Curator Dashboard

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

Portal for Global Mouse Models for COVID-19 consortium. Presents consortium, its statement and membership, and URLs for mouse COVID-19 resources worldwide.

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• RRID-Legacy
• 6 years ago - submitted by Edyta Vieth

Software R package for estimation of effect size indices and standardized parameters. Used to work with indices of effect size and standardized parameters, allowing computation and conversion of indices such as Cohen’s d, r, odds-ratios, etc.

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• RRID
• 1 year ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 27,2023.Interactive multimedia educational outreach resource promoting awareness and understanding of key microbiological issues to adult and youth audiences, and showcases the significance of microbes in our lives. It is an online community for sharing the latest news, blog posts, videos, podcasts, images, research and resources related to microbiology and the life sciences. Join today and help contribute to the fastest growing networks for science information on the web. The anthrax attacks of 2001 and the ensuing focus on bioterrorism, the potential of viral and bacterial infections for victims of Hurricane Katrina, the emergence of avian flu, and the public''s growing interest in alternative fuel sources have thrust microbes into unprecedented prominence in the headlines. MicrobeWorld informs the public about how science works. The various outreach methods feature the process of discovery, historical changes in research, and a variety of scientific careers in industry, academia, and government. One of the first MicrobeWorld Radio podcasts explained how microbes enter the initially sterile bodies of infants just hours after birth, establishing the microbial communities that stay with them for life. Other topics have included why the overuse of antibiotics is a growing problem, how microbes are key in the making of chocolate, and how microbiologists are on the front line in the war against infectious diseases that threaten human and animal health. Objectives * Leverage emerging communications technologies to promote the science of microbiology to the public and provide educational resources for all levels. * Repurpose the American Society for Microbiology''s resources for the wired generation. * Increase public understanding and appreciation of the vital role microbes play on our planet. * Use new technology to promote ASM''s resources to students, educators and other potential members of the Society. * Establish ASM as a leader in online science content.

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• SciCrunch
• 15 years ago - by Anonymous

Software tool to evaluate and visualize statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per variable,diversity, and joining gene of given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. Antibody clonotype analysis based on NGS sequences.

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• RRID-Legacy
• 6 years ago - by Anonymous

Core provides services including project evaluation and design, sample processing and biochemical purifications, mass spectrometry measurements, data processing, and bioinformatics analysis performed by the experienced core personnel.

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• SciCrunch
• 1 year ago - submitted by Edyta Vieth

Center that produces knockout mice and carries out high-throughput phenotyping of each line in order to determine function of every gene in mouse genome. These mice will be preserved in repositories and made available to scientific community representing valuable resource for basic scientific research as well as generating new models for human diseases.

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• SciCrunch
• 15 years ago - by Anonymous

Provided core services include Sanger DNA Sequencing, Next Generation DNA Sequencing (Four Illumina MiSeqs, four Illumina NextSeq 500s and one Illumina NovaSeq 6000),Next Generation Automated Library Sample Prep (Perkin Elmer Sciclone Genomic, ChIP, RNAseq and other methods), Single Cell DNA and RNA-Seq (10X Genomics Chromium), Bioanalyzer Analysis DNA and RNA (Two Agilent 2100 BioAnalyzers and two Agilent 2200 TapeStations), Qiagen Qiacube Automated DNA / RNA Prep (single to multiple samples), Oligonucleotide Ordering (IDT Portal), Reagents and Supplies Ordering (multiple vendors / products). Facility web based Laboratory Information Management System (LIMS) provides users with access to order services and supplies as well as retrieve data and review and pay invoices all online.

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• SciCrunch
• 13 years ago - by Anonymous

Research institute focused on the study of plants at the molecular level.IBMP is a major CNRS center for plant sciences. Located at the Strasbourg site, it collaborates closely with the University of Strasbourg and our international partners in the Upper Rhine Valley region. Conducts research in areas of plant biology, including gene expression and RNA regulation, plant metabolism, organelles, and virology.

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• RRID
• 1 year ago - submitted by Edyta Vieth

Software package that provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs (single nucleotide variants).

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• SciCrunch
• 13 years ago - by Anonymous

Atlas includes co-registered templates constructed from MR images frequently used to characterize macroscopic brain structure T2/SPACE and T1/MP-RAGE, and diffusion tensor imaging template.

