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http://www.mmc.edu/education/sogsr/academicprograms/phd_program/pharmacology/

Graduate Program in Pharmacology at Meharry Medical College embraces the broad definition of pharmacology as the study of how chemical agents affect living processes; the chemicals involved include agents such as endogenous hormones, neurotransmitters, and/or growth factors; toxic substances in our environment; and pharmaceutically developed drugs. The breadth of our scientific environment is manifested by faculty who study the fate of drugs once ingested and the variability of drug response in varying patient populations (a discipline known as pharmacokinetics), as well as faculty who study the mechanisms by which drugs and endogenous agents work (a discipline known as pharmacodynamics). A unique strength of our research and training environment is the inter-disciplinary nature of the program, which encompasses faculty from the four divisions of the Department of Biomedical Science and Departments of Internal Medicine and Neurology.

Proper citation: Meharry Medical College Pharmacology (RRID:SCR_003477) Copy   

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http://genecloud.org/

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.

Proper citation: Gene Cloud: Exploring Connections in the Mouse Genome (RRID:SCR_003503) Copy   

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http://archive.gramene.org/plant_ontology/ontology_browse.html#to

A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part.

Proper citation: Plant Trait Ontology (RRID:SCR_003461) Copy   

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http://www.ispa.pt/ui/uie/ibbg/TilapiaBrainAtlas/index.html

Digital three-dimensional MRI atlas of the Mozambique tilapia brain, supported by Nissl staining. Images were viewed and analyzed in all orientations (transverse, sagittal, and horizontal) and manually labelled to reveal structures in the olfactory bulb, telencephalon, diencephalon, optic tectum, and cerebellum. The MRI atlas data (16-bit int) and delineation data (8-bit int) are provided in Raw data (file_name.raw), Amira format (file_name.am) and in Analyze format (file_name.img and file_name.hdr).

Proper citation: Brain Atlas of the Mozambique Tilapia Oreochromis mossambicus (RRID:SCR_003501) Copy   

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http://www.montana.edu/cbn/

The academic programs and scientific research interests in our department cover a wide range of topics, with special emphasis on Cell Biology, Neurobiology, Developmental Biology, Physiology, Anatomy, Biophysics, and Neuroinformatics. Together, faculty and students in our department study biological processes that span the continuum from single cells to the entire human body. The Department of Cell Biology and Neuroscience offer both an Undergraduate and Graduate Program, which includes Ph.D. or M.S. degrees in Neuroscience or Biological Science. Two different undergraduate degree options are available within the Cell Biology and Neuroscience major: Biomedical Sciences and Cell Biology & Neuroscience. The Department of Cell Biology and Neuroscience offers exciting opportunities to work with nationally and internationally recognized faculty on a wide range of research topics, including cognitive neuroscience, neurophysiology, neuroinformatics, developmental biology, cell biology, biophysics and computational neuroscience.

Proper citation: Montana State University, Department of Cell Biology and Neuroscience (RRID:SCR_003467) Copy   

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http://www.utoledo.edu/med/depts/neurosciences/index.html

The Department of Neurosciences is highly committed to advancing the state of knowledge of nervous system structure and function through a tripartite mission of innovative research, state-of-the-art teaching methods, and dedicated service to the broader academic and surrounding communities. The teaching mission of our Department effectively communicates the current state of knowledge in neuroscience to the medical, graduate, and post-graduate students of the University using innovative methods. We are nationally known for using the most current technologies to teach human anatomy, embryology, and neurobiology to medical and graduate students. We teach critical thinking and problem solving skills and also provide opportunities for the students to excel in the laboratory and develop as life-long learners. Faculty participate in our Neurosciences and Neurological Disorders (NND) training track which awards both Ph.D. and M.S. degrees. We also train students towards the M.D./Ph.D and M.D./ M.S.B.S. joint degrees. Our research mission incorporates molecular, cellular, and systems neuroscience and cuts across the boundaries of traditional departments and disciplines. Our funded research in neurodevelopment, neurodegeneration, regeneration and repair, sensory function, and drug abuse comprise just a few of our interests. We employ cutting edge technologies and focus on the solution of fundamentally important problems pertinent to nervous system diseases and processes that can be translated feasibly to clinical issues. We work towards a synergistic interaction between the clinical and basic sciences that prompts unexpected discoveries of causes and novel treatments for the diseased nervous system. We also coordinate the Human Body Donation Program at the University of Toledo College of Medicine.

Proper citation: University of Toledo Health Sciences Campus; Neurosciences (RRID:SCR_003466) Copy   

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http://socialbrain.wordpress.com/2009/09/30/neurovia-download-neuro-imaging-tools-software-brain-project-matlab-program-package-for-the-analysis-of-functional-neuroimages/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 24, 2013. These distribution sets contain software modules and/or data sets extracted from the Visualization and Analysis Software Tools (VAST) library developed at the Minneapolis VA Medical Center, the University of Minnesota and/or the International Consortium for Neuroimaging (INC) (partially funded by the Human Brain Project )

Proper citation: Software Distribution Sets (RRID:SCR_003465) Copy   

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http://www.gru.edu/mcg/phy/

Department that trains independent, creative, productive scholars in the physiological sciences. The department offers programs leading to the Ph.D. degree. A combined M.D./Ph.D. or D.M.D./Ph.D. degree program is available for students who obtain prior or concurrent admission to the Schools of Medicine or Dentistry respectively. The primary research interests of the department are Cardiovascular Physiology, Endocrinology, and Neuroscience. Physiology faculty currently hold more than $7,000,000 in extramural funding, ranking 21st out of Medical School Physiology Departments nationally. Members of the Department teach in the Medical and Graduate Schools including Medical Physiology and Intergated Systems Biology, Neuroscience and advanced courses in cardiovascular and endocrine physiology.

Proper citation: Medical College of Georgia Department of Physiology (RRID:SCR_003458) Copy   

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http://www.loria.fr/~coulet/sopharm2.0_description.php

A domain ontology implemented in OWL-DL, which proposes a formal description of pharmacogenomic knowledge. It articulates different ontologies that represent complementary sub-domains of pharmacogenomics, i.e. related to genotype, phenotype, drugs, and clinical trials. SO-Pharm enables the representation of pharmacogenomic relationships between a drug, a genomic variation and a phenotype trait. In addition, it enables the representation of a patient and more largely a panel included in trials, and populations. SO-Pharm enables the representation of measured items on patients such as results from the observation of a phenotype trait or of genomic variations. SO-Pharm supports knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. SO-Pharm is designed to facilitate data integration and knowledge discovery in pharmacogenomics. In addition it provides a consistent articulation of ontologies of pharmacogenomic sub-domains.

Proper citation: Suggested Ontology for Pharmacogenomics (RRID:SCR_003497) Copy   

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https://bioportal.bioontology.org/ontologies/REX?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FREX_0000000

An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. It includes both microscopic processes (involving molecular entities or subatomic particles) and macroscopic processes. Some biochemical processes from Gene Ontology (GO Biological process) can be described as instances of REX.

Proper citation: Physico-Chemical Process (RRID:SCR_003530) Copy   

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http://code.google.com/p/popoolation/

A collection of tools to facilitate population genetic studies of next generation sequencing data from pooled individuals. It builds upon open source tools (bwa, samtools) and uses standard file formats (gtf, sam, pileup) to ensure a wide compatibility. PoPoolation allows to calculate Tajima's Pi, Watterson's Theta and Tajima's D for reference sequences using a sliding window approach. Alternatively these population genetic estimators may be calculated for a set of genes (provided as gtf). One of the main challenges in population genomics is to identify regions of intererest on a genome wide scale. PoPoolation will greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools.

Proper citation: PoPoolation (RRID:SCR_003495) Copy   

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https://github.com/delt0r/msms

A coalescent simulation software program for a structured population including recombination, demographic structure and selection at a single diploid locus.

Proper citation: MSMS (RRID:SCR_003532) Copy   

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http://theswo.sourceforge.net

An ontology for describing software tools, their types, tasks, versions, provenance and data associated (the input and output data types and the uses the software can be put to).

