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Protein sets from fully sequenced genomes. Proteomes portal offers protein sequence sets obtained from translation of completely sequenced genomes. Published genomes from NCBI Genome are brought into UniProt if genome is annotated and set of coding sequences is available. Number of predicted coding sequences falls within statistically significant range of published proteomes from neighbouring species.

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• RRID-Legacy
• 7 years ago - by Anonymous

Mechanical Core provides variety of fabrication, customization and repair services for mechanical devices and equipment. Offers precision machining of metals and plastics, welding of structural and exotic metals, instrument refurbishing and mechanical repair.

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• 1 year ago - submitted by Matthew Rudy

A website containing the complete sequenced genome of the medaka fish. It presents a high-quality draft genome sequence of a small egg-laying freshwater teleost, medaka (Oryzias latipes). Medaka is native to East Asia and an excellent model system for a wide range of biology, including ecotoxicology, carcinogenesis, sex determination4, 5, 6 and developmental genetics7. In the assembled medaka genome (700 megabases), which is less than half of the zebrafish genome, we predicted 20,141 genes, including approx2,900 new genes, using 5’-end serial analysis of gene expression tag information. We found single nucleotide polymorphisms (SNPs) at an average rate of 3.42% between the two inbred strains derived from two regional populations; this is the highest SNP rate seen in any vertebrate species. Analyses based on the dense SNP information show a strict genetic separation of 4 million years (Myr) between the two populations, and suggest that differential selective pressures acted on specific gene categories. Four-way comparisons with the human, pufferfish (Tetraodon), zebrafish and medaka genomes revealed that eight major interchromosomal rearrangements took place in a remarkably short period of approx 50 Myr after the whole-genome duplication event in the teleost ancestor and afterwards, intriguingly, the medaka genome preserved its ancestral karyotype for more than 300 Myr.

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• SciCrunch
• 17 years ago - by Anonymous

Software R package for structural variant analysis. Contains helper functions for dealing with structural variants in VCF format. Contains functions for parsing VCFs from number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects.

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• RRID-Legacy
• 6 years ago - by Anonymous

Core provides biomechanical testing of biological structures and biomaterials. Allows investigators to conduct research of mechanical properties of existing biological structures and constructs, as well as to quantify potential for new technologies and clinical advancements. Robotic simulators are built around the simVITRO software platform and are designed for in vitro simulation of major joints including knee, spine, foot, ankle, hip, shoulder, elbow, wrist and more. Provides testing capabilities for range of biomechanical modalities and will offer expert advice and support for development of new test protocols, innovative techniques for instrumentation and data collection. Modalities include tissues, joints, and multi-articular units, such as foot or spine segments.

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• 1 year ago - by Anonymous

International, curated, digital repository that makes the data underlying scientific publications discoverable, freely reusable, and citable. Particularly data for which no specialized repository exists. Provides the infrastructure for, and promotes the re-use of, data underlying the scholarly literature. Governed by a nonprofit membership organization. Membership is open to any stakeholder organization, including but not limited to journals, scientific societies, publishers, research institutions, libraries, and funding organizations. Most data are associated with peer-reviewed articles, although data associated with non-peer reviewed publications from reputable academic sources, such as dissertations, are also accepted. Used to validate published findings, explore new analysis methodologies, repurpose data for research questions unanticipated by the original authors, and perform synthetic studies.UC system is member organization of Dryad general subject data repository.

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• SciCrunch
• 15 years ago - by Anonymous

Software R package to obtain estimated marginal means for linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and other displays.

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• RRID-Legacy
• 6 years ago - submitted by Kate Kennedy

Core provides imaging systems for advanced microscopy including confocal, multi-photon and super-resolution modalities, enabling users to address research questions in living systems across temporal and spatial scales. Staff offers training to use equipment, expertise about experimental strategy, design, image processing and analysis.

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• 1 year ago - by Anonymous

Listing of institutional repositories for depositing preprints of published materials with the aim of promoting the development of open access by providing timely information about the growth and status of repositories throughout the world. Open access to research maximizes research access and thereby also research impact, making research more productive and effective. Repository Types: * Research Institutional or Departmental * Research Multi-institution Repository * Research Cross-Institutional * e-Journal/Publication * e-Theses * Database/A&I Index * Research Data * Open and Linked Data * Learning and Teaching Objects * Demonstration * Web Observatory * Other Repository Software: * ARNO * Bepress * CDS Invenio * ContentDM by OCLC * DIGIBIB * DigiTool * DiVA * DoKS * DSpace * EDOC * EPrints * Equella * ETD-db * Fedora ** Fez * Greenstone * HAL * i-Tor * IntraLibrary * Keystone DLS * MiTOS * MyCoRe * Open Journal System * Open Repository * OPUS (Open Publications System) * Other softwares (various) * PMB Services * SBCAT * SciX * SobekCM * WIKINDX * Zentity

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• SciCrunch
• 15 years ago - by Anonymous

Core provides collection of diversity-oriented, drug-like, and natural small molecules in non-redundant libraries, variety of automated liquid handling and assay detection systems such as EnVision Multiplate reader and ArrayScan HCA System, modern equipment for medicinal and analytical chemistry including NMR, LC-QTOF MS, HPLC, Peptide Synthesizer, and sophisticated chemoinformatics tools. Besides traditional high-throughput screening and hit compound optimization services, newly adapted technologies include arrayed CRISPR screening, phage display, and SAR by NMR.

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• SciCrunch
• 6 years ago - submitted by Edyta Vieth

AGMP provides researchers with platform from which they can retrieve existing information regarding genetic associations to disease-related phenotypes in African populations.

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• 1 year ago - by Anonymous

To satisfy the need for standardized terminologies several ontologies, we are developing the Ontology of Craniofacial Development and Malformation. When complete, this ontology will describe several realms of anatomy and development relevant to FaceBase, including: * Human craniofacial anatomy, including developmental progressions * Craniofacial malformations * Mouse craniofacial anatomy * Mappings between mouse and human anatomy These ontologies are currently undergoing active development. As a result, these files should be considered very preliminary. They may not work correctly, and contents will almost certainly undergo significant change. Five (sub) ontologies in this zip archive correspond to the categories described above. * OCDM - Ontology of Craniofacial Development and Malformation: currently imports the CHO, CMO, and the CHMMO. * CHO - Craniofacial Human Ontoloogy: normal adult human craniofacial anatomy derived from the FMA. * CMO - Craniofacial Mouse Ontology: normal adult mouse craniofacial anatomy * CHMMO - Craniofacial Human-Mouse Mapping Ontology: mappings of classes in the * CHO to related (homologous) structures in the CMO. CFMO - Craniofacial Malformation Ontology: abnormal human anatomy, includes the CHO All ontologies are in Protege Frames format (requires Protege 3.x). Ontologies refer to other ontologies via the Protege include mechanism. The CHMMO includes the CHO and the CMO. The OCDM (which is the umbrella ontology) includes all of the rest. Future releases will include translations to the OWL language.

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• SciCrunch
• 15 years ago - by Anonymous

Provides service and expert advice to researches in their projects related to nanoimaging studies of molecular systems at single molecule and single cell levels utilizing Atomic Force Microscope, combination of Atomic Force Microscope with Fluorescence Optical Microscope, combination of Atomic Force Microscope with Raman Spectroscopy.

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• SciCrunch
• 6 years ago - submitted by Edyta Vieth

NIDA IRP Confocal and Electron Microscopy Core serves NIDA-IRP researchers by providing access to confocal and electron microscopic technologies to characterize cellular and ultrastructural properties of organelles, tissue culture and brain tissue. Provides expertise, consultations and training in adaptation and execution of confocal and electron microscopic techniques and procedures.

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• SciCrunch
• 1 year ago - submitted by Edyta Vieth

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

Software tool as fully integrated online platform for performing systematic reviews of preclinical studies.

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• RRID-Legacy
• 6 years ago - submitted by Alexandra Bannach-Brown

Software R package for splitting, applying and combining data. Used to split up big data structure into homogeneous pieces, apply function to each piece and then combine all the results back together.

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• 1 year ago - by Anonymous

The database of protein-chemical structural interactions includes all existing 3D structures of complexes of proteins with low molecular weight ligands. When one considers the proteins and chemical vertices of a graph, all these interactions form a network. Biological networks are powerful tools for predicting undocumented relationships between molecules. The underlying principle is that existing interactions between molecules can be used to predict new interactions. For pairs of proteins sharing a common ligand, we use protein and chemical superimpositions combined with fast structural compatibility screens to predict whether additional compounds bound by one protein would bind the other. The current version includes data from the Protein Data Bank as of August 2011. The database is updated monthly.

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• SciCrunch
• 15 years ago - by Anonymous

Database for evolutionary biochemical studies of caspase functional divergence and ancestral sequence inference. Tool to rapidly disseminate organized caspase sequence data. Includes all animal species with currently available annotated genomes in NCBI genome database. Manually curated and not curated sequences are available to download.

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• RRID-Legacy
• 6 years ago - by Anonymous

Software function as Matlab implementation of the TFA as specified in the White Paper (2015). An example of use on the supplied data (tfa_sample_data.txt) is given in tfa_demo.m and results are reported at the end of this report.

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• RRID
• 1 year ago - by Anonymous