17,000 words. For automatic extraction of brain region mentions we evaluated simple dictionary methods and complex natural language processing techniques. The dictionary methods based on neuroanatomical lexicons recalled 36% of the mentions with 57% precision. The best performance was achieved using a conditional random field (CRF) with a rich feature set. Features were based on morphological, lexical, syntactic and contextual information. The CRF recalled 76% of mentions at 81% precision, by counting partial matches recall and precision increase to 86% and 92% respectively. We suspect a large amount of error is due to coordinating conjunctions, previously unseen words and brain regions of less commonly studied organisms. We found context windows, lemmatization and abbreviation expansion to be the most informative techniques. We encourage you to test new methods and applications of the dataset. Please contact us if you do, we would like to hear about and link to your work. The abstracts are from PubMed/Medline, specifically The Journal of Comparative Neurology.

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• SciCrunch
• 17 years ago - by Anonymous

Provides molecular and anatomical foundational framework for study of brain function and disorders.Comprehensive Center on Human and Non-Human Primate Brain Cell Atlases with goal to build reference brain cell atlases that will be used throughout research community.

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• RRID
• 4 years ago - submitted by Edyta Vieth

An ontology that formalized the genomic element by defining an upper class genetic interval using BFO as its framework. The definition of genetic interval is the spatial continuous physical entity which contains ordered genomic sets (DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic_Acid_Base_Residue) on a chromosome or RNA molecule which must have a liner primary sequence structure.

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• SciCrunch
• 13 years ago - by Anonymous

Special interest society focused on basic mechanisms involved in human urinary stone formation.

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• dkNET
• 4 years ago - submitted by Ko-Wei Lin

An ontology including concepts, definitions, terms, and resources for a standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1. These terms will enable structure queries of elements of the experiments. Furthermore, the terms will also enable unambiguous descriptions of how the experiment was performed.

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• SciCrunch
• 16 years ago - by Anonymous

Research on microbial agents, which cause lethal diseases in humans and for which effective drugs or preventive vaccines are not available, must be conducted by well-trained investigators in specially built, well-maintained laboratories. Core provides the triad of service, research and development, and education and training.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Database and resource that provides sequence and annotation data for the rice genome. This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. All structural and functional annotation is viewable through our Rice Genome Browser which currently supports 75 tracks of annotation. Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads. Rice is a model species for the monocotyledonous plants and the cereals which are the greatest source of food for the world''s population. While rice genome sequence is available through multiple sequencing projects, high quality, uniform annotation is required in order for genome sequence data to be fully utilized by researchers. The existence of a common gene set and uniform annotation allows researchers within the rice community to work from a common resource so that their results can be more easily interpreted by other scientists. The objective of this project has always been to provide high quality annotation for the rice genome. They generated, refined and updated gene models for the estimated 40,000-60,000 total rice genes, provided standardized annotation for each model, linked each model to functional annotation including expression data, gene ontologies, and tagged lines. They have provided a resource to extend the annotation of the rice genome to other plant species by providing comparative alignments to other plant species. Analysis/Tools are available including: BLAST, Locus Name Search, Functional Term Search, Protein Domain Search, Anatomy Expression Viewer, Highly Expressed Genes

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• SciCrunch
• 17 years ago - by Anonymous

Provides services and expertise that facilitate behavioral, psychosocial, community, translational, and population based oncology research. Services include coordinating recruitment and retention of diverse study participants representative of Sylvester South Florida catchment area;supporting development of culturally and linguistically tailored study materials; facilitating data collection and management, including for biospecimens, in clinical and community setting; assisting with development and delivery of evidence based interventions across cancer continuum from prevention to survivorship; offering, seminars, workshops and training.Offers consultation on culturally appropriate approaches for study implementation and provides translation of study materials into Spanish and/or Haitian Creole. Engages diverse stakeholders throughout South Florida in dialogue about cancer prevention and collaborative research opportunities.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Core facility that provides the following services: DNA sequencing service.

The BIDMC DNA Sequencing Facility is equipped with an ABI 3130xl Automated DNA Sequencer. Turn around time is 24 hours: drop off samples by 10am (at CLS-426E or SL-232) and obtain results by 11am of the following day. Some results can be posted the same day of sample submission. Sample pick up is available in Longwood Medical Area - please send requests by email. Also available through the BIDMC DNA sequencing core to the Harvard Research community is the newest model of the Arcturus Laser Capture Microdissection System!

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• SciCrunch
• 13 years ago - by Anonymous

Nanomaterials and nanostructures grown in INML are used in lasers, solar cells, detectors, transistors, modulators, and a wide range of other electronic and photonic devices.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth