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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   

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https://rwjms.rutgers.edu/departments/pharmacology/message-from-the-chair

Department of Pharmacology is committed to fulfilling its roles in education, research and service, both locally and on a broader scale. Our faculty contributes to the education of medical, graduate and undergraduate students in the classroom and in the laboratory; carries out research at the forefront of biomedical science while training the next generation of research scientists; and serves the medical school, university, national and international scientific communities.

Proper citation: Rutgers University Robert Wood Johnson Medical School Department of Pharmacology (RRID:SCR_007470) Copy   

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http://www.mcmp.purdue.edu/

The Department of Medicinal Chemistry and Molecular Pharmacology is one of the three departments comprising the School of Pharmacy and Pharmaceutical Sciences. There are currently over 80 graduate students enrolled in the Department, the vast majority of whom are engaged in studies leading to the Ph.D. degree. The presence of approximately 30 postdoctoral associates and other research staff professionals further enriches the intellectual atmosphere. Graduate students in the Department have the opportunity to interact with researchers in a wide variety of fields, including many who are associated with other departments at Purdue. Various research groups actively collaborate with groups from departments such as biochemistry, biological sciences, chemical engineering, chemistry, foods and nutrition, horticulture, and physics. In addition, approximately half of our faculty belong to the Purdue Cancer Center, the Neuroscience Program, the Graduate Program in Virology and/or the Purdue University Biochemistry and Molecular Biology Program (BMB), leading to extensive, formalized interactions campus-wide. Graduate students attend research seminars across campus, -affording the opportunity to observe firsthand many of the world's foremost researchers.

Proper citation: Purdue University School of Pharmacy and Pharmaceutical Sciences Department of Medicinal Chemistry and Molecular Pharmacology (RRID:SCR_007468) Copy   

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http://www.nei.nih.gov/funding/

The National Eye Institute Research funding resource provides notifications of funding opportunities in eye and vision research. National Eye Institute supports the 28 grant mechanisms listed on the site and lists extramural funding data. The National Eye Institute (NEI) was established by Congress in 1968 to protect and prolong the vision of the American people. NEI research leads to sight-saving treatments reduces visual impairment and blindness and improves the quality of life for people of all ages. NEI-supported research has advanced our knowledge of how the visual system functions in health and disease. Vision research is supported by the NEI through approximately 1600 research grants and training awards made to scientists at more than 250 medical centers hospitals universities and other institutions across the country and around the world. The NEI also conducts laboratory and patient-oriented research at its own facilities located on the NIH campus in Bethesda Maryland.

Proper citation: NEI Research Funding (RRID:SCR_007417) Copy   

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http://human.brain-map.org/static/brainexplorer

Multi modal atlas of human brain that integrates anatomic and genomic information, coupled with suite of visualization and mining tools to create open public resource for brain researchers and other scientists. Data include magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), histology and gene expression data derived from both microarray and in situ hybridization (ISH) approaches. Brain Explorer 2 is desktop software application for viewing human brain anatomy and gene expression data in 3D.

Proper citation: Allen Human Brain Atlas (RRID:SCR_007416) Copy   

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http://www.pharmacy.utah.edu/pharmtox/

The Department of Pharmacology and Toxicology at the University of Utah is located in Salt Lake City at the foot of the beautiful Wasatch Range of the Rocky Mountains. Our Department focuses on research, graduate and professional training, and service. The faculty of this department place a high priority on the teaching and research training of graduate students for the Ph.D. degree. Our program features close working relationships between individual students and their faculty mentor, rich and diverse research opportunities, and individualized programs of study based on the needs of the students. Doctoral graduates of our program gain employment in research and teaching positions at colleges and universities, engage in research and development in the biotechnology and pharmaceutical industries, and have additional opportunities in research institutes, government agencies, environmental protection organizations, and many other arenas. Our Summer Undergraduate Research Fellowship (SURF) Program provides enriching research experiences for undergraduate students anticipating research careers in the biological sciences.

Proper citation: University of Utah Salt Lake City Utah. Pharmacology & Toxicology (RRID:SCR_007537) Copy   

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http://www.idars.org/

IDARS is an international scientific organization that promotes and fosters the research and collaboration of scientists around the world in the area of substances of abuse and addiction. Our focus is to foster research in molecular, cellular and systems biology and includes neuropharmacological, neurobehavioral, neurochemical and neuroanatomical themes. The purposes of IDARS are scientific, educational and charitable. We strive to promote excellence in: advancing the understanding of drug abuse, substance abuse and addictions, including the part they play in behaviors of humans and in animal models bringing together scientists of varying backgrounds and disciplines within the field of drug abuse research integrating drug abuse research directed at all levels of biological organization and its translation to improvement in clinical prevention and treatment efforts promoting education in the addiction sciences informing the general public on the results and implications of current research in the addiction sciences promoting other activities that will contribute to the development of addiction sciences IDARS is a 501c3 nonprofit organization.

Proper citation: International Drug Abuse Research Society (RRID:SCR_007411) Copy   

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http://www.neurosci.tufts.edu/

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.

Proper citation: Tufts University Department of Neuroscience (RRID:SCR_007491) Copy   

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https://medicine.tulane.edu/departments/basic-sciences/pharmacology

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.

Proper citation: Tulane University Medical Center Department of Pharmacology (RRID:SCR_007492) Copy   

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http://www.usal.es/webusal/en

Spanish higher education institution, located in the city of Salamanca, west of Madrid, in the autonomous community of Castile and León. It was founded in 1134 and given the Royal charter of foundation by King Alfonso IX in 1218.

Proper citation: University of Salamanca; Salamanca; Spain (RRID:SCR_007833) Copy   

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http://bmserver.sce.ntu.edu.sg/INVERTER/

Software for a de novo exact match tandem repeat finder which main advantage is without the need to specify either the pattern or a particular pattern size, integrated with a data visualization tool and has a built-in user-friendly Graphical User Interface.

Proper citation: INVERTER (RRID:SCR_007956) Copy   

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http://zmf.umm.uni-heidelberg.de/apps/zmf/argonaute/single.php

A database is a of mammalian miRNAs and their known or predicted regulatory targets. It provides information on origin of miRNAs, tissue specificity of their expressions and their known or proposed functions, their potential target genes as well as data on miRNA families based on their co-expression and proteins known to be involved in miRNA processing. This database also contains three other navigation tools that can be used to find information relating to miRNA: 1.) Gene Annotations is an information retrieval system for miRNA target genes. It provides comprehensive information from sequence databases and allows to simultaneously search PubMed with all synonyms of a given gene. 2.) miRNA Motif Finder - Argonaute predicts miRNA motifs binding to the gene sequence of the user. The miRNA mature sequences are taken from Agronaute 2 database. miRNA Motif Finder - Custom predicts miRNA motifs binding to the gene sequence, both the gene sequence and miRNA mature sequences provided by the user. 3.) miRNA Statistics provides statistics for the mature miRNA sequences from Argonaute 2 as well as for the miRNA sequences uploaded by the user. It provides statitics on the individual nucleotide as well as pattern of nucleotides apperaing in the sequence.

Proper citation: ARGONAUTE 2 - A database on mammalian microRNAs and their function in gene and pathway regulation (RRID:SCR_007553) Copy   

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http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

Allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser.

Proper citation: BigWig and BigBed (RRID:SCR_007708) Copy   

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

Software that predicts microsatellites with Tandem Repeats Finder (TRF).

Proper citation: HighSSR (RRID:SCR_007949) Copy   

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http://ekhidna.biocenter.helsinki.fi/sqgraph/pairsdb

This is a web interface for ADDA, an automatic algorithm for domain decomposition and clustering of all protein domain families. We use alignments derived from an all-on-all sequence comparison to define domains within protein sequences based on a global maximum likelihood model. ADDA is downloadable. There are three ways in which you can retrieve a protein sequence and its domains from ADDA. Sequences can be located using sequence identifiers and/or accession numbers, using a identical fragment lookup, or by running BLAST against all sequences in ADDA. ADDA is a protein sequence clustering algorithm. It takes a set of sequences and returns domain families. ADDA has two steