Curator Dashboard

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 6,2023. EMMA (Extensible MATLAB Medical image Analysis) is a toolkit designed to ease the use of MATLAB in the analysis of medical imaging data. It provides functions for reading and writing MINC files, viewing images, performing ROI operations, and performing several popular analyses. Also, there are toolkits for performing kinetic analysis of dynamic PET rCBF (regional cerebral blood flow) and FDG data. The goal for this site is to provide a centrally available listing of all image analysis tools that are available to the neuroscience community in order to facilitate the development, identification, and sharing of tools that are of use to the general community.

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• SciCrunch
• 17 years ago - by Anonymous

The AARSs database is the collection of amino acid sequences of all published AARSs. Currently it contains 1047 primary structures of cytoplasmic and organellar AARSs from various organisms. The entries are grouped according to AARS amino acid specificity. They are based on EMBL/SWISS-PROT format. Each includes the AARS amino acid sequence, its SWISS-PROT name and the accession number, a short description of the sequence, its source (organism name with taxonomic classification) and bibliographic information. For the enzymes whose sequences were determined at the nucleotide level, the appropriate EMBL/GenBank or TIGR entries are included, and for those with already known 3D structure, the cross-references to the Brookhaven Protein Data Base are indicated. The partial sequences of AARSs are also included in the database. According to the original SWISS-PROT description, some of the entries have been marked as putative or probable.

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• SciCrunch
• 17 years ago - by Anonymous

DINO is a realtime 3D visualization program for structural biology data. It runs under X-Windows and uses OpenGL. Supported architectures are Linux-i586 and Mac OSX. Versions for IRIX, OSF1 and SunOS are made available sporadically, usually upon request. DINO is distributed in binary form only, the current DINO version is 0.9.1. Structural Biology is a multidisciplinary research area, including x-ray crystallography, structural NMR, electron microscopy, atomic-force microscopy and bioinformatics (molecular dynamics, structure predictions, surface calculations etc). The data produced by these different research areas is very diverse: atomic coordinates (models and predictions), electron density maps, surface topographs, trajectories, molecular surfaces, electrostatic potentials, sequence alignements etc... DINO aims to visualize all this structural data in a single program and to allow the user to explore relationships between the data. There are five data-types supported: structure (atomic coordinates and trajectories), surface (molecular surfaces), scalar fields (electron densities and electrostatic potentials), topographs (surface topography scans) and geom (geometric primitives such as lines). The number and size of the data the program can handle is only limited by the amount of RAM present in the system. No artifical limits are set. Supported input file formats are PDB (coordinates), X-PLOR/CNS (coordinates, electron densities and trajectories), CHARMM (coordinates, trajectories and scalar fields), CCP4 (electron densities), UHBD (el, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

A graphical tool designed for detection of errors in relationship specification in general pedigrees by use of genome scan marker data. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

EPSRC is the main UK government agency for funding research and training in engineering and the physical sciences, investing more than £850 million a year in a broad range of subjects from mathematics to materials science, and from information technology to structural engineering. We support research into engineering, mathematics, physics, chemistry, materials science, information and communications technologies. EPSRC is a non-departmental public body funded by the UK government through the Department for Universities, Innovation and Skills. We employ around 300 staff in Swindon. We manage our portfolio through programmes. Research base programmes focus on investigator-led research and training. Business innovation programmes deliver our priority research themes and maximise the economic and social impact of the research and training we fund.

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• SciCrunch
• 16 years ago - submitted by Andrea Stagg

Software program to systematically design gene specific long oligonucleotide probes for entire genomes, for the purpose of developing whole genome microarrays. For each open reading frame, the program optimizes the oligo selection based upon several parameters, including uniqueness in the genome, sequence complexity, lack of self-binding, GC content and proximity to the 3''end of the gene.

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• SciCrunch
• 13 years ago - by Anonymous

An Antibody supplier

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• SciCrunch
• 14 years ago - by Anonymous

An Antibody supplier

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• SciCrunch
• 14 years ago - by Anonymous

It is a comprehensive database of Gene Expression Profiles, which enable to compare the transcriptome of various tissues, organs and experiments. mRNA expression levels of thousands of genes are measured with oligo-nucleotide DNA microarray "GeneChip". All gene expression data in this database is produced by LSBM (Laboratory for Systems Biology and Medicine) and the collaborators. SBM DB provides two different databases: A reference database for fur expression analysis (RefEXA) and LSMB GeNet, a database of various organisms, tissues, and experiences. RefEXA provides a comprehensive gene expression database of Human normal tissues, normal cultured cells and cancer cell lines with GeneChip HG-U133A, can help investigation of Human disease. LSMB provides

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• SciCrunch
• 17 years ago - by Anonymous

Software application that selects high resolution mapping subsamples and performs bin mapping (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

Voltage-gated potassium channel database (VKCDB) is designed to serve as a resource for research on voltage-gated potassium channels. Protein sequences, references, functional data and many other relevant data are included in this database. Mysql is used as the underlying database management system to meet the requirements of future development plans. VKCDB will allow you to browse and search using different annotation criteria, and search against the sequences in VKCDB with VKCBLAST. Displayed entries can be selected to download as multiple sequences in FASTA format for further analyses, such as ClustalW alignment. Several computational tools are being developed to help guide structure function analysis of voltage-gated potassium channels and other protein families in general. VKCDB currently stores 346 voltage-gated potassium channel entries, including some "unknown proteins" annotated by automatic genome annotation projects which share a high degree of sequence similarity with voltage-gated potassium channels. VKCDB was populated using automatic parsing of BLASTP search output. Entries were checked manually for redundancy, sequence conflicts, and isoforms, and they are hyperlinked to their variant entries as well as to entries with sequence conflicts. All entries contain GenBank annotations and Swissprot annotations if available. Current annotations were updated with Swissprot release 43.1 (Apr 2004) and GenBank as of Apr 2004. The snapshot version 3 of VKCDB in XML format as of Apr 2004 can be downloaded here. We collected available electrophysiological data and pharmacological data from over 200 journal articals and stored them in VKCDB. VKCDB is updated regularly from BLAST searches of new entries in GenBank and Swissprot. VKCBLAST are updated to include new sequences within a few days after new entries are added into VKCDB. Sequences of all VKCDB entries were sent to TMHMM and PHD for membrane domain prediction. Both results were parsed and linked to each VKCDB entry page. Multiple alignment of T1 and six transmembrane domains of Kv1-4 and KCNQ (Kv7) family are also presented here. VKCDB is a part of an ongoing high throughput voltage-gated potassium channel sequencing project in the laboratories of Dr. Warren J. Gallin and Dr. Andy N. Spencer at the University of Alberta, Canada.

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• SciCrunch
• 17 years ago - by Anonymous

A suit of algorithms and tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.

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• SciCrunch
• 13 years ago - by Anonymous

DOLOP is an exclusive knowledge base for bacterial lipoproteins by processing information from 510 entries to provide a list of 199 distinct lipoproteins with relevant links to molecular details. Features include functional classification, predictive algorithm for query sequences, primary sequence analysis and lists of predicted lipoproteins from 43 completed bacterial genomes along with interactive information exchange facility. This website along will have additional information on the biosynthetic pathway, supplementary material and other related figures. DOLOP also contains information and links to molecular details for about 278 distinct lipoproteins and predicted lipoproteins from 234 completely sequenced bacterial genomes. Additionally, the website features a tool that applies a predictive algorithm to identify the presence or absence of the lipoprotein signal sequence in a user-given sequence. The experimentally verified lipoproteins have been classified into different functional classes and more importantly functional domain assignments using hidden Markov models from the SUPERFAMILY database that have been provided for the predicted lipoproteins. Other features include: primary sequence analysis, signal sequence analysis, and search facility and information exchange facility to allow researchers to exchange results on newly characterized lipoproteins.

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• SciCrunch
• 17 years ago - by Anonymous

A pathway-based graphical interface for navigating the glycoenzyme database. The goal of the project is to define the paradigms by which carbohydrate binding proteins function in cellular communication. These pages are divided into six categories: -Glycosphingolipid: Sub-categories are Isogloboseries, Globoseries, Neo-lactoseries, Lactoseries and Ganglioseries - N-linked: Sub-categories are High-mannose, Hybrid and Complex -Mucin -Terminal Core 1 -Other O-linked -Terminal All: Includes all potential terminal structures for each glycan category

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• SciCrunch
• 17 years ago - by Anonymous

An Antibody supplier

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• SciCrunch
• 14 years ago - by Anonymous

An Antibody supplier

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• SciCrunch
• 14 years ago - by Anonymous

Software package providing an interactive graphical interface for computations in dynamical systems and visualization of resulting geometric structures, designed for researchers and educators studying dynamical systems (both differential equations and discrete time systems). DsTool readily produces nice pictures for both discrete and continuous systems.

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• SciCrunch
• 17 years ago - by Anonymous

The HUGE protein database has been created to publicize the Human cDNA project at the Kazusa DNA Research Institute. This project will sequence and analyze long (>4 kb) human cDNAs and establish methods by using the sequence data how to predict the primary structure of proteins of various biological activities. Currently, it focuses on the analysis of cDNA clones encoding particularly large proteins (>50 kDa). The HUGE protein database contains various types of information derived from the predicted primary structure data of newly identified human proteins. The HUGE protein database are expected to cover various sets of large human proteins of hitherto unidentified functions. They are likely to be involved in cellular structure/motility (such as cytoskeleton, membrane skeleton, and motor proteins), gene expression and nucleic acid metabolism, cell signaling/communication (such as cellular adhesion, signal transduction, channels, and receptors), and so on.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of virus-specific oligonucloetides and their primers. It allows users to search based on virus name, PMID, VirOligoID, or taxonomy ID. The VirOligo database is part of an effort to provide methods suitable for assessing what viruses are present in samples. Such methods should faciliate studies of the spatial and temporal distribution of viruses and their diversity at any one time and place. To this end, researchers are also exploring Virus Signature Hybridization (ViSH) and Virus Signature Amplification (ViSA), microarray-based methods for hybridization and PCR amplification. The site employs Universal PCR techniques, a PCR that amplifies DNA fragments from more than one viral species, such as family- or genus-specific PCR.

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• SciCrunch
• 17 years ago - by Anonymous

Software application for Bayesian estimation of the population inbreeding coefficient f (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous