Curator Dashboard

A platform composed of three modules: the Database, the Search Engine, and rSNPs, for the computational identification of transcription factor binding sites (TFBSs) in multiple genomes, that combines TRANSFAC and JASPAR data with the search power of profile hidden Markov models (HMMs). The Database contains putative TFBSs found in the upstream sequences of genes from the human, mouse and D.melanogaster genomes. For each gene, they scanned the region from 10,000 base pairs upstream of the transcript start to 50 base pairs downstream of the coding sequence start against all their models. Therefore, the database contains putative binding sites in the gene promoter and in the initial introns and non-coding exons. Information displayed for each putative binding site includes the transcription factor name, its position (absolute on the chromosome, or relative to the gene), the score of the prediction, and the region of the gene the site belongs to. If the selected gene has homologs in any of the other two organisms, the program optionally displays the putative TFBSs in the homologs. The Search Engine allows the identification, visualization and selection of putative TFBSs occurring in the promoter or other regions of a gene from the human, mouse, D.melanogaster, C.elegans or S.cerevisiae genomes. In addition, it allows the user to upload a sequence to query and to build a model by supplying a multiple sequence alignment of binding sites for a transcription factor of interest. rSNPs MAPPER is designed to identify Single Nucleotide Polymorphisms (SNPs) that may have an effect on the presence of one or more TFBSs.

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• SciCrunch
• 17 years ago - by Anonymous

Core offers specialized expertise for analysis of proteins and peptides using mass spectrometry. Develops new methods and customized approaches for proteomic analysis and suggests experimental strategies and sample preparation prior to mass spectrometry analysis. Services include:comprehensive protein identification ,analysis of affinity purified complexes,characterizing protein post-translational modifications,de novo sequencing,label and label-free quantitation ,multiplexed quantitation global phosphorylation and ubiquitin analysis,analysis of laser-capture microdissected formalin-fixed paraffin-embedded tissue,secretome analysis,crosslinking analysis,disulfide mapping.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

The Oomycete Genomics Database is a publicly accessible resource that includes functional assays and expression data, combined with transcript and genomic analysis and annotation. OGD builds upon data available from the Phytophthora Genome Consortium, Syngenta Phytophthora Consortium and the Phytophthora Functional Genomics Database. Data are analyzed and annotated using NCGR''s XGI System. The knowledge gained from these studies provide significant insight into key molecular processes regulating an economically important pathosystem and will provide novel tools for improvement of disease resistance in crop plants.

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• SciCrunch
• 17 years ago - by Anonymous

AMRDC Repository provides archival, preservation, access, and metadata authoring services for Antarctic meteorological data, managing data from submission to end-user retrieval. The repository hosts data collected by the Antarctic Meteorological Research Center and Automatic Weather Station projects, as well as campaign meteorological datasets deposited by other Antarctic investigators.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Software tool to evaluate de novo genome assemblies with RNA transcripts.

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• SciCrunch
• 13 years ago - by Anonymous

Provides open access to Climate and Earth System Data from scientists at the centre and their collaborators. Helps to make your data open, FAIR and visually appealing. Each dataset and source code in the Bolin Centre Database is assigned a unique DOI. This makes it easy to cite and find your data. If dataset has more than one version, each version will have its own DOI.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 08, 2013. A repository for physical mapping data of the human X chromosome that aims at providing a global view of genomic data at a chromosomal level including an integrated physical, genetic, transcript and sequence map of the human X chromosome. This implies acquiring, understanding and formatting an enormous amount of experimental results and can only be accomplished progressively. We have chosen to start the integration process with YAC maps generated by the community. These provide the basis for future higher resolution physical maps, as well as emerging transcript and sequence maps. The current content of IXDB therefore reflects this situation, with the emphasis placed on YAC mapping data. Due to their immediate value, IXDB has also started to systematically include bacterial clone contig maps and EST data. Currently IXDB does not store sequence data, although links to nucleic sequence databases are provided.

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• SciCrunch
• 15 years ago - by Anonymous

Core facility is available for use by any researcher at university whose work requires manipulation of biological agents that may cause serious or potentially lethal disease as result of exposure by inhalation route.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Portal and tools for sharing and editing neurophysiological and behavioral data for brain-machine interface research. Users can search for existing data or login with their Google, Facebook, or Twitter account and upload new data. Their main focus is on supporting brain-machine interface research, so we encourage users to not just provide recordings of brain activity data, but also information about stimuli, etc., so that statistical relationships can be found between stimuli and/or subject behavior and brain activity. The Matlab tools are for writing, reading, and converting Neuroshare files, the common file format. A free, open source desktop tool for editing neurophysiological data for brain-machine interface research is also available: https://github.com/ATR-DNI/BrainLiner Since data formats aren''''t standardized between programs and researchers, data and analysis programs for data cannot be easily shared. Neuroshare was selected as the common file format. Neuroshare can contain several types of neurophysiological data because of its high flexibility, including analog time-series data and neuronal spike timing. Some applications have plug-ins or libraries available that can read Neuroshare format files, thus making Neuroshare somewhat readily usable. Neuroshare can contain several types of neurophysiological data, but there were no easy tools to convert data into the Neuroshare format, so they made and are providing a Neuroshare Converter Library and Simple Converter using the library. In future work they will make and provide many more useful tools for data sharing. Shared experiments include: EMG signal, Takemiya Exp, Reconstruct (Visual image reconstruction from human brain activity using a combination of multi-scale local image decoders), SPIKE data, Speech Imagery Dataset (Single-trial classification of vowel speech imagery using common spatial patterns), Functional Multineuron Calcium Imaging (fMCI), Rock-paper-scissors (The data was obtained from subject while he make finger-form of rock/paper/scissors). They also have a page at https://www.facebook.com/brainliner where you can contact us

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• SciCrunch
• 16 years ago - by Anonymous

Software to interpret undetected homolog.Method that calculates probability that homolog of given gene would fail to be detected by homology search in given species, even if homolog were present and evolving normally.

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• RRID
• 4 years ago - by Anonymous

SerbGO is a web-based tool intended to assist researchers determine which microarray tools for gene expression analysis which make use of the GO ontologies are best suited to their projects. SerbGO is a bidirectional application. The user can ask for some features by checking on the Query Form to get the appropriate tools for their interests. The user can also compare tools to check which features are implemented in each one. Platform: Online tool

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• SciCrunch
• 15 years ago - by Anonymous

Leading collaborative interdisciplinary organization that advances research, education, and training in quantum science and engineering. Helps to unify and promote research in quantum science and engineering in the Pittsburgh area. PQI members have faculty appointments from Carnegie Mellon University, Duquesne University, and the University of Pittsburgh in physics, chemistry, and engineering disciplines. Connects with team based science intitiatives and shared facilities.Resources and Facilities for Quantum Research include Carnegie Mellon Nanofabrication Facility,Center for Research Computing, Gertrude E. and John M. Petersen Institute of NanoScience and Engineering (PINSE), Materials Characterization Facility, Pittsburgh Supercomputing Center,QCFD (Quantum Computing/Computational Fluid Dynamics).

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Newt-omics is a database, which enables researchers to locate, retrieve and store data sets dedicated to the molecular characterization of newts. Newt-omics is a transcript-centered database, based on an Expressed Sequence Tag (EST) data set from the newt, covering ~50,000 Sanger sequenced transcripts and a set of high-density microarray data, generated from regenerating hearts. Newt-omics also contains a large set of peptides identified by mass spectrometry, which was used to validate 13,810 ESTs as true protein coding. Newt-omics is open to implement additional high-throughput data sets without changing the database structure. Via a user-friendly interface Newt-omics allows access to a huge set of molecular data without the need for prior bioinformatical expertise. The newt Notopthalmus viridescens is the master of regeneration. This organism is known for more than 200 years for its exceptional regenerative capabilities. Newts can completely replace lost appendages like limb and tail, lens and retina and parts of the central nervous system. Moreover, after cardiac injury newts can rebuild the functional myocardium with no scar formation. To date only very limited information from public databases is available. Newt-Omics aims to provide a comprehensive platform of expressed genes during tissue regeneration, including extensive annotations, expression data and experimentally verified peptide sequences with yet no homology to other publicly available gene sequences. The goal is to obtain a detailed understanding of the molecular processes underlying tissue regeneration in the newt, that may lead to the development of approaches, efficiently stimulating regenerative pathways in mammalians. * Number of contigs: 26594 * Number of est in contigs: 48537 * Number of transcripts with verified peptide: 5291 * Number of peptides: 15169

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• SciCrunch
• 15 years ago - by Anonymous

Software for short read alignment and mapping of sequencing reads where the DNA sequence is somehow modified and/or there is more divergence between sample and reference than what fast mappers will handle.

• SciCrunch
• 9 years ago - submitted by Isabella Froman

An open bioinformatis software repository with no tie to any organization or institution. Contact them to host your software.

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• SciCrunch
• 14 years ago - by Anonymous

PhenomeNet is a cross-species phenotype similarity network. It contains the experimentally observed phenotypes of multiple species as well as the phenotypes of human diseases. PhenomeNet provides a measure of phenotypic similarity between the phenotypes it contains. The latest release (from 22 June 2012) contains 124,730 complex phenotype nodes taken from the yeast, fish, worm, fly, rat, slime mold and mouse model organism databases as well as human disease phenotypes from OMIM and OrphaNet. The network is a complete graph in which edge weights represent the degree of phenotypic similarity. Phenotypic similarity can be used to identify and prioritize candidate disease genes, find genes participating in the same pathway and orthologous genes between species. To compute phenotypic similarity between two sets of phenotypes, we use a weighted Jaccard index. First, phenotype ontologies are used to infer all the implications of a phenotype observation using several phenotype ontologies. As a second step, the information content of each phenotype is computed and used as a weight in the Jaccard index. Phenotypic similarity is useful in several ways. Phenotypic similarity between a phenotype resulting from a genetic mutation and a disease can be used to suggest candidate genes for a disease. Phenotypic similarity can also identify genes in a same pathway or orthologous genes. PhenomeNet uses the axioms in multiple species-dependent phenotype ontologies to infer equivalent and related phenotypes across species. For this purpose, phenotype ontologies and phenotype annotations are integrated in a single ontology, and automated reasoning is used to infer equivalences. Specifically, for every phenotype, PhenomeNet infers the related mammalian phenotype and uses the Mammalian Phenotype Ontology for computing phenotypic similarity. Tools: * PhenomeBLAST - A tool for cross-species alignments of phenotypes * PhenomeDrug - method for drug-repurposing

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• SciCrunch
• 15 years ago - by Anonymous

A suite of tools to address common questions raised in genomic studies - mostly with regard to overlap and proximity relationships between data sets.

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• SciCrunch
• 13 years ago - by Anonymous

A network for supporting resting-state fMRI (R-fMRI) related studies. It connects R-fMRI researchers (as nodes) by their sharings (as edges). Through the network, ideas, comments, resources, tools, experiences, and data can be shared. Researchers (nodes) with basic neuroscience, methodological, or clinical backgrounds can connect with each other in the network. It also contains a preprint server that allows neuroscientists to share their preprints, comment on each others research and get back valuable information about their experiments from their colleagues. This is based on the arXiv model. Ultimately, the network aims to enhance collaborations among researchers, especially to translate knowledge of basic neuroscience and methodology to clinical applications (bench to bedside).

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• SciCrunch
• 12 years ago - by Anonymous

A utility, whose output is a PostScript file of aligned sequences with graphical enhancements. Its main input is an ascii file of pre-aligned sequences. Optional files allow further rendering. The program calculates a similarity score for each residue of the aligned sequences. The output shows: * Secondary Structures * Aligned sequences * Similarities * Accessibility * Hydropathy * User-supplied markers * Intermolecular contacts In addition, similarity score can be written in the bfactor column of a pdb file, to enable direct display of highly conserved areas. You can run ESPript from this server with the HTML interface. It is configured for a maximum of 1,000 sequences. Links to webESPript * ENDscript: you can upload a PDB file or enter a PDB code such as 1M85. The programs DSSP and CNS are executed via the interface, so as to obtain an ESPript figure with a lot of structural information (secondary structure elements, intermolecular contacts). You can also find homologous sequences with a BLAST search, perform multiple sequence alignments with MULTALIN or CLUSTALW and create an image with BOBSCRIPT or MOLSCRIPT to show similarities on your 3D structure. * ProDom: you can enter a sequence identifier to find homologous domains, perform multiple sequence alignments with MULTALIN and click on the link to ESPript. * Predict Protein: you can receive a mail in text (do not use the HTML option when you submit your request in Predict Protein) with aligned sequences and numerous information including secondary structure prediction. Click on a special html link to upload your mail in ESPript. * NPS(at): you can execute the programs BLAST and CLUSTALW to obtain multiple alignments. You can predict secondary structure elements and click on the link to ESPript. This program started in the laboratory of Dr Richard Wade at the Institut de Biologie Structurale, Grenoble. It moved later to the Laboratory of Molecular Biophysics in Oxford, then to the Institut de Pharmacologie et de Biologie Structurale in Toulouse. It is now developed in the Laboratoire de BioCristallographie of Dr Richard Haser, Institut de Biologie et de Chimie des Prot��������ines, Lyon and in the Laboratoire de Biologie Mol��������culaire et de Relations Plantes-Organismes, group of Dr Daniel Kahn, Institut National de la Recherche Agronomique de Toulouse.

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• SciCrunch
• 17 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