Curator Dashboard

Web-accessible digital brain atlas of the common marmoset (Callithrix jacchus), prepared from histological sections of the marmoset brain using various staining techniques.

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• SciCrunch
• 15 years ago - by Anonymous

Software for scaffolding to address some of the challenges encountered when analyzing metagenomes. Scaffolding represents the task of ordering and orienting contigs by incorporating additional information about their relative placement along the genome. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.

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• SciCrunch
• 13 years ago - by Anonymous

Service to align and optionally taxonomically classify your rRNA gene sequences. The results can be combined with any other sequences aligned by SINA or taken from the SILVA databases by concatenation of FASTA files or using the ARB MERGE tool. Note: Submission is currently limited to at most 1000 sequences of at most 6000 bases each. If your requirements exceed this limitation, get Opens internal link in current windowSINA for local installation.

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• SciCrunch
• 13 years ago - by Anonymous

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• SciCrunch
• 17 years ago - submitted by Andrea Stagg

Center that supplies access to wild-type, mutant, and transgenic zebrafish lines, EST's/cDNAs, antibodies and fish health services. ZIRC Health Services include diagnostic pathology testing for zebrafish and other small laboratory fish species.

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• SciCrunch
• 17 years ago - by Anonymous

Medical school of the University of Iowa, located in Iowa City, in the U.S. state of Iowa.

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• SciCrunch
• 15 years ago - submitted by Andrea Stagg

Neuron Navigator (NNG) integrates a 3D neuron image database into an easy-to-use visual interface. Via a flexible and user-friendly interface, NNG is designed to help researchers analyze and observe the connectivity within the neural maze and discover possible pathways. With NNG''s 3D neuron image database, researchers can perform volumetric searches using the location of neural terminals, or the occupation of neuron volumes within the 3D brain space. Also, the presence of the neurons under a combination of spatial restrictions can be shown as well. NNG is a result of a multi-discipline collaboration between neuroscientists and computer scientists, and NNG has now been implemented on a coordinated brain space for the Drosophila (fruit fly) brain. Account is required.

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• SciCrunch
• 15 years ago - by Anonymous

A GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST. It can produce exactly the same results as NCBI-BLAST, and it also has very similar user commands. It also supports a pipeline mode, which can fully utilize the GPU and CPU resources when handling a batch of medium to large sized queries.

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• SciCrunch
• 13 years ago - by Anonymous

Ontodog is a web-based ontology view generator. It can generate inSubset annotation ontology, user preferred label annotation ontology and subset of source ontology. Simply provide Ontodog input term file (Microsoft Excel file or tab-delimited text file), select one source ontology or enter your own source ontology and SPARQL endpoint, then set the settings for Ontodog output files and get the OWL (RDF/XML) Output files. Ontodog performs the basic ontology modularization-like function, i.e.,it automatically extracts all axioms and related terms associated with user-specified signature term(s). In addition, Ontodog includes extra features: (1) extracting all instance data associated with the retrieved class terms and annotations; and (2) recursively extracting all axioms and related terms indirectly associated with signature terms. More features are being added to Ontodog, such as relabeling preferred names for various ontology terms to fit in with the needs from a specific community. The Ontodog input data requires a source ontology and a list of user-specified signature terms in tab-delimited format. Ontodog provides the template files for generating the signature terms as the input terms file to download. There are several output options that the users can choose based on their needs. With more and more ontologies being developed, Ontodog offers a timely web-based package of solutions for ontology view generation. Ontodog provides an efficient approach to promote ontology sharing and interoperability. It is easy to use and does not require knowledge of SPARQL, script programming, and command line operation. Ontodog is developed to serve the ontology community for ontology reuse. It is freely available under the Apache License 2.0. The source code is made available under Apache License 2.0.

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• SciCrunch
• 15 years ago - by Anonymous

An open web-accessible resource for gene functional annotations in the plant sciences to facilitate improvement, consolidation and visualization of gene annotations across several plant species. It is based on the MapMan ontology, organized in the form of a hierarchical tree of biological concepts, which describe gene functions. Currently, genes of the model species Arabidopsis, potato, tomato, rice, and tobacco are included. The main features are (i) dynamic and interactive gene product annotation through various curation options; (ii) consolidation of gene annotations for different plant species through the integration of orthologue group information; (iii) traceability of gene ontology changes and annotations; (iv) integration of external knowledge about genes from different public resources; and (v) providing gathered information to high-throughput analysis tools via dynamically generated export files. All of the GoMapMan functionalities are openly available, with the restriction on the curation functions, which require prior registration to ensure traceability of the implemented changes.

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• SciCrunch
• 13 years ago - by Anonymous

University of Kerala, formerly the University of Travancore, is an affiliating university located in Thiruvananthapuram, capital of the state of Kerala, India.

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• SciCrunch
• 16 years ago - submitted by Andrea Stagg

An Antibody supplier, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 14 years ago - by Anonymous

A stand-alone software program for scaffolding pre-assembled contigs using paired-read data. Main features are: a short runtime, multiple library input of paired-end and/or mate pair datasets and possible contig extension with unmapped sequence reads.

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• SciCrunch
• 13 years ago - by Anonymous

Tool to search for targets of conserved microRNAs in Caenorhabditis elegans by weighting RISC-immunoprecipitation-enriched parameters.

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• SciCrunch
• 13 years ago - by Anonymous

Created by the Government of Canada in 1997 to undertake world-class research and technology development to benefit Canadians by investing in facilities and equipment, universities, colleges, research hospitals and non-profit research institutions to attract and retain the world's top talent, training the next generation of researchers, supporting private-sector innovation and creating high-quality jobs.

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• SciCrunch
• 15 years ago - by Anonymous

Brain Canada is a national non-profit organization that develops and supports collaborative, multidisciplinary, multi-institutional research across the neurosciences. Through partnering with the public, private and voluntary sectors, Brain Canada connects the knowledge and resources available in this area to accelerate neuroscience research and funding and maximize the output of Canada''s world-class scientists and researchers. Brain Canada was created to address the twin challenges of increasing the scale of brain research funding in Canada and widening its scope to encourage interdisciplinary collaboration to produce insights for treating multiple disorders. Brain Canada is built on the successes and model of NeuroScience Canada (NSC). Established in 1999, NSC raised more than $11.5 million, leveraged over $20 million with partnered funding, and funded 100 individual and teams of researchers in Canada. Brain Canada is the new vision for Canadian brain researchthe voice for the brain and the grouping of brain disorders, raising awareness about their prevalence and impact on individuals, families, the economy and society. But most important, through the research we are funding, we are giving hope to the millions of Canadians who are directly or indirectly touched by diseases, disorders, and injuries of the brain, spinal cord and nervous system.

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• SciCrunch
• 15 years ago - by Anonymous

A set of tools designed to cluster large numbers (>1 million) of pre-aligned nucleotide sequences. It performs the clustering of sequences using the Hierarchical Clustering Algorithm (HCA). There are currently three different cluster metrics implemented: single-linkage, complete-linkage, and average-linkage. In addition, there are currently four sequence distance functions implemented, these are: identity (gap-gap counting as match), nogap (gap-gap being ignored), nogap-single (like nogap, but consecutive gap-nogap''s count as a single mismatch), tamura (distance is calculated with the knowledge that transitions are more likely than transversions). One advantage that HCA has over other algorithms is that instead of producing only the clustering at a given threshold, it produces the set of merges occuring at each threshold. With this approach, the clusters can afterwards very quickly be reported for every arbitrary threshold with little extra computation. This approach also allows the plotting of the variation of number of clusters with clustering threshold without requiring the clustering to be run for each threshold independently. Another feature of the way HPC-CLUST is implemented is that the single-, complete-, and average-linkage clusterings can be computed in a single run with little overhead.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented on August 18,2021.Research in the Department of Pharmacology addresses fundamental questions relevant to understanding the actions of drugs, hormones, neurotransmitters, and growth factors at the molecular and cellular level, as well as their effects on the whole organism. Current areas of focus, employing a wide variety of approaches and model systems, are neuropharmacology and mechanisms of signal transduction. Seminars, Journal Clubs and Interest Groups create a stimulating, supportive and collegial environment in which intra and interdepartmental collaborations flourish. Postdoctoral fellows and graduate students from the interdisciplinary Molecular and Cell Biology and Neuroscience training programs enrich this environment, and faculty are actively encouraged to participate all aspects of graduate education. In addition to modern, well-equipped laboratories within the Department, the Biomedical Instrumentation Center provides core facilities for imaging, flow cytometry, proteomics and protein and DNA sequencing. Other University resources, as well as our proximity to the National Institutes of Health, provide easy access to additional state-of the-art technologies that enhance the research programs of our faculty.

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• SciCrunch
• 17 years ago - by Anonymous

Project that developed an open access discovery platform, called Open Pharmacological Space (OPS), via a semantic web approach, integrating pharmacological data from a variety of information resources and tools and services to question this integrated data to support pharmacological research. The project is based upon the assimilation of data already stored as triples, in the form subject-predicate-object. The software and data are available for download and local installation, under an open source and open access model. Tools and services are provided to query and visualize this data, and a sustainability plan will be in place, continuing the operation of the Open PHACTS Discovery Platform after the project funding ends. Throughout the project, a series of recommendations will be developed in conjunction with the community, building on open standards, to ensure wide applicability of the approaches used for integration of data.

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• SciCrunch
• 15 years ago - by Anonymous

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