Curator Dashboard

This tool creates an Atlas image as an average of several DTI images that will be registered. The registration will be done in two steps : - Affine Registration with BRAINSFit - Non Linear Registration with GreedyAtlas A final step will apply the transformations to the original DTI images so that the final average can be computed. The main function writes a python script that will be executed to compute the Atlas. By running DTIAtlasBuilder, you will need to fill in informations in a Graphical User Interface, and then compute the Atlas. You can also run the tool in command line without using the GUI. Using the GUI, you will be able to save or load a dataset file or a parameter file. The tool needs these other tools to work, so be sure to have these installed on your computer: - ImageMath - ResampleDTIlogEuclidean - CropDTI - dtiprocess - BRAINSFit - GreedyAtlas - dtiaverage - DTI-Reg - unu - MriWatcher If you download the package, be sure to have the glut library installed.

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• SciCrunch
• 13 years ago - by Anonymous

The pursuit of the Department of Physiology & Pharmacology at Wake Forest University School of Medicine is excellence in research and education. Graduate education and training includes quality introductory and advanced courses in physiology, pharmacology and neuroscience, as well as seminars and journal clubs in several major research areas. Laboratory rotations encourage the graduate student to explore various experimental approaches and provide a diverse training experience. The department and Medical Center are frequented by distinguished visitors from other universities who further enrich the stimulating academic environment. Departmental faculty are active in the medical education as well as in residency training programs in Neurology, Psychiatry, Urology, and Surgery.

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• SciCrunch
• 17 years ago - by Anonymous

General-purpose unsupervised data-analysis tool, most often used for brain imaging data.

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• SciCrunch
• 13 years ago - by Anonymous

A tool for the gene-set (or pathway) analysis of a genome-wide association study result. It accepts a genome-wide list of SNPs and their association P-values. It summarizes the SNP P-values into nearby genes. The gene-by-gene summary results are then further summarized by gene-sets such as Gene Ontology, KEGG pathways, or user-created gene-sets. Various standardization and statistical tests can be performed and the resulting gene-sets that pass a significance level after multiple-testing correction are reported. The tool is written in Java and is available as a standalone version.

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• SciCrunch
• 13 years ago - by Anonymous

Software tools for the processing of liver images. These tools consist of a level set based variational approach that incorporates shape priors and appearance models. It uses ITK-SNAP 1.4 as interface. The tools are capable of automatic liver segmentation and semi-automatic injury segmentation.

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• SciCrunch
• 13 years ago - by Anonymous

Database that contains the complete entries of human ARE-containing full-length mRNAs.<BR/> ARED is further clustered into five groups depending on the number of motifs in the ARE stretch. Groups 1-4 contain five, four, three and two pentameric (AUUUA) repeats, respectively, while Group 5 contains only one repeat within the 13-bp pattern. Clustering was performed in such a way that, for example, Group 1 included not only exact five or more continuous ARE pentamers but also those with 10% ambiguity, so that a stretch of NUUUAUUUAUUUAUUUAUUUN would fall in this category. This process was verified by a phylogenic tree relationship using Clustal-W alignment of ARE stretches and their variations. As could be expected, this analysis showed that the lower the number of ARE motifs in a group, the higher the number of sequences that were included, and apparently the more functionally diverse the corresponding ARE-genes.<BR/>

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• SciCrunch
• 17 years ago - by Anonymous

This Matlab toolkit is a general purpose tool for editing, visualizing, and analyzing EEG data (both Event Related Potential - ERP and spectral) whose most recent version has been downloaded over 1000 times. Its three chief highlights are: 1) an optimized automatic artifact correction function that includes ICA correction for eye blinks and saccades. 2) Extensive support for easily conducting PCA and ICA through all stages of the procedure, including inspection of reconstituted waveforms and batch ANOVAs. 3) Implementation of robust ANOVAs, including McCarthy-Wood vector test. It has a graphical user interface for point and click usage and comes with an extensive illustrated tutorial. A description of the toolkit was published in Dien (2010) in Journal of Neuroscience Methods. It relies on both internal functions as well as borrowed functions from both EEGlab and FieldTrip.

