Curator Dashboard

Software program for phylogenetic analyses of large datasets under maximum likelihood.

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• SciCrunch
• 13 years ago - by Anonymous

A free, open source authoring and publishing platform that is designed to make it easy for authors to write long-form, born-digital scholarship online. Scalar enables users to assemble media from multiple sources and juxtapose them with their own writing in a variety of ways, with minimal technical expertise required. This semantic web authoring tool brings a considered balance between standardization and structural flexibility to all kinds of material including a built-in reading interface as well as an API that enables Scalar content to be used to drive custom-designed applications. Scalar also gives authors tools to structure essay- and book-length works in ways that take advantage of the unique capabilities of digital writing, including nested, recursive, and non-linear formats. The platform also supports collaborative authoring and reader commentary.

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• SciCrunch
• 15 years ago - by Anonymous

Videos from the National Center for Biotechnology Information including presentations and tutorials about NCBI biomolecular and biomedical literature databases and tools.

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• SciCrunch
• 15 years ago - by Anonymous

nature.com blogs is the new home for blogs written by Nature Publishing Group editors, staff and occasional guest bloggers. If you''re looking for the nature.com blogs catalogue of science blogs, this has been temporarily taken offline. In the meantime, the data in the catalogue is still accessible via the blogs API. If you''d like to submit your blog to the catalogue or suggest someone else''s, please email blogs (at) nature.com All nature.com blogs * Nature News Blog * Of Schemes and Memes Blog * Spoonful of Medicine * The Sceptical Chymist * Nature Jobs Blog * Trade Secrets * Stepwise * Soapbox Science * London Blog * Boston Blog * New York Blog * House of Wisdom * Indigenus * Methagora * Action Potential * Free Association * The Seven Stones Archived blogs * Climate Feedback * In The Field * Inherently Responsive * Nascent * Nature''s Journal Club * Nautilus * Peer-to-Peer * The Niche

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• SciCrunch
• 15 years ago - by Anonymous

ZiFDB is a database of zinc finger arrays and zinc finger proteins organized for use by molecular biologists. ZiFDB organizes information on both individual zinc finger modules and engineered ZFAs. There are currently four sets of zinc finger modules available: 1) Sangamo BioScience researchers have identified fingers recognizing all 5''-GNN-3'' and a few of 5''-ANN-3'', 5''-CNN-3'' and 5''-TNN-3'' triplets using phage display, targeted mutagenesis and SELECT methods (Liu et al., 2002); 2) the Barbas group constructed another set of models, which recognize all 5''-GNN-3'', most 5''-ANN-3'', 5''-CNN-3'' and a few 5''-TNN-3'' triplets (Dreier et al., 2001; Dreier et al., 2005; Dreier et al., 2000;); 3) Toolgen, Inc. isolated a set of naturally-occurring zinc finger modules from human transcription factors (Bae et al., 2003); 4) the Joung lab has made a large number of ZFAs by OPEN, and the constituent zinc fingers are included in the database. For the engineered ZFAs, we have collected information on 3-finger ZFAs, since this is the architecture advocated by the Zinc Finger Consortium (http://www.zincfingers.org), a group of academic laboratories dedicated to the development of improved methods to engineer zinc finger proteins. Currently, all ZFAs in ZiFDB are described in the published literature. In the future, unpublished ZFAs will also be included. It is hoped that the information in this database will help molecular biologists develop zinc finger reagents that meet their needs for genome modification. Further, we hope the analysis of the collected information will aid in improving modular design.

