Curator Dashboard

A web-based application designed from a genetic epidemiology point of view to analyze association studies using single nucleotide polymorphisms (SNPs). For each selected SNP, you will receive: * Allele and genotype frequencies * Test for Hardy-Weinberg equilibrium * Analysis of association with a response variable based on linear or logistic regression * Multiple inheritance models: co-dominant, dominant, recessive, over-dominant and additive * Analysis of interactions (gene-gene or gene-environment) If multiple SNPs are selected: * Linkage disequilibrium statistics * Haplotype frequency estimation * Analysis of association of haplotypes with the response * Analysis of interactions (haplotypes-covariate)

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• SciCrunch
• 14 years ago - by Anonymous

Software package that implements and enhances circular visualization in R. Due to natural born feature of R to draw statistical graphics, this package can provide more general and flexible way to visualize huge information in circular style.

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• SciCrunch
• 12 years ago - by Anonymous

High resolution, compact and robust confocal that enables immunohistochemical colocalization analysis of florescent markers. Leica TCS SPE confocal point-scanning, spectral system for fluorescence imaging of live or fixed cells.

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• SciCrunch
• 12 years ago - by Anonymous

Set of programs and Tk/Tcl scripts, with a GUI wrapper, for extracting the inner and outer cortical surfaces from a T1-weighted MR image of the human brain. It is based on the TFI C++ library and is written for a Unix-based environment (specifically 64-bit and 32-bit versions of Ubuntu). As a courtesy to Apple users a version for Apple/X11 is maintained but the OS X version will always lag the Linux version; also, because some of the third-party libraries SurfRelax relies on may not be supported in or compatible with future versions of OS X, there is no guarantee that the OS X version will be supported indefinitely. Although in principle SurfRelax could be run under Windows (using Cygwin), because of the difficulties of maintaining multiple platforms and the limited support libraries available under Cygwin, there will no longer be support for SurfRelax on this platform. The surfaces are guaranteed to be topologically equivalent to a sphere, thereby obviating the need for handle removal. SurfRelax requires no user intervention, although minor manual editing is recommended for optimal results (normally less than 10 minutes per hemisphere). SurfRelax has several properties that compare favorably with other software packages for surface reconstruction: * Free software - The binaries (written in C++ and Tcl/Tk) are in the public domain. The source code will be released once legacy code issues have been resolved (i.e. replacing with GPL code). * Uses standard public file formats: Analyze file format (SPM/FSL-compatible) for volumes and OOGL OFF binary format for surfaces (see www.geomview.org (http://www.geomview.org/docs/html/geomview_26.html#OOGLRef)) * Combines advantages of volumetric and surface-based methods for surface generation * Correct topology of output surface guaranteed * Requires little or no user intervention - no need for manual handle removal * Relatively robust to noise - multi-scale method compensates for partial volume effects and intensity inhomogeneities * Relatively fast (an entire brain is segmented, extracted and unfolded in less than 2 hours of CPU time) * Powerful editing and visualization tools for volumes and surfaces * Readily extendable - for instance for use with monkey brains or children's brains * Can be used to visualize functional data from SPM or FSL * Includes tools for integration with Stanford's VISTASOFT tools for FMRI data analysis (white.stanford.edu)

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• SciCrunch
• 17 years ago - by Anonymous

Database of confirmed translation initiation sites (TISs) for prokaryotic genomes. The confirmed data has supporting evidence from different sources, including experiments records in the public protein database Swiss-Prot, literature, conserved domain search and sequence alignment among orthologous genes. Combing with predictions from the-state-of-the-art TIS predictor MED-Start/MED-StartPlus (in release 1.0 & 1.2) and TriTISA (since release 1.4) and annotations on potential regulatory signals, the database can serve as a refined annotation resource for the public database RefSeq.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. It investigates mitochondrial genome diversity and evolution by systematically determining the complete mitochondrial DNA (mtDNA) sequences of a phylogenetically broad selection of protists. The mtDNAs of lower fungi and choanoflagellates are being analyzed by the Fungal Mitochondrial Genome Project (FMGP), a sister project to the OGMP.

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• SciCrunch
• 17 years ago - by Anonymous

A curated database that strives to annotate gene promoters identified from ChIP-Seq experiment results. The long term goal of the database is to provide an integrated resource for mammalian gene transcriptional regulation and epigenetics. Users can search based on Enterz gene id/symbol, or by tissue/cell specific activity and filter results based on any combination of tissue/cell specificity, known/novel, CpG/NonCpG, and protein-coding/non-coding gene promoters. It is also integrated with GBrowse genome browser for visualiztion of ChIP-seq profiles and display the annotations.

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• SciCrunch
• 13 years ago - by Anonymous

This is a portal to the consensus yeast metabolic network as reconstructed from the genome sequence and literature. It is a highly annotated metabolic map that is periodically updated by a team of collaborators from various research groups. The first version of this reconstruction was published in Herrgrd, Swainston et al. (2008) A consensus yeast metabolic reconstruction obtained from a community approach to systems biology Nature Biotechnol. 26, 1155-1160 (you can access that network here). A second version has now been released and is awaiting publication. We plan on continuing to update this resource towards a complete metabolic network of yeast. All versions will remain accessible for historical purposes, however it is highly recommended that you always use the latest one since that is the most up to date. This effort started on the shoulders of a number of reconstructions of the metabolic network of yeast based on genomic and literature data that were published separately. (iMM904 and iLL672) However, due to the different approaches utilized in them, those earlier reconstructions had a significant number of differences. In addition they suffered from the use of non-standard names and overall they were not annotated with methods that are machine-readable. A community effort in 2007, led by the Manchester Centre for Integrative Systems Biology and the YSBN resulted in a consensus network representation of yeast metabolism, reconciling the earlier results. That effort is now ongoing under the leadership of the MCISB and with collaboration with colleagues under the UNICELLSYS FP7 project. Availability The network reconstruction is primarily assembled and provided as an SBML file enriched with MIRIAM-compliant annotations (which are embedded in the SBML through RDF). All small and macro- molecules are referenced to an authoritative database (e.g. Uniprot, ChEBI, etc.). All molecules and reactions are also annotated with appropriate publications that contain supporting evidence. Thus this network is entirely traceable and is presented in a computational framework. SBML is a format that is understood by a large number of software applications (see sbml.org). While the SBML file is the most efficient computational resource for these data, casual users also need access to the network. That is provided by a searchable relational database accessed directly from this website. The database pages also allow readers to add comments to any chemical species or reaction. Such comments are taken into consideration by the team collating new versions of the network and can lead to corrections and additions to the network. This reconstruction is provided in the following formats: :* an SBML file containing the reaction network and annotations, located to specific sub-cellular compartments :* an SBML file containing the reaction network and annotations without subcellular compartmentation (all reactions happening in a single compartment). :* a searcheable relational database, which uses the B-Net software from Pedro Mendes' group. The database version of this data set is managed with the B-Net software created in Pedro Mendes' group at the Virginia Bioinformatics Institute. B-Net's schema is a detailed representation of the underlying biochemistry and regulation. A number of reconstructions of the metabolic network of yeast based on genomic and literature data have been published. However, due to different approaches utilized in the reconstruction as well as different interpretations of the literature, the earlier reconstructions have significant number of differences. A community effort resulted in a consensus network model of yeast metabolism, combining results from previous models.

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• SciCrunch
• 17 years ago - by Anonymous

Open and collaborative platform dedicated to curation of biological pathways. Each pathway has dedicated wiki page, displaying current diagram, description, references, download options, version history, and component gene and protein lists. Database of biological pathways maintained by and for scientific community.

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• SciCrunch
• 17 years ago - by Anonymous

A bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone.

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• SciCrunch
• 12 years ago - by Anonymous

Collection of eukaryotic promoters derived from published articles. Annotated non-redundant collection of eukaryotic POL II promoters, for which transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.

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• SciCrunch
• 14 years ago - by Anonymous

Database of biotic and abiotic stress responsive genes in Arabidopsis thaliana and Oryza sativa L. with options to identify probable Transcription Factor Binding Sites in their promoters. In the response to biotic stress like Bacteria and abiotic stresses like ABA, drought, cold, salinity, dehydration, UV-B, high light, heat,heavy metals etc, ten specific families of transcription factors in Arabidopsis thaliana and six in Oryza sativa L. are known to be involved. HMM-based models are used to identify binding sites of transcription factors belonging to these families. They have also consulted literature reports to cross-validate the Transcription Factor Binding Sites predicted by the method.

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.The TFe provides details of transcription factor binding sites in close collaboration with Pazar, a public database of transcription factor and regulatory sequence information. The long-term goal of TFe is to create an online encyclopedic collection of well-studied transcription factor proteins in the human, mouse, and rat genomes, combining a mixture of both expert-curated and automatically-populated content to provide users with a wide set of information relevant to a transcription factor protein of their interest.

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• SciCrunch
• 17 years ago - by Anonymous

The SEED is a framework to support comparative analysis and annotation of genomes. The cooperative effort focuses on the development of the comparative genomics environment and, more importantly, on the development of curated genomic data. Curation of genomic data (annotation) is done via the curation of subsystems by an expert annotator across many genomes, not on a gene by gene basis. From the curated subsystems we extract a set of freely available protein families (FIGfams). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free RAST-Server (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the Metagenomics-RAST-Server freely available. We also provide a SEED-Viewer that allows read-only access to the latest curated data sets. We currently have 58 Archaea, 902 Bacteria, 562 Eukaryota, 1254 Plasmids and 1713 Viruses in our database. All tools and datasets that make up the SEED are in the public domain and can be downloaded at ftp://ftp.theseed.org

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• SciCrunch
• 16 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project on the release 5 of the TIGR-assembly of Oryza sativa japonica cv. Nipponbare genome sequenced by IRGSP.

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• SciCrunch
• 14 years ago - by Anonymous

A computer program and web-based service for the rapid retrieval of linkage disequilibrium proxy single nucleotide polymorphism (SNP) results given input of one or more query SNPs and based on empirical observations from the International HapMap Project and the 1000 Genomes Project. A series of filters allow users to optionally retrieve results that are limited to specific combinations of genotyping platforms, above specified pairwise r2 thresholds, or up to a maximum distance between query and proxy SNPs. SNAP can also generate linkage disequilibrium plots

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• SciCrunch
• 13 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 28,2022. InterPare is a database server for protein interaction interface information. It contains large-scale interface data of proteins whose 3D-structures are known. Protein interface information is derived from three different methods. InterPare introduces a large-scale protein domain interaction interface database called InterPare. InterPare uses three methods: 1) the Euclidean distance method for checking the distance among subunits in multidomain proteins, 2) Accessible Surface Area (ASA) for detecting the buried region of a protein that is detached from a solvent when forming multimers or complexes, 3) the Voronoi diagram, a computational geometry method, that uses a mathematical definition of interface regions. InterPare includes tools with different display modes for viewing protein interior, surface, and interaction interfaces.

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• SciCrunch
• 17 years ago - by Anonymous

LSPD provides liver specific gene. It lists ~300 promoter regions responsible for liver specific transcriptions, collect ~400 experimentally verified regulatory regions and elements, provide information on transcription regulation of liver genes, compare transcription regulation of functionally or evolutionarily related genes, and retrieve sequences of the promoter region. Its regulatory elements provides information on transcription regulatory elements, reports the methods for verification of the elements, records binding affinity and regulatory function, and summarizes the site distribution and sequence consensus.

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 29,2022. This database is an attempt to catalog in a convenient, searchable fashion the publicly available information about the identities of mammalian proteins that become covalently adducted by chemically-reactive metabolites of xenobiotic agents. At present all entries pertain to well-identified proteins that become adducted following defined exposures to known chemical agents in vivo or in cell culture experiments. Results from studies using enzymatic or chemical model systems have not been included but may be in the future. The search functions are relatively simple and intuitive, so most users can go straight to the Search page and begin searching. Additional explanations, examples and information about possible future expansions may be found.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. An online database of two-hybrid protein interactions in B. Subtilis. Interactions stored in SPID are either characterized by experimental evidence or by bibliographic references. A graphical user interface is provided to explore interaction networks as well as to view the details of each piece of evidence. The database contains 112 interactions between 79 proteins.

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• SciCrunch
• 17 years ago - by Anonymous