Curator Dashboard

Freely accessible, public repository of vetted and annotated microscopic images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. Explore by Cell Process, Cell Component, Cell Type or Organism. The Cell includes images acquired from historical and modern collections, publications, and by recruitment.

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• SciCrunch
• 14 years ago - by Anonymous

A hybrid software system for feature selection and sample classification of high-dimensional datasets. It is designed for microarray but can be applied to any other high-dimensional datasets. It uses multiple filters to produce a normalized score for each feature. The score is an indication of the usefulness of each feature. It is then translated into a frequency map with more useful features receive a higher frequency in the map.

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• SciCrunch
• 13 years ago - by Anonymous

The Neuroscience Graduate Program (NGP) at OHSU provides outstanding, multidisciplinary training in neuroscience in one of the best-recognized neuroscience programs in the United States. Our graduates are distributed at top research institutions throughout the world, and the success of our faculty ensures that graduates have ready access to their next step ����?? be it postdoctoral fellowships in academia or industry, or other science-related careers. The program is particularly strong in cellular neuroscience, neuronal signaling, gene regulation, biophysics of channels and transporters, sensory systems, and neuroendocrinology with increasing strength in developmental neuroscience and disease-oriented neuroscience research. Faculty members are located within research institutes at OHSU including the Vollum Institute, the Oregon National Primate Research Center (ONPRC), Oregon Hearing Research Center, Jungers Center and the Center for Research on Occupational and Environmental Toxicology (CROET); as well as the basic and clinical departments in the OHSU School of Medicine. As time spent in the lab is the most important component of graduate science training, our program is designed such that core coursework is completed in the first year. During that first year, students also are immersed in research through lab rotations in several labs, eventually choosing one that gives a mutual fit. Because of the relatively small number of students compared to the number of neuroscience laboratories at OHSU, students have many options for a thesis lab. Our well funded faculty provide state-of-the-art exposure to the concepts and technology of modern neuroscience. OHSU also offers certificate and degree programs, e.g. technology transfer and translational science, for advanced students in the NGP who want to broaden their career options.

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• SciCrunch
• 16 years ago - by Anonymous

CATs Tower of London test is a free, computer-based software test originally developed by Shallice (1982) to investigate problem solving in subjects with damage to the frontal lobes. The CATs Tower of London Test comes with one preprogrammed test along with extensive normative data for that test. You can also create a test using your design. Briefly, subjects are required to move colored beads from a window on the left (working area) until they achieve the arrangement in the window on the right (goal position). Subjects are instructed to try to achieve the goal arrangement in as few moves as possible. The software contains a Tower of London test. The test contains trials with 3 beads and 3 pegs, 4 beads and 4 pegs, and 5 beads and 5 pegs. You can use the Setup screen to create a test using your design. A test can contain 3, 4, and 5 bead problems with varying number of moves required for the optimal solution. In Shallice's initial investigation using the Tower of London, patients with damage to the left anterior frontal lobe demonstrated impaired planning (i.e., greater number of moves required for solution). Patients with damage to the right anterior, and left or right posterior areas of the frontal lobes were not impaired. Thus, results from this initial study provided support for the view that the left anterior frontal lobe area is involved in the planning required for solving the Tower of London test. Recent studies using neuroimaging techniques support this notion. Studies using regional cerebral blood flow (rCBF) imaging indicate an involvement of the left frontal lobes in the planning required for successfully completing the Tower of London puzzle. Studies of patients with damage to the frontal lobes indicate less cortical specificity, but are consistent with the view that the frontal lobes are involved in the planning required for solving this puzzle.

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• SciCrunch
• 17 years ago - by Anonymous

HEFalMp (Human Experimental/FunctionAL MaPper) is a tool developed by Curtis Huttenhower in Olga Troyanskaya's lab at Princeton University. It was created to allow interactive exploration of functional maps. Functional mapping analyzes portions of these networks related to user-specified groups of genes and biological processes and displays the results as probabilities (for individual genes), functional association p-values (for groups of genes), or graphically (as an interaction network). HEFalMp contains information from roughly 15,000 microarray conditions, over 15,000 publications on genetic and physical protein interactions, and several types of DNA and protein sequence analyses and allows the exploration of over 200 H. sapiens process-specific functional relationship networks, including a global, process-independent network capturing the most general functional relationships. Looking to download functional maps? Keep an eye on the bottom of each page of results: every functional map of any kind is generated with a Download link at the bottom right. Most functional maps are provided as tab-delimited text to simplify downstream processing; graphical interaction networks are provided as Support Vector Graphics files, which can be viewed using the Adobe Viewer, any recent version of Firefox, or the excellent open source Inkscape tool.

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• SciCrunch
• 17 years ago - by Anonymous

A comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. It provides: systematic and alternate names, atomic formulas and masses, enzyme activities generating the modifications, keywords, literature citations, Gene Ontology cross-references, Protein Information Resource (PIR) and SWISS-PROT protein sequence database feature table annotations, structure diagrams and molecular models. Each RESID Database entry presents a chemically unique modification and shows how that modification is currently annotated in the protein sequence databases, Swiss-Prot and the Protein Information Resource (PIR). The RESID Database provides a table of corresponding equivalent feature annotations that is used in the UniProt project, an international effort to combine the resources of the Swiss-Prot, TrEMBL and PIR. As an annotation tool, the RESID Database is used in standardizing and enhancing modification descriptions in the feature tables of Swiss-Prot entries.

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• SciCrunch
• 17 years ago - by Anonymous

An online electronic lab notebook designed for lab scientists at research organizations that allows the creation and import research data, controlled sharing between lab members, and lets lab members communicate via messages and tasks. It also allows lab members to work from home or when travelling, in a secure, integrated collaborative environment.

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• SciCrunch
• 17 years ago - by Anonymous

Gene Cloud is a novel tool presenting gene-gene associations based on the scientific literature. It was developed by the Knockout Mouse Repository (www.komp.org) to help our customers find products related to other products they chose. We have built a detailed graph model of gene-gene associations based on how many times two genes are cited in the same article. If two genes are cited in many papers together, they are considered strongly connected. Each instance of Gene Cloud is centered around a specific gene. A list of the top most related genes is plotted as a branching structure from the center. A secondary branch can occur if a gene in the graph is more related a non-central gene than it is to the center gene. The font size of a branched gene indicates the relative strength of connection--always to the center gene. The distribution of genes in space is randomized each time Gene Cloud is run so a different picture will result for the same central gene. Color is used to indicate the availability of Knockout Mouse products at the KOMP Repository. If a gene is colored green in the graph there are products (mutant ES cells, sperm, embryos, or mice) ready to be ordered. Blue colored genes do not yet have products available, but you can follow the links back to the KOMP Repository and register interest to be alerted when products do become available. Gene Cloud is driven by a database of gene-gene associations that currently contains 82,000 genes and other biotypes, 113,000 annotated publications, and 467 million connections. The latest gene symbols, names and gene-publication annotation information is updated daily from the Mouse Genome Informatics database. The graphing is accomplished through the use of a modified version of jsViz.

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• SciCrunch
• 17 years ago - by Anonymous

Dataset of resting state fMRI scans obtained using two different TR's in healthy college-aged volunteers. Specifically, for each participant, data is being obtained with a short TR (0.4 seconds) and a long TR (2.0 seconds). In addition this dataset contains a 64-direction DTI scan for every participant. The following data are released for every participant: * 8-minute resting-state fMRI scan (TR = 2 seconds, # repetitions = 240) * 8-minute resting-state fMRI scans (TR = 0.4 seconds, # repetitions = 1200) * MPRAGE anatomical scan, defaced to protect patient confidentiality * 64-direction diffusion tensor imaging scan (2mm isotropic) * Demographic information

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• SciCrunch
• 13 years ago - by Anonymous

Digital three-dimensional MRI atlas of the Mozambique tilapia brain, supported by Nissl staining. Images were viewed and analyzed in all orientations (transverse, sagittal, and horizontal) and manually labelled to reveal structures in the olfactory bulb, telencephalon, diencephalon, optic tectum, and cerebellum. The MRI atlas data (16-bit int) and delineation data (8-bit int) are provided in Raw data (file_name.raw), Amira format (file_name.am) and in Analyze format (file_name.img and file_name.hdr).

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• SciCrunch
• 13 years ago - by Anonymous

Wiki dedicated to neurosurgical topics, maintained by the Congress of Neurological Surgeons. Members can log in to contribute by adding or editing an article. A wiki is a collaborative technology for organizing information. Visitors can add, remove, and edit content. Like all other wikis, the CNS University's NeuroWiki allows linking among any number of pages. This ease of interaction and operation will engender collaborative authoring.

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• SciCrunch
• 17 years ago - by Anonymous

Database on transcriptional regulation in Escherichia coli K-12 containing knowledge manually curated from original scientific publications, complemented with high throughput datasets and comprehensive computational predictions. Graphic and text-integrated environment with friendly navigation where regulatory information is always at hand. They provide integrated views to understand as well as organized knowledge in computable form. Users may submit data to make it publicly available.

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• SciCrunch
• 17 years ago - by Anonymous

Software package that performs genetic association tests between SNPs (one-at-a-time) and multiple phenotypes (separately or in joint model).