Proper citation: Software Ontology (RRID:SCR_003493) Copy   

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http://www.humanvariomeproject.org/

Project facilitating the establishment and maintenance of standards systems and infrastructure for the worldwide collection and sharing of all genetic variations effecting human disease. The Human Variome Project produces two categories of recommendations: HVP Standards and HVP Guidelines. HVP Standards are those systems, procedures and technologies that the Human Variome Project Consortium has determined should be used by the community. These carry more weight than the less prescriptive HVP Guidelines, which cover those systems, procedures and technologies that the Human Variome Project Consortium has determined would be beneficial for the community to adopt. HVP Standards and Guidelines are central to supporting the work of the Human Variome Project Consortium and cover a wide range of fields and disciplines, from ethics to nomenclature, data transfer protocols to collection protocols from clinics. They can be thought of as both technical manuals and scientific documents, and while the impact of HVP Standards and Guidelines differ, they are both generated in a similar fashion. A document has been generated both as a guide for those collecting and distributing data and for those developing policy. Items should include those generated by HGVS/HVP collaborators as well as those generated by groups of individual Societies and Standards bodies in all relevant fields worldwide.

Proper citation: Human Variome Project (RRID:SCR_003492) Copy   

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http://www.humanconnectomeproject.org/

A multi-center project comprising two distinct consortia (Mass. Gen. Hosp. and USC; and Wash. U. and the U. of Minn.) seeking to map white matter fiber pathways in the human brain using leading edge neuroimaging methods, genomics, architectonics, mathematical approaches, informatics, and interactive visualization. The mapping of the complete structural and functional neural connections in vivo within and across individuals provides unparalleled compilation of neural data, an interface to graphically navigate this data and the opportunity to achieve conclusions about the living human brain. The HCP is being developed to employ advanced neuroimaging methods, and to construct an extensive informatics infrastructure to link these data and connectivity models to detailed phenomic and genomic data, building upon existing multidisciplinary and collaborative efforts currently underway. Working with other HCP partners based at Washington University in St. Louis they will provide rich data, essential imaging protocols, and sophisticated connectivity analysis tools for the neuroscience community. This project is working to achieve the following: 1) develop sophisticated tools to process high-angular diffusion (HARDI) and diffusion spectrum imaging (DSI) from normal individuals to provide the foundation for the detailed mapping of the human connectome; 2) optimize advanced high-field imaging technologies and neurocognitive tests to map the human connectome; 3) collect connectomic, behavioral, and genotype data using optimized methods in a representative sample of normal subjects; 4) design and deploy a robust, web-based informatics infrastructure, 5) develop and disseminate data acquisition and analysis, educational, and training outreach materials.

Proper citation: MGH-USC Human Connectome Project (RRID:SCR_003490) Copy   

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http://www2.mrc-lmb.cam.ac.uk/

The MRC Laboratory of Molecular Biology (LMB) has long been, and remains, a world-class research laboratory. Our primary goal is to understand biological processes at the molecular level, through the application of methods drawn from physics, chemistry and genetics. This quest extends from structural studies of individual macromolecules, through their interactions and beyond to the functioning of subcellular systems, cells and multicellular systems in whole organisms, with the ultimate aim of using this knowledge to tackle specific problems in human health and disease. The LMB is one of the birthplaces of modern molecular biology. Many techniques were pioneered at the laboratory, most notably methods for determining the three-dimensional structure of proteins and DNA sequencing. Whole genome sequencing was initiated at the LMB. Another landmark discovery was the invention of monoclonal antibodies. Over the years, the work of LMB scientists has attracted 9 Nobel Prizes, shared between 13 LMB scientists, as well as numerous other prizes and scientific awards.

Proper citation: MRC Laboratory of Molecular Biology (RRID:SCR_003527) Copy   

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http://altmetrics.org/manifesto/

altmetrics is the creation and study of new metrics based on the Social Web for analyzing, and informing scholarship. No one can read everything. We rely on filters to make sense of the scholarly literature, but the narrow, traditional filters are being swamped. However, the growth of new, online scholarly tools allows us to make new filters; these alt-metrics reflect the broad, rapid impact of scholarship in this burgeoning ecosystem. We call for more tools and research based on alt-metrics. * Tools: Browse a directory of noteworthy altmetrics apps. * Media: Watch videos of altmetrics presentations.

Proper citation: alt-metrics: a manifesto (RRID:SCR_003528) Copy   

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http://ccdb.ucsd.edu/SAO

Ontology that describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules. It is built according to ontology development best practices (re-use of existing ontologies; formal definitions of terms; use of foundational ontologies). It describes the parts of neurons and glia and how these parts come together to define supracellular structures such as synapses and neuropil. Molecular specializations of each compartment and cell type are identified. The SAO was designed with the goal of providing a means to annotate cellular and subcellular data obtained from light and electron microscopy, including assigning macromolecules to their appropriate subcellular domains. The SAO thus provides a bridge between ontologies that describe molecular species and those concerned with more gross anatomical scales. Because it is intended to integrate into ontological efforts at these other scales, particular care was taken to construct the ontology in a way that supports such integration.

Proper citation: Subcellular Anatomy Ontology (RRID:SCR_003486) Copy   

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http://www.msm.edu/Research/research_centersandinstitutes/NI/

The mission of the Morehouse School of Medicine Neuroscience Institute (MSMNI) is to create a supportive and challenging environment for the investigation and teaching of the functional organization of the nervous system, and to seek ways to reduce suffering brought about by neurological disorders. Members of the MSM NI are involved in teaching graduate students, medical students, and health care professionals about researching and treating medical conditions that are caused by or are rooted in the central nervous system. Additionally, MSM NI offers an 8-week Summer Research Program to qualified undergraduate, post-baccalaureate and first-year medical school students. Funding and administrative support were secured from the National Institutes of Health Office on Research for Minority Health and the National Institute for Neurological Disorders and Stroke (NINDS), respectively. The Neuroscience Institute is composed of selected faculty members from the Department of Neurobiology and the Department of Pharmacology at Morehouse School of Medicine who are conducting grant supported research. MSMNI research areas cover a broad range of cellular and molecular neuroscience and include the molecular biology and physiology of circadian rhythm, mechanisms of sleep and sleep disorders, mechanisms of stroke and stroke prevention, photoreceptor and retinal physiology, glutamate receptor physiology and mechanisms of hyperexcitability in epilepsy. Investigators use a variety of experimental preparations including whole animals, the intact portions of the central nervous system, and simplified preparations, such as tissue slices and single cells, to study cellular activities and cell-cell communication under more controlled conditions.

Proper citation: Morehouse School of Medicine Neuroscience Institute (RRID:SCR_003484) Copy   

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http://www.phmtox.msu.edu/

At the Department of Pharmacology & Toxicology at Michigan State University, we combine integrative research, active learning and intellectual enrichment to prepare the student for advancement and leadership in their chosen field. The Department provides courses for undergraduate students, graduate students, medical students of the allopathic, osteopathic and veterinary colleges, and nursing students. In addition, specialized courses of study are offered in areas of professional development and life-long learning. From molecular and cellular levels to organ systems and whole animal models, our graduate and undergraduate programs encompass multiple areas of study, empowering students to challenge the boundaries of knowledge and chart their own unique path in the biomedical sciences. The disciplines of pharmacology and toxicology play a momentous role in human health today, and their applications in the professional world are vast. The department offers: * Pharmacology & Toxicology Graduate Doctoral Program * Online MS Programs ** Online Professional Science Masters in Integrative Pharmacology ** Online Masters in Pharmacology * Undergraduate Courses in Pharmacology & Toxicology * Dual Major Graduate Program in Toxicology (joint Pharmacology & Toxicology/Environmental Toxicology graduate program) * NIGMS Integrative and Organ Systems Pharmacology Short Course * Summer Undergraduate Research Fellowships

Proper citation: Michigan State University, Department of Pharmacology and Toxicology (RRID:SCR_003483) Copy   

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