Curator Dashboard

An interface between MATLAB and the Polhemus Fastrak digitizer used to digitize fiducial locations and scalp EEG electrode locations. There are 5 versions all of which work under MATLAB R14 (on both linux and windows platforms), # polgui_ver1_r14 : works with 1 receiver (stylus pen) # polgui_ver2_r14 : works with 2 receivers (including the pen) # polgui_ver3_r14 : works with 3 receivers(including the pen) # polgui_ver4_r14 : works with 4 receivers (including the pen) # polgui_ver5_r14 : Generic version which works with 1/2/3/4 receivers (WARNING: Ver 5 might be buggy; not fully tested) Requirements: MATLAB R14 (Linux/Windows)

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• SciCrunch
• 14 years ago - by Anonymous

Core facility for the Vanderbilt Digestive Disease Research Center. Provides professional expertise in biostatistics for all DDRC projects, investigators, and participants. Functions provided by this component include development of experimental designs, power analysis, and sample size computation; data acquisition and database development; statistical analysis and interpretation of findings; collaboration on presentation of results; education in biostatistical methods; and development of tools with application to clinical trials and laboratory research.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.

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• SciCrunch
• 13 years ago - by Anonymous

A large multi-site pediatric MRI and genetics data resource to facilitate studies of the genomic landscape of the developing human brain. It includes information about the developing mental and emotional functions of the children to understand the genetic basis of individual differences in brain structure and connectivity, cognition, and personality. Investigators on the project are studying 1400 children between the ages of 3 and 20 years so that links between genetic variation and developing patterns of brain connectivity can be examined. Investigators interested in the effects of a particular gene will be able to search the database for any brain areas or connections between areas that differ as a function of variation in a particular gene, and also to determine if the genes appear to affect the course of brain development at some point during childhood. A data exploration tool has been created for mapping and analyzing MRI data sets collected for PING and related developmental studies. Approved investigators will be able to view raw image sets and derived 3D brain maps of MRI and DTI data, conduct hypothesis testing, and graph brain area measures as they change across the time course of development. PING Cores * Coordinating Core: Functions include project management, screening of participants and maintaining the database * Neuroimaging Core: applying a standardized high-resolution structural MRI protocol involving 3-D T1-weighted scans, a T2-weighted volume, and a set of diffusion-weighted scans with multiple b values and diffusion directions, scans to estimate MRI relaxation rates, and gradient echo EPI scans for resting state fMRI. Importantly, adaptive motion compensation, using ����??PROMO����??, a novel real-time motion correction algorithm will be used. Specific PING protocols for each scanner manufacturer: ** PING MRI Protocol - GE ** PING MRI Protocol - Philips ** PING MRI Protocol - Siemens * Assessment Core: Cognitive assessments for the PING project are conducted using the NIH Toolbox for Cognition. * Genomics Core: functions as a central repository for receipt of saliva samples collected for each study participant. Once received, samples are catalogued, maintained, and DNA is extracted using state-of-the-field laboratory techniques. Ultimately, genome-wide genotyping is performed on the extracted DNA using the Illumina Human660W-Quad BeadChip. PING involves 10 sites throughout the country including UCSD, University of Hawaii, Scripps Genomics, UCLA, UC Davis, Kennedy Krieger Institute/Johns Hopkins, Sacker Institute/Cornell University, University of Massachusetts, Massachusetts General Hospital/Harvard, and Yale. Families who may want to participate in the study, or others who want to know more about it, may email questions to ping (at) ucsd.edu.

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• SciCrunch
• 13 years ago - by Anonymous

Software as R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding. Used for high-dimentional data visualisation.

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• SciCrunch
• 8 years ago - submitted by Edyta Vieth

A meta-list that is a compilation of other biology related wikipedia pages. These listings include the wiki name, description, year of inception, pages, new pages, users, active users, new edits, and wiki logo. The table can also be downloaded in a csv formatted table.

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• SciCrunch
• 17 years ago - by Anonymous

A MATLAB toolbox which implements the joint Independent Component Analysis (ICA), parallel ICA and CCA with joint ICA methods. It is used to to extract the shared information across modalities like fMRI, EEG, sMRI and SNP data. * Environment: Win32 (MS Windows), Gnome, KDE * Operating System: MacOS, Windows, Linux * Programming Language: MATLAB * Supported Data Format: ANALYZE, NIfTI-1

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• SciCrunch
• 17 years ago - by Anonymous

Software tool bridges in vitro drug screening with in vivo drug and biomarker discovery. Predicts in vivo or cancer patient drug response and biomarkers to enrich for response from cell line screening data. Builds model using ridge regression, and enables biomarker discovery by imputing drug response in large cancer molecular datasets. Enables drug specific biomarker identification by correcting for general level of drug sensitivity shared among the population.

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• RRID
• 3 years ago - submitted by dongliang leng

Academy scientists, journalists, adventurers and other staff members are blogging their stories and inviting questions and comments. Read current science news, hear from researchers in the field (Philippines, Sao Tome, Papua New Guinea), ask a question of an Academy naturalist, and much more.

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• SciCrunch
• 15 years ago - by Anonymous

A statistical and graphical visualization MATLAB toolbox for the analysis of fMRI data, called the Bayesian Spatial Model for activation and connectivity (BSMac). BSMac simultaneously performs whole-brain activation analyses at the voxel and region of interest levels as well as task-related functional connectivity (FC) analyses using a flexible Bayesian modeling framework (Bowman et al., 2008). BSMac allows for inputting data in either Analyze or Nifti file formats. The user provides information pertaining to subgroup memberships, scanning sessions, and experimental tasks (stimuli), from which the design matrix is constructed. BSMac then performs parameter estimation based on MCMC methods and generates plots for activation and FC, such as interactive 2D maps of voxel and region-level task-related changes in neural activity and animated 3D graphics of the FC results.

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• SciCrunch
• 14 years ago - by Anonymous

Core used to develop custom monoclonal antibodies and obtain large scale quantities of existing ones for experiments. Core provides cell line distribution service and tests samples for mycoplasma contamination.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A database of proteolytic pathways. Its goal is to contribute to the scientific community and the understanding of proteolysis by providing better tools and data to researchers and medical researchers.

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• SciCrunch
• 17 years ago - by Anonymous

An open-source C++ application that performs pair-wise DTI registration, using scalar FA map to drive the registration. Individual steps of the pair-wise registration pipeline are performed via external applications - some of them being 3D Slicer modules. Starting with two input DTI images, scalar FA maps are generated via dtiprocess. Registration is then performed between these FA maps, via BRAINSFit/BRAINSDemonWarp or ANTS -Advanced Normalization Tools-, which provide different registration schemes: rigid, affine, BSpline, diffeomorphic, logDemons. The final deformation is then applied to the source DTI image via ResampleDTI.

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• SciCrunch
• 14 years ago - by Anonymous

Scientific Instrument Services provides technical support functions including repair and maintenance of lab equipment; custom design and fabrication of new fixtures and devices using CAD, 3-D printing, and traditional machining; protocol development and performance optimization of wide variety of automated liquid handlers deployed in many of our institutions core services.Services are provided for JAX faculty.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A database of information from the Center for Tobacco Use Prevention and Research. Materials include depositions, trial testimony and opening and closing statements, expert reports, jury instructs, and verdicts. Some transcripts are rough copies and others may be marked as confidential although they no longer retain that status. This resource is in French.

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• SciCrunch
• 14 years ago - by Anonymous

Atlas that contains new anatomical, DTI, HARDI templates and probabilistic gray matter labels of the adult human brain in ICBM-152 space. Artifact-free MRI data from 72 human subjects was used in the development of the atlas. All diffusion MRI data collection was conducted using Turboprop, and spatial normalization was accomplished in a population-based fashion. A description of the contents of the atlas can be found in the Downloads link. NOTE: The files of the older IIT2 DTI Brain Template are still available. However, the new DTI template of the IIT Human Brain Atlas (v.3) is of superior quality and allows more accurate registration across subjects.

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• SciCrunch
• 14 years ago - by Anonymous

Web application for visualizing pathogen evolution.Interactive web app for visualizing phylogenomic data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A loose collection of programs and configuration options that intend to make working with data more transparent to formats. Currently available is a basic specification for NIfTI-1 for the UNIX file command and proof of concept code for the concept of treating data as an abstract concept and instantiating physical instances on demand.

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• SciCrunch
• 14 years ago - by Anonymous

A toolbox for SPM which provides routines for region of interest analysis. Features include region of interest definition, combination of regions of interest with simple algebra, extraction of data for regions with and without SPM preprocessing (scaling, filtering), and statistical analyses of ROI data using the SPM statistics machinery.

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• SciCrunch
• 14 years ago - by Anonymous

Software tools for manipulating Common Assembly Format files text format for describing sequence assemblies,that can be downloaded from the Sanger ftp site.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth