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• SciCrunch
• 16 years ago - by Anonymous

A wiki all about medical imaging. Anyone may contribute who registers. Popular pages include Optical Imaging, Imaging brain function with optical topography, Optical mammography, Introduction to optical imaging, Comparison of time domain and frequency domain systems, Forward problem in diffuse optical imaging, Optical molecular imaging.

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• SciCrunch
• 16 years ago - by Anonymous

This tool will take a DNA sequence and find the large, non-overlapping open reading frames using the E.coli genetic code and the sites for all Type II and commercially available Type III restriction enzymes that cut the sequence just once. By default, only enzymes available from NEB are used, but other sets may be chosen. Just enter your sequence and submit. Further options will appear with the output. The maximum size of the input file is 1 MByte, and the maximum sequence length is 300 KBases. NEBcutter produces a variety of outputs including restriction enzyme maps, theoretical digests and links into the restriction enzyme database, REBASE (http://rebase.neb.com/rebase/rebase.html). Importantly, its table of recognition sites is updated daily from REBASE and it marks all sites that are potentially affected by DNA methylation (Dam, Dcm, etc.). Many options exist to choose the enzymes used for digestion, including all known specificities, subsets of those that are commercially available or sets of enzymes that produce compatible termini.

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• SciCrunch
• 16 years ago - by Anonymous

Action for Autism: Supporting Autistic People Blog

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• SciCrunch
• 16 years ago - by Anonymous

The CTB (Chernobyl Tissue Bank) is an international cooperation that collects, stores and disseminates biological samples from tumors and normal tissues from patients for whom the aetiology of their disease is known - exposure to radioiodine in childhood following the accident at the Chernobyl power plant. The main objective of this project is to provide a research resource for both ongoing and future studies of the health consequences of the Chernobyl accident. It seeks to maximize the amount of information obtained from small pieces of tumor by providing multiple aliquots of RNA and DNA extracted from well documented pathological specimens to a number of researchers world-wide and to conserve this valuable material for future generations of scientists. It exists to promote collaborative, rather than competitive, research on a limited biological resource. Tissue is collected to an approved standard operating procedure (SOP) and is snap frozen; the presence or absence of tumor is verified by frozen section. A representative paraffin block is also obtained for each case. Where appropriate, we also collect fresh and paraffin-embedded tissue from loco-regional metastases. Currently we do not issue tissue but provide extracted nucleic acid, paraffin sections and sections from tissue microarrays from this material. The project is coordinated from Imperial College, London and works with Institutes in the Russian Federation (the Medical Radiological Research Centre in Obninsk) and Ukraine (the Institute of Endocrinology and Metabolism in Kiev) to support local scientists and clinicians to manage and run a tissue bank for those patients who have developed thyroid tumors following exposure to radiation from the Chernobyl accident. Belarus was also initially included in the project, but is currently suspended for political reasons.

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 2nd, 2022. Tissue bank and service organization for bioimplants.

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• SciCrunch
• 16 years ago - by Anonymous

Not yet vetted by NIF curator

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• SciCrunch
• 16 years ago - by Anonymous

A biobank of human biological material and genetic information. It provides samples and information to researchers in order to identify new genes and clarify pathogenic mechanisms of diseases. The biobank offers biochemical and molecular diagnoses of genetic dystonias, Parkinson's disease and NBIA disorders, as well as storage of biological samples for external institutions.

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• SciCrunch
• 16 years ago - by Anonymous

Not yet vetted by NIF curator

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• SciCrunch
• 16 years ago - by Anonymous

Science-specific search engine with over 575 million scientific items indexed at last count (May 2013), it allows researchers to search for not only journal content but also scientists'' homepages, courseware, pre-print server material, patents and institutional repository and website information. Scirus helps you quickly locate scientific information on the Web: * Filters out non-scientific sites. For example, if you search on REM, Google finds the rock group - Scirus finds information on sleep, among other things * Finds peer-reviewed articles such as PDF and PostScript files, which are often invisible to other search engines. * Searches the most comprehensive combination of web information, preprint servers, digital archives, repositories and patent and journal databases. Scirus goes deeper than the first two levels of a Web site, thereby revealing much more relevant information. Scirus has proved so successful at locating science-specific results on the Web that the Search Engine Watch Awards voted Scirus ''Best Specialty Search Engine'' in 2001 and 2002 and ''Best Directory or Search Engine Website'' WebAward from Web Marketing Association in 2004, 2005, 2006 and 2007. Give your Web site greater functionality and enhance the experience of your users, by adding Scirus to your home page for free. Scirus uses the latest in search engine technology to pinpoint precise scientific information that other search engines can not reach, including pdf files and peer reviewed articles. Make your Web site more visible to the scientific community, by submitting it for inclusion on Scirus. You will increase the chance of scientists finding your site when looking for information and you could increase your visitor rate.

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• SciCrunch
• 16 years ago - by Anonymous

A component of EcoliHub, EcoliWiki is a wiki-based system for finding, editing, and adding information about E. coli K-12 and other model organism strains of E. coli. EcoliWiki is being constructed to include information about bacteriophage, plasmids, and mobile genetic elements. Information should be easily accessible and correct, and users have the right to edit any information they feel is incorrect. Most of the E. coli information was initially seeded with a subset of information from parsing EcoCyc data dumps. For phage gamma and the F plasmid, Genbank accessions were converted to GFF, which was parsed into the appropriate tables. Other sources of content include: * user additions * monthly addition of annotations from EcoCyc * structural data from the PDB * domains and motif information from InterPro * various databases including EcoGene, RegulonDB, Genbank, GenoBase, ASAP * many many scientific papers EcoliWiki participates in the RefGenome project. EcoliWiki provides REST web services as part of the EcoliHub Web Services infrastructure project.

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• SciCrunch
• 16 years ago - by Anonymous

VAST is a computer algorithm developed at NCBI and used to identify similar protein 3-dimensional structures by purely geometric criteria, and to identify distant homologs that cannot be recognized by sequence comparison. Related structures for every structure in MMDB are pre-computed using VAST and accessible via links on the MMDB Structure Summary pages. The VAST Search page also allows you to compare the coordinates of a newly resolved structure in PDB format against all structures in MMDB to find its neighbors. Protein structure neighbors in Entrez are determined by direct comparison of 3-dimensional protein structures with the VAST algorithm. Each of the more than 87,804 domains in MMDB is compared to every other one. From the MMDB Structure summary pages, retrieved via Entrez, structure neighbors are available for protein chains and individual structural domains. If you already know a PDB/MMDB-Id you can try this at once, using the input form in the right column. VAST Search is a service that allows searching for structural neighbors starting with a set of 3D-coordinates specified by the user. This service is meant to be used with newly determined protein structures that are not yet part of MMDB. Structure neighbors for proteins already in MMDB have been pre-computed and can simply be looked up from MMDB''s Structure summary pages!

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core performs research activities to create a wide array of industrial technologies using genomes and the other biological information to fulfill their mission. CBRC hosts research staff experts in diverse fields spanning computer science, mathematics, physics, chemistry, and biology and scientists affiliated with other institutions, with whom they work closely on joint, collaborative projects. Core offers internally developed and maintained software applications and databases, with corresponding external resources.

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• SciCrunch
• 16 years ago - by Anonymous

The Microbe Division in RIKEN-BRC has been collecting, preserving, and distributing cultured microbial strains as one of the leading culture collections in the world since established as Japan Collection of Microorganisms (JCM) in 1981. JCM aims to contribute to scientific communities by maintaining and serving high-quality microbial resources useful for general microbial studies and various research fields particularly in health and environmental science. JCM has participated in the National BioResource Project supported by the Ministry of Education, Culture, Sports, Science and Technology of Japan as the core facility for General Microbes. JCM maintains approximately 19,900 strains as of Sept. 2010, and the approximate numbers of the available strains from JCM are: 7,400 strains of aerobic and anaerobic bacteria including actinomycetes, 300 strains of archaea, and 4,100 strains of fungi including yeasts (in total ca. 12,000 strains). Strains held at JCM are limited to those classified in Risk Group 1 or 2. Information of the available strains is opened to the public through the JCM On-line Catalogue Database. Genomic DNA samples of some strains are also distributed in cooperation with RIKEN BRC-DNA Bank. More than 3,500 strains are annually distributed to domestic and overseas researchers. JCM welcomes a deposit of microbial strains published or designed to be published in scientific papers as well as an order for microbial cultures.

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Integrated RNA-Seq read analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

It is a prospective cohort study designed to investigate the relationship between sleep disordered breathing and cardiovascular disease. Participants were recruited from nine existing epidemiological studies in which data on cardiovascular risk factors had been collected previously.

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• SciCrunch
• 14 years ago - by Anonymous

The purpose of these three Banks (SUDDEN DEATH BRAIN AND TISSUE BANK, HIV BRAIN AND TISSUE BANK, and CJD BRAIN AND TISSUE BANK) is to collect donated samples from the brain and other organs of the body during post mortem examination, and to make these available for medical research. All the samples stored in the Edinburgh Banks are fully authorized for research by families and ethically approved for research use in accordance with the terms of current UK Human Tissue legislation. During the last 100 years or so, much of our knowledge of brain disorders has come from the study of post mortem tissues, based on identifying the differences between diseased and control (normal) brains. Advances in the diagnosis and treatment, as well as understanding the genetic background, of disorders such as Alzheimer''s disease, dementia with Lewy bodies, Parkinson''s disease and the effects of head injury have all depended on research using Brain Bank resources in different countries. Brain Banking in Edinburgh commenced in 1990, focusing specifically on HIV infection of the brain and on Creutzfeldt-Jakob disease (CJD). Significant progress in understanding these two brain infections has resulted both from the research in Edinburgh and from the work of scientists worldwide who have used tissue samples from the Edinburgh Brain Banks. These resources proved vital in establishing variant CJD as a new disease, different from the classic sporadic form and in demonstrating the brain changes in pre-AIDS and AIDS, particularly in drug abusers. In 2005 a third brain bank was established in Edinburgh with the specific aim of collecting donated normal brain tissue samples from the forensic post mortem service since there is a worldwide shortage of such material. This Bank also collects samples donated from individuals with psychiatric disorders or a history of head injury or of drug and alcohol addiction.

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• SciCrunch
• 16 years ago - by Anonymous

A software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification. Crux analyzes shotgun proteomics tandem mass spectra, associating peptides with observed spectra. This software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification is provided as a single executable. Crux is implemented in C and is distributed with source code freely to noncommercial users. Mass spectrometry, the core technology in the field of proteomics, promises to enable scientists to identify and quantify the entire complement of proteins in a complex biological sample. Currently, the primary bottleneck in this type of experiment is computational. Existing algorithms for interpreting mass spectra are slow and fail to identify a large proportion of the given spectra. We describe a database search program called Crux that reimplements and extends the widely used database search program Sequest. For speed, Crux uses a peptide indexing scheme to rapidly retrieve candidate peptides for a given spectrum. For each peptide in the target database, Crux generates shuffled decoy peptides on the fly, providing a good null model and, hence, accurate false discovery rate estimates. Crux also implements two recently described postprocessing methods: a p value calculation based upon fitting a Weibull distribution to the observed scores, and a semisupervised method that learns to discriminate between target and decoy matches. Both methods significantly improve the overall rate of peptide identification.

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• SciCrunch
• 16 years ago - by Anonymous

The intellectual system GenExpress designed for analysis of genomic regulatory sequences of higher eukaryotes comprises the following major units: (1) the database of transcription regulatory regions of eukaryotic genes TRRD that contains the description of regulatory regions of 427 eukaryotic genes, including 2133 transcription factor binding sites, 78 composite regulatory elements, 593 enhancers, and other types of transcription-regulating elements; (2) the database Activity that comprises the available data on the activity of the sites involved in the regulation of gene expression as well as the physico-chemical, conformational, and statistical DNA/RNA properties significant for the activity of these sites; (3) the database for gene networks GeneNet that contains the information on groups of the genes functioning coordinately to provide expression of genetic information; (4) a set of programs for detecting functional sites and predicting their activity; (5) programs for visualization of the information contained in the listed databases and the results of analysis; (6) semantic means to provide user''s navigation in the system. SRS (Sequence Retrieval System) query language was chosen for the system GenExpress, as it is widespread and Internet-compatible. GenExpress is available at /mgs/systems/geneexpress/. Applications of the system to analysis of the structure-function organization of human genomic nucleotide sequences are considered.

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• SciCrunch
• 16 years ago - by Anonymous

Databases which provide clustered sets of sequences from UniProt Knowledgebase and selected UniParc records, in order to obtain complete coverage of sequence space at several resolutions while hiding redundant sequences from view. The UniRef100 database combines identical sequences and sub-fragments with 11 or more residues (from any organism) into a single UniRef entry. The sequence of a representative protein, the accession numbers of all the merged entries, and links to the corresponding UniProtKB and UniParc records are all displayed in the entry. UniRef90 and UniRef50 are built by clustering UniRef100 sequences with 11 or more residues such that each cluster is composed of sequences that have at least 90% (UniRef90) or 50% (UniRef50) sequence identity to the longest sequence (UniRef seed sequence). All the sequences in each cluster are ranked to facilitate the selection of a representative sequence for the cluster.

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• SciCrunch
• 16 years ago - by Anonymous