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NSR Physiome Project Resource Report Resource Website 1+ mentions |
NSR Physiome Project (RRID:SCR_007379) | NSR Physiome Project | portal, data or information resource, simulation software, training resource, software application, topical portal, software resource, professional program | Database of physiological, pharmacological, and pathological information on humans and other organisms and integration through computational modeling. Models include everything from diagrammatic schema, suggesting relationships among elements composing a system, to fully quantitative, computational models describing the behavior of physiological systems and an organism''s response to environmental change. Each mathematical model is an internally self-consistent summary of available information, and thereby defines a working hypothesis about how a system operates. Predictions from such models are subject to test, with new results leading to new models.BR /> A Tool developed for the NSR Physiome project is JSim, an open source, free software. JSim is a Java-based simulation system for building quantitative numeric models and analyzing them with respect to experimental reference data. JSim''s primary focus is in physiology and biomedicine, however its computational engine is quite general and applicable to a wide range of scientific domains. JSim models may intermix ODEs, PDEs, implicit equations, integrals, summations, discrete events and procedural code as appropriate. JSim''s model compiler can automatically insert conversion factors for compatible physical units as well as detect and reject unit unbalanced equations. JSim also imports the SBML and CellML model archival formats. All JSim models are open source. Goals of the Physiome Project: - To develop and database observations of physiological phenomenon and interpret these in terms of mechanism (a fundamentally reductionist goal). - To integrate experimental information into quantitative descriptions of the functioning of humans and other organisms (modern integrative biology glued together via modeling). - To disseminate experimental data and integrative models for teaching and research. - To foster collaboration amongst investigators worldwide, to speed up the discovery of how biological systems work. - To determine the most effective targets (molecules or systems) for therapy, either pharmaceutic or genomic. - To provide information for the design of tissue-engineered, biocompatible implants. | physiome, computational modeling, cell, organ, organism, human, model, physiological, pharmacological, pathological, model repository, sbml, cellml, biophysics, biochemistry, database, proteome, jsim simulation analysis system, data analysis tool, parameter optimization tool, integrating biological system | has parent organization: University of Washington; Seattle; USA | NSF BE08407; NHLBI T15 HL88516-01; NSF BES-0506477; NHLBI R01HL073598; NIBIB R01EB001973 |
nif-0000-00532 | SCR_007379 | National Simulation Resource Physiome Project | 2026-08-12 10:49:45 | 3 | |||||||
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UA Neuroscience GIDP Resource Report Resource Website |
UA Neuroscience GIDP (RRID:SCR_007494) | UA Neuroscience GIDP | data or information resource, department portal, portal, organization portal | The University of Arizona offers a Ph.D. through the Graduate Interdisciplinary Program in Neuroscience. The Program, administered by the Committee on Neuroscience, is designed to provide students with the knowledge and tools that they will need to embark on careers as educators and researchers in the field of neuroscience. Students participate in designing their own individually tailored programs that provide a thorough base of knowledge in the many facets of neuroscience as well as depth in chosen areas of specialization, and that enhance their abilities to think creatively and express themselves clearly. Because of the breadth of expertise represented by the faculty, students have access to educational and research training opportunities in areas ranging through molecular, cellular, systems, behavioral, cognitive, theoretical, and clinical neuroscience. The program currently enrolls 27 students. | has parent organization: University of Arizona; Arizona; USA | nif-0000-02132 | SCR_007494 | Program in Neuroscience, University of Arizona Graduate Interdisciplinary Program in Neuroscience | 2026-08-12 10:49:43 | 0 | |||||||||
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T-One weighted Perfusion imaging Parameter CAlculation Toolkit Resource Report Resource Website 1+ mentions |
T-One weighted Perfusion imaging Parameter CAlculation Toolkit (RRID:SCR_007376) | data processing software, image processing software, software resource, software application | TOPPCAT stands for T-One weighted Perfusion imaging Parameter CAlculation Toolkit. TOPPCAT creates quantitative maps of Ktrans (volume transfer constant between blood plasma and the extravascular extracellular space) and fPV (fractional plasma volume) from dynamic T1-weighted perfusion images. At the current time, analysis using the method of Patlak plots (most appropriate for first pass dynamic contrast-enhanced MR imaging) is supported. As a preliminary step for the parameter calculation, TOPPCAT also creates maps of T1 and S0 (equilibrium magnetization) from multi-flip angle T1-weighted SPGR (or FLASH) sequences.Daniel P. Barboriak, James R. MacFall, Anthony O. Padua,Gerald E. York, Benjamin L. Viglianti, and Mark W. Dewhirst. Standardized software for calculation of Ktrans and vp from dynamic T1-weighted MR images. Presented at the International Society for Magnetic Resonance in Medicine Workshop on MR in Drug Development: From Discovery to Clinical Therapeutic Trials, McLean VA, April 2004. | has parent organization: Duke University; North Carolina; USA | nif-0000-00349 | SCR_007376 | TOPPCAT | 2026-08-12 10:49:45 | 2 | ||||||||||
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University of California Santa Cruz, Department of Molecular, Cell and Developmental Biology Resource Report Resource Website |
University of California Santa Cruz, Department of Molecular, Cell and Developmental Biology (RRID:SCR_007497) | data or information resource, department portal, portal, organization portal | The Department of Molecular, Cell & Developmental Biology (MCD), with 20 faculty members, focuses on fundamental problems in the molecular, cell and developmental biology of animals and plants. The scope of research conducted in this group spans the broad range of modern biological research; from classical and molecular genetics to biochemistry and molecular biology. Research laboratories in the MCD Biology Department use both simple model organisms and vertebrate systems to study important biological processes, ranging from the mechanism of protein synthesis to the development and function of the nervous system. | nif-0000-02139 | http://www.mcd.ucsc.edu/ | SCR_007497 | UCSC | 2026-08-12 10:49:43 | 0 | ||||||||||
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Tufts University Department of Neuroscience Resource Report Resource Website 10+ mentions |
Tufts University Department of Neuroscience (RRID:SCR_007491) | data or information resource, department portal, portal, organization portal | The Graduate Program in Neuroscience at Tufts University School of Medicine is a member of the Sackler School Integrated Studies Program (ISP). The research programs of the 20 faculty members incorporate a broad range of approaches - from molecular to systems analysis - to understand the form and function of the nervous system, with a particular emphasis on the synapse. The graduate course of study, likewise, strongly emphasizes multidisciplinary training to prepare students for research careers in the complex field of neuroscience. Such training is additionally promoted through the technical expertise and research facilities offered by the Tufts Center for Neuroscience Research (CNR).It is based in newly renovated space in the Neuroscience Department, occupying three floors of the Tufts Medical School research complex in downtown Boston. | nif-0000-02118 | SCR_007491 | Tufts | 2026-08-12 10:49:43 | 27 | |||||||||||
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Brain Architecture Management System Resource Report Resource Website 1+ mentions |
Brain Architecture Management System (RRID:SCR_007251) | BAMS | ontology, service resource, data or information resource, database, controlled vocabulary, data repository, storage service resource | Knowledge management system designed to handle neurobiological information at different levels of organization of vertebrate nervous system. Database and repository for information about neural circuitry, storing and analyzing data concerned with nomenclature, taxonomy, axonal connections, and neuronal cell types. Handles data and metadata collated from original literature, or inserted by scientists that is associated to four levels of organization of vertebrate nervous system. Data about expressed molecules, neuron types and classes, brain regions, and networks of brain regions. | neurobiology, vertebrate, nervous, system, database, repository, neural, circuitry, analysis, data, nomenclature, taxonomy, axonal, connection, cell, |
is used by: NIF Data Federation is used by: Integrated Nervous System Connectivity is related to: Integrated Manually Extracted Annotation has parent organization: University of Southern California; Los Angeles; USA is parent organization of: BAMS Nested Regions is parent organization of: BAMS Connectivity is parent organization of: BAMS Cells is parent organization of: BAMS Neuroanatomical Ontology |
NIBIB ; Human Brain Project ; NIMH MH61223; NINDS NS16686; NINDS NS50792 |
Restricted | nif-0000-00018 | http://brancusi.usc.edu/bkms/ | SCR_007251 | Brain Architecture Management System, The Brain Architecture Management System | 2026-08-12 10:49:41 | 6 | |||||
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NeuroLens Resource Report Resource Website 10+ mentions |
NeuroLens (RRID:SCR_007372) | NeuroLens | data visualization software, image analysis software, image processing software, software application, data processing software, software resource | An integrated environment for the analysis and visualization of functional neuroimages. It is intended to provide extremely fast and flexible image processing, via an intuitive user interface that encourages experimentation with analysis parameters and detailed inspection of both raw image data and processing results. All processing operations in NeuroLens are built around a Plugin architecture, making it easy to extend its functionality. NeuroLens runs on Apple computers based on the G4, G5, or Intel chipsets and running MacOSX 10.4 (Tiger) or later. It is available free for academic and non-profit research use. * Operating System: MacOS * Programming Language: Objective C * Supported Data Format: AFNI BRIK, ANALYZE, COR, DICOM, MGH/MGZ, MINC, Other Format | image-to-image, linear, temporal convolution - deconvolution, multivariate analysis, neuroimaging, fmri, brain structure, neural structure, brain, temporal convolution, temporal deconvolution, afni brik, analyze, cor, dicom, image display, macos, mgh/mgz, minc, magnetic resonance, objective c, registration, regression, rendering, software, spatial transformation, statistical operation, surface rendering, temporal transformation, three dimensional display, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of Montreal; Quebec; Canada |
MGH CSRL License, - free for academic and non-profit research use. | nif-0000-00333 | http://www.nitrc.org/projects/nldo | SCR_007372 | 2026-08-12 10:49:43 | 10 | |||||||
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University of Alabama Neurobiology Resource Report Resource Website |
University of Alabama Neurobiology (RRID:SCR_007493) | data or information resource, department portal, portal, organization portal | The Department of Neurobiology offers students interested in the nervous system a program of study that leads to the Ph.D. in Neurobiology or a combined M.D./Ph.D. through The University of Alabama School of Medicine located at UAB. The graduate program has numerous faculty members with active research programs from a broad range of areas in contemporary neuroscience with a major focus on topics of biomedical importance. Molecular, cellular and biophysical approaches are emphasized to address fundamental problems of brain function, development and disease. All students take a series of graduate courses in biochemistry and molecular biology, cell biology, ion channel biophysics, synaptic function, developmental neurobiology and medical neurobiology. Evidence of the faculty's national and international impact in fundamental Neuroscience research includes: their substantial number of publications in high impact journals; appointments to editorial boards and editorships of leading neuroscience journals; appointments to NIH and NSF study sections and review boards; awards of over 28 million dollars in annual research grant funds; and numerous invitations to speak at national and international research symposia. Faculty members also have received numerous national and international awards recognizing excellence in research and training. | nif-0000-02130 | http://www.neurobiology.uab.edu/ | SCR_007493 | UAB Department of Neurobiology | 2026-08-12 10:49:47 | 0 | ||||||||||
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Tulane University Medical Center Department of Pharmacology Resource Report Resource Website 10+ mentions |
Tulane University Medical Center Department of Pharmacology (RRID:SCR_007492) | data or information resource, department portal, portal, organization portal | Department to educate and train medical and graduate students in principles of pharmacology using modern techniques and to conduct state of art research in pharmacology related fields in order to expand frontiers of science and medicine. | nif-0000-02122 | http://tulane.edu/som/departments/pharmacology/ | SCR_007492 | Tulane | 2026-08-12 10:49:37 | 10 | ||||||||||
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CASPLab: Comet Assay Software Project Laboratory Resource Report Resource Website 10+ mentions |
CASPLab: Comet Assay Software Project Laboratory (RRID:SCR_007249) | organization portal, portal, data or information resource, software resource, laboratory portal | CASP is a tool to image analysis in comet assay. CASP has been developed to work with either color, or gray-scale images of fluorescence-stained comets saved in TIF format. In its present version CASP does not control a video or CCD camera. Comets stained with silver (dark cells on white background) must be converted into negative images in order to be analysed correctly. An unlimited number of images can be marked, CASP will load them successively into a image view window (see screenshot). Only comets oriented from left (head) to right (tail) can be analysed correctly. The user can adjust various thresholds of sensitivity and save the adjustments for future use. A measurement frame is drawn on the screen and its size adjusted. The adjustments are frozen to prevent accidental modification. The frame is moved onto a cell and measurement is activated. An intensity profile shows up on a profile window together with selected result values (right window on figure 1) and the result can be saved. In addition to such parameter as head radius, tail length etc, the program calculates the tail moment (TM) and the Olive tail moment (OTM). If several cells are present on the same picture, the user can proceed with the measurement of another cell on the same picture or can load a new picture. The saved results can be visualized during the working session in a spreadsheet in view results window. When measurements are terminated, the results can be exported into a text file and imported into a commercial spreadsheet calculation program. CASP is optimized for a 600x800 resolution. Sponsors: This work has been supported by the University of Wroclaw. Keywords: Comet, Assay, Software, Laboratory, Camera, Negative, Cell, Analysis, Image, | has parent organization: University of Wroclaw; Wroclaw; Poland | nif-0000-30299 | SCR_007249 | CASPLab | 2026-08-12 10:49:43 | 47 | ||||||||||
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FisWidgets Resource Report Resource Website |
FisWidgets (RRID:SCR_007367) | data processing software, data analysis software, software resource, software application | A set of Java libraries for rapidly creating GUIs for software modules (C, C++, Fortan, PERL scripts, etc.), and graphically controlling process flow among them. This allows a GUI to be created for existing image processing and analysis routines, which provides: 1) graphic elements for setting parameters, arguments, etc. (i.e., text dialogs, file browsers, etc.); 2) links to web based documentation; 3) simple point-and-click interface for setting up a path for data flow from one module to another. The purpose of FisWidgets is to provide an integrated and user-friendly environment for using the disparate and growing array of image processing and analysis tools created by different laboratories. | has parent organization: University of Pittsburgh; Pennsylvania; USA | nif-0000-00302 | http://neurocog.lrdc.pitt.edu/fiswidgets/ | SCR_007367 | 2026-08-12 10:49:45 | 0 | ||||||||||
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Thomas Jefferson University Neurology Resource Report Resource Website |
Thomas Jefferson University Neurology (RRID:SCR_007488) | portal, postdoctoral program resource, data or information resource, medical school program resource, degree granting program, training resource, organization portal, people resource | The Department of Neurology at Jefferson Medical College has a long tradition of excellence in clinical training and care. They are committed to providing an active and exciting research program, exemplified by the Farber Institute for the Neurosciences, established in the spring of 2002. Consolidation of our academic and research base with the neurology ambulatory care facility at the new Jefferson Hospital for the Neurosciences underscores the continuing evolution of the Neurology department, and of its many functions, including, our fully approved residency program. | nif-0000-02114 | http://www.jefferson.edu/neurology/index.cfm | SCR_007488 | Jefferson | 2026-08-12 10:49:43 | 0 | ||||||||||
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Image Pro Plus Resource Report Resource Website 10000+ mentions |
Image Pro Plus (RRID:SCR_007369) | software toolkit, data acquisition software, image analysis software, software application, data processing software, image acquisition software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18,2023. Software package to capture, process, measure, analyze and share images and data. | morphometric, image analysis, image acquisition, automation, classification, microscope control | is listed by: SoftCite | nif-0000-00313, SCR_015803, SCR_016879 | SCR_007369 | Image-Pro Plus, Image-Pro Plus Morphometric Analysis Software | 2026-08-12 10:49:43 | 18774 | |||||||||
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Texas Tech University Department of Pharmacology and Neuroscience Resource Report Resource Website |
Texas Tech University Department of Pharmacology and Neuroscience (RRID:SCR_007483) | TTU Department of Pharmacology and Neuroscience, | data or information resource, department portal, portal, organization portal | The Department of Pharmacology and Neuroscience at Texas Tech University is committed to providing a strong education experience for all trainees. The department's primary areas of training emphasis are neuroscience/ neuropharmacology and cardiovascular/ autonomic pharmacology.Our objective is to prepare students for careers in research and teaching. We currently have 14 faculty and who conduct research in a broad variety of subjects ranging from environmental toxicology to molecular pharmacology. This allows a broad basis for a strong theoretical as well as 'hands-on' education in pharmacology. The faculty of the program work hard to foster a creative and productive research atmosphere, to provide encouragement and positive challenges, and to equip students with the intellectual tools they will need to be good teachers and investigators. | has parent organization: Texas Tech University Health Sciences Center; Texas; USA | nif-0000-02098 | http://www.ttuhsc.edu/som/pharmacology/ | SCR_007483 | Texas Tech University Department of Pharmacology Neuroscience | 2026-08-12 10:49:37 | 0 | ||||||||
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COLELMS: Stata module to calculate Coles LMS values for growth data Resource Report Resource Website 1+ mentions |
COLELMS: Stata module to calculate Coles LMS values for growth data (RRID:SCR_007244) | data processing software, data analysis software, software resource, software application | COLELMS calculates LMS values, smoothed LMS, and growth reference centiles based in smoothed LMS values. df value is set to when calculating smoothed LMS values. You are responsible for setting an appropriate df for your data. This is version 0.2 of the software. Sponsors: This resource is supported by Boston College. Keywords: Software, LMS, Calculation, Growth, Data, Stata, Module, | nif-0000-30264 | SCR_007244 | COLELMS | 2026-08-12 10:49:41 | 7 | |||||||||||
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XFido Resource Report Resource Website |
XFido (RRID:SCR_007365) | data processing software, data visualization software, software resource, software application | An interactive, graphic, fiducial marking software for placing, editing and tracking fiducial marks on images in a tomography tilt series. You can also use this tool to view the tilt series as well as crop it. | has parent organization: National Center for Microscopy and Imaging Research | nif-0000-00300 | SCR_007365 | XFido | 2026-08-12 10:49:43 | 0 | ||||||||||
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UTHealth at Houston Neuroscience Research Center Resource Report Resource Website |
UTHealth at Houston Neuroscience Research Center (RRID:SCR_007486) | UTHealth NRC | portal, postdoctoral program resource, data or information resource, training resource, topical portal, graduate program resource | The Neuroscience Research Center (NRC) is a university-wide center where diverse and multidisciplinary research is conducted to further the understanding of neural and behavioral disorders. Whether conducting cellular research in laboratories or clinical trials in patient care settings, the work of NRC researchers may someday contribute to preventing and treating such devastating disorders as: * Dementias resulting from Alzheimer''s disease and stroke * Mental retardation and other learning disabilities * Mental illnesses, including schizophrenia and manic-depressive illness * Alcoholism and other substance abuse problems * Inability to process knowledge due to factors such as aging and head trauma * Disabilities due to disorders of the developing nervous system More than 280 faculty hold NRC appointments, and are on the faculties of the Medical School, School of Public Health, School of Nursing, Dental Branch, and School of Biomedical Informatics. Departments with significant NRC research activities within the Medical School include Neurobiology and Anatomy; Neurology; Neurosurgery; Ophthalmology and Visual Science; Psychiatry and Behavioral Sciences and Radiology. NRC activities are guided by an executive committee appointed by the President of the Health Science Center. The Neuroscience Research Center (NRC) is affiliated with educational opportunities at the graduate and postdoctoral levels. | neuroscience, brain | has parent organization: University of Texas Health Science Center at Houston; Texas; USA | nif-0000-02108 | http://nba.uth.tmc.edu/nrc/ | SCR_007486 | University of Texas Health Science Center at Houston Neuroscience Research Center | 2026-08-12 10:49:37 | 0 | |||||||
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Texas A and M Health Science Center College of Medicine Department of Neuroscience and Experimental Therapeutics Resource Report Resource Website |
Texas A and M Health Science Center College of Medicine Department of Neuroscience and Experimental Therapeutics (RRID:SCR_007482) | data or information resource, department portal, portal, organization portal | The Department of Neuroscience and Experimental Therapeutics (NExT) at the Texas A&M Health Science Center College of Medicine has 16 full-time faculty members and is one of four basic science departments within the College of Medicine. Program strengths within the department include brain development, cellular/molecular basis of drug addiction, circadian biology, ocular pharmacology and experimental therapeutics, neurobiology of aging, neurodegenerative diseases such as stroke and Alzheimer''s disease, neuro-oncology and neuroteratology of alcohol, nicotine and other drugs of abuse. The Department of Neuroscience and Experimental Therapeutics participates in an interdisciplinary graduate program in the Medical Sciences that leads primarily to the Ph.D. degree with special emphasis in interdisciplinary training in Neurosciences or Pharmaceutical Sciences. The Ph.D. program in Medical Science usually requires 4-5 years to complete. Graduates from our program are prepared for leadership roles in research and teaching in academic, industrial, or governmental positions. Faculty within the department are affiliated with university-wide interdisciplinary faculties including the TAMU Faculty of Neuroscience rand our clinical science partner, the Texas Brain and Spine Institute. The department is also home to the Women''s Health in Neuroscience Program, consisting of interdisciplinary research faculty and a clinical advisory group aimed at developing a cohesive preclinical approach to the impact of puberty, pregnancy and menopause on brain development, mental health and brain disease. | has parent organization: Texas A and M Health Science Center College of Medicine; Texas; USA | Aging | nif-0000-02093 | SCR_007482 | TAMHSC College of Medicine NExT, TAMHSC COM NExT | 2026-08-12 10:49:43 | 0 | |||||||||
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SUNY Upstate Medical University, Pharmacology Resource Report Resource Website |
SUNY Upstate Medical University, Pharmacology (RRID:SCR_007481) | data or information resource, department portal, portal, organization portal | Research in the Department of Pharmacology focuses on three major areas: 1) cardiovascular science 2) cell signaling 3) cancer biology and therapeutics. Within those areas, research ranges from basic biological problems to those with clinical orientations. The cardiovascular science research strives to understand the normal and abnormal functioning of the heart at the molecular, cellular and organ levels, and is exceptionally strong in cardiac electrophysiology and the mechanisms of cardiac arrhythmia. The cell signaling research concerns regulation of cell function by extracellular factors, the molecular biology of signaling pathways, cell communication, and intracellular proteolysis. The cancer biology and therapeutics research is focused on molecular mechanisms regulating cell death and survival in human malignancies, development and testing of novel cancer therapeutics, novel tumor markers, oncogenic transformation and apoptosis, regulation of tumor suppressors and molecular mechanisms of leukemogensis. The Pharmacology Department has multiple research grants for the next five years. Most of the funding comes from the National Institutes of Health (NIH), with additional funding from the Association for International Cancer Research, the American Society of Hematology, the Department of Defense and the American Heart Association. | nif-0000-02084 | SCR_007481 | SUNY Upstate | 2026-08-12 10:49:47 | 0 | |||||||||||
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BraInSitu: A homepage for molecular neuroanatomy Resource Report Resource Website 1+ mentions |
BraInSitu: A homepage for molecular neuroanatomy (RRID:SCR_008081) | BraInSitu | image, data or information resource, database, narrative resource, experimental protocol, atlas, expression atlas | Database of detailed protocols for single and double in situ hybridization (ISH) method, probes used by Yamamori lab and others useful for studies of brain, and many photos of mammalian (mostly mouse and monkey) brains stained with various gene probes. Also includes a brain atlas of gene expression. Currently, the atlas comprises a series of un-annotated images showing the localization of a particular probe or molecule, e.g., AChE. | function, gene expression, gene, anatomical structure, brain, central nervous system, cerebral cortex, in situ hybridization, mammalian, neocortex, pcr cloning, probe, molecular neuroanatomy resource, neuroanatomy, in situ hybridization protocol | has parent organization: National Institute for Basic Biology; Okazaki; Japan | nif-0000-11633 | SCR_008081 | 2026-08-12 10:49:39 | 4 |
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