Curator Dashboard

A software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data.

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• SciCrunch
• 13 years ago - by Anonymous

FishNet is a collaborative effort by natural history museums and other biodiversity institutions to establish a global network of Ichthyology collections. There is an open invitation for any institution with a fish collection to join. The current portal is an outgrowth of the original FishNet project with improvements in network stability, georeferencing capabilities, and technical support. Users are provided access to searchable, mappable and downloadable data that are cached on a regular basis from participating institutions who have published their data via the DiGIR or TAPIR protocols with a Darwin Core schema. FishNet is also one of four (along with MaNIS, HerpNET, and ORNIS) vertebrate network portals that provide access to specimen collection records from around the world. These web portals, together, comprise VertNet and serve georeferenced, taxon-based data from 72 global institutions. VertNet is a cooperative project working to maintain and expand these distributed database projects. Future plans for VertNet include biodiversity informatics workshops, enhancement of the portal design, better searching capabilities, and a dynamic cache to expand performance and analytic features. :Sponsors: This resource is supported by the National Science Foundation :.

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• SciCrunch
• 17 years ago - by Anonymous

A de novo assembly algorithm for Next-Generation Sequencing technology.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool which predicts possible impact of amino acid substitution on structure and function of human protein using straightforward physical and comparative considerations. PolyPhen-2 is new development of PolyPhen tool for annotating coding nonsynonymous SNPs.

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• SciCrunch
• 17 years ago - by Anonymous

R package intended to implement a program for multiple alignment-free sequence comparison based on long genome sequence or NGS data.

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• SciCrunch
• 13 years ago - by Anonymous

This portal describes Professor Kitaoka Akiyoshi''s research in the science of visual illusions. Working as an associate professor at the Ritsumeiken University, Department of Psychology, he is one of the few researchers in Japan to be actively researching in this field of study. Professor Kitaoka defines an illusion as a misperception of a real object, adding that defining what is real is a difficult task that depends on recognition and epistemology. An illusion is formed when the perceived characteristics of the object differ from the physical characteristics. Professor Kitaoka first started studying visual illusions when working at the Tokyo Metropolitan Institute for Neuroscience, before coming to RU. He currently researches geometrical, color, lightness, and motion illusions and visual completion, and has become a prominent expert in the field, publishing a wide range of articles on the subject as well as the popular books Trick Eyes, Trick Eyes 2, Trick Eyes Graphics, and the Handbook of the Science of Illusion. To create his illusions, Professor Kitaoka uses graphic design software such as CorelDRAW, Adobe Illustrator, and the drawing software included in Microsoft Word in addition to making use of programming languages like Borland Delphi (Pascal). All of the images set out to test hypotheses that serve to advance his study of illusions and their applications for other visual functions. The goal of his research is to test visual mechanisms through visual illusions.

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• SciCrunch
• 16 years ago - by Anonymous

Set of different illusions, including color illusions, motion illusions, and optic illusions. Most illusions are from Professor Akiyoshi Kitaoka of the Ritsumeikan University in Kyoto, Japan.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. An online database containing information aboutMyxococcus xanthus. It provides a genome browser, microarray data, and BLAST functions. MyxoPedia is an online, community driven encyclopedia for information about ''anything Myxo''. Registered community members are welcome to add and edit articles on any aspect of Myxococcus xanthus here. Myxopedia faciliates M.xanthus and other myxobacterial researchers to contribute directly towards the ongoing genome annotation.

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• SciCrunch
• 17 years ago - by Anonymous

• Organization
• SciCrunch
• 15 years ago - submitted by Andrea Stagg

The incidence of Creutzfeldt-Jakob disease (CJD) is monitored in the UK by the National CJD Surveillance Unit (NCJDSU) based at the Western General Hospital in Edinburgh, Scotland. The Unit brings together a team of clinical neurologists, neuropathologists and scientists specialising in the investigation of this disease. This document is intended to summarise the research in progress at the NCJDSU and also provide some background information about CJD and other human spongiform encephalopathies. We have also provided some links to other resources and contrary points of view available on the Web.

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• SciCrunch
• 14 years ago - by Anonymous

SYFPEITHI is a database comprising more than 7000 peptide sequences known to bind class I and class II MHC molecules. The entries are compiled from published reports only. It contains a collection of MHC class I and class II ligands and peptide motifs of humans and other species, such as apes, cattle, chicken, and mouse, for example, and is continuously updated. Searches for MHC alleles, MHC motifs, natural ligands, T-cell epitopes, source proteins/organisms and references are possible. Hyperlinks to the EMBL and PubMed databases are included. In addition, ligand predictions are available for a number of MHC allelic products. The database is based on previous publications on T-cell epitopes and MHC ligands. It contains information on: -Peptide sequences -anchor positions -MHC specificity -source proteins, source organisms -publication references Since the number of motifs continuously increases, it was necessary to set up a database which facilitates the search for peptides and allows the prediction of T-cell epitopes. The prediction is based on published motifs (pool sequencing, natural ligands) and takes into consideration the amino acids in the anchor and auxiliary anchor positions, as well as other frequent amino acids. The score is calculated according to the following rules: The amino acids of a certain peptide are given a specific value depending on whether they are anchor, auxiliary anchor or preferred residue. Ideal anchors will be given 10 points, unusual anchors 6-8 points, auxiliary anchors 4-6 and preferred residues 1-4 points. Amino acids that are regarded as having a negative effect on the binding ability are given values between -1 and -3. Sponsors: SYFPEITHI is supported by DFG-Sonderforschungsbereich 685 and theEuropean Union: EU BIOMED CT95-1627, BIOTECH CT95-0263, and EU QLQ-CT-1999-00713.

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• SciCrunch
• 17 years ago - by Anonymous

Software package that implements gene and gene-set level analysis methods for somatic mutation studies of cancer.

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• SciCrunch
• 13 years ago - by Anonymous

http://www.cdc.gov/niosh/oep/funding.html

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• SciCrunch
• 15 years ago - submitted by Andrea Stagg

A simple arithmetic coding based compressor for the SAM and BAM (DNA sequence alignment) file format.

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• SciCrunch
• 13 years ago - by Anonymous

Tissue bank for collecting, cataloging and storing postmortem brain tissue samples from subjects with and without neurological disorders. Specimens are available for research on cognitive impairment, Alzheimer's, dementia and other disorders along with clinical data such as demographic information, health and family history and neuropsychological test scores. The bank provides services to distribute postmortem brain tissue and other samples to investigators for use in research that will provide qualitative and quantitative diagnostic information to physicians, families, and researchers.

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• SciCrunch
• 15 years ago - by Anonymous

Software application for identifying all Mendelian inconsistencies in complex pedigree data with thousand of individuals, including many loops and several errors. Can also infer missing genotypes. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.

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• SciCrunch
• 13 years ago - by Anonymous

Software package to explore high-throughput ''C'' data such as 5C or Hi-C.

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• SciCrunch
• 13 years ago - by Anonymous

A perl script that finds microsatellite repeat elements directly from raw 454 or Illumina paired-end sequencing reads.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. It provides annotated sequence data and classifications for the genomes of eighteen species of hemiascomycete yeasts, including nine complete genomes. The Gnolevures web resources provides genetic element pages, orthologs defined by syntenic homology, protein families, a genome browser for interspecies comparison, and data sets for downloading. An advanced search facility permits a number of criterion-based and full text queries. Classification data, including protein families and orthologs, and the most up-to-date genome annotations, are for the most part not available in general-purpose sequence data bases such as EMBL/GenBank/DDBJ.

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• SciCrunch
• 17 years ago - by Anonymous