Curator Dashboard

Software package for aligning long sequencing reads as a diploid-aware genome assembler. Used for assembling non-inbred or rearranged heterozygous genomes.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

A Python-based environment of open-source software for mathematics, science, and engineering. The core packages of SciPy include: NumPy, a base N-dimensional array package; SciPy Library, a fundamental library for scientific computing; and IPython, an enhanced interactive console.

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• SciCrunch
• 13 years ago - by Anonymous

A software package written in OpenCL (Open Computing Language) that can be used for parallel analysis of fMRI data on a large variety of hardware configurations. If BROCCOLI is running on a GPU, it can perform non-linear spatial normalization to a 1 mm brain template in 4-6 s and run a second level permutation test with 10,000 permutations.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software package as probabilistic framework for structural variant discovery. Capable of integrating any number of SV detection signals including those generated from read alignments or prior evidence. Simplified wrapper for standard analyses, LUMPY Express, can also be executed.

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• SciCrunch
• 12 years ago - by Anonymous

Voluntary, non-profit organization dedicated to collecting and disseminating statistical data. Resource for gathering and disseminating epidemiologic data on all primary benign and malignant brain and other CNS tumors.

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• SciCrunch
• 16 years ago - by Anonymous

A project which aims to simplify the preparation of accurate electromagnetic head models for EEG forward modeling. It builds off of the seminal SimNIBS tool for electromagnetic field modelling of transcranial magnetic stimulation and transcranial direct current stimulation. Human skin, skull, cerebrospinal fluid, and brain meshing pipelines have been rewritten with Nipype to ease access parallel processing and to allow users to start/stop the workflows. Conductivity tensor mapping from diffusion-weighted imaging is also included.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A C++ software framework to develop, simulate and run magnetic resonance sequences on different platforms.

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• SciCrunch
• 14 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented on November 05, 2013. It has been superseeded by the CALATK, available here http://www.calatk.org c++ libraries and applications for performing fluid registration based operations on 2D and 3D images. The registration method is based on the large displacement diffeomorphic mapping (LDDM) registration method and implements discretized fluid registration. This registration method is then applied to time series analysis, cross-sectional atlas building, and longitudinal atlas building. The individual tool components are: * LDDM: Fluid registration between two images. * TimeSeries: Time series analysis of longitudinal data for a single subject. * AtlasBuilder: Cross-sectional atlas building for a population of images. * LongitudinalAtlasBuilder: Longitudinal atlas building for a population of subjects, each with a longitudinal data set. * FRATUtils: A collection of utility functions for working with volumes and time series files

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• SciCrunch
• 14 years ago - by Anonymous

An international symposium held initially to assess the new technology and innovation in the various established fields of genetics and imaging, and to facilitate the transdisciplinary fusion needed to optimize the development of the emerging field of Imaging Genetics

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software fast and lightweight tool for processing sequences in FASTA or FASTQ format.

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• SciCrunch
• 6 years ago - by Anonymous

Ontology that provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities. It provides vocabulary for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects.

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• SciCrunch
• 13 years ago - by Anonymous

A Matlab-based tool for computational neuroscience-based analysis and data visualization. Its features include: surface mesh visualization in PLY, PIAL, NV, STL,VTK, and GIFTI formats; conversion of NIfTI voxel images to surface meshes and saving as PLY or VTK; track (TRK files) visualization; connectome data (BrainNet Viewer .node and .edge files) visualization; intuitive GUI; that availability of all functions available in the GUI through scripting (automated scripts can be created); and exporting of rendered image as bitmap.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software tool as de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. It assembles raw reads without error correction and then builds consensus from intermediate assembly output. Desiged to assemble huge genomes in very limited time.

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• SciCrunch
• 8 years ago - submitted by Jie Yang

Community model organism database for laboratory mouse and authoritative source for phenotype and functional annotations of mouse genes. MGD includes complete catalog of mouse genes and genome features with integrated access to genetic, genomic and phenotypic information, all serving to further the use of the mouse as a model system for studying human biology and disease. MGD is a major component of the Mouse Genome Informatics.Contains standardized descriptions of mouse phenotypes, associations between mouse models and human genetic diseases, extensive integration of DNA and protein sequence data, normalized representation of genome and genome variant information. Data are obtained and integrated via manual curation of the biomedical literature, direct contributions from individual investigators and downloads from major informatics resource centers. MGD collaborates with the bioinformatics community on the development and use of biomedical ontologies such as the Gene Ontology (GO) and the Mammalian Phenotype (MP) Ontology.

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• SciCrunch
• 16 years ago - by Anonymous

A Matlab toolbox that computes the Q-Ball Imaging Orientation Distribution Function in Constant Solid Angle (CSA-ODF) for diffusion-weighted MRI.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Project features single board real time input/output system including touch sensing joysticks to quantify mouse forelimb trajectories with micron millisecond spatiotemporal resolution, which resolves mouse forelimb kinematics and further allows extraction of primitives. Joystick increases spatial precision, and reduces displacement force. Joystick is then integrated into automated home cage system to train mice in center out reach task.

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• RRID
• 3 years ago - submitted by Samantha White

The Epilepsy Foundation of America is the national voluntary agency dedicated solely to the welfare of the almost 3 million people with epilepsy in the U.S. and their families. The organization works to ensure that people with seizures are able to participate in all life experiences; to improve how people with epilepsy are perceived, accepted and valued in society; and to promote research for a cure. :Typical of the Foundations national programs are its Jeanne A. Carpenter Epilepsy Legal Defense Fund, the H.O.P.E. (Helping Other People with Epilepsy) Mentoring Program, a Public Policy Institute, Seniors and Womens Health Initiatives, the Kids Speak Up advocacy program, a school personnel training program, outreach to youth and to the Hispanic community, employment programs and a research grants program. Services commonly provided in local communities are information and referral, counseling, patient and family advocacy, school and community education, support groups and camps for children. Its Web site offers the most comprehensive, medically approved consumer information about epilepsy and seizures on the Internet and is the trusted source for millions of people who seek reliable information about epilepsy. : Each year the Foundation also invites research investigators to apply for grants and fellowships to test new ideas and follow new research leads. The applications, more than a hundred in an average year, are ranked according to merit by a blue ribbon panel of research scientists, and funded according to available resources. Additionally, the Epilepsy Foundation offers a series of training fellowships in basic, clinical and behavioral science to scientists at the start of their careers. These fellowships, awarded to young people at the nation's leading research institutes, have in many cases been the first steps on a lifetime commitment to solving the medical and scientific puzzle of why epilepsy develops and how it can be treated or prevented. Specifically, the Gowers Fellowship is awarded annually to a physician/scientist who is embarking on a career in academic clinical medicine and who wishes to undertake a specific project in epilepsy research. Sponsors: The Epilepsy Foundation is funded primarily through individual donations from the general public and receives restricted grant support from the federal government, foundations and private industry.

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• SciCrunch
• 17 years ago - by Anonymous

A software package for computational modeling of neural maps developed as part of the NIMH Human Brain Project. Topographica focuses on the large-scale structure and function that is visible only when many thousands of such neurons are connected into topographic maps containing millions of connections. The software package provides a general-purpose framework for building models at this level, at an appropriate level of detail and complexity, as determined by the available computing power, phenomena of interest, and amount of biological data available for validation. It is intended to complement low-level neuron simulators that are available, such as General Neural Simulation System and NEURON.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

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• NIF
• 3 years ago - by Anonymous

Software functions for data analysis and graphical displays for developmental microarray time course data.

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• SciCrunch
• 13 years ago - by Anonymous