Curator Dashboard

Software tool as simulator for spiking neural network models that focuses on dynamics, size and structure of neural systems rather than on exact morphology of individual neurons. Used for any size spiking neurons networks including models of information processing, models of network activity dynamics, models of learning and plasticity.

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 23, 2013. Database for resting state functional connectivity studies. Functional connectivity has shown tremendous promise in mapping the intrinsic functional topography of the brain, evaluating neuroanatomical models, and investigating neurological and psychiatric disease. Brainscape includes a repository of public and private data and an analysis engine for exploring the correlation structure of spontaneous fluctuations in the fMRI BOLD signal. (DICOM data is the image format that can be uploaded.) With Brainscape you can upload, analyze, and share your own data. You can search for, download, and analyze studies in the repository of shared data. The analysis engine works by selecting one or more studies, typing in the coordinates of a brain region of interest, and the seed-region correlation engine computes the correlation structure across the whole brain. (T1, T2 and EPI data are the scan types Brainscape can process.) You decide who can access your data. You can keep it to yourself, share with select colleagues, or share it with everyone. The Brainscape database and analysis tools are open source and freely available.

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• SciCrunch
• 17 years ago - by Anonymous

An application for the automatic segmentation and tracing of three-dimensional neuronal images.

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• SciCrunch
• 12 years ago - by Anonymous

The Grass Foundation is a small, not-for-profit, private foundation chartered to support research and education in neuroscience. The hallmark program of The Grass Foundation is the Grass Fellowship Program at the Marine Biological Laboratory in Woods Hole, Massachusetts. This program provides a first opportunity for neuroscientists during late stages of predoctoral training or during postdoctoral years to conduct independent research for scientific discovery on their own at the MBL each summer. While sharing the Grass Laboratory, Fellows function as an intellectual and social group within the MBL community. The number of fellowships awarded varies annually. Additional programs supported by The Grass Foundation include the Robert S. Morison Fellowship, The Grass-MBL Faculty Grant Program, the Ricardo Miledi Program for Neuroscience Training, several neuroscience courses at the MBL, and yearly funding of a few lectureships and prizes. Please see our Program Grants section for more information.

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• SciCrunch
• 17 years ago - by Anonymous

A Bioconductor package that organizes, annotates, analyses and validates fusions reported by different fusion detection tools. The current implementation can deal with output from bellerophontes, chimeraScan, deFuse, fusionCatcher, FusionFinder, FusionHunter, FusionMap, mapSplice, Rsubread, tophat-fusion, tophat-fusion-post and STAR. The core of Chimera is a fusion data structure that can store fusion events detected with any of the aforementioned tools.

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• SciCrunch
• 12 years ago - by Anonymous

A powerful web-based platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphism loci.

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• SciCrunch
• 17 years ago - by Anonymous

Database of known and predicted mammalian and eukaryotic protein-protein interactions, it is designed to be both a resource for the laboratory scientist to explore known and predicted protein-protein interactions, and to facilitate bioinformatics initiatives exploring protein interaction networks. It has been built by mapping high-throughput (HTP) data between species. Thus, until experimentally verified, these interactions should be considered predictions. It remains one of the most comprehensive sources of known and predicted eukaryotic PPI. It contains 490,600 Source Interactions, 370,002 Predicted Interactions, for a total of 846,116 interactions, and continues to expand as new protein-protein interaction data becomes available.

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• SciCrunch
• 14 years ago - by Anonymous

A freeware Macintosh program for simulating and testing polymerase chain reactions (PCRs) that can also be used as a tool for designing primers by evaluating candidates. It's a program to simulate the polymerase chain reaction. You specify a target sequence and primers, and it predicts the result. It's useful for planning experiments, testing primers and teaching about PCR. Amplify draws a diagram of the predicted results showing all expected primer matches and amplified fragments. Clicking on any of these objects gives additional information about them.