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• SciCrunch
• 17 years ago - by Anonymous

The Foundation is dedicated to advancing environmental conservation, scientific research, and patient care, as well as helping to improve quality of life in the San Francisco Bay Area--Gordon and Betty Moore''s home for more than 70 years. The Foundation is devoted to the inspirational vision articulated by our founders: creating positive outcomes for future generations. This vision guides our mission: to achieve significant, lasting and measurable results in environmental conservation, science, patient care, and the San Francisco Bay Area. A set of core valuesimpact, integrity, disciplined approach, and collaborationdirects our work. The Foundation carries out its work through the following frameworks: * Programs. The enduring management unit designed to achieve transformational change in a selected field of interest through a portfolio of integrated interventions. * Initiatives. Initiatives are built around well-developed strategies for concentrated investments, focused on the long-term and achieving significant impact. Initiatives are characterized by a portfolio approach to grantmaking, and other engagements of the Foundation, to pursue ambitious, large-scale outcomes. * Program grants. The Foundation devotes some of its grantmaking to experimentation, focused innovation, and agile response to time-sensitive, high-impact opportunities in its areas of focus. Across all initiatives and program grants, the Foundation''s grantees and partners seek to make positive changes in the world. The Foundation''s headquarters are in Palo Alto, in a building renovated with an emphasis on the environment and sustainability.

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• SciCrunch
• 15 years ago - by Anonymous

Online GEne Essentiality database containing genes that were tested experimentally for essentiality and their features; it also provides a set of tools to systematically explore and analyze these data. The main purpose of this project is to better understand gene essentiality by facilitating the comparisons of the differences and similarities between essential and non-essential genes. This is achieved by collecting not only experimentally tested essential and non-essential genes, but also associated gene features such as expression profiles, duplication status, conservation across species, evolutionary origins and involvement in embryonic development. We focus on large-scale experiments and complement our data with text-mining results. Genes are organized into data sets according to their sources. Genes with variable essentiality status across data sets are tagged as conditionally essential, highlighting the complex interplay between gene functions and environments. Linked tools allow the user to compare gene essentiality among different gene groups, or compare features of essential genes to non-essential genes, and visualize the results. Why is it different from existing databases? * we included both essential and non-essential genes so that we could better understand the gene essentiality by comparing the similarities and differences between the two gene sets; * we compiled a list of features for each gene, including whether they are duplicates or involved in development, the number of other homologous genes in the same genome, as well as their earliest expression stages during development. These features are keys to understand the essentiality of genes; * we also provide a set of tools to explore our data and visualize the results. For example, users can simply divide genes into two groups according to whether they are duplicates, calculate the proportion of essential genes (PE%) in each group and then visualize the results in a bar plot; or they can classify genes into multiple groups according to their earliest expression stages during evolution, compare the essentiality of genes that were expressed earlier with those were latter, and plot the results in a line chart.

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• SciCrunch
• 15 years ago - by Anonymous

NRG-CING presents a complete validation report for all 9,000+ wwPDB NMR entries including remediated experimental data such as chemical shifts from BMRB and restraints from NRG . These CING reports are compiled from internal analyses and those by CCPN, DSSP, PROCHECK-NMR/Aqua, ShiftX, Talos+, Vasco, Wattos, and WHAT_CHECK. The NRG-CING website is a collection of CING reports that has been pre-calculated for all PDB files solved by NMR. (See website for more information on CING.) In case the underlying experimental data is available, these have been cleaned up and made syntactically and semantically correct and homogeneous. For many macromolecular NMR ensembles from the Protein Data Bank (PDB) the experiment-based restraint lists used in the structure calculation are accessible, while other experimental data, mainly chemical shift values, are often available from the BioMagResBank. Assessment of the quality of the structural result is paramount to their usage and a combined, integrated repository of both input data and structural results greatly facilitates such an analysis. In addition, the accuracy and precision of the coordinates in these macromolecular NMR ensembles can be improved by recalculations using the available experimental data and present-day software with improved protocols and force fields. Such efforts, however, generally fail on over half of all deposited structures due to the syntactic and semantic heterogeneity of the data and the wide variety of formats used for their deposition. We have combined the cleaned-up restraints information from the NMR Restraints Grid (NRG) database with available chemical shifts from the BioMagResBank in the weekly updated NRG-CING database. Eleven programs, in addition to CING itself, have been included in the NRG-CING production pipeline to arrive at validation reports that list for each entry the potential inconsistencies between the coordinates and the available restraint and chemical shift data. The longitudinal validation of this data yielded a set of indicators that can be used to judge the quality of every macromolecular structure solved with NMR. The cleaned up NMR experimental datasets and the validation reports are freely available.

