Curator Dashboard

Collection of human embryonic and fetal material (Tissue and RNA) ranging from 3 to 20 weeks of development available to the international scientific community. Material can either be sent to registered users or our In House Gene Expression Service (IHGES) can carry out projects on user''''s behalf, providing high quality images and interpretation of gene expression patterns. Gene expression data emerging from HDBR material is added to our gene expression database which is accessible via our HUDSEN (Human Developmental Studies Network) website. A significant proportion of the material has been cytogenetically karyotyped, and normal karyotyped material is provided for research.

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• SciCrunch
• 14 years ago - by Anonymous

Database of a set of standard 3D virtual models at different stages of development from Carnegie Stages (CS) 12-23 (approximately 26-56 days post conception) in which various anatomical regions have been defined with a set of anatomical terms at various stages of development (known as an ontology). Experimental data is captured and converted to digital format and then mapped to the appropriate 3D model. The ontology is used to define sites of gene expression using a set of standard descriptions and to link the expression data to an ''''anatomical tree''''. Human data from stages CS12 to CS23 can be submitted to the HUDSEN Gene Expression Database. The anatomy ontology currently being used is based on the Edinburgh Human Developmental Anatomy Database which encompasses all developing structures from CS1 to CS20 but is not detailed for developing brain structures. The ontology is being extended and refined (by Prof Luis Puelles, University of Murcia, Spain) and will be incorporated into the HUDSEN database as it is developed. Expression data is annotated using two methods to denote sites of expression in the embryo: spatial annotation and text annotation. Additionally, many aspects of the detection reagent and specimen are also annotated during this process (assignment of IDs, nucleotide sequences for probes etc). There are currently two main ways to search HUDSEN - using a gene/protein name or a named anatomical structure as the query term. The entire contents of the database can be browsed using the data browser. Results may be saved. The data in HUDSEN is generated from both from researchers within the HUDSEN project, and from the wider scientific community. The HUDSEN human gene expression spatial database is a collaboration between the Institute of Human Genetics in Newcastle, UK, and the MRC Human Genetics Unit in Edinburgh, UK, and was developed as part of the Electronic Atlas of the Developing Human Brain (EADHB) project (funded by the NIH Human Brain Project). The database is based on the Edinburgh Mouse Atlas gene expression database (EMAGE), and is designed to be an openly available resource to the research community holding gene expression patterns during early human development.

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• SciCrunch
• 14 years ago - by Anonymous

Forum for researchers in human developmental biology and related fields to meet and establish links.

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• SciCrunch
• 14 years ago - by Anonymous

A web-based software system that allows users to upload lists of mammalian genes/proteins onto a server-based program for integrated analysis. The system includes web-based tools to manipulate lists with different set operations, to expand lists using existing mammalian networks of protein-protein interactions, co-expression correlation, or background knowledge co-annotation correlation, as well as to apply gene-list enrichment analyses against many gene-list libraries of prior biological knowledge such as pathways, gene ontology terms, kinase-substrate, microRNA-mRAN, and protein-protein interactions, metabolites, and protein domains. Such analyses can be applied to several lists at once against many prior knowledge libraries of gene-lists associated with specific annotations. The system also contains features that allow users to export networks and share lists with other users of the system.

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• SciCrunch
• 13 years ago - by Anonymous

Dissemination of public datasets containing raw crystallography data (known as ''diffraction images''), along with rich metadata for search and persistent handles for citation in publications. Storage is federated, meaning the public index contains no data itself and merely points to data stored in external labs and institutions. TARDIS is scheduled to be replaced by the Bioscience Data Platform (https://www.nectar.org.au/bioscience-data-platform-tardis-cloud)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 14 years ago - by Anonymous

Web-based linked data server and browser specifically designed for ontology terms, it supports ontology visualization, query, and development. Ontobee provides a web interface for displaying the details and hierarchy of a specific ontology term. Meanwhile, Ontobee provides a RDF source code for the particular web page, which supports remote query of the ontology term and the Semantic Web. Ontobee provides an efficient and publicly available method to promote ontology sharing, interoperability, and data integration.

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• SciCrunch
• 14 years ago - by Anonymous

Centre is committed to free and open exchange of scientific data and is working collaboratively with international centres, networks and scientists to build sustainable polar data commons. Delivers professional data management and analysis services to Antarctic scientists and environmental managers. Supports logistical operations of Australian Antarctic Program. Data held in AADC data stores are qualified with metadata and discoverable through Catalogue of Australian Antarctic and Sub-antarctic Metadata (CAASM http://data.aad.gov.au/aadc/metadata) or through customized applications accessible via the website. All data is archived in AADC to permit its re-use. AADC has capability to create DOIs for datasets.

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• SciCrunch
• 14 years ago - by Anonymous

University of Ottawa often referred to as uOttawa or U of O, is a bilingual public research university in Ottawa, Ontario, Canada.

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• SciCrunch
• 13 years ago - submitted by Stephen Larson

A multidisciplinary repository of public data sets such as the Human Genome and US Census data that can be seamlessly integrated into AWS cloud-based applications. AWS is hosting the public data sets at no charge for the community. Anyone can access these data sets from their Amazon Elastic Compute Cloud (Amazon EC2) instances and start computing on the data within minutes. Users can also leverage the entire AWS ecosystem and easily collaborate with other AWS users. If you have a public domain or non-proprietary data set that you think is useful and interesting to the AWS community, please submit a request and the AWS team will review your submission and get back to you. Typically the data sets in the repository are between 1 GB to 1 TB in size (based on the Amazon EBS volume limit), but they can work with you to host larger data sets as well. You must have the right to make the data freely available.

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• SciCrunch
• 14 years ago - by Anonymous

Data repository to preserve and provide access to agricultural and environmental data produced during research projects undertaken at the University of Guelph including datasets on topics such as crop yield, soil moisture, weather and agroforestry. A special emphasis is placed on research funded by Ontario Ministry of Agriculture and Food (OMAF) and MRA.

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• SciCrunch
• 14 years ago - by Anonymous

General purpose simulation platform developed to support the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, simulations of large networks, and systems-level models. As such, GENESIS, and its version for parallel and networked computers (PGENESIS) was the first broad scale modeling system in computational biology to encourage modelers to develop and share model features and components. User contributed GENESIS models and simulations are available. You may to contribute a model or simulation. Educational tutorials for instruction in both neurobiology and computational methods have been developed. These tutorials and GENESIS are now being widely used in graduate and undergraduate instruction. These uses include full semester courses in computational neuroscience or neural modeling, short intensive courses or workshops, an option for a course project, and short units on computational neuroscience within courses on artificial neural nets. They also have a repository of user-contributed tutorials and materials for use in neuroscience education. If you have course descriptions, syllabi, exercises, tutorials, or short HOWTO documents, please upload them to Education.

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• SciCrunch
• 13 years ago - by Anonymous

The world''s largest private, nonprofit ocean research, engineering and education organization.

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• SciCrunch
• 17 years ago - submitted by Andrea Stagg

Authoritative, need-to-know information from Johns Hopkins available for mobile devices and the web. Guides provide up to date information and break down details of diagnosis, drug indications, dosing, pharmacokinetics, side effects and interactions, pathogens, management, and vaccines into frequently-updated, quick-read entries. Available for infectious disease (ABX), diabetes, and HIV.

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• SciCrunch
• 14 years ago - by Anonymous

Images and movies of plant organelle dynamics that were obtained from plant research, based on the Plant Organelles Database. This educational tool is written in layman''''s terms to engage members of the non-scientific community such as students and school teachers. Additional content: ''''What happens, if organelle functions become defective '''' was added in anticipation that readers will be interested in this subject. The Scientific Research of Priority Areas on Organelle Differentiation as the Strategy for Environmental Adaptation in Plants was started on 2004 to promote a comprehensive understanding of plant organelle research, and research with plant scientists all over Japan has been conducted for the past five years. The Plant Organelles Database (PODB), which contains images and movies of various plant organelles that were obtained from this project''''s research was constructed but was designed for scientists. ''''The Plant Organelles World'''' was created for the non-scientific community to understand. Plants have developed mechanisms to adapt to the environment, which is different from the mammalian system of adaption. From recent plant research, the small compartments in cells, ''''organelles'''', have been shown to be involved in various responses to environmental changes. The dramatic development of bio-imaging analysis tools such as green fluorescent protein (GFP), which won a Nobel prize for chemistry in 2008, has contributed to recent plant science, because it has become easier to biotechnologically introduce GFP and its derivatives into cells, leading to convenient methods of observing the inside of cells. As a result, we can analyze organelle dynamics and obtain insights related to understanding the way plants live, as well as forming a deeper understanding of organelles.

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• SciCrunch
• 14 years ago - by Anonymous

Software application that plots measures of pairwise linkage disequilibria for SNPs (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

Community-wide effort (Challenge) for evaluating text mining and information extraction systems applied to the biological domain. It is focused on the comparison of methods and the community assessment of scientific progress, rather than on the purely competitive aspects. There is a considerable difficulty in constructing suitable gold standard data for training and testing new information extraction systems which handle life science literature. Thus the data sets derived from the BioCreAtIvE challenge - because they have been examined by biological database curators and domain experts - serve as useful resources for the development of new applications as well as helping to improve existing ones. Two main issues are addressed at BioCreAtIvE, both concerned with the extraction of biologically relevant and useful information from the literature. The first one is concerned with the detection of biologically significant entities (names) such as gene and protein names and their association to existing database entries. The second one is concerned with the detection of entity-fact associations (e.g. protein - functional term associations ).

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• SciCrunch
• 14 years ago - by Anonymous

Data set of almost 2,000 neurosurgical images using a variety of search options.

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 19,2021.Designed with the neurosurgeon in mind, this portal contains everything you need to acquire new skills and techniques, including courses, an image database, and the world''s largest neurosurgical wiki reference - NeuroWiki. The new University of Neurosurgery includes: * More than 40 new online courses - in all neurosurgical subspecialties. * Archived webinars. * Lectures from the CNS Annual Meetings. * Neurosurgical image database. We are continuing to add new content - check back often.

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• SciCrunch
• 16 years ago - by Anonymous

Software program for constructing linkage disequilibrium (LD) maps. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data.

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• SciCrunch
• 14 years ago - by Anonymous