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Software for automated anatomical labeling of activations in SPM (Statistical Parametric Mapping) using a macroscopic anatomical parcellation of the MNI MRI single-subject brain. The software was used for an automated anatomical parcellation of the spatially normalized single-subject high-resolution T1 volume provided by the Montreal Neurological Institute (MNI) (D. L. Collins et al., 1998, Trans. Med. Imag. 17, 463468, PubMed). Using this parcellation method, three procedures to perform the automated anatomical labeling of functional studies were proposed: (1) labeling of an extremum defined by a set of coordinates, (2) percentage of voxels belonging to each of the anatomical volumes of interest (AVOI) intersected by a sphere centered by a set of coordinates, and (3) percentage of voxels belonging to each of the AVOI intersected by an activated cluster. An interface with the Statistical Parametric Mapping package is provided as a freeware to researchers of the neuroimaging community.

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• SciCrunch
• 13 years ago - by Anonymous

Program consisting of three Task Forces and one Working Group to promote data exchange and integration in the neurosciences by developing terminology standards and formal ontologies for neural structures. Closely linked to the Program on Digital Brain Atlasing, the Program aims to establish a structured lexicon for the translation and definition of terms describing neural structures at multiple levels of granularity. The three Task Forces and one Working Group involved in the PONS effort: * Structural lexicon * Neuron registry * Representation and deployment * KnowledgeSpace Working Group Structural lexicon, Neuron registry, Representation and deployment, and KnowledgeSpace Working Group.

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• SciCrunch
• 13 years ago - by Anonymous

Provides animal and human serums, plasmas, purified proteins, and antisera.

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• SciCrunch
• 14 years ago - by Anonymous

Private comprehensive research university in South Korea. Starting as a church-run kindergarten in 1918, CAU transformed into a school for female kindergarten teachers in 1922 and was granted university status in 1953.

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• SciCrunch
• 13 years ago - submitted by Timothy Tsui

Database for molecular interaction information integrated with various other bio-entity information, including pathways, diseases, gene ontology (GO) terms, species and molecular types. The information is obtained from several manually curated databases and automatic extraction from literature. There are protein-protein interaction, gene/protein regulation and protein-small molecule interaction information stored in the database. The interaction information is linked with relevant GO terms, pathway, disease and species names. Interactions are also linked to the PubMed IDs of the corresponding abstracts the interactions were obtained from. Manually curated molecular interaction information was obtained from BioGRID, IntAct, NCBI Gene, and STITCH database. Pathway related information was obtained from KEGG database, Pathway Interaction database and Reactome. Disease information was obtained from PharmGKB and KEGG database. Gene ontology terms and related information was obtained from Gene Ontology database and GOA database.

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• SciCrunch
• 13 years ago - by Anonymous

A file format for graphs that consists of a language core to describe the structural properties of a graph and a flexible extension mechanism to add application-specific data. It is based on XML and is ideally suited as a common denominator for all kinds of services generating, archiving, or processing graphs. Its main features include support of * directed, undirected, and mixed graphs, * hypergraphs, * hierarchical graphs, * graphical representations, * references to external data, * application-specific attribute data, and * light-weight parsers.

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• SciCrunch
• 13 years ago - by Anonymous

TACMASS collects, preserves, and banks biospecimens obtained from Arizona Cancer Center surgical patients who are seen by University Medical Center surgeons and oncologists. Biospecimens collected at the time of surgery include fresh surgical tissue, blood and urine. Serum, plasma and genomic DNA are harvested from the whole blood. AZCC Members and collaborators may request the use of banked biospecimens through TACMASS. The patient's surgeon or oncologist is responsible for consenting the patient for submission of surgical specimens to the AZCC BioRepository (IRB #06-0609-04, Setsuko Chambers, PI). The surgeon and the Department of Pathology attending physicians and residents are responsible for identifying appropriate tissue for banking that will not compromise pathological diagnosis. Tumor and/or normal adjacent tissue, identified by gross examination, that will not be needed for pathological diagnosis are preserved by fixing in formalin, snap freezing, and/or fixing in RNALater. Histological diagnosis is rendered on each piece of formalin-fixed and snap frozen tissue by Hematoxylin and Eosin staining (H&E). Everyone involved in submitting specimens to the Tumor Bank must maintain a current CITI Certification.