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• SciCrunch
• 13 years ago - by Anonymous

Commissioned Corps of the United States Public Health Service, is the federal uniformed service of the U.S. Public Health Service, and is one of the eight uniformed services of the United States.

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• SciCrunch
• 16 years ago - submitted by Andrea Stagg

This software can be used to analyze EEG data either using a graphical interface (GUI) or using Matlab scripts, which make use of the functions provided by the MeanMachine. As compared to other libraries, MeanMachine can handle even very large data sets like, for example, 256 channels recorded at 2KHz.

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• SciCrunch
• 13 years ago - by Anonymous

Blog that examines the intersection of traditional genealogical techniques and modern genetic research.

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• 13 years ago - by Anonymous

A mutation registry for X-linked agammaglobulinemia (XLA). BTKbase lists mutation entries of 1,111 patients from 973 unrelated families showing 602 unique molecular events. Agammaglobulinemia is characterized by failure to produce mature B lymphocyte cells and is associated with a failure of Ig heavy chain rearrangement. Two thirds of cases are familial, and one third of cases are believed to arise from new mutations. Mutations of the BTK gene are found in approximately 80% of patients with agammaglobulinemia. The localization of the mutations on the gene and protein for BTK can be analyzed by clicking sequences on the web pages. It includes a mutation browser, which gives users access to mutations in Bruton tyrosine kinase (BTK) protein sequences, and XLA fact file, and forms for users to submit mutation to the dataset.

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• SciCrunch
• 17 years ago - by Anonymous

ColiSNP is a website made up of two databases focused on SNPS. The first database is a database of Single Nucleotide Polymorphism (SNP) located in the protein coding region, and the second is a database of Single Nucleotide Polymorphism (SNP) located in the gene regulation region. The database of Single Nucleotide Polymorphism (SNP) located in the protein coding region is a database of Single Nucleotide Polymorphism (SNP) mapped on protein structure. Users can search the data of SNP on this web site and display the structure of protein with SNP by RasMol. The database of Single Nucleotide Polymorphism (SNP) located in the gene regulation region is a database of Single Nucleotide Polymorphism (SNP) mapped on regulation region. Users can search genes mapped snp on regulation region.

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• SciCrunch
• 17 years ago - by Anonymous

The Catalytic Site Atlas (CSA) is a database documenting enzyme active sites and catalytic residues in enzymes of 3D structure. We defined a classification of catalytic residues which includes only those residues thought to be directly involved in some aspect of the reaction catalyzed by an enzyme. The CSA contains 2 types of entry: 1. Original hand-annotated entries, derived from the primary literature. References for these entries are given. 2. Homologous entries, found by PSI-BLAST alignment (using an e value cut-off of 0.00005) to one of the original entries. The equivalent residues, which align in sequence to the catalytic residues found in the original entry are documented. Access to the CSA is via PDB code, SWISS-PROT entry or E.C. number. Accessing via PDB code takes you straight to the CSA entry for that PDB, while accessing via SWISS-PROT or E.C. number gives a list of all PDB codes for structures assigned that particular SWISS-PROT identifier or E.C. number. Structures with entries in the CSA are given as hyperlinks. Each CSA entry lists the catalytic residues found in that entry, using PDB residue numbering. Each site is also marked with an evidence tag, which is either Literature reference or PSI-BLAST hit. If the entry is a PSI-BLAST hit you can follow the link to the original entry. You may download the CSA. JESS, an algorithm for constraint-based structural template matching and its application to 3D templates used by the CSA, is available for download.

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• SciCrunch
• 17 years ago - by Anonymous

Data analysis service for the prediction of multi-label protein subcellular localization based on gene ontology and support vector machines. Web services are also available.