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• NIF
• 6 years ago - by Anonymous

Software R package implements time series z-normalization, SAX, HOT-SAX, VSM, SAX-VSM, RePair, and RRA algorithms facilitating time series motif (i.e., recurrent pattern), discord (i.e., anomaly), and characteristic pattern discovery along with interpretable time series classification.

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• RRID
• 1 year ago - submitted by Marybeth Baumgartner

An open-membership International community to promote mechanisms that standardize the description of genomes and the exchange and integration of genomic data. Community-driven standards have the best chance of success if developed within the auspices of international working groups. Participants in the GSC include biologists, computer scientists, those building genomic databases and conducting large-scale comparative genomic analyses, and those with experience of building community-based standards. The mission of the GSC is to work with the wider community towards: * the implementation of new genomic standards * methods of capturing and exchanging metadata * harmonization of metadata collection and analysis efforts across the wider genomics community

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• SciCrunch
• 14 years ago - by Anonymous

Web tool for executing broad range of modeling studies and visualizing their results. Provides web interface for reusing any model. Models, simulations, and visualizations are available under licenses specified for each resource.

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• SciCrunch
• 6 years ago - by Anonymous

Public research university founded in 1828. One of the largest Universities of Technology in Germany.

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• SciCrunch
• 16 years ago - submitted by Stephen Larson

A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data.

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• SciCrunch
• 14 years ago - by Anonymous

Open source pipeline to automatically identify embryo dysmorphology from 3D volumetric images. Automated image analysis for developmental phenotyping of mouse embryos.

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• RRID-Legacy
• 6 years ago - submitted by Anita Bandrowski

Core is utilized in medical biotechnology and in research focused on mammalian cells. Offers analyzing of impact of new drugs and pharmaceuticals on individual cells in vitro. Provides sorting of cell populations with desired characteristics, including fluorescent dye-stained cell sorting (FACS) analysis of cell populations for presence of specific factors, e.g. introduced fluorescent protein, surface markers, DNA content determining the size, granulation and shape of animal and other cells.

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• SciCrunch
• 1 year ago - submitted by Edyta Vieth

A comprehensive biochemical knowledge-base on human metabolism, this community-driven, consensus metabolic reconstruction integrates metabolic information from five different resources: * Recon 1, a global human metabolic reconstruction (Duarte et al, PNAS, 104(6), 1777-1782, 2007) * EHMN, Edinburgh Human Metabolic Network (Hao et al., BMC Bioinformatics 11, 393, 2010) * HepatoNet1, a liver metabolic reconstruction (Gille et al., Molecular Systems Biology 6, 411, 2010), * Ac/FAO module, an acylcarnitine/fatty acid oxidation module (Sahoo et al., Molecular bioSystems 8, 2545-2558, 2012), * a human small intestinal enterocytes reconstruction (Sahoo and Thiele, submitted). Additionally, more than 370 transport and exchange reactions were added, based on a literature review. Recon 2 is fully semantically annotated (Le Nov��re, N. et al. Nat Biotechnol 23, 1509-1515, 2005) with references to persistent and publicly available chemical and gene databases, unambiguously identifying its components and increasing its applicability for third-party users. Here you can explore the content of the reconstruction by searching/browsing metabolites and reactions. Recon 2 predictive model is available in the Systems Biology Markup Language format.

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• SciCrunch
• 14 years ago - by Anonymous

Core provides professional scientific expertise in light microscopy. Offers access to hardware and software as well as expert guidance at any step of imaging project, from experimental design to image analysis.Comprises eight microscope systems including two laser scanning confocal microscopes including one Olympus inverted confocal microscope system (FV1000) and one Zeiss inverted confocal microscope system (LSM-980) equipped with Airy scan 2 for super resolution and 2-photon technology for in-vivo deep imaging with temperature controlled chamber. One spinning disk confocal including Nikon inverted spinning disk microscope system with incubation chamber (Eclipse Ti with Yokogawa disk CSU-W1), two Zeiss widefield microscopes for brightfield and epifluorescence illumination (Zeiss Apotome and Zeiss Colibri), three macroscopes systems to observe large samples or complete model organisms in brightfield and epifluorescence including one Olympus stereomicroscope system (MVX10) and two Zeiss stereomicroscope systems (SteREO Discovery V12), fully automated and one AxioZoom V16 , fully automated with ApoTome attachment.

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• SciCrunch
• 6 years ago - submitted by Edyta Vieth