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http://www.nmpdr.org/FIG/wiki/view.cgi
The National Microbial Pathogen Data Resource provides curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma. This edition of the NMPDR includes 47 archaeal, 725 bacterial, and 29 eukaryal genomes with 3,257,100 genetic features, of which 1,338,895 are in FIGfams curated using 616 active subsystems. ''''''Notice to NMPDR Users'''''' - The NMPDR BRC contract ended in December 2009. At that time we ceased maintenance of the NMPDR web resource and data. Bacterial data from NMPDR has been transferred to PATRIC (http://www.patricbrc.org), a new consolidated BRC for all NIAID category A-C priority pathogenic bacteria. NMPDR was a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois.
Proper citation: NMPDR (RRID:SCR_007821) Copy
https://www.mc.vanderbilt.edu/victr/dcc/projects/acc/index.php/Main_Page
A national consortium formed to develop, disseminate, and apply approaches to research that combine DNA biorepositories with electronic medical record (EMR) systems for large-scale, high-throughput genetic research. The consortium is composed of seven member sites exploring the ability and feasibility of using EMR systems to investigate gene-disease relationships. Themes of bioinformatics, genomic medicine, privacy and community engagement are of particular relevance to eMERGE. The consortium uses data from the EMR clinical systems that represent actual health care events and focuses on ethical issues such as privacy, confidentiality, and interactions with the broader community.
Proper citation: eMERGE Network: electronic Medical Records and Genomics (RRID:SCR_007428) Copy
Project focused on cerebral aneurysms and provides integrated decision support system to assess risk of aneurysm rupture in patients and to optimize their treatments. IT infrastructure has been developeded for management and processing of vast amount of heterogeneous data acquired during diagnosis.
Proper citation: aneurIST (RRID:SCR_007427) Copy
A computer-readable format for representing models of biochemical reaction networks in software. It''s applicable to models of metabolism, cell-signaling, and many others. This website is the portal for the global SBML development effort; you can find information about all aspects of SBML.
Proper citation: SBML (RRID:SCR_007422) Copy
http://www.pharmacy.wsu.edu/prospectivestudents/graduateprograms.html
The research-oriented program in pharmacology and toxicology prepares students for careers in independent research and teaching in pharmacology, toxicology and related areas.The research interests of the faculty are very broad and active areas of research include cancer biology, pharmacogenomics, pharmacokinetics, immuno-pharmacology and -toxicology and neuroscience. The diversity in faculty research interests provides students with a solid foundation in many areas of molecular and cellular pharmacology and toxicology and gives them a wide variety of research programs from which a dissertation proposal may be selected.
The curriculum provides exposure of students to virtually all areas of current research in molecular and cellular biochemistry, immunology, molecular biology, pharmacology and toxicology and formal course requirements are flexible to tailor programs to individual needs.Our graduates have been successfully placed in careers in universities and colleges, the pharmaceutical and biotech industries, and in federal and state agencies. The program awards Ph.D. and M.S. degrees.
Proper citation: Washington State University Pullman WA. Pharmacology and Toxicology (RRID:SCR_007543) Copy
http://www.gene-regulation.com/pub/programs.html
In an effort to strongly support the collaborative nature of scientific research, BIOBASE offers access to their tools. Programs that are available through this portal are: * AliBaba 2.1: AliBaba2 is a program for predicting binding sites of transcription factor binding sites in an unknown DNA sequence. Therefore it uses the binding sites collected in TRANSFAC. AliBaba2 is currently the most specific tool for predicting sites. * Boxshade 3.3.1: Pretty Printing and Shading of Multiple-Alignment files. * ClustalW 1.8: ClustalW Multiple Sequence Alignment Program. * Dialign2.0: Multiple Sequence Alignment Program. * F-Match 1.0: F-MATCH is a program for identifying statistically overrepresented Transcription Factor Binding Sites (TFBS) in a set of sequences compared against a control set, assuming a binomial distribution of TFBS frequency. The program reads MATCH output files for the query and control sets. F-Match uses a library of mononucleotide weight matrices from TRANSFAC 6.0 * Match 1.0 Public: Match is designed for searching potential binding sites for transcription factors (TF binding sites) nucleotide sequences. MatchTM uses a library of mononucleotide weight matrices from TRANSFAC 6.0 * molwSearch 1.0: Search for transcription factors with a certain molecular weight. * P-Match 1.0: P-Match is a new tool for identifying transcription factor binding sites (TF binding sites) in DNA sequences. It combines