Curator Dashboard

An on-demand, cloud based computational virtual machine pre-installed with popular NITRC neuroimaging tools built using NeuroDebian. For a listing of current NITRC-CE packages visit: http://www.nitrc.org/ce-packages. You can also use the "public Amazon Machine Interface (AMI)" to conduct your analyses on the Amazon EC2 platform.

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• SciCrunch
• 14 years ago - by Anonymous

An fMRI analysis software package with a GUI (Graphical User Interface) front end. Stimulate offers a comprehensive set of fMRI analysis tools integrated into a single package for convenient and flexible data processing. Users can point and click with the mouse to modify analysis or display variables. Activation maps can be calculated from the fMRI data and overlaid onto structural MRI image displays.

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• SciCrunch
• 17 years ago - by Anonymous

Provieds acess to light microscopy techniques and instruments, consultation, training, and assists with project collaborations.Provides support with selecting imaging techniques, microscope systems, and setting up imaging experiments.Offers expertise in imaging techniques, such as Spinning disk confocal microscopy,Laser scanning confocal microscopy, 2-photon microscopy, Light sheet microscopy,Wide-field microscopy,Total internal reflection fluorescence (TIRF) microscopy ,Laser capture microdissection,Extended resolution microscopy,Quantitative phase imaging,Live cell and organoid imaging,Photomanipulation

• Resource
• SciCrunch
• 4 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE, Documented on March 24, 2014. A resource for gene expression studies, storing highly curated MIAME-compliant studies (i.e. experiments) employing a variety of technologies such as filter arrays, 2-channel microarrays, Affymetrix chips, SAGE, MPSS and RT-PCR. Data were available for querying and downloading based on the MGED ontology, publications or genes. Both public and private studies (the latter viewable only by users having appropriate logins and permissions) were available from this website. Specific details on protocols, biomaterials, study designs, etc., are collected through a user-friendly suite of web annotation forms. Software has been developed to generate MAGE-ML documents to enable easy export of studies stored in RAD to any other database accepting data in this format. RAD is part of a more general Genomics Unified Schema (http://gusdb.org), which includes a richly annotated gene index (http://allgenes.org), thus providing a platform that integrates genomic and transcriptomic data from multiple organisms. NOTE: Due to changes in technology and funding, the RAD website is no longer available. RAD as a schema is still very much active and incorporated in the GUS (Genomics Unified Schema) database system used by CBIL (EuPathDB, Beta Cell Genomics) and others. The schema for RAD can be viewed along with the other GUS namespaces through our Schema Browser.

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• SciCrunch
• 17 years ago - by Anonymous

A simulation program that simulates and plots (in real time) ancestral recombination graphs. This is currently primarily a teaching/educational tool. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

Software that assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2.

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• SciCrunch
• 13 years ago - by Anonymous

Gene Cloud is a novel tool presenting gene-gene associations based on the scientific literature. It was developed by the Knockout Mouse Repository (www.komp.org) to help our customers find products related to other products they chose. We have built a detailed graph model of gene-gene associations based on how many times two genes are cited in the same article. If two genes are cited in many papers together, they are considered strongly connected. Each instance of Gene Cloud is centered around a specific gene. A list of the top most related genes is plotted as a branching structure from the center. A secondary branch can occur if a gene in the graph is more related a non-central gene than it is to the center gene. The font size of a branched gene indicates the relative strength of connection--always to the center gene. The distribution of genes in space is randomized each time Gene Cloud is run so a different picture will result for the same central gene. Color is used to indicate the availability of Knockout Mouse products at the KOMP Repository. If a gene is colored green in the graph there are products (mutant ES cells, sperm, embryos, or mice) ready to be ordered. Blue colored genes do not yet have products available, but you can follow the links back to the KOMP Repository and register interest to be alerted when products do become available. Gene Cloud is driven by a database of gene-gene associations that currently contains 82,000 genes and other biotypes, 113,000 annotated publications, and 467 million connections. The latest gene symbols, names and gene-publication annotation information is updated daily from the Mouse Genome Informatics database. The graphing is accomplished through the use of a modified version of jsViz.

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• SciCrunch
• 17 years ago - by Anonymous

The Care Connectivity Consortium (CCC) is working to address and overcome the most critical and key challenges to effective health information exchange (HIE), to make HIE technologies more versatile and valuable for patients, caregivers, and health care organizations. By developing improved technologies for comprehensive, secure, reliable and innovative HIE, the CCC aims to enable health care provider organizations nationwide to deliver better, timelier, and more informed patient care.

• Organization
• Consortia-pedia, a FasterCures Project
• 12 years ago - submitted by Taylor Cronin

A software to map short sequencer reads to reference genomes. It is able to detect not only mismatches but also insertions and deletions. Furthermore, it is not limited to a specific read length and is able to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping.

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• SciCrunch
• 13 years ago - by Anonymous

Collection of biology-focused teaching materials created and administered by the Howard Hughes Medical Institute including free lectures, videos and animations for science education. Many of the resources are also available on DVD and CD-ROM. In addition to the resources on the website, BioInteractive offers DVDs of HHMI''s annual Holiday Lectures on Science and CD-ROMs of the Virtual Lab series. These materials are available to educators for free and can be ordered from the catalog at http://catalog.hhmi.org. Each Holiday Lectures on Science is a set of four one-hour lectures presented each December at the headquarters of the Howard Hughes Medical Institute in Chevy Chase, Maryland . The lectures give students and teachers the opportunity to learn about cutting-edge biomedical research directly from some of the world''s leading scientists. Intended to inspire young students to pursue careers in science, the lectures bring the latest developments in a rapidly moving field of research into the classroom. The lectures are primarily geared to high school students in honors and Advanced Placement biology classes. Other high school students and undergraduates can certainly benefit from the content of the lectures. Some of the related materials on the biointeractive website (http://www.biointeractive.org/) are aimed at a broader audience. With a teacher''s guidance, middle school students can also enjoy learning about the topic. Holiday Lectures are webcast live at http://www.hhmi.org/biointeractive/hl/. Following the live event, they are available as on-demand streaming video at the same Web address. Webcasts of all past Holiday Lectures are available as on-demand streaming video at http://www.hhmi.org/biointeractive/lectures/index.html. Holiday Lectures are also available as podcasts from http://www.hhmi.org/biointeractive/podcast_popup.html

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• SciCrunch
• 16 years ago - by Anonymous

The Multiple Sclerosis Outcome Assessments Consortium (MSOAC) is a public-private partnership which aims to accelerate the development of new therapies for MS by generating new tools for measuring outcomes in clinical trials. It is collecting, standardizing, and analyzing data about MS with the goal of qualifying new measures of disability for the disease. MSOAC is the newest of the eight consortia of Critical Path Institute (C-Path), a nonprofit organization that is dedicated to accelerating drug development by delivering on the mission outlined by FDA''''s critical path initiative.

• Organization
• Consortia-pedia, a FasterCures Project
• 12 years ago - submitted by Taylor Cronin

Error correction algorithm designed for short-reads from next-generation sequencing platforms such as Illumina''s Genome Analyzer II.

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• SciCrunch
• 13 years ago - by Anonymous

RTI Donor Services is a not-for-profit, American Association of Tissue Banks (AATB) accredited organization, working with organ and tissue agencies to provide responsible stewardship of the gift of donation. By working with RTI Donor Services, you will receive the benefit of the science, safety and innovation of RTI Biologics, Inc. (RTI). While RTI Biologics and RTI Donor Services are separate but affiliated organizations, our missions are symbiotic ����?? both are aimed at improving the lives of others with a focus on maximizing the gift of tissue donation, providing safe tissue implants for recipients, and providing education and support programs to donor families and the donation community. Please visit http://www.rtidonorservices.org/about_rti_donor_services for more information.

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• SciCrunch
• 16 years ago - by Anonymous

A software registry containing digital research tools ranging from content management systems to statistical analysis packages and mind mapping software. The site contains detailed descriptions, license information, and links to software developer websites and downloads.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

Web service that converts all 30 reconstruction formats (and 65 variations) described in scientific literature into SWC standard. Service is available open-source through user-friendly browser interface and Application Programming Interface.

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• RRID
• 4 years ago - by Anonymous

Biospecimen repository of normal and diseased human material from a variety of tissues and conditions along with clinical annotation. Both frozen aliquots and paraffin embedded tissue are available. Biospecimens are available to qualified researchers with IRB approval. * Preliminary inquires please contact Cheryl Spencer at cheryl.spencer (at) bmc.org

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• SciCrunch
• 15 years ago - by Anonymous

A web application which organizes current scientific literature by fields, people, institutes, labs, places, and historical sets they are a part of. Sciencscape allows users to subscribe to topics to receive new material, as well as provides visual representations to organize recent and most cited papers.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

Facility with two locations:Marley and Life Sciences North. Dedicated to acquisition of images for research, industrial and clinical applications.Marley location features inverted point scanning confocal microscope, upright confocal/multiphoton microscope with superresolution capabilities, fluorescence stereo microscope and research quality microwave. Life Sciences North location features superresolution fluoresence microscope:structured illumination, SIM; inverted multifunction widefield microscope:color brightfield, polarized light, fluorescence; image analysis workstation.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A collection of software plug-ins developed for the automatic segmentation of magnetic resonance brain images. The tools include multiple published algorithms developed at Johns Hopkins University. The SPECTRE algorithm performs brain extraction. The TOADS algorithm generates a topology-preserving tissue classification into cortical, subcortical, and cerebellar structures. The CRUISE algorithm produces inner, central, and outer cortical surfaces suitable for computing thickness and other geometric measures. Tools are also included for performing gyral labeling, lesion segmentation, thickness computation, surface visualization, and surface file conversion. All tools are released as plug-ins for the MIPAV software package and were developed using the Java Image Science Toolkit (both available at NITRC: http://nitrc.org). They are therefore cross-platform and compatible with a wide variety of file formats.

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• SciCrunch
• 15 years ago - by Anonymous

A software registry which offers links to various free statistical software programs for stand-alone computing. The software programs are split into different categories: General Packages, Subset Packages, Curve Fitting and Modeling, Biostatistics and Epidemiology, Surveys, Testing and Measurement, Excel Spreadsheets and Add-ins, Programming Languages and Subroutine Libraries, Scripts and Macros, Miscellaneous, and Other Collections.

• Resource
• SciCrunch
• 12 years ago - submitted by Kristen Jensen