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• SciCrunch
• 12 years ago - by Anonymous

A domain ontology implemented in OWL-DL, which proposes a formal description of pharmacogenomic knowledge. It articulates different ontologies that represent complementary sub-domains of pharmacogenomics, i.e. related to genotype, phenotype, drugs, and clinical trials. SO-Pharm enables the representation of pharmacogenomic relationships between a drug, a genomic variation and a phenotype trait. In addition, it enables the representation of a patient and more largely a panel included in trials, and populations. SO-Pharm enables the representation of measured items on patients such as results from the observation of a phenotype trait or of genomic variations. SO-Pharm supports knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. SO-Pharm is designed to facilitate data integration and knowledge discovery in pharmacogenomics. In addition it provides a consistent articulation of ontologies of pharmacogenomic sub-domains.

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• SciCrunch
• 13 years ago - by Anonymous

Collection of curated, non-redundant genomic DNA, transcript RNA, and protein sequences produced by NCBI. Provides a reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. Accessed through the Nucleotide and Protein databases.

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• SciCrunch
• 17 years ago - by Anonymous

A collection of tools to facilitate population genetic studies of next generation sequencing data from pooled individuals. It builds upon open source tools (bwa, samtools) and uses standard file formats (gtf, sam, pileup) to ensure a wide compatibility. PoPoolation allows to calculate Tajima's Pi, Watterson's Theta and Tajima's D for reference sequences using a sliding window approach. Alternatively these population genetic estimators may be calculated for a set of genes (provided as gtf). One of the main challenges in population genomics is to identify regions of intererest on a genome wide scale. PoPoolation will greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools.

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• SciCrunch
• 13 years ago - by Anonymous

A MATLAB toolbox which implements the joint Independent Component Analysis (ICA), parallel ICA and CCA with joint ICA methods. It is used to to extract the shared information across modalities like fMRI, EEG, sMRI and SNP data. * Environment: Win32 (MS Windows), Gnome, KDE * Operating System: MacOS, Windows, Linux * Programming Language: MATLAB * Supported Data Format: ANALYZE, NIfTI-1

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• SciCrunch
• 17 years ago - by Anonymous

An ontology for describing software tools, their types, tasks, versions, provenance and data associated (the input and output data types and the uses the software can be put to).

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• SciCrunch
• 13 years ago - by Anonymous

Project facilitating the establishment and maintenance of standards systems and infrastructure for the worldwide collection and sharing of all genetic variations effecting human disease. The Human Variome Project produces two categories of recommendations: HVP Standards and HVP Guidelines. HVP Standards are those systems, procedures and technologies that the Human Variome Project Consortium has determined should be used by the community. These carry more weight than the less prescriptive HVP Guidelines, which cover those systems, procedures and technologies that the Human Variome Project Consortium has determined would be beneficial for the community to adopt. HVP Standards and Guidelines are central to supporting the work of the Human Variome Project Consortium and cover a wide range of fields and disciplines, from ethics to nomenclature, data transfer protocols to collection protocols from clinics. They can be thought of as both technical manuals and scientific documents, and while the impact of HVP Standards and Guidelines differ, they are both generated in a similar fashion. A document has been generated both as a guide for those collecting and distributing data and for those developing policy. Items should include those generated by HGVS/HVP collaborators as well as those generated by groups of individual Societies and Standards bodies in all relevant fields worldwide.

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• SciCrunch
• 15 years ago - by Anonymous

A multi-center project comprising two distinct consortia (Mass. Gen. Hosp. and USC; and Wash. U. and the U. of Minn.) seeking to map white matter fiber pathways in the human brain using leading edge neuroimaging methods, genomics, architectonics, mathematical approaches, informatics, and interactive visualization. The mapping of the complete structural and functional neural connections in vivo within and across individuals provides unparalleled compilation of neural data, an interface to graphically navigate this data and the opportunity to achieve conclusions about the living human brain. The HCP is being developed to employ advanced neuroimaging methods, and to construct an extensive informatics infrastructure to link these data and connectivity models to detailed phenomic and genomic data, building upon existing multidisciplinary and collaborative efforts currently underway. Working with other HCP partners based at Washington University in St. Louis they will provide rich data, essential imaging protocols, and sophisticated connectivity analysis tools for the neuroscience community. This project is working to achieve the following: 1) develop sophisticated tools to process high-angular diffusion (HARDI) and diffusion spectrum imaging (DSI) from normal individuals to provide the foundation for the detailed mapping of the human connectome; 2) optimize advanced high-field imaging technologies and neurocognitive tests to map the human connectome; 3) collect connectomic, behavioral, and genotype data using optimized methods in a representative sample of normal subjects; 4) design and deploy a robust, web-based informatics infrastructure, 5) develop and disseminate data acquisition and analysis, educational, and training outreach materials.

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• SciCrunch
• 13 years ago - by Anonymous