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• SciCrunch
• 13 years ago - by Anonymous

An American global biotechnology company that manufactures drug therapies for cancer and inflammatory disorders. The company's major products are Thalomid (thalidomide), which is approved for the acute treatment of the cutaneous manifestations of moderate to severe erythema nodosum leprosum (ENL), as well as in combination with dexamethasone for patients with newly diagnosed multiple myeloma, and Revlimid (lenalidomide), for which the company has received FDA and EMA approval in combination with dexamethasone for the treatment of multiple myeloma patients who have received at least one prior therapy. Revlimid is also approved in the United States for the treatment of patients with transfusion-dependent anemia due to Low- or Intermediate-1-risk Myelodysplastic syndromes (MDS) associated with a deletion 5q cytogenetic abnormality with or without additional cytogenetic abnormalities. Both Thalomid and Revlimid are sold through proprietary risk-management distribution programs to ensure safe and appropriate use of these pharmaceuticals. Vidaza is approved for the treatment of patients with MDS. Celgene also receives royalties from Novartis Pharma AG on sales of the entire Ritalin family of drugs, which are widely used to treat Attention Deficit Hyperactivity Disorder (ADHD). (Adapted from Wikipedia) There are numerous clinical trials at major medical centers using compounds from Celgene. Investigational compounds are being studied for patients with incurable hematological and solid tumor cancers, including multiple myeloma, myelodysplastic syndromes, chronic lymphocyte leukemia (CLL), non-Hodgkin's lymphoma (NHL), glioblastoma, and ovarian, pancreatic and prostate cancer.

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• SciCrunch
• 17 years ago - by Anonymous

HvrBase++ is the improved and extended version of HvrBase. Extensions are made by adding more population-based sequence samples from all primates including humans. The current collection comprises 13,873 hypervariable region I (HVRI) sequences and 4940 hypervariable region II (HVRII) sequences. In addition, we included 1376 complete mitochondrial genomes, 205 sequences from X-chromosomal loci and 202 sequences from autosomal chromosomes 1, 8, 11 and 16. In order to reduce the introduction of erroneous data into HvrBase++, we have developed a procedure that monitors GenBank for new versions of the current data in HvrBase++ and automatically updates the collection if necessary. For the stored sequences, supplementary information such as geographic origin, population affiliation and language of the sequence donor can be retrieved. As a new key feature, HvrBase++ provides an interactive graphical tool to easily access data from dynamically created geographical maps.

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• SciCrunch
• 17 years ago - by Anonymous

National public repository system for mutant mice. Archives and distributes scientifically valuable spontaneous and induced mutant mouse strains and ES cell lines for use by biomedical research community. Includes breeding/distribution facilities and information coordinating center. Mice strains are cryopreserved, unless live colony must be established. Live mice are supplied from production colony, from colony recovered from cryopreservation, or via micro-injection of cell line into host blastocysts. MMRRC member facilities also develop technologies to improve handling of mutant mice, including advances in assisted reproductive techniques, cryobiology, genetic analysis, phenotyping and infectious disease diagnostics.

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• SciCrunch
• 17 years ago - by Anonymous

Database for the diploid genome sequence of J. Craig Venter as published in PLoS Biology. Its graphical interface depicts the haploid sequence with SNP and insertion/deletion DNA variants as identified by genome assembly and comparison methods, as well as represents the haplotype blocks from which diploid genome sequence can be inferred and gene annotations.

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• SciCrunch
• 17 years ago - by Anonymous

Software application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), it will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, it provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichement and more). AltAnalyze can be run through an intuitive graphical user interface or command-line and requires no advanced knowledge of bioinformatics programs or scripting. Alternative regulated exons can be subsequently visualized in the context of proteins, domains and microRNA binding sites with the Cytoscape Plugin DomainGraph.

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• SciCrunch
• 17 years ago - by Anonymous

A cross-reactive allergen prediction program built on a combination of Support Vector Machine (SVM) and pairwise sequence similarity. Cross-reactivity is based on similarity of proteins to allergens. However, not all proteins with similar sequence or structure to known allergens are cross-reactive allergens. AllerHunter aims to predict allergens and non-allergens with high sensitivity and specificity, without compromising efficiency at classification of proteins with similar sequence to known allergens. There are distinct differences between prediction of allergenicity and cross-reactivity of allergens. Allergenicity is the immunogenic potential of an allergen to induce IgE antibody production, whereas cross-reactivity is the potential of a substance to bind to IgE previously induced by a known allergen. It is difficult to predict allergenicity because causes of immunogenicity of allergens are still not completely clear. However it is possible to predict cross-reactivity since it implies similarity in IgE binding sites. Please provide protein sequence in fasta format.

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• SciCrunch
• 17 years ago - by Anonymous

Database of interrupted coding sequences detected by a similarity-based approach in complete prokaryotic genomes. The definition of each interrupted gene is provided as well as the ICDS genomic localization with the surrounding sequence. To facilitate the experimental characterization of ICDS, optimized primers are proposed for re-sequencing purposes. The database is accessible by BLAST search or by genome. 118 Genomes are available in the database.

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• SciCrunch
• 13 years ago - by Anonymous

A community portal for sharing and integration of human protein data that allows research laboratories to contribute and maintain protein annotations. The Human Protein Reference Database (HPRD) integrates data that is deposited along with the existing literature curated information in the context of an individual protein. Data pertaining to post-translational modifications, protein-protein interactions, tissue expression, expression in cell lines, subcellular localization and enzyme substrate relationships can be submitted.

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• SciCrunch
• 17 years ago - by Anonymous

This site provides access to mutation databases and software including the human hprt database, Human p53 database, Transgenic lacZ database, and Transgenic lacI database. Other avaialble programs include Mutational spectra comparison and relational database data entry. The most recent hprt database contains information on over 2,300 mutations found in vivo and in vitro in the human hprt gene and runs under Windows. The version for evaluation on this homepage has fewer mutations and is a DOS program. The database contains information on the mutagen, dose, spontaneous and induced mutant fraction, base position, amino acid position, amino acid change, local DNA sequence, cell type, citation, and other items. In addition, information regarding the cause and effect of mutations affecting splicing is given. Routines have been developed for the analysis of single base substitutions. The p53 database contains information on nearly 5,867 mutations found in the human p53 gene. The database itself has been updated in April of 1997. The database contains information on the cancer type, loss of heterozygosity, base position, amino acid position, amino acid change, local DNA sequence,citation, and other items. Routines have been developed for the analysis of single base substitutions. The Transgenic lacZ database contains information on 405 mutations found in vivo in the transgenic lacZ gene. It has last been updated in January of 1998. It provides information on the mutagen, dose, organ, mutant fraction, base position, amino acid position, amino acid change, local DNA sequence, citation, and other items. The Transgenic lacI database contains information on over 1700 mutations found in vivo in the transgenic lacI gene and on nearly 8000 mutations in the lacI gene in native E. coli. The database was updated in January 1998. The database contains information on the mutagen, dose, organ, mutant fraction, base position, amino acid position, amino acid change, local DNA sequence, citation, and other items. Routines have been developed for the analysis of single base substitutions for each of the databases. The software runs only on IBM-compatible PCs.

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• SciCrunch
• 15 years ago - by Anonymous

Research institute which investigates chronic disease and its triggers.

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• SciCrunch
• 17 years ago - by Anonymous

A database of human mitochondrial genomes containing mtDNA sequences, polymorphic sites, and the ability to search for specific variants. It contains 1865 complete sequences and 839 coding region sequences.

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• SciCrunch
• 17 years ago - by Anonymous

Software package for analyzing transcriptome sequencing data from different sequencing platforms.

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• SciCrunch
• 13 years ago - by Anonymous