Curator Dashboard

Ontology of clinical trial terminology.

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• SciCrunch
• 13 years ago - by Anonymous

A powerful software for model-based analysis of peripheral psychophysiology (e.g. skin conductance, heart rate, pupil size etc.). General linear modelling and dynamic causal modelling of these signals provide for inference on neural states/processes. SCRalyze includes flexible data import and display, statistical inference and results display and export. Easy programming of add-ons for new data formats, signal channels, and models.

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• SciCrunch
• 14 years ago - by Anonymous

Software toolbox for resting state HRF estimation and deconvolution analysis. Matlab and Python toolbox that implements HRF estimation and deconvolution from resting state BOLD signal. Used to retrieve optimal lag between events and HRF onset, as well as HRF shape. Once that HRF has been retrieved for each voxel/vertex, it can be deconvolved from time series or one can map shape parameters everywhere in brain and use it as pathophysiological indicator. Input can be 2D GIfTI, 3D or 4D NIfTI images, but also on time series matrices/vectors. Output are three HRF shape parameters for each voxel/vertex, plus deconvolved time series, and number of retrieved pseudo events. All can be written back to GIfTI or NIfTI images.

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• RRID
• 3 years ago - submitted by Guorong Wu

Atlas of segmented and normalized high-resolution postmortem MRI of the human hippocampus. Additional data (raw images) is available through the SCM link. It requires knowing how to use CVS.

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• SciCrunch
• 14 years ago - by Anonymous

Simple, menu-driven software toolbox for SPM 5/8 for exploratory data analysis for functional or structural images (.img / .nii) provides the user with several options: # a histogram of all non-zero voxel values in a brain image; # a scatter plot, Q-Q plot, or Bland-Altman plots comparing two images; # a surface plot of all voxel values at a particular axial slice; # easy Region of Interst (ROI)-based extraction of voxel values. Note: the toolbox calls various SPM 5/8 functions. The Q-Q plot function requires the MATLAB stats toolbox.

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• SciCrunch
• 14 years ago - by Anonymous

Facility houses research equipment for evaluating materials and biological preparations, and offers 3D printing and 3D scientific illustration services. Available instruments include Cytation3 Automated Microscope Plate Reader, BioTek Inc.; Zetasizer Nano ZSP, Malvern Inc.; Lyophilizers FreeZone 6 and 6 Plus, Labconco; Azure300, Chemiluminescent Gel Imager, Azure Biosystems; Real-Time PCR I-cycler CFX-Connect, Bio-Rad Laboratories; Centrifuge Sorvall X1R, ThermoFisher; MCR302 Rheometer, Anton Paar Inc.; Plasma Cleaner, Harrick Plasma; NanoSight300, Malvern Instruments (Evanston); IncuCyte Live Cell Analysis System, Sartorius; Piuma Nanoindenter, Optics 11; Freezer/Mill, SPEX Sample Prep; J-1500 Circular Dichroism Spectrometer, JASCO.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Information framework and knowledge base to facilitate research about nervous system regeneration. It includes minimal information standards, an ontology that is linked to other ontologies, and a knowledge base built with a triple store and a relational database.

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• SciCrunch
• 13 years ago - by Anonymous

Network that brings together researchers in imaging genomics, to understand brain structure and function, based on MRI, DTI, fMRI and genomewide association scan (GWAS) data. The ENIGMA Network has several goals: * to create a network of like-minded individuals, interested in pushing forward the field of imaging genetics * to ensure promising findings are replicated via member collaborations, in order to satisfy the mandates of most journals * to share ideas, algorithms, data, and information on promising findings or methods * to facilitate training, including workshops and conferences on key methods and emerging directions in imaging genetics. Data sharing with other members of the ENIGMA Network is optional and by no means a requirement of joining the network. Genetics and Imaging Protocols are available.

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• SciCrunch
• 15 years ago - by Anonymous

Core catalyzes translation of scientific discoveries into novel protein cancer therapies. Offers therapeutic antibody and enzyme discovery, engineering, and optimization services.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Center for patient care, education and research on cancer. The institute focuses its research on prevention methods, early detection, treatment and finding cures.

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• SciCrunch
• 16 years ago - by Anonymous

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