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• SciCrunch
• 16 years ago - by Anonymous

Software tool that displays large genomics datasets (e.g. gene expression data from Arabidopsis Affymetrix arrays) onto diagrams of metabolic pathways or other biological processes.

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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 September 6, 2016. Sage Bionetworks video podcasts feature the plenary talks from the April 2011 Commons Congress in San Francisco. The Keynote and project update video posts are in reverse chronological order; the full agenda is available at www.sagecongress.org. There are also several excellent podcasts from the January 2011 Symposium on Human Data Interoperability. The podcasts are also available on iTunes where you can subscribe and receive new podcasts automatically when posted. Upcoming posts will feature presentations and interviews on network biology, genomics, healthcare and open science. All these podcasts feature research and thought leaders as well as policy advocates, scientists working at the coal-face and patients. The topics span technical and strategic issues and include fact and opinion. The goal is to engage, educate and inspire non-scientists and scientists alike.

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• SciCrunch
• 16 years ago - by Anonymous

Archive and access films from the field of Ophthalmology for free on highly secure servers for permanent access and citeability. A citeable identification number (specific addressing using DOI), allows for citation of individual films in journal publications. Films may be commented by the author either in speech, or in text. Key wording provided by the authors at the time of submission, make each film recognizable to internet search machines.

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• SciCrunch
• 13 years ago - by Anonymous

Data sets resulting from glaucoma research including visual fields, various imaging modalities and other data from both glaucomatous and normal subjects. The Longitudinal Glaucomatous Visual Fields data set contains IOP (Intraocular pressure) measurements and 24-2 Full Threshold visual fields obtained with a Humphrey Field Analyzer (Zeiss). Data of both eyes of 139 patients over a mean period of over 9 years is included, with on average more than 17 fields per eye. Local threshold and total deviation values are included.

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• SciCrunch
• 13 years ago - by Anonymous

Public university in Newport News, Virginia. Academic programs at CNU encompass more than 80 areas of study, from biology to business administration and political science to performing arts.

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• SciCrunch
• 17 years ago - submitted by Andrea Stagg

Resting state datasets, including an anatomical as well as a resting state fMRI scan, collected from a community sample in Valencia, Spain. The first release includes data for 45 participants. Participants were instructed to keep their eyes open during the resting state scan, no visual stimulus was presented. The following data are released for every participant: * Scanner Type: Philips Achieva 3T-TX * One high-resolution T1-weighted mprage, defaced to protect patient confidentiality * At least one 6-minute resting state fMRI scan (R-fMRI), eyes open, no visual stimulus presented * Demographic Information

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• SciCrunch
• 13 years ago - by Anonymous

Dataset consisting of a community sample of individuals ranging in age from 18 to 60 years old with at least two 7.5-minute resting state fMRI scans. During the resting state scan participants were instructed to relax while keeping their eyes open. In part of the sample eye status was randomized between scans. The particular eye status for each scan is indicated in the phenotypic information. No visual stimulus was presented. A subset of participants completed the ICS and PANAS affective behavior scales. The following data are released for every participant: * Scanner Type: Siemens, 3T Trio Tim * 7.5-minute resting state fMRI scan (R-fMRI) * MPRAGE anatomical scan, defaced to protect patient confidentiality * Demographic information, inluding ICS and PANAS scores (included in the release file).

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• SciCrunch
• 13 years ago - by Anonymous

