Curator Dashboard

Analysis-tool which identifies singular node motifs in a network. Network nodes can be described by node-motifs. It is an improvement to the method described in Costa et al. (2009).

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• SciCrunch
• 15 years ago - by Anonymous

A database of scents. Users can search their structure or by scent tree, and can also add or search for specific scents by name. The database SuperScent was established to supply users with detailed information on the variety of odor components. The version of the database presented here comprises the 2D/3D structures of approximately 2100 volatiles and around 9200 synonyms as well as physicochemical properties, commercial availability and references. The volatiles are classified according to their origin, functionality and odorant groups. The information was extracted from the literature and web resources. SuperScent offers several search options, e.g. name, Pubchem ID number, species, functional groups, or molecular weight.

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• SciCrunch
• 17 years ago - by Anonymous

A sample script on how to map some numbers to brain regions, using the Talairach-Tournoux Atlas database. For example, put the value 0.379 in each hippocampus voxel, and the value 0.666 in each superior temporal gyrus voxel.

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• SciCrunch
• 15 years ago - by Anonymous

The FMRIB Centre is a multi-disciplinary neuroimaging research facility, which focuses on the use of Magnetic Resonance Imaging (MRI) for neuroscience research, along with related technologies such as Transcranial Magnetic Stimulation, transcranial Direct Cortical Stimulation and EEG. FMRIB is composed of research groups in all aspects of brain imaging research, including physics, analysis, basic science and clinical neuroscience. We were recently awarded 8 million pounds by the MRC, EPSRC, Wolfson Foundation and University of Oxford to purchase and install new 7T and 3T leading-edge MRI systems to enable us to image brain structure and function at even higher resolution than currently possible.

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• SciCrunch
• 15 years ago - by Anonymous

A commercial database of the substructures of natural compounds. Their conformers are available for purchase. Although tremendous effort has been put into synthetic libraries, most drugs on the market are still natural compounds or derivatives thereof. There are encyclopaedias of natural compounds, but the availability of these compounds is often unclear and catalogues from numerous suppliers have to be checked. To overcome these problems we have compiled a database of approximately 50,000 natural compounds from different suppliers. To enable efficient identification of the desired compounds, we have implemented substructure searches with typical templates. Starting points for in silico screenings are about 2500 well-known and classified natural compounds from a compendium that we have added. Possible medical applications can be ascertained via automatic searches for similar drugs in a free conformational drug database containing WHO indications. Furthermore, we have computed about three million conformers, which are deployed to account for the flexibilities of the compounds when the 3D superposition algorithm that we have developed is used.

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• SciCrunch
• 17 years ago - by Anonymous

A linear average model atlas produced by the International Consortium for Brain Mapping (ICBM) project. A set of full- brain volumetric images from a normative population specifically for the purposes of generating a model were collected by the Montreal Neurological Institute (MNI), UCLA, and University of Texas Health Science Center at San Antonio Research Imaging Center (RIC). 152 new subjects were scanned using T1, T2 and PD sequences using a specific protocol. These images were acquired at a higher resolution than the original average 305 data and exhibit improved contrast due predominately to advances in imaging technology. Each individual was linearly registered to the average 305 and a new model was formed. In total, three models were created at the MNI, the ICBM152_T1, ICBM152_T2 and ICBM152_PD from 152 normal subjects. This resulting model is now known as the ICBM152 (although the model itself has not been published). One advantage of this model is that it exhibits better contrast and better definition of the top of the brain and the bottom of the cerebellum due to the increased coverage during acquisition. The entirely automatic analysis pipeline of this data also included grey/white matter segmentation via spatial priors. The averaged results of these segmentations formed the first MNI parametric maps of grey and white matter. The maps were never made publicly available in isolation but have formed parts of other packages for some time including SPM, FSL AIR and as models of grey matter for EEG source location in VARETTA and BRAINWAVE. Again, as these models are an approximation of Talairach space, there are differences in varying areas, to continue our use of origin shift as an example, the ICBM models are approximately 152: +3.5mm in Z and +-co-ordinate -3.5mm and 2.0mm in Y as compared to the original Talairach origin. In addition to the standard analysis performed on the ICBM data, 64 of the subjects data were segmented using model based segmentation. 64 of the original 305 were manually outlined and a resulting parametric VOI atlas built. The native data from these acquisitions was 256x256 with 1mm slices. The final image resolution of this data was 181x217x181 with 1mm isotropic voxels. Refer to the ICBM152 NonLinear if you are fitting an individual to model and do not care about left/right comparisons. A short history of the various atlases that have been produced at the BIC (McConnell Brain Imaging Center, Montreal Neurological Institute) is provided.

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• SciCrunch
• 15 years ago - by Anonymous

The goal of our laboratory is to develop new MR technologies to improve the resolution and contrast of MRI and apply them to observe brain anatomy to answer various types of biological questions. Currently we have three major research targets: Characterization of mouse brain development; Human white matter anatomy and development; and Development of diffusion tensor imaging technique and technology dissemination. The DTI database (Under the DTI Download Tab) contains raw and processed DTI data of normal population. Currently we have 2.5 mm isotropic resolution images and 2.2 mm isotropic resolution images. Only 2.5 mm data are available from this site. If you are interested in the high-resolution images, please contact susumu @ mri.jhu.edu. This database is open to public once the user is registered. Basic imaging parameters can be also downloaded.

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• SciCrunch
• 15 years ago - by Anonymous

DTI white matter atlases with different data sources and different image processing. These include single-subject, group-averaged, B0 correction, processed atlases (White Matter Parcellation Map, Tract-probability maps, Conceptual difference between the WMPM and tract-probability maps), and linear or non-linear transformation for automated white matter segmentation. # Adam single-subject white matter atlas (old version): These are electronic versions of atlases published in Wakana et al, Radiology, 230, 77-87 (2004) and MRI Atlas of Human White Matter, Elsevier. ## Original Adam Atlas: 256 x 256 x 55 (FOV = 246 x 246 mm / 2.2 mm slices) (The original matrix is 96x96x55 (2.2 mm isotropic) which is zerofilled to 256 x 256 ## Re-sliced Adam Atlas: 246 x 246 x 121 (1 mm isotropic) ## Talairach Adam: 246 x 246 x 121 (1 mm isotropic) # New Eve single-subject white matter atlas: The new version of the single-subject white matter atlas with comprehensive white matter parcellation. ## MNI coordinate: 181 x 217 x 181 (1 mm isotropic) ## Talairach coordinate: 181 x 217 x 181 (1 mm isotropic) # Group-averaged atlases: This atlas was created from their normal DTI database (n = 28). The template was MNI-ICBM-152 and the data from the normal subjects were normalized by affine transformation. Image dimensions are 181x217x181, 1 mm isotropic. There are two types of maps. The first one is the averaged tensor map and the second one is probabilistic maps of 11 white matter tracts reconstructed by FACT. # ICBM Group-averaged atlases: This atlas was created from ICBM database. All templates follow Radiology convention. You may need to flip right and left when you use image registration software that follows the Neurology convention.

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• SciCrunch
• 15 years ago - by Anonymous

A database of haptens. It compiles 2D/3D structures, physicochemical properties and references for about 7500 haptens and 25,000 synonyms. Commercial availability is documented for about 6300 haptens and 450 related antibodies, enabling experimental approaches on cross-reactivity. The immune system protects organisms from foreign proteins, peptide epitopes and a multitude of chemical compounds. Among these, haptens are small molecules, eliciting an immune response when conjugated with carrier molecules. Known haptens are xenobiotics or natural compounds, which can induce a number of autoimmune diseases like contact dermatitis or asthma. Furthermore, haptens are utilized in the development of biosensors, immunomodulators and new vaccines. Although hapten-induced allergies account for 6-10% of all adverse drug effects, the understanding of the correlation between structural and haptenic properties is rather fragmentary. We have developed a manually curated hapten database, SuperHapten, integrating information from literature and web resources. The current version of the database compiles 2D/3D structures, physicochemical properties and references for about 7500 haptens and 25,000 synonyms. The commercial availability is documented for about 6300 haptens and 450 related antibodies, enabling experimental approaches on cross-reactivity. The haptens are classified regarding their origin: pesticides, herbicides, insecticides, drugs, natural compounds, etc. Queries allow identification of haptens and associated antibodies according to functional class, carrier protein, chemical scaffold, composition or structural similarity. keywords: hapten

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 9, 2025. A database which retains extensive clinical information about study subjects recruited by the Alzheimer's Disease Research Center Clinical Core, as well as other individuals with neurological diseases. In addition to clinical information, the database has basic demographics, medical history (including risk factors such as smoking), and a detailed family history from all subjects. Some entries have neuropsychological measures. Users can access a Summary Database which contains the most commonly requested variables. A data dictionary describing the variables in the Summary Database is available.

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• SciCrunch
• 15 years ago - by Anonymous

The core mission of the AXA Research Fund is to finance basic research contributing to understand and prevent risks. We support innovative and cutting-edge projects within three areas: environmental, life, and socio-economic risks. Only research institutions may submit applications. * Funding for research projects, postdoc and graduate fellowships, and long and short term projects * Encourages international applicants and research around the world Research projects funded by the Fund must fall within the scope of one of the themes identified by the AXA Scientific Board. The themes for 2011 are identified below: * Life risks ** Aging & Long-term care ** Biomedical risks ** Addictions and risky behaviors * Socio-economic risks ** Geopolitical risks ** Macroeconomic and financial systemic risks ** Individual and collective behaviors when facing uncertainties ** Large corporate risks * Environmental risks ** Climate change ** Natural hazards ** Human driven environmental changes

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• SciCrunch
• 15 years ago - by Anonymous

Software package to comprehensively evaluate different aspects of RNA-seq experiments, such as sequence quality, GC bias, polymerase chain reaction bias, nucleotide composition bias, sequencing depth, strand specificity, coverage uniformity and read distribution over the genome structure. RSeQC takes both SAM and BAM files as input, which can be produced by most RNA-seq mapping tools as well as BED files, which are widely used for gene models.

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• SciCrunch
• 13 years ago - by Anonymous

Algorithm for sequencing error correction of RNA-seq data sets. SEECER removes mismatch and indel errors from the raw reads and improves downstream analysis of the data.

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• SciCrunch
• 13 years ago - by Anonymous

Software aimed at using RNA-Seq short reads to build de novo gene models. First, candidate exons are built directly from the positions of the reads mapped on the genome (without any ab initio assembly of the reads), and all the possible splice junctions between those exons are tested against unmapped reads : the testing of junctions is directed by the information available in the RNA-Seq dataset rather than a priori knowledge about the genome. Exons can thus be chained into stranded gene models.

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• SciCrunch
• 13 years ago - by Anonymous

Software focusing on calling indels from the next-generation paired-end sequencing data.

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• SciCrunch
• 13 years ago - by Anonymous

Using robotic devices to investigate human motor behavior, this group develops computational models to understand the underlying control and learning processes. By simulating novel objects or dynamic environments they study how the brain recalibrates well-learned motor skills or acquires new ones. These insights are used to design fMRI studies to investigate how these processes map onto the brain. They have developed a number of novel techniques of how to study motor control in the MRI environment, and how to analyze MRI data of the human cerebellum. They also study patients with stroke or neurological disease to further determine how the brain manages to control the body.

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• SciCrunch
• 15 years ago - by Anonymous

A fast and accurate alignment tool for RNA-Seq data.

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• SciCrunch
• 13 years ago - by Anonymous

Software for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio. The statistical methods to estimate read coverage significance are also applicable to other sequencing data. Scripture also has modules for ChIP-Seq peak calling.

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• SciCrunch
• 13 years ago - by Anonymous

The Subviral RNA database facilitates the research and analysis of viroids, satellite RNAs, satellite viruses, the human hepatitis delta virus, and related RNA sequences. It integrates a large number of Subviral RNA sequences, their respective RNA motifs, analysis tools, related publication links and additional pertinent information to allow users to efficiently retrieve and analyze relevant information about these small RNA agents. The Subviral RNA Database contains 2877 sequences indexed in 83 species and 4 main groups.

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• SciCrunch
• 17 years ago - by Anonymous

A Java application to investigate alternative mRNA splicing patterns in data from high-throughput mRNA sequencing studies. Sequence reads are mapped to splice graphs that unambiguously quantify the inclusion level of each exon and splice junction. The graphs are then traversed to predict the protein isoforms that are likely to result from the observed exon and splice junction reads. UniProt annotations are mapped to each protein isoform to identify potential functional impacts of alternative splicing. This tool may be used on a single RNASeq sample to identify genes with multiple spliceforms, on a pair of samples to identify differential splicing between the two, or on groups of samples to identify statistically significant group level differences in splicing patterns. SpliceSeq can be run from the install page as a java web start application to explore the sequencing data on their server or can be installed locally to analyze your own mRNA-Seq data.

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• SciCrunch
• 13 years ago - by Anonymous