pattern matching and weight matrix approaches thus providing higher accuracy of recognition than each of the methods alone. P-Match uses a library of mononucleotide weight matrices from TRANSFAC 6.0 along with the site alignments associated with these matrices. * Patch 1.0: Search for potential transcription factor binding sites in your own sequences with the pattern search program using TRANSFAC 6.0 public sites. * m2transfac 1.0: m2transfac is a PWM-PWM alignment interface for the TRANSFAC(R) database. For given user motifs, m2transfac reports all non-overlapping pairwise alignments to a TRANSFAC(R) matrix which satisfy a specified threshold. * MatrixCatch 2.7: The MatrixCatch tool is designed for searching potential composite elements (CEs) for transcription factors (TFs) in any DNA sequence, which may be of interest. MatrixCatch uses a library of CE matrix models, which were compiled on a basis of experimentally identified CEs collected in TRANSCOMPEL database and mononucleotide weight matrices for single TF-binding sites collected in TRANSFAC 6.0 public database. * Composite Module Analyst (CMA) 1.0: CMA reads output of Match program and applies a genetic algorithm in order to define promoter models based on the composition of transcription factor binding sites and their pairs. * PolyA Scan 0.000707: Scanning a Sequence for potential Polyadenylation Sites. * ReadSeq 2.0: ReadSeq reads and writes nucleic/protein sequences in various formats. * SignalScan: Analysis of DNA Sequences for known Eukaryotic Signals * SbBlast 1.0: Search Tool for Sequence Search in the S/MARt Binder Database. SbBlast makes use of the BLAST Sequence Similarity Search Tool - Version 2.0.13 (May-26-2000). * SnpFind 0.3: SNPFIND is a tool for searches in the Database of Single Nucleotide Polymorphisms. The search algorithm used for the database search is the BLAST algorithm. * TfBlast 0.1: Search Tool for Sequence Search in the TRANSFAC Factor Table. SbBlast makes use of the BLAST Sequence Similarity Search Tool - Version 2.0.13 (May-26-2000).
Proper citation: Gene Regulation Programs (RRID:SCR_007787) Copy
https://www.schulich.uwo.ca/physpharm/
Research-based medical science department of physiology and pharmacology in the Schulich School of Medicine and Dentistry at the University of Western Ontario that focus on biological processes from the cellular-molecular level to the integrative-systemic level, and on the effects of drugs and environmental agents on these processes. Their areas of research excellence include the physiology and pharmacology of the cardiovascular, neural, reproductive, endocrine and musculoskeletal systems. Several faculty work in the area of developmental biology related to these organ systems. Faculty members in this Department are leaders in nationally-funded collaborative research programs studying skeletal / bone development and biology, heart and vascular biology, cell communication and gap junctions, neural control of vision and movement, and osteoarthritis and pain. Funding from several large infrastructure grants from both national and provincial governments has facilitated the development of state-of-the-art research laboratories and core facilities.
Proper citation: University of Western Ontario London Ontario Canada Physiology and Pharmacology (RRID:SCR_007541) Copy
http://purl.bioontology.org/ontology/CPRO
A uniform core set of data elements (whose formal semantics are captured in OWL) for use in a Computer-Based Patient Record (CPR)
Proper citation: Computer-Based Patient Record Ontology (RRID:SCR_007540) Copy
The GPCRDB is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on G protein-coupled receptors (GPCRs). :The GPCRDB contains data on sequences, ligand binding constants and mutations. In addition, t he system provides computationally derived data such as multiple sequence alignments, homology models, and a series of query and visualization tools. :The GPCRDB is designed to be a data storage medium, as well as a tool to aid biomedical scientists with answering questions by offering a single point of access to many types of data that are integrated and visualized in a user-friendly way. Although most parts of the GPCRDB are self-explanatory, if you have not used this resource before it is adviced that you to take a look at the usage page. Sponsors: This resource is supported by Organon and Unilever, and the NIH. Keywords: G protein, Coupled, receptor, Molecular, Heterogenous, Data, Sequence, Ligand, Mutation, Computational, Software, Alignment, Homology, Model, Visualization, Tool, Biomedical, Scientist, Integration,
Proper citation: G Protein-Coupled Receptor Data Base (RRID:SCR_007419) Copy
https://www.kent.edu/neuroscience
Neuroscience is dedicated to understanding how the brain and nervous system function in health, disease and repair. Neuroscience research at Kent State University is supported by over 50 faculty members from numerous departments and disciplines. Our researchers have a wide range of expertise including behavioral neuroscience, sensory neuroscience, developmental neuroscience and neurodegenerative diseases.
Proper citation: Kent State University Department of Neuroscience (RRID:SCR_007458) Copy
The Neuroscience Training Program at The Johns Hopkins University School of Medicine addresses the broad areas encompassed by modern neuroscience. The purpose of the Program is to train doctoral students for independent research and teaching in neuroscience. It is the goal of the Program to ensure that candidates for the Ph.D. and M.D./Ph.D. degrees obtain a background covering molecular/cellular and systems/cognitive approaches to neuroscience, as well as receive training that brings them to the forefront of research in their particular area of interest. A series of core courses in neuroscience, along with advanced electives, seminar series, laboratory rotations and original independent dissertation research form the Neuroscience Graduate Training Program. The Neuroscience Training Program and the Neuroscience Department are among the oldest in the United States and date back to 1980. The faculty of the Neuroscience Training Program have trained about 250 Ph.D. and M.D./Ph.D. students and 500 postdoctoral fellows over the past ten years. All doctoral candidates receive full tuition remission and a stipend. Research within the department ranges from investigating the development of the nervous system, synaptic plasticity and the molecular and cellular mechanisms of learning and memory to the neural basis of higher brain function such as perception and decision-making. Our faculty are also at the forefront of research into the molecular mechanisms of neurological and psychiatric diseases, including Parkinson''s, Alzheimer''s'' disease, amyotrophic lateral sclerosis (ALS), schizophrenia, depression, drug addiction, mental retardation and autism.
Proper citation: Johns Hopkins University Neuroscience (RRID:SCR_007455) Copy
http://healthsciences.howard.edu/education/colleges/medicine/departments/pharmacology/Overview
The Department of Pharmacology offers programs leading to the Master of Science and Doctor of Philosophy degrees. The primary objective of these programs is to prepare candidates for research and teaching careers. The first few semesters are devoted primarily to core course work designed to give the student a broad background in the fundamental theories and techniques of pharmacology.During this time, the student gains exposure to methods for the solution of research problems by working in the laboratories of various faculty members culminating in a selection of a thesis advisor. The department has spacious laboratories equipped with modern instruments that are used by both faculty and students in such research areas as biochemical, molecular, cardiovascular, autonomic, clinical, and neuropharmacology, drug metabolism, cancer research and toxicology.
Proper citation: Howard University Washington D.C Department of Pharmacology (RRID:SCR_007454) Copy
http://ki.se/ki/jsp/polopoly.jsp?l=en&d=4329
Department of Clinical Neuroscience at Karolinska Institutet conducts research and teaching regarding the function of the brain - from a molecular level to the effect on society. This activity is closely integrated with medical clinics within Stockholm.
Proper citation: Karolinska Institute Department of Clinical Neuroscience (RRID:SCR_007456) Copy
The establishment of the Neuroscience Center at Dartmouth (NCD) in 2002 has produced a new and unique interdisciplinary group whose mission is to foster collaborative and interactive research and education in the neurosciences. Training opportunities in neuroscience include undergraduate minor/major in Neuroscience, graduate training toward a Ph.D., and postdoctoral training. The NCD draws from the strengths in three key areas: Clinical, Cognitive & Behavioral, and Molecular/Cellular/Systems Neuroscience. It is the vision of its researchers to produce and disseminate new knowledge, and in doing so train and educate the next generation of neuroscientists. Interactions among members of the neuroscience community are enhanced and foster a highly interactive atmosphere through the development of this integrated Center. By promoting multidisciplinary efforts in both basic and applied research, the Center''s scientists will contribute to human health and well being by increasing our understanding of the mechanisms underlying nervous system function, both in health and disease. This will lead to valuable discoveries that translate into novel pharmaceutical agents and therapeutic approaches for the treatment of a variety of central nervous system diseases and disorders. The research facilities are located in Hanover, NH, Lebanon, NH (Dartmouth-Hitchcock Medical Center) and the Veteran Affairs Medical Center in White River Junction, Vt. Research interests comprise a broad range of studies within the neurosciences and provide a wide range of research opportunities for students. In addition, the NCD augments the education of residents and fellow at the clinical level who have academic neuroscience interests.
Proper citation: Dartmouth Medical School Neuroscience (RRID:SCR_007449) Copy
Database that provides human protein interaction information and integrated interaction and also finds proteins from databases that can potentially react with proteins submitted by users. The human protein interaction information was pre-computed by a statistical method from existing structural and experimental data, while the integrated human protein interactions are derived from BIND, DIP and HPRD. A score composed of three parts is assigned to the predicted interaction data, and those interactions with high scores were found reliable. HPID allows the user to use the protein IDs in EMBL, Ensembl, MIM, RefSeq, HPRD and NCBI to search protein interactions of interest. A set of web-based software tools has also been developed so that users can visualize and analyze protein interaction networks.
Proper citation: HPID - Human Protein Interaction database (RRID:SCR_007724) Copy
http://www.pharmacy.umaryland.edu/graduate/psc/
The School of Pharmacys Department of Pharmaceutical Sciences has a rapidly expanding research program in the areas of cellular and molecular biology, chemistry, neuroscience and pharmacology, biopharmaceutics and drug delivery and clinical pharmaceutical sciences. Faculty and graduate students in the Department of Pharmaceutical Sciences are organized into Research Areas. The mission of the graduate program is to foster individual and collaborative research, faculty growth, and a graduate student education which provides a strong, broad background in the drug development process along with intensive expertise in a focal research area of the pharmaceutical sciences. The department also provides opportunities to conduct research in the area of Clinical Pharmaceutical Sciences. This is one of only 4 such programmatic themes of its kind in the U.S. This program is a collaborative effort between the departments of Pharmacy Practice and Science and Pharmaceutical Sciences in the School of Pharmacy. The clinical pharmaceutical research scientists trained by this program will be well-suited to meet the demand expressed by federal agencies (FDA, NIH), academia, and the pharmaceutical industry, with the potential to develop new therapeutic strategies to optimize patient care in Maryland, the U.S., and worldwide.
Proper citation: University of Maryland School of Pharmacy, Pharmaceutical Sciences Graduate Program (RRID:SCR_007513) Copy
http://www.louisville.edu/medschool/pharmacology/
The Department of Pharmacology & Toxicology in the School of Medicine at the University of Louisville focuses upon the interaction of drugs and other chemicals with biological systems ranging from individual molecules, to cells, to tissues, to organ systems or individuals. The two disciplines are a continuum incorporating the therapeutic to toxic effect of every drug and chemical. Our departmental programs incorporate pharmacology and/or toxicology, and graduates are well trained to accept employment in either or both disciplines. Our research and curriculum incorporate molecular biology, genetics, neuroscience, biochemistry, physiology and other biomedical sciences, providing maximum flexibility for our graduates.
Proper citation: University of Louisville, Department of Pharmacology (RRID:SCR_007510) Copy
http://purl.bioontology.org/ontology/HCPCS
Ontology for the healthcare common procedure coding system.
Proper citation: Healthcare Common Procedure Coding System (RRID:SCR_007598) Copy
https://renaissance.stonybrookmedicine.edu/neurology
The Department of Neurology has a commitment to teaching, clinical care, and research. They include divisions of Clinical Neurophysiology (with training in EEG and EMG, including inpatient and outpatient monitoring facilities, intraoperative monitoring, and access to a sleep laboratory), Neuropsychology (both adult and pediatrics), Child Neurology (including special interest groups in Epilepsy, Developmental Disabilities, Pediatric AIDS, and Autism), and Vascular Neurology (with an accredited training program, board certified faculty, close cooperation with Vascular Surgery, Interventional Radiology, and Cardiology, and an emphasis on clinical trials and neuroimaging research). They have a very strong program in Multiple Sclerosis/Neuroimmunology (including multiple clinical trials, Neuroimaging research, the only Pediatric MS Center in the country, and a focus on gender issues in MS). They also have strong programs in Neuromuscular Disease (with a particular interest in ALS, and nerve/muscle biopsies), Neurologic Infections (with a particular interest in emerging pathogens), Parkinson's Disease, Neurorehabilitation, and Behavioral Neurology.
Proper citation: SUNY Stony Brook Department of Neurology Stony Brook NY (RRID:SCR_007479) Copy
http://neurology.stanford.edu/
The Department of Neurology and Neurological Sciences offers comprehensive evaluation and treatment of adults and children with neurological disorders. Clinical programs include general neurology, epilepsy, stroke, movement disorders, memory disorders, multiple sclerosis, neuromuscular diseases, neuro-oncology, neurophysiology, and child neurology. Their educational programs offer outstanding residency training in adult and child neurology and post-residency fellowship training in many neurological subspecialties. Many current faculty members are international leaders in their field. Included among its former trainees and faculty are many department chairs and other leaders in American neurology. The Department provides care and consultative services to patients referred from throughout California and from throughout the nation. The combination of recent and current enhanced development of clinical facilities at Stanford and its allied medical centers along with continued robust population growth in Northern California and the Bay Area provides a remarkable breadth and depth of clinical neurology experience. Research in the Department of Neurology and Neurological Sciences covers a wide range of multidisciplinary programs ranging from basic neuroscience studies, preclinical studies and clinical trials. In addition, Stanford is well known for its outstanding neuroscience community. The outstanding academic milieu at Stanford along with cutting edge programs promoting multidisciplinary research makes possible an exceptional degree of research integration that links Department faculty members and trainees with those from multiple schools and departments, each with major national stature, across the Stanford campus. The Department has a particularly rich tradition of integrating cutting edge advances in basic science with novel clinical approaches.
Proper citation: Stanford University School of Medicine Neurology and Neurological Sciences (RRID:SCR_007478) Copy
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