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http://www.umassmed.edu/bmp/index.aspx

Department of Biochemistry and Molecular Pharmacology seeks to foster interactive, innovative environment in which faculty, students and postdoctoral fellows bring molecular perspective to problems in biology. By establishing interface between biology and disciplines of chemistry, mathematics and physics, this department encourages development and application of quantitative approaches to complex problems in life sciences. Department also serves to strengthen and, in turn, be strengthened by close interactions with other basic science and clinical departments at medical school.

Proper citation: University of Massachusetts at Worcester Medical School Department of Biochemistry and Molecular Pharmacology (RRID:SCR_007431) Copy   

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http://vcell.org/

V-Cell is a remote user modeling and simulation environment utilizing Java''s Remote Method Invocation (RMI). The biologically oriented user interface allows experimentalists to create models, define cellular geometry, specify simulations and analyze the simulation results. The results are run and stored on a remote server and can be reviewed in the software and/or exported in a variety of popular formats. The design of the biological to mathematical mapping allows for separate use of biological and math components, and includes automatic mathematical simplification using pseudo-steady approximations and mass conservation relationships. This allows for direct specification of mathematical problems, performing simulations and analysis on those systems. The stand alone mathematics user interface is also a powerful tool for modeling reaction-diffusion systems. A transparent general purpose solver is used to translate the initial biological description into a set of concise mathematical problems. The solver is transparent to the average user, but is accessible to the theorist as the Math Editor component. The software is composed of three main components: 1. The modeling framework represents the physiological models of the Virtual Cell and allows for persistence and database support. 2. The mathematics framework transparently solves an important class of mathematical problems encountered in the cellular modeling. 3. The WWW accessible graphical user interface provides access to the technology mentioned above. The user interface has been developed using Java 2 Applets.

Proper citation: Virtual Cell at the National Resource for Cell Analysis and Modeling (RRID:SCR_007421) Copy   

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http://www.translatingtime.net

Web tool for translating neurodevelopemental time across species and predicting neurodevelopemental events. This tool was created because clinicians and researchers rely on neurodevelopment data obtained from a variety of non-human species, it is essential to be able to relate studies across the different experimental animals, and ultimately to humans, in an easily accessible format. This web site is based on a mathematical model originally described by Finlay and Darlington (Science, 268:1578-84) that predicts post conception (PC) dates using log transformations. It integrates hundreds of empirically-derived neural events to translate neurodevelopmental time across hamsters, mice, rats, rabbits, spiny mice, guinea pigs, ferrets, cats, rhesus monkeys and humans.

Proper citation: Translating Time across developing mammalian brains (RRID:SCR_007424) Copy   

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http://www.depts.washington.edu/phcol/

The Department of Pharmacology are involved in diverse areas of research with special emphasis on molecular pharmacology, cellular regulation, neuropharmacology, and environmental toxicology. Active areas of research include evaluating the effects of drugs and chemicals on humans and animals; studying the actions of hormones, neurotransmitters, and other physiological regulators on individual cells; examining the detailed molecular structure of cellular constituents; and exploring how the cell regulates it's vital processes through transcriptional and post-transcriptional mechanisms. Through our research, we'd ultimately like to gain detailed insights into drug action and cellular regulation at many different levels of inquiry: the human patient, the experimental animal, the individual cell, its complement of proteins, and the genetic code.

Proper citation: University of Washington Seattle WA. Pharmacology (RRID:SCR_007539) Copy   

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https://www.queensu.ca/sgs/pharmacology-toxicology

This program is now part of the new interdisciplinary program of Biomedical and Molecular Sciences.

Proper citation: Queens University at Kingston Department of Pharmacology and Toxicology Graduate Program (RRID:SCR_007450) Copy   

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https://code.google.com/p/peakrots/

Bioinformatics analysis software tool for optimized ChIP-seq peak detection written in R.

Proper citation: peakrots (RRID:SCR_007453) Copy   

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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://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.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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https://njms.rutgers.edu/departments/neurology/graduate_programs.php

The Graduate Program in Neuroscience is committed to educating and training outstanding young scientists in the multidisciplinary concepts and contemporary techniques at the heart of modern Neuroscience. Students selected for this program generally have had exceptional undergraduate training in the physical, biological and social sciences. It offers students an outstanding opportunity for graduate training in a rapidly growing joint program of the Graduate School of Rutgers University and the Graduate School of Biomedical Sciences of the University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, both located in Piscataway/New Brunswick, New Jersey. A major goal of the Graduate Program in Neuroscience is to prepare students-in the classroom and in active research laboratories-for careers of independent research in universities, medical schools, governmental facilities and industry.

Proper citation: University of Medicine and Dentistry of New Jersey Neuroscience Graduate Program (RRID:SCR_007515) Copy   

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http://www.dental.umaryland.edu/dentaldepts/neural_pain_sciences/nps_orc_dubner.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 25,2022. Research unit in the University of Maryland School of Dentistry specializing in neural pain. The program includes a major Program Project on Plasticity and Modulation in Models of Persistent Pain and the University of Maryland, Baltimore Research Center for Neuroendocrine Influences on Pain.

Proper citation: University of Maryland Dental School, Organized Research Center on Persistant Pain (RRID:SCR_007512) Copy   

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http://www.umanitoba.ca/faculties/medicine/units/pharmacology/

The Department of Pharmacology and Therapeutics at the University of Manitoba consists of 15 full time faculty, 21 joint faculty, and 1 senior scholar, with research interests including cardiovascular pharmacology, clinical pharmacology, hepatic pharmacology, neuropharmacology, and renal pharmacology, teaching in Medicine and Pharmacy, and offering courses of study leading to M.Sc. and Ph.D. degrees in Pharmacology. It is a modern well equipped facility with a thriving graduate program, based on the 2nd, 3rd, and 4th floors of the Chown Building on the Bannatyne Campus next to the Health Science Centre and at the Division of Neurodegenerative Disorders at St. Boniface General Hospital Research Centre in Winnipeg, Manitoba Canada.

Proper citation: University of Manitoba, Faculty of Medicine, Department of Pharmacology (RRID:SCR_007511) 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.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://neuroscience.uc.edu/

The Graduate Program in Neuroscience at the University of Cincinnati was established in 1988 as an interdisciplinary program offering the Ph.D. degree. More than 80 faculty members from 22 departments the Colleges of Medicine, Pharmacy, the Arts and Sciences are members of the Neuroscience Program. Research interests of the faculty are diverse and reflect a variety of state of the art approaches toward understanding the brain. Many faculty have research programs with a clinical focus on brain diseases such as stroke, Alzheimer's Disease, brain tumors, substance abuse, schizophrenia, bipolar disorder and obesity.

Proper citation: University of Cincinnati, Neuroscience Graduate Program (RRID:SCR_007506) Copy   

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http://www.medicine.uiowa.edu/pharmacology/

The Department of Pharmacology is one of five basic science departments in the Roy J. and Lucille A. Carver College of Medicine at The University of Iowa. The Department currently consists of 25 faculty members, holding either primary or joint appointments in Pharmacology, many of whom are nationally and internationally recognized for their research. The Department occupies almost 32,000 square feet of newly renovated space in the Bowen Science Building, a component of the Health Sciences Complex on the west bank of the Iowa River. Departmental laboratories are well-equipped for the pursuit of research, and our faculty members use a wide variety of experimental methodologies to address contemporary issues in cellular and molecular pharmacology.

Proper citation: University of Iowa College of Medicine Department of Pharmacology (RRID:SCR_007502) Copy   

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https://neuroscience.uchicago.edu/

The Integrative Neuroscience graduate program at the University of Chicago is designed to provide the training and research opportunities for the next generation of behavioral, cognitive, and social neuroscientists. Behavioral, cognitive, and social neuroscience represent three complementary and partially overlapping aspects of this integrative neuroscience of mind and behavior. Behavioral neuroscience places an emphasis on the biological mechanisms underlying basic behavioral processes; cognitive neuroscience places an emphasis on the biological mechanisms underlying cognition, with a specific focus on the neural substrates of mental processes and their behavioral manifestations; and social neuroscience places an emphasis on the biological mechanisms underlying social processes and behavior, including the ability to perceive and communicate mental states including the beliefs and desires of others and to form and maintain interpersonal and group relationships. The University of Chicago is optimally positioned to meet this challenge because its unique academic structure facilitates interactions across disciplinary perspectives.

Proper citation: University of Chicago Department of Neuroscience (RRID:SCR_007505) Copy   

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