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• SciCrunch
• 15 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. It contains a complete, curated list of yeast genes encoding mitoproteins. The ORF name for each mitoprotein is linked to a page presenting a summary of the Baysian prior-based profile for conserved segments of that protein and statistics describing profile quality. The page also contains a list of homologs identified by the profile that span the widest possible taxonomic breadth. A multi-domain diagram at the bottom of the page displays the relationships between the conserved segments of different homologs and shows any additional sequence domains. Clicking on these initiates BLAST searches against the database of all fully sequenced genomes. A clickable button accesses a full multiple alignment of the profile-matched segments for the homolog set. Phylogenetic trees based on these alignments can also be displayed by clicking appropriate buttons (See How to use YMPD). A complete list of the known mitoproteins classified by functional category has links to the pages for individual mitoproteins in each category

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• SciCrunch
• 17 years ago - by Anonymous

This database presents the entire DNA sequence of the first diploid genome sequence of a Han Chinese, a representative of Asian population. The genome, named as YH, represents the start of YanHuang Project, which aims to sequence 100 Chinese individuals in 3 years. It was assembled based on 3.3 billion reads (117.7Gbp raw data) generated by Illumina Genome Analyzer. In total of 102.9Gbp nucleotides were mapped onto the NCBI human reference genome (Build 36) by self-developed software SOAP (Short Oligonucleotide Alignment Program), and 3.07 million SNPs were identified. The personal genome data is illustrated in a MapView, which is powered by GBrowse. A new module was developed to browse large-scale short reads alignment. This module enabled users track detailed divergences between consensus and sequencing reads. In total of 53,643 HGMD recorders were used to screen YH SNPs to retrieve phenotype related information, to superficially explain the donor's genome. Blast service to align query sequences against YH genome consensus was also provided.

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• SciCrunch
• 17 years ago - by Anonymous

A curated repository of more than 206000 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1300 bibliographic references. It also includes the description of 326 specific DNA binding sites shared among 113 characterized TFs. Further information about each Yeast gene has been extracted from the Saccharomyces Genome Database (SGD). For each gene the associated Gene Ontology (GO) terms and their hierarchy in GO was obtained from the GO consortium. Currently, YEASTRACT maintains a total of 7130 terms from GO. The nucleotide sequences of the promoter and coding regions for Yeast genes were obtained from Regulatory Sequence Analysis Tools (RSAT). All the information in YEASTRACT is updated regularly to match the latest data from SGD, GO consortium, RSA Tools and recent literature on yeast regulatory networks. YEASTRACT includes DISCOVERER, a set of tools that can be used to identify complex motifs found to be over-represented in the promoter regions of co-regulated genes. DISCOVERER is based on the MUSA algorithm. These algorithms take as input a list of genes and identify over-represented motifs, which can then be compared with transcription factor binding sites described in the YEASTRACT database.

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• SciCrunch
• 17 years ago - by Anonymous

ProQuest Dissertation Publishing has been publishing dissertations and theses since 1938. In that time, we have published over 2 million graduate works from graduate schools around the world. We have over 700 active university publishing partners, and publish more than 70,000 new graduate works each year. In addition to publishing, we provide access to graduate works for thousands of libraries around the world. Based on your interests, you should find the information you need below: * Authors - Information for authors on why and how to publish their graduate work with us. * Grad Schools & Libraries - Learn about the benefits of publishing, and why to submit online. * Researchers - We can help you find the dissertation or thesis you need.

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• SciCrunch
• 15 years ago - by Anonymous

Public research university in Albuquerque, New Mexico. Founded in 1889, UNM offers bachelor's, master's, doctoral, and professional degree programs.

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• SciCrunch
• 17 years ago - submitted by Eddy Kim

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

This database presents a PartiGene analysis of the Bombus terrestris worker caste normalised Sanger ESTs produced by Sadd et al.

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• SciCrunch
• 15 years ago - by Anonymous

As part of our effort in PhyloGenomics, we have developed the PartiGene ARTHROPODA Database. In these databases, we have analyzed the EST datasets for sixty different arthropod species. To aid searching we have split the interface between four class-based views: Chelicerata, Hexapoda, Crustacea, Myriapoda. Amongst other analyses, we have included Alfried Vogler's lab's PartiGene analysis of ~30 different arthropod species ESTs. A separate access point for that dataset is also available.

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• SciCrunch
• 15 years ago - by Anonymous

NEMBASE is a comprehensive Nematode Transcriptome Database including 63 nematode species, over 600,000 ESTs and over 250,000 proteins. Nematode parasites are of major importance in human health and agriculture, and free-living species deliver essential ecosystem services. The genomics revolution has resulted in the production of many datasets of expressed sequence tags (ESTs) from a phylogenetically wide range of nematode species, but these are not easily compared. NEMBASE4 presents a single portal into extensively functionally annotated, EST-derived transcriptomes from over 60 species of nematodes, including plant and animal parasites and free-living taxa. Using the PartiGene suite of tools, we have assembled the publicly available ESTs for each species into a high-quality set of putative transcripts. These transcripts have been translated to produce a protein sequence resource and each is annotated with functional information derived from comparison with well-studied nematode species such as Caenorhabditis elegans and other non-nematode resources. By cross-comparing the sequences within NEMBASE4, we have also generated a protein family assignment for each translation. The data are presented in an openly accessible, interactive database. An example of the utility of NEMBASE4 is that it can examine the uniqueness of the transcriptomes of major clades of parasitic nematodes, identifying lineage-restricted genes that may underpin particular parasitic phenotypes, possible viral pathogens of nematodes, and nematode-unique protein families that may be developed as drug targets.

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• SciCrunch
• 15 years ago - by Anonymous

A database housing EST information from nine mollusc species, including Lymnaea stagnalis, the pond snail. Co-curated with Angus davison of Nottingham University.

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• SciCrunch
• 15 years ago - by Anonymous

A collaborative wiki that collates information on completed, ongoing and planned genome and transcriptome sequencing projects on species from phylum Nematoda. The intention is to encourage genome sequencing across the diversity of the phylum Nematoda. Wiki includes: * Published complete nematode genomes: A dynamically generated table of all species for which the genome is published. * Nematode species with genomes in progress: A dynamically generated table of all species for which a genome project is underway. Users may add species to the list * Proposed nematode genome projects: To propose a species for genome sequencing, edit its species page, and set the genome project status to proposed. * BLAST server: Search a number of the nematode-genomes-in-progress with genes of your choice. Currently there are 12 draft genomes available... * Genomes with Data available: Genomes with data available for download. Users may add more data URLs to strain pages or update the URLs.

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• SciCrunch
• 15 years ago - by Anonymous

There are over 120 faculty, postdoctoral fellows, graduate students and support staff collaborate in state-of-the-art research facilities on the University of Nebraska Medical Center campus. The Department of Pharmacology and Experimental Neuroscience is rapidly growing, not only in terms of facilities, personnel and research support, but in terms of national and international reputation as well. The department offers graduate education in pharmacology and neurosciences, and a summer undergraduate research program. Pharmacology continues to be among the most dynamic of the biomedical sciences. Neuroscience research has been a major emphasis of the Department of Pharmacology at UNMC from its earliest days. This has been expanded with the 2004 merger of UNMC''s internationally recognized Center for Neurovirology and Neurodegenerative Disorders (CNND) into the Department of Pharmacology and Experimental Neuroscience.

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• SciCrunch
• 17 years ago - by Anonymous