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• SciCrunch
• 13 years ago - by Anonymous

The EzCatDB database analyzes and classifies enzyme catalytic mechanisms on the basis of information from literature and data that are derived from entries in the Protein Data Bank (PDB). Each data set contains corresponding enzyme information, such as E.C. number, PDB entries with their annotated ligand information and active site residues, information on catalytic mechanisms, and links to other databases, such as Swiss-prot, CATH, KEGG, PDBsum, and PubMed.

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• SciCrunch
• 17 years ago - by Anonymous

Transcriptomic information (spatiotemporal gene expression profile data) on the postnatal cerebellar development of mice (C57B/6J & ICR). It is a tool for mining cerebellar genes and gene expression, and provides a portal to relevant bioinformatics links. The mouse cerebellar circuit develops through a series of cellular and morphological events, including neuronal proliferation and migration, axonogenesis, dendritogenesis, and synaptogenesis, all within three weeks after birth, and each event is controlled by a specific gene group whose expression profile must be encoded in the genome. To elucidate the genetic basis of cerebellar circuit development, CDT-DB analyzes spatiotemporal gene expression by using in situ hybridization (ISH) for cellular resolution and by using fluorescence differential display and microarrays (GeneChip) for developmental time series resolution. The CDT-DB not only provides a cross-search function for large amounts of experimental data (ISH brain images, GeneChip graph, RT-PCR gel images), but also includes a portal function by which all registered genes have been provided with hyperlinks to websites of many relevant bioinformatics regarding gene ontology, genome, proteins, pathways, cell functions, and publications. Thus, the CDT-DB is a useful tool for mining potentially important genes based on characteristic expression profiles in particular cell types or during a particular time window in developing mouse brains.

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• SciCrunch
• 17 years ago - by Anonymous

A tool for structural biology and drug design.

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• SciCrunch
• 13 years ago - by Anonymous

Database on the sequence of the euchromatic genome of Drosophila melanogaster In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterizing the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community. Resources * Universal Proteomics Resource: Search for clones for expression and tissue culture * Materials: Request genomic or cDNA clones, library filters or fly stocks * Download Sequence data sets and annotations in fasta or xml format by http or ftp * Publications: Browse or download BDGP papers * Methods: BDGP laboratory protocols and vector maps * Analysis Tools: Search sequences for CRMs, promoters, splice sites, and gene predictions * Apollo: Genome annotation viewer and editor September 15, 2009 Illumina RNA-Seq data from 30 developmental time points of D. melanogaster has been submitted to the Short Read Archive at NCBI as part of the modENCODE project. The data set currently contains 2.2 billion single-end and paired reads and over 201 billion base pairs.

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• SciCrunch
• 17 years ago - by Anonymous

Software developed at Celera Genomics as part of Celera''s sequencing and annotation of the human genome, and released as open source in 2006.

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• SciCrunch
• 13 years ago - by Anonymous

Genetic Codes is a summary resource of the taxonomy of each record and assignment of the correct genetic code for every entry in the GenBank database. GenBank format by historical convention displays mRNA sequences using the DNA alphabet. Thus, for the convenience of people reading GenBank records, the genetic code tables shown here use T instead of U. The following genetic codes are described here: The Standard Code The Vertebrate Mitochondrial Code The Yeast Mitochondrial Code The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code The Invertebrate Mitochondrial Code The Ciliate, Dasycladacean and Hexamita Nuclear Code The Echinoderm and Flatworm Mitochondrial Code The Euplotid Nuclear Code The Bacterial, Archaeal and Plant Plastid Code The Alternative Yeast Nuclear Code The Ascidian Mitochondrial Code The Alternative Flatworm Mitochondrial Code Blepharisma Nuclear Code Chlorophycean Mitochondrial Code Trematode Mitochondrial Code Scenedesmus Obliquus Mitochondrial Code Thraustochytrium Mitochondrial Code

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• SciCrunch
• 17 years ago - by Anonymous