Curator Dashboard

A resource for online accredited courses in a wide variety of areas, including accounting, animal care, beauty, building and construction, business, education, design and writing. This resource is based in Australia.

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• SciCrunch
• 12 years ago - by Anonymous

Software for segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.

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• SciCrunch
• 11 years ago - by Anonymous

Understanding the mechanisms underlying the expression and perception of auditory communication in nonhuman primates provides important insights for understanding the neural systems that mediate nonverbal auditory communication in humans. Our research is devoted to understanding the changes in vocal behavior that are associated with maturation and social experience under normative conditions, and to investigating neural systems to define their roles in auditory communication. The anterior cingulate gyrus, in the frontal cerebral cortex, is an essential neural system for the expression of the primate isolation call, a structural and functional equivalent of the cry sounds of humans. Bilateral removal of this structure in adult squirrel monkeys resulted in a long-lasting inability to emit isolation calls. Partial recovery, often over many weeks, initially took the form of production of short, faint and uninflected versions of the typical isolation call. Humans suffering infarct damage to this region likewise show an initial recovery in the form of short, faint, monosyllabic sounds, suggesting that the anterior cingulate gyrus of nonhuman primates is the evolutionary precursor of a neural structure involved in human affective expression and speech. Our working model of isolation call production is that the anterior cingulate gyrus is the site where the command to produce this vocalization is initiated. Since the anterior cingulate region also has reciprocal connections with temporal lobe auditory cortex, a presumptive feedback pathway exists for registering commands to initiate vocalization with the temporal lobe cortex, which plays a major role in perceiving and decoding the acoustic details of species-specific vocalizations. At present, we do not know the role of the anterior cingulate gyrus in the production of infant vocalizations. However, we have found that neonatal removal of the amygdala, an important forebrain component of the limbic system, or portions of the inferotemporal gyrus, which sends projections to the amygdala, result in significant changes in the vocal behavior of infant rhesus macaques. Vocal development is a dynamic process, and a pattern shared by several nonhuman primates has emerged regarding the nature of this process. Infants are highly vocal during periods of brief separation from their caregiver, and we take advantage of this to document the range of vocalizations produced by infants of different ages. In the neonatal period, infants of 3 species of nonhuman primate (rhesus macaque, squirrel monkey and common marmoset) all produce sounds that vary widely in their acoustic structure. Many of these bear a striking similarity to sounds used in a variety of social settings by adults, suggesting that neural systems responsible for generating adult vocalizations are already in place during early infancy. As infants mature, their vocal behavior during brief periods of social separation becomes much more stereotyped. It isn't until much later in development, as individuals engage in a variety of social interactions with peers and adults, that the sounds expressed in early infancy begin to re-appear in adult contexts. The role of individual experience during development is currently being explored to determine the mechanisms leading to the acquisition of adult vocal skills.

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• SciCrunch
• 14 years ago - by Anonymous

A software package for control of automated microscopes that runs as a plugin in ImageJ, works with virtually all scientific grade microscope equipment, and has a simple interface towards routine image acquisition strategies such as time-lapse, z- stacks, multi-channel, and multi-position acquisition. In addition, it uses a device abstraction layer available from various programming environments (such a C, Java, Python, Matlab and LabView), facilitating development of novel approaches to image acquisition. Manager has a simple and clean user interface, through which it lets users execute common microscope image acquisition strategies such as time-lapses, multi-channel imaging, z-stacks, and combinations thereof. Manager works with microscopes from all four major manufacturers (Leica, Nikon, Olympus and Zeiss), most scientific-grade cameras and many peripherals (stages, filter wheels, shutters, etc.) used in microscope imaging.

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• SciCrunch
• 12 years ago - by Anonymous

R software package for transcription factor (TF) target gene prediction based on ChIP-seq data. Version 0.4 contains code to compute FDR-corrected q-values via permutations of the peak-to-gene assignments (ClosestGene only).

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• SciCrunch
• 12 years ago - by Anonymous

An OpenGL based medical image viewer that contains useful tools such as a DICOM anonymizer and format conversion utility. MIView can read DICOM, Analyze/Nifti, and raster images, and can write Analyze/Nifti and raster images.

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• SciCrunch
• 12 years ago - by Anonymous

The packaged tools perform Local Binary Pattern on Three Orthogonal Planes (LBP-TOP) analysis on MR brain images. One can use them to extract LBP texture features for machine learning applications or other advance analysis. Bash scripts performing simple preprocessing with FSL and AFNI as well as LBP mapping programs written by Java are both including in this package. The output is the histogram describing the brain morphology.

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• SciCrunch
• 12 years ago - by Anonymous

Discussion forum on licensing issues in software and data. All are invited to participate or join the project and contribute. A listing of software licenses are available.

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• SciCrunch
• 12 years ago - by Anonymous

A Bioconductor package that can import gates defined by the commercial package FlowJo and work with them in a manner consistent with the other flow packages in Bioconductor. FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the FlowJo Workspace. This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm.

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• SciCrunch
• 11 years ago - by Anonymous

An R/Bioconductor package that interfaces the X!Tandem protein identification algorithm.

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• SciCrunch
• 11 years ago - by Anonymous

Software R package for meta-analysis for microarrays. It combines either p-values or modified effect sizes from different studies to find differentially expressed genes.

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• SciCrunch
• 11 years ago - by Anonymous

Software for fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.

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• SciCrunch
• 11 years ago - by Anonymous

Input either normalized MNI coordinates from a 3D image, or input real world XYZ matrix coordinates, and this code will convert coordinates of one type to the other.

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• SciCrunch
• 12 years ago - by Anonymous

Software which integrates a comprehensive, automated genome annotation engine with the VAAST and Phevor disease gene prioritization tools to rank gene variants on the severity of their impact on protein function and likelihood to cause disease. Each variant in a gene is analyzed for its impact on protein function, conservation and frequency. Each gene is ranked rather than filtered in order to ensure critical targets are not prematurely removed.

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• SciCrunch
• 12 years ago - by Anonymous

Blog about random findings from data written by Leon French.

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• SciCrunch
• 13 years ago - by Anonymous

Database of processed seismic reflection / refraction data providing access to metadata, SEG-Y files, navigation files, seismic profile images, processing histories and more. The main features of the web site include a geographic search engine using Google Plugins, a metadata search engine, and metadata pages for the various seismic programs. Metadata are uploaded into mySQL, a public-domain SQL server, and then PHP scripts query the metadata and directories, creating web pages, displaying images, and providing ftp links. The minimum requirements for data submission are: * unrestricted access to the navigation and small raster image (about 300 x 600 pixels) * file format is SEG-Y (they can help with this) * information relating geographic location to the traces in the file (this is often a big part of what they create) They also need basic descriptive information (metadata) about acquisition, navigation geometry, processing sequence and provenance (and pass some of our consistency tests). The submitted metadata is naturally highly variable but could include cruise reports, processing reports, important citations, etc.

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• SciCrunch
• 13 years ago - by Anonymous

A data resource, map repository, and GIS service provider for federally-funded scientists conducting research in the Arctic and Antarctic. The PGC holds an extensive collection of satellite imagery and aerial photography at varying resolutions. They can process and deliver imagery to federally-funded researchers, but most datasets are directly available for download from the satellite imagery page or aerial photography page. Included are the Alaskan High Altitude Aerial Photography (AHAP) Program, Antarctic TMA Aerial Photographs, Landsat and MODIS imagery, among others. The PGC also has staff trained in cartography and GIS to specifically create custom maps for your project. The PGC also holds a large collection of Antarctic maps in digital form. Included are series from the Antarctic and Arctic from many organizations and decades. In collaboration with the United States Geological Survey's Antarctic Resource Center, the PGC holds and digitally preserves the entire reconnaissance mapping series and satellite maps. The PGC also digitally stores geologic maps from the American Geographical Society, historic Antarctic nautical charts, and many others. If you cannot find a map of a specific region or time, it may still exist, especially since the PGC creates more than 100 maps per year and are still adding to the collection. Due to licensing and other restrictions, some of the maps are not be publicly available; send your request and they may be able to provide these maps to you. They also employ a remote sensing staff to assist in remote sensing analysis of your imagery. They provide analysis such as NDVI or land-use/land-cover. The PGC employs both full-time and student staff trained in the latest GIS software and techniques. Although not a primary data creator for the polar regions, they use and distribute many datasets for basemaps and operations. The GIS data page displays links to external resources or data direct for download. They provide analysis with geospatial data (raster and vector) including, but not limited to, imagery/spectral analysis, modeling, DEM creation and manipulation, raster processing, line-of-sight and transect analysis, and database creation and maintenance. In the past, the PGC has been a tremendous resource for researchers and logistics staff alike to make sense of their field or logistics data. Even if it's as simple as plotting coordinates on a map, the PGC can assist!

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• SciCrunch
• 13 years ago - by Anonymous

Automated benchtop flow cytometry system. It allows measuring four fluorochrome-conjugates, forward and side scatter.

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• SciCrunch
• 12 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, as of October 1, 2013; however, the site is still accessible. NCBI resource that contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites. STS sequences are incorporated into the STS Division of GenBank. The dbSTS database offers a route for submission of STS sequences to GenBank. It is designed especially for the submission of large batches of STS sequences.

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• SciCrunch
• 15 years ago - by Anonymous

Software using statistical methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the flowCore package.

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• SciCrunch
• 11 years ago - by Anonymous