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http://www.ncigt.org/

Biomedical Technology Resource Center that serves as a national resource for all aspects of research into medical procedures that are enhanced by imaging. Its common goal is to provide more effective patient care. The center is focused on the multidisciplinary development of innovative image-guided intervention technologies to enable effective, less invasive clinical treatments that are not only more economical, but also produce better results for patients. The NCIGT is helping to implement this vision by serving as a proving ground for some of the next generation of medical therapies.

Proper citation: National Center for Image-Guided Therapy (RRID:SCR_001419) Copy   

•   Source: SciCrunch Registry

https://reich.hms.harvard.edu/software

XP-CLR (Chen et al. 2010) uses allele frequency differentiation at linked loci to detect selective sweeps. Source code and documentation are available.

Proper citation: XP-CLR (RRID:SCR_004961) Copy   

•   Source: SciCrunch Registry

http://rsync.samba.org/

Software that provides rapid incremental file transfer.

Proper citation: rsync (RRID:SCR_003113) Copy   

•   Source: SciCrunch Registry

http://harvard.eagle-i.net/i/0000012e-3517-ac53-550e-f59280000000

Core facility that provides metals analytical capabilities to biomedical and non-biomedical researchers and serves as a source for study design consultation and sample QA/QC requirements. The transport, fate, exposure, and toxic effects of heavy metals is a primary focus of research at the Center. It operates as a modified fee-for-service laboratory. Researchers have the option of having the samples run by the Service staff, or of receiving instruction (for themselves or a doctoral or post doctoral trainee) on how to operate the analytical equipment and analyze their own samples. Both options have associated fees and, as with other services, facility access funds can be requested internal or external services when individual grant support is not yet available.

Proper citation: HSPH Trace Metals Laboratory (RRID:SCR_002819) Copy   

•   Source: SciCrunch Registry

http://www.fmri.org

THIS RESOURCE IS NO LONGER IN SERVICE, documented on 7/28/13. Core facility of Columbia Neuroscience with the goal of establishing a collaborative and multi-investigator neuroimaging environment that is focused on the investigation of the neurocircuitry of the brain that underlies cognition, perception and action, and also the development of clinical applications that enhance the goals of personalized medicine. Within this environment the specific current research interests of the Hirsch group include several related directions of investigation. The first is conscious and subconscious neural processes that mediate emotion and cognition in healthy individuals and in patients with psychiatric disorders. This direction also includes neurocircuitry that is characteristic of disorders of consciousness such as minimally conscious or vegetative states, self and visual awareness, and attention. Neurocircuitry of other complex cognitive processes such as decisions, inductive and deductive reasoning, language, truthfulness and top-down influences of expectation, reward, and regulation on early visual and mid-level perceptual and emotional systems. On-going projects targeted for clinical applications include benefits for neurosurgery such as the development of task batteries to map the cortical locations of essential functions such as language, motor, sensation, memory, emotion and sensory functions including visions, audition and the chemical senses. Computational innovations for labeling correspondence between brain structure and specific functional regions are under development to achieve the highest interpretive precision. Current projects include integration of EEG and fMRI techniques to localize seizuregenic cortex in relation to eloquent and functioning cortex for neurosurgical planning; integration of TMS and fMRI to discriminate essential and associative language-sensitive cortical areas; and integration of VEP, EEG and fMRI to inform assessments of visual disease secondary to stroke or neural degeneration. Projects intended to refine and enhance diagnosis of psychiatric disorders such as anxiety, depression, and eating disorders include development of specialized paradigms to target dysfunctional neurocircuitry such as emotional systems (amygdala and basal ganglia) and control and regulatory systems (cingulate and pre-frontal cortex). Comparison of before-treatment images with after-treatment images to inform models of both treatment and disease and investigation of the hypothesis that individual genetic and functional differences have predictive value for treatment options and outcome are currently underway. The lab has pioneered techniques for functional mapping of single patients, and operates an active clinical service for mapping individuals for neurosurgical planning, assessments of the neurocircuitry that underlie acquired or inherited disabilities and the mechanisms of neuroplasticity that restore lost functions are actively investigated using both groups and single subject studies. :

Proper citation: fMRI Research Center at Columbia (RRID:SCR_002658) Copy   

•   Source: SciCrunch Registry

http://depts.washington.edu/yeastrc/

Biomedical technology research center that (1) exploits the budding yeast Saccharomyces cerevisiae to develop novel technologies for investigating and characterizing protein function and protein structure (2) facilitates research and extension of new technologies through collaboration, and (3) actively disseminates data and technology to the research community. Through collaboration, the YRC freely provides resources and expertise in six core technology areas: Protein Tandem Mass Spectrometry, Protein Sequence-Function Relationships, Quantitative Phenotyping, Protein Structure Prediction and Design, Fluorescence Microscopy, Computational Biology.

Proper citation: Yeast Resource Center (RRID:SCR_007942) Copy   

•   Source: SciCrunch Registry

http://alchemy.sourceforge.net/

ALCHEMY is a genotype calling algorithm for Affymetrix and Illumina products which is not based on clustering methods. Features include explicit handling of reduced heterozygosity due to inbreeding and accurate results with small sample sizes. ALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods. It has been developed for and tested on Affymetrix GeneChip Arrays, Illumina GoldenGate, and Illumina Infinium based assays. Primary motivations for ALCHEMY''s development was the lack of available genotype calling methods which can perform well in the absence of heterozygous samples (due to panels of inbred lines being genotyped) or provide accurate calls with small sample batches. ALCHEMY differs from other genotype calling methods in that genotype inference is based on a parametric Bayesian model of the raw intensity data rather than a generalized clustering approach and the model incorporates population genetic principles such as Hardy-Weinberg equilibrium adjusted for inbreeding levels. ALCHEMY can simultaneously estimate individual sample inbreeding coefficients from the data and use them to improve statistical inference of diploid genotypes at individual SNPs. The main documentation for ALCHEMY is maintained on the sourceforge-hosted MediaWiki system. Features * Population genetic model based SNP genotype calling * Simultaneous estimation of per-sample inbreeding coefficients, allele frequencies, and genotypes * Bayesian model provides posterior probabilities of genotype correctness as quality measures * Growing number of scripts and supporting programs for validation of genotypes against control data and output reformating needs * Multithreaded program for parallel execution on multi-CPU/core systems * Non-clustering based methods can handle small sample sets for empirical optimization of sample preparation techniques and accurate calling of SNPs missing genotype classes ALCHEMY is written in C and developed on the GNU/Linux platform. It should compile on any current GNU/Linux distribution with the development packages for the GNU Scientific Library (gsl) and other development packages for standard system libraries. It may also compile and run on Mac OS X if gsl is installed.

Proper citation: ALCHEMY (RRID:SCR_005761) Copy   

•   Source: SciCrunch Registry

http://noble.gs.washington.edu/proj/segtools/

Segtools is a Python package designed to put genomic segmentations back in the context of the genome! Using R for graphics, Segtools provides a number of modules to analyze a segmentation in various ways and help you interpret its biological relevance. Segmentations should be in BED4+ or GFF format, with the ''name'' field of each line used specifying the segment label of that line. The Segtools commands allow you to compare the properties of the segment labels with one another.

Proper citation: Segtools (RRID:SCR_004394) Copy   

•   Source: SciCrunch Registry

http://omicsoft.com/osa/

A fast and accurate alignment tool for RNA-Seq data.

Proper citation: Omicsoft Sequence Aligner (RRID:SCR_005270) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.udel.edu/Research/skategenomeproject

Core facility provides a model for collaborative approaches to use specialized resources and expertise in an integrated process. Core builds on the expertise and resources provided by the Bioinformatics Cores of the five northeastern states that form NECC. The Skate Genome Annotation Workshops and Jamborees offer training and opportunities for faculty and students to work with and annotate genome sequences. Workshops include lectures, tutorials and exercises annotating the genome of the little skate, Leucoraja erinacea.

Proper citation: University of Delaware Skate Genome Project (RRID:SCR_005300) Copy   

•   Source: SciCrunch Registry

http://www.neurospin-wiki.org/pmwiki/Main/NeurospinMEG

A magnetoencephalography facility hosted at NeuroSpin (CEA Saclay, France) equipped with a 306-channel MEG system from Elekta Neuromag, EEG and EGI systems, and an Eyelink 1000 eye-tracker from SR research. A large set of MEG data analysis tools are being used in the lab including mne-python, fieldtrip, brainstorm, spm, adjust and in-house techniques are also being developed.

Proper citation: NeuroSpin MEG (RRID:SCR_002398) Copy   

•   Source: SciCrunch Registry

http://bamview.sourceforge.net/

A free interactive display of read alignments in BAM data files that can be launched with Java Web Start or downloaded. This interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence can be used in a number of contexts including SNP calling and structural annotation. It has been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features. The source code is available as part of the Artemis code which can be downloaded from GitHub.

Proper citation: BamView (RRID:SCR_004207) Copy   

•   Source: SciCrunch Registry

http://owlapi.sourceforge.net/

The OWL API is a Java API and reference implementation for creating, manipulating and serializing OWL Ontologies. The latest version of the API is focused towards OWL 2. The OWLAPI underpins ontology browsing and editing tools and platforms such as SWOOP and Protege4. Note that this API, or any other OWL-based API, can be used without an integrated OWL parser if you download a pre-converted OWL file generated from OBO. See OBO Ontologies List for all OBO ontologies converted to OWL (we do not list the full complement of OWL-based APIs here, only those of direct relevance to GO). The OWL API includes the following components: * An API for OWL 2 and an efficient in-memory reference implementation * RDF/XML parser and writer * OWL/XML parser and writer * OWL Functional Syntax parser and writer * Turtle parser and writer * KRSS parser * OBO Flat file format parser * Reasoner interfaces for working with reasoners such as FaCT++, HermiT, Pellet and Racer Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: OWL API (RRID:SCR_005734) Copy   

•   Source: SciCrunch Registry

https://www.ngvbcc.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Archiving services, insertional site analysis, pharmacology and toxicology resources, and reagent repository for academic investigators and others conducting gene therapy research. Databases and educational resources are open to everyone. Other services are limited to gene therapy investigators working in academic or other non-profit organizations. Stores reserve or back-up clinical grade vector and master cell banks. Maintains samples from any gene therapy related Pharmacology or Toxicology study that has been submitted to FDA by U.S. academic investigator that require storage under Good Laboratory Practices. For certain gene therapy clinical trials, FDA has required post-trial monitoring of patients, evaluating clinical samples for evidence of clonal expansion of cells. To help academic investigators comply with this FDA recommendation, the NGVB offers assistance with clonal analysis using LAM-PCR and LM-PCR technology.

Proper citation: National Gene Vector Biorepository (RRID:SCR_004760) Copy   

•   Source: SciCrunch Registry

http://proteomics.ucsd.edu/

Biomedical technology research center that focuses on the computational bottlenecks that impair the interpretation of data, bringing modern algorithmic approaches to mass spectrometry and building a new generation of reliable, open-access software tools to support both new mass spectrometry instrumentation and emerging applications.

Proper citation: Center for Computational Mass Spectrometry (RRID:SCR_008161) Copy   

•   Source: SciCrunch Registry

http://www.equitech-bio.com/

Provides animal and human serums, plasmas, purified proteins, and antisera.

Proper citation: Equitech-Bio (RRID:SCR_003548) Copy   

•   Source: SciCrunch Registry

http://neurofitter.sourceforge.net

Neurofitter is software for parameter tuning of electrophysiological neuron models. It automatically searches for sets of parameters of neuron models that best fit available experimental data, and therefore acts as an interface between neuron simulators, like Neuron or Genesis, and optimization algorithms, like Particle Swarm Optimization, Evolutionary Strategies, etc.

Proper citation: Neurofitter (RRID:SCR_005843) Copy   

•   Source: SciCrunch Registry

http://www.panlab.com/panlabWeb/Software/php/displaySoft.php?nameSoft=SMART%20VIDEO-TRACKING

Software for the automated evaluation of behavior in a range of pre-clinical and neuroscience applications in basic and clinical psychopharmacology. Applications include phenotype characterization and studying the behavioral effects of pharmacologic substances.

Proper citation: SMART Video-tracking (RRID:SCR_002852) Copy   

•   Source: SciCrunch Registry

http://www.cmrr.umn.edu/

Biomedical technology research center that focuses on development of unique magnetic resonance (MR) imaging and spectroscopy methodologies and instrumentation for the acquisition of structural, functional, and biochemical information non-invasively in humans, and utilizing this capability to investigate organ function in health and disease. The distinctive feature of this resource is the emphasis on ultrahigh magnetic fields (7 Tesla and above), which was pioneered by this BTRC. This emphasis is based on the premise that there exists significant advantages to extracting biomedical information using ultrahigh magnetic fields, provided difficulties encountered by working at high frequencies corresponding to such high field strengths can be overcome by methodological and engineering solutions. This BTRC is home to some of the most advanced MR instrumentation in the world, complemented by human resources that provide unique expertise in imaging physics, engineering, and signal processing. No single group of scientists can successfully carry out all aspects of this type of interdisciplinary biomedical research; by bringing together these multi-disciplinary capabilities in a synergistic fashion, facilitating these interdisciplinary interactions, and providing adequate and centralized support for them under a central umbrella, this BTRC amplifies the contributions of each of these groups of scientists to basic and clinical biomedical research. Collectively, the approaches and instrumentation developed in this BTRC constitute some of the most important tools used today to study system level organ function and physiology in humans for basic and translational research, and are increasingly applied world-wide. CMRR Faculty conducts research in a variety of areas including: * High field functional brain mapping in humans; methodological developments, mechanistic studies, and neuroscience applications * Metabolism, bioenergetics, and perfusion studies of human pathological states (tumors, obesity, diabetes, hepatic encephalopathy, cystic fibrosis, and psychiatric disorders) * Cardiac bioenergetics under normal and pathological conditions * Automated magnetic field shimming methods that are critical for spectroscopy and ultrafast imaging at high magnetic fields * Development of high field magnetic resonance imaging and spectroscopy techniques for anatomic, physiologic, metabolic, and functional studies in humans and animal models * Radiofrequency (RF) pulse design based on adiabatic principles * Development of magnetic resonance hardware for high fields (e.g. RF coils, pre-amplifiers, digital receivers, phased arrays, etc.) * Development of software for data analysis and display for functional brain mapping.

Proper citation: Center for Magnetic Resonance Research (RRID:SCR_003148) Copy   

•   Source: SciCrunch Registry

http://genetherapy.unc.edu/jvl.htm

Core facility to access a comprehensive range of resources and services for gene transfer research including vector production services for research, preclinical and clinical materials. Services include: * Adeno-associated Virus (AAV) Custom Production; * AAV In-Stock Aliquots: Reporters, Deisseroth, Boyden, Roth, Uchida, Shah; * Lentivirus Custom Production

Proper citation: UNC Joint Vector Laboratories (RRID:SCR_002448) Copy   

•   Source: SciCrunch Registry