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http://www.hms.harvard.edu/dms/

The Division of Medical Sciences was established at Harvard University in 1908. The Division was designed to provide students wishing to pursue careers in research and teaching with a broad education in basic biomedical science fields and specialization in one of them. Classroom and laboratory instruction are conducted primarily by the 450 faculty members of the basic sciences departments and affiliated hospital laboratories of the Harvard Medical School (HMS) in Boston. The Ph.D. degree is awarded by the Graduate School of Arts and Sciences (GSAS) of Harvard University. For 100 years, this fruitful collaboration has spawned research achievements across the spectrum from basic science to experimental medicine. Since 1909, over 2,000 Division graduates, including six Nobel Laureates, have gone on to distinguished careers in biomedical research, university teaching, and a number of increasingly diverse careers.

Proper citation: Harvard Medical School Division of Medical Sciences (RRID:SCR_007452) Copy   

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https://www.vet.cornell.edu/education/biological-biomedical-sciences-bbs-phd-program/phd-program-overview/fields-study/pharmacology/program-study

Pharmacology training program offers an intensive course of study and research emphasizing molecular, cellular, and systems pharmacology that prepares students for productive careers in biomedical research and teaching. The program accepts outstanding college graduates as well as physicians and veterinarians seeking advanced training in pharmacology.

Proper citation: Cornell University College of Veterinary Medicine Program of Study (RRID:SCR_007448) Copy   

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http://cran.r-project.org/web/packages/evora/

R package for quantifying variation in DNA methylation as a cancer biomarker.

Proper citation: EVORA (RRID:SCR_007329) Copy   

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http://www.nia.nih.gov/research/dab/nia-mutant-mouse-aging-colony-handbook

THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 09, 2013. Supply aged mutant and transgenic mice for NIH-supported research directly related to the biology of aging. The mice are raised by the NIA's contractor, Taconic Farms, in Specific Pathogen-Free (SPF) barrier facilities. The strains in the mutant mouse aging colony have been donated by the investigators who developed the models, and those investigators are still the legally recognized owners of the intellectual property. A Material Transfer Agreement (MTA) is required to purchase the mice (a one-time requirement per strain). There are restrictions to the use of this colony as described in the MTA. These restrictions include a prohibition against breeding the mice purchased from the NIA Mutant Mouse Aging Colony, agreement that the mice will not be used for commercial purposes, and agreement that the mice and all derivatives will not be transferred to third parties. The restrictions are further spelled out in the MTA. Animals are sold by age, not weight, and ages are stated in 1 month intervals only; all animals born within a calendar month are considered to be the same age, so date of birth (DOB) is given as month/year. All mice are virgins. The mutant mouse aging colony is slated to end in September 2013. Old mice will be available until September 2013 but the availability of young mice will end earlier. Entries of different strains into the mutant mouse aging colony will end at different times, dependent on the lifespan and pattern of use of the strain. Mouse models include: * Snell Dwarf (3623) ??????????????? last entry will be the November 2011 DOB (date of birth) * Ames Dwarf (324) ??????????????? last entry will be the October 2012 DOB * A53T ???????????????????????-synuclein Transgenic (322) ??????????????? last entry will be the December 2012 DOB * GFP Transgenic (317) ??????????????? last entry will be the January 2013 DOB

Proper citation: NIA Mutant Mouse Aging Colony Handbook (RRID:SCR_007328) Copy   

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http://www.nntc.org/

Collects, stores, and distributes samples of nervous tissue, cerebrospinal fluid, blood, and other tissue from HIV-infected individuals. The NNTC mission is to bolster research on the effects of HIV infection on human brain by providing high-quality, well-characterized tissue samples from patients who died with HIV, and for whom comprehensive neuromedical and neuropsychiatric data were gathered antemortem. Researchers can request tissues from patients who have been characterized by: * degree of neurobehavioral impairment * neurological and other clinical diagnoses * history of drug use * antiretroviral treatments * blood and CSF viral load * neuropathological diagnosis The NNTC encourages external researchers to submit tissue requests for ancillary studies. The Specimen Query Tool is a web-based utility that allows researchers to quickly sort and identify appropriate NNTC specimens to support their research projects. The results generated by the tool reflect the inventory at a previous time. Actual availability at the local repositories may vary as specimens are added or distributed to other investigators.

Proper citation: National NeuroAIDS Tissue Consortium (RRID:SCR_007323) Copy   

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http://seurat.r-forge.r-project.org/

Software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data. Visual analytics for the integrated analysis of microarray data.

Proper citation: SEURAT (RRID:SCR_007322) Copy   

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http://www.bumc.bu.edu/busm-bns/

The Behavioral Neuroscience program''s focus is on the delineation and analysis of perceptual, cognitive, linguistic, affective, and behavioral disorders observed in neurologic disease, as these disorders contribute to an understanding of normal brain function and its modification by pathology. The subject matter derives chiefly, but not exclusively, from clinical populations with neurological disorders affecting higher processes, particularly from the study of syndromes involving selective impairment of functional systems such as memory, language, or purposeful movement. Current methods of clinical assessment, cognitive psychology, experimental design, and the neurosciences are integrated into a broad program of clinical and basic research. The Behavioral Neuroscience Ph.D. Program is administered through the Division of Graduate Medical Sciences, BUSM, by faculty members of the Department of Neurology, Division of Psychiatry, and Anatomy & Neurobiology, BUSM (holding joint appointments at the Department of Veterans Affairs [VA] Medical Centers in Boston or Bedford, MA). Only the doctoral program is offered (no master''s degree). The Program is not designed to meet requirements for accreditation as to clinical competence in psychology nor in any discipline which has a certification procedure. It does, however, accept students in the M.D./Ph.D. Program at Boston University School of Medicine, or other students enrolled elsewhere in related programs (including the Master of Arts in Medical Sciences Program), to take some or all of the offerings. Boston University School of Medicine is an accredited institution. Behavioral Neuroscience is a degree-granting Program having the same representation as other Ph.D.-granting Departments in the Division of Graduate Medical Sciences.

Proper citation: Boston University School of Medicine Department of Behavioral Neuroscience (RRID:SCR_007443) Copy   

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http://www.mitochondrial.net/

Website with multiple information including curent news and publications, clinical trials, and a mitochondria database. :clinical trials related to mitochondria; publications related to mitochondria, mitochondria database : :

Proper citation: Mitochondria News and Research (RRID:SCR_007325) Copy   

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http://www.med.cornell.edu/neuro/

The Department of Neurology and Neuroscience at NewYork-Presbyterian Hospital/Weill Cornell Medical Center is considered one of the premier academic neurology departments in the world. The department has over eighty faculty members focusing on the education of medical students, interns, residents and graduate students, on all aspects of the Neurological systems. The department also offers a two-year postdoctoral specialty training program and CME courses. The Department currently has several thousand square feet of research space, 25,000 square feet of clinical outpatient office space, a 30-bed dedicated inpatient unit and an 11-bed Neurological Intensive Care Unit. Last year, our clinical neurologists had over 23,000 patient care visits in our offices. In 2008, five of our faculty members were voted Best Doctors in New York Magazine and US News and World Report ranked NewYork-Presbyterian Hospital services in neurology and neurosurgery #1 in New York City and #5 in the United States. Our Department attracts the best and brightest graduates of medical schools from around the world to our residency training program, and many of our trainees go on to lead other academic departments. Our department continues to expand in all of its fundamental missions treating patients with neurologic disorders, performing research, and teaching medical students and residents in Neurology. One of the key missions of the department is to translate critical research advances discovered in our laboratories to benefit, treat and possibly cure a wide array of neurological diseases.

Proper citation: Weill Cornell Medicine Department of Neurology (RRID:SCR_007446) Copy   

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http://www.geisha.arizona.edu/geisha/

Online repository for chicken in situ hybridization information. This site presents whole mount in situ hybridization images and corresponding probe and genomic information for genes expressed in chicken embryos in Hamburger Hamilton stages 1-25 (0.5-5 days). The GEISHA project began in 1998 to investigate using high throughput whole mount in situ hybridization to identify novel, differentially expressed genes in chicken embryos. An initial expression screen of approximately 900 genes demonstrated feasibility of the approach, and also highlighted the need for a centralized repository of in situ hybridization expression data. Objectives: The goals of the GEISHA project are to obtain whole mount in situ hybridization expression information for all differentially expressed genes in the chicken embryo between HH stages 1-25, to integrate expression data with the chicken genome browsers, and to offer this information through a user-friendly graphical user interface. In situ hybridization images are obtained from three sources: 1. In house high throughput in situ hybridization screening: cDNAs obtained from several embryonic cDNA libraries or from EST repositories are screened for expression using high throughput in situ hybridization approaches. 2. Literature curation: Agreements with journals permit posting of published in situ hybridization images and related information on the GEISHA site. 3. Unpublished in situ hybridization information from other laboratories: laboratories generally publish only a small fraction of their in situ hybridization data. High quality images for which probe identity can be verified are welcome additions to GEISHA.

Proper citation: GEISHA - Gallus Expression in Situ Hybridization Analysis: A Chicken Embryo Gene Expression Database (RRID:SCR_007440) Copy   

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http://www.cerefy.com/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 19, 2015. Commercial brain atlases distributed by Theime Medical Publishers. It supports a complete electronic version of the Talairach Atlas, as well as gyral-level description of the human brain and atlases for cerebral vasculature, cranial nerves and a probabilistic functional atlas. In addition, this tool permits the incorporation of user image data, both structural and functional, into the viewer for direct co-visualization with the atlas. This CD-ROM provides numerous tools for the analysis of functional images: It contains the fully color-coded and labeled Talairach-Tournoux brain atlas in the axial, coronal and sagittal orientations, along with Brodmann''s areas and gyri in the axial orientation. -Allows anatomical and functional images to be loaded and registered. -Enables interactive placement of the Talairach landmarks in 3D Space. -Provides automatic data-to-atlas warping based on the Talairaich proportional grid system transformation. In addition, real-time interactive warping for fine tuning is available. -Allows the user to place marks on the activation loci in the warped functional images, display these marks with the atlas, and edit them simultaneously on the axial, cornal and sagittal orientations. Mark placement is assisted by a grey-value thresholding feature. -Provides simultaneous display of the atlas, anatomical image and functional image withing one interactively blended image. Atlas-data blending and anatomical-functional image blending are controlled independently. -Labels the data by means of the atlas. The atlas can be flipped left/right so that Brodmann''s areas areas and gyri can be labeled on both hemispheres. -Provides additional functions such as friendly navigation, simultaneous display of axial, coronal and sagittal atlas plates, cross-referenced display, image and atlas sequencing, readout of the Talairach coordinates and intensities, save, print, help.

Proper citation: Brain Atlas for Functional Imaging (RRID:SCR_007356) Copy   

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https://www.icts.uiowa.edu/confluence/dashboard.action

A group of software packages for image analysis, mainly used in MRI image processing. BRAINS (Brain Research: Analysis of Images, Networks, and Systems) contains manual and automated tools for structural identification and methods for tissue classification and cortical surface generation. BRAINS2 is most commonly used to analyze magnetic resonance (MR) scans, but the package can also be used to analyze images acquired with positron emission tomography (PET), single photon emission computed tomography (SPECT), and functional magnetic resonance (fMR). It is implemented in an object-oriented, cross-platform compatible manner and includes a toolbar and command line interface, a graphical interface, and a computational kernel.

Proper citation: Brain Research: Analysis of Images, Networks and Systems (RRID:SCR_007357) Copy   

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https://njms.rutgers.edu/sgs/current_students/phd/intergrative_neuroscience/index.php

Neuroscience program offers a multidisciplinary curriculum and research opportunities to provide students with a comprehensive understanding of the basic tenets and underpinnings of this modern discipline. Emphasis is placed on early entrance into research laboratories, seminar programs and journal clubs. Students have the opportunity to experience the breadth of Neuroscience -- from Cellular and Molecular approaches to Translational and Clinical Neuroscience. Advanced students also have opportunity to assist in teaching Graduate and Medical students. The goal of the Graduate Program in Neuroscience is to couple broad educational opportunities with intense laboratory experiences so our graduates are prepared to excel as research scientists, academicians, and educators.

Proper citation: Rutgers University Integrative Neuroscience Graduate Program (RRID:SCR_007472) Copy   

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http://www.brainvisa.info/

BrainVISA is a modular an customizable software platform built to host heterogeneous tools dedicated to neuroimaging research. Many toolboxes have already been developed for BrainVISA (T1 MRI, sulcal identification and morphometry, cortical surface analysis, diffusion imaging and tractography, fMRI, nuclear imaging, EEG and MEG, TMS, histology and autoradiography, etc.). Anatomist is a software for interactive visualization of multimodal data and for manipulation of structured 3D objects. It allows to build scenes that merge or combine images, meshes, regions of interest, fibers, textures, color palettes, referential changes, etc. A user can interact in 3D and in real time with the objects of an Anatomist scene: change point of view, select objects, add/suppress objects, change colors, draw regions of interests, do manual registration, etc. BrainVISA main features are: * Harmonization of communications between different software. For instance, BrainVISA toolboxes are using home-made software but also third-party software such as FreeSurfer, FSL, SPM, nipy, R-project, Matlab, etc. * Ontology-based data organization allowing database sharing and automation of mass of data analysis. * Fusion and interactive visualization of multimodal data (using Anatomist software). * Automatic generation of graphical user interfaces. * Workflow monitoring and data quality checking. * Full customization possible. * Runs on Linux, Mac and Windows. * Programming Language: C++, Python * Supported Data Format: ANALYZE, DICOM, GIfTI, MINC, NIfTI-1, Other Format

Proper citation: BrainVISA / Anatomist (RRID:SCR_007354) Copy   

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http://www.fei.com/software/amira-3d-for-life-sciences/

Software tool for visualizing, manipulating, and understanding data from tomography, microscopy, MRI and other imaging processes.Used to import and export options, to processes 3D image filtering and DTI based fiber tracking to visualization, volume and surface rendering, author tools for virtual reality navigation, video generation, and more.

Proper citation: Advanced 3D Visualization and Volume Modeling (RRID:SCR_007353) Copy   

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http://www.utsouthwestern.edu/utsw/home/research/cbn/

The mission of the Department of Neuroscience at the University of Texas Southwestern Medical Center at Dallas is to advance fundamental knowledge in this field by conducting cutting edge research and by providing training to the next generation of neuroscientists. The research activities within the Department of Neuroscience focus on cellular, molecular, genetic, and developmental mechanisms underlying behavior, neural circuits and related neurological disorders. Scientists within the Department of Neuroscience participate in a vibrant, interdisciplinary, interdepartmental, and highly collaborative research community within the University.

Proper citation: University of Texas Southwestern Medical Center Neuroscience (RRID:SCR_007474) Copy   

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https://github.com/steinmann/peakzilla

An algorithm to identify transcription factor binding sites from ChIP-seq data.

Proper citation: Peakzilla (RRID:SCR_007471) Copy   

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http://dicom.offis.de/dscope/

DICOMscope is a free DICOM viewer which can display uncompressed, monochrome DICOM images from all modalities and which supports monitor calibration according to DICOM part 14 as well as presentation states. The application is rather a feasibility study for DICOM presentation states. DICOMscope offers a print client (DICOM Basic Grayscale Print Management) which also implements the optional Presentation LUT SOP Class.

Proper citation: DICOMscope (RRID:SCR_007344) Copy   

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https://www.pomona.edu/academics/departments/neuroscience-department

Provides opportunity to learn fundamentals of neuroscience, perform experimental techniques in state-of-the-art teaching laboratories, and discover how neuroscience provides insight into other liberal arts disciplines, including psychology, economics, computer science and philosophy. Areas of neuroscience include:cell and molecular neuroscience;systems-level neuroscience;nervous system disorders such as anxiety and depression;neuroscientific models of social behavior and interaction;and imaging the mind at work.Majors have the opportunity to assist faculty in research or conduct their own project through the Summer Undergraduate Research Program.

Proper citation: Pomona College Department of Neuroscience (RRID:SCR_007467) Copy   

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https://cgc.umn.edu

Center that acquires, maintains, and distributes genetic stocks and information about stocks of the small free-living nematode Caenorhabditis elegans for use by investigators initiating or continuing research on this genetic model organism. A searchable strain database, general information about C. elegans, and links to key Web sites of use to scientists, including WormBase, WormAtlas, and WormBook are available.

Proper citation: Caenorhabditis Genetics Center (RRID:SCR_007341) Copy   

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