World's open biospecimen research database where biobanks and biomedical researchers meet to exchange human biospecimen needs and supply: whole blood, serum, plasma, solid tissue samples and more. The connection is accelerated so researchers save valuable time and money and tissue banks utilize inventory. The pace of specimen procurement remains unacceptably slow to the biomedical research community. Specimen Central is the foremost global resource to aid biomedical researchers in expediting their search for high quality human biospecimens, tissues, samples and specimens. They facilitate your search for blood, whole blood, buccal swab, DNA, RNA, protein, cell lines, plasma, serum, RBC, white cells, buffy coat, fluid, marrow, urine, stem cells, and solid tissue such as tumor, tumor and biopsy materials spanning all manner of common and rare pathologies and indications including Alzheimer's, basal cell carcinoma, bladder cancer, bone cancer, brain cancer, breast cancer, cerebrospinal fluid, amniotic fluid, colorectal cancer, colon cancer, hodgkins and non-hodgkins lymphoma, kidney/renal cancer, leukemia, liver cancer, lung cancer, melanoma, multiple sclerosis, myeloma neuroblastoma, neurodegenerative diseases, ovarian cancer, pancreatic cancer, prostate cancer, urinary cancer. This includes adult and pediatric indications. Specimen Central users specify a number of variables in their Specimen Requests, including preparation, preservation and handling requirements such as cryo-preserved, FFPE (Formalin-fixed paraffin-embedded), formalin, frozen, refrigerated, OCT, snap frozen, paraffin block, fresh, prospective, autopsy or cadaveric, etc. Many users require clinically annotated date associated with their specimens, as well as documentation of IRB or ethics committee approval and informed consents. For Researchers Most specimen databases require researchers to waste time and effort entering lengthy registrations and search queries that yield poor results, if anything. Specimen Central solves this problem by having tissue banks search for you. From years to months, months to weeks, and weeks to days, Specimen Central seeks to reduce delays and costs in the research & development life cycle by expediting connections between demand and supply. For Biobanks The capital costs of maintaining a biobank infrastructure are substantial and growing. Biobanks use Specimen Central as a marketing tool to augment their business development efforts. By routinely checking Specimen Central's Specimen Requests, biobanks can uncover market demand for their inventories and develop new connections and revenue streams to defray costs. Specimen Central supplements - not displaces - the efforts of your sales representatives, agents, brokers and commercial partners.

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• SciCrunch
• 16 years ago - by Anonymous

The RNA modification database provides a comprehensive listing of posttranscriptionally modified nucleosides from RNA. Information provided for each nucleoside includes: the type of RNA in which it occurs and phylogenetic distribution; common chemical name and symbol; Chemical Abstracts registry number and index name; chemical structure; initial literature citations for structural characterization or occurrence, and for chemical synthesis. Both the structural diversity and extent of posttranscriptional modification in RNA is remarkable, with 107 different nucleosides presently known in all types of RNA. The discovery of new modified nucleosides as well as increasing knowledge of the array of functional roles of modification, based largely on extensive studies of tRNA, mandates a need for a comprehensive database of RNA nucleosides. The RNA Modification Database is maintained as an extension of the initial version published in mid-1994. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA. The information provided permits access to the modified nucleoside literature through provision of both computer-searchable Chemical Abstracts registry numbers and key literature citations. This database also provides an historical record of the initial reports of occurrence, characterization and chemical synthesis of modified nucleosides from RNA. It is our judgement that the total number of RNA nucleosides listed, and the chemical structures reported, are very accurate. However, the distributions listed are in some cases a matter of concern, due primarily to the possibility of inhomogeneity of the RNA isolate and the use of methods of nucleoside identification that are not sufficiently rigorous. Reinvestigation of some of the unusual or single-report source distributions is warranted, and will likely lead to future refinements in the listings. The authors invite comments concerning new entries, errors or omissions and on the format presently used for electronic access to the database.

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• SciCrunch
• 17 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 September 6, 2016. FSSP (families of structurally similar proteins) is a database of structural alignments of proteins in the Protein Data Bank. The database currently contains an extended structural family for each of 330 representative protein chains. Each data set contains structural alignments of one search structure with all other structurally significantly similar proteins in the representative set (remote homologs, below 30%% sequence identity), as well as all structures in the Protein Data Bank with 70-30%% sequence identity relative to the search structure (medium homologs). Very close homologs (above 70 % sequence identity) are excluded as they rarely have marked structural differences. The alignments of remote homologs are the result of pairwise all-against-all structural comparisons in the set of 330 representative protein chains. All such comparisons are based purely on the 3D co-ordinates of the proteins and are derived by automatic (objective) structure comparison programs. The significance of structural similarity is estimated based on statistical criteria. The FSSP database is available electronically and by anonymous ftp (file transfer protocol).

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• SciCrunch
• 16 years ago - by Anonymous

An Antibody supplier

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• SciCrunch
• 14 years ago - by Anonymous

A coalescent simulation software program for a structured population including recombination, demographic structure and selection at a single diploid locus.

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• SciCrunch
• 12 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023.BAMS is an online resource for information about neural circuitry. The BAMS Cell view focuses on the major brain regions and which cells are contained therein.

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• SciCrunch
• 16 years ago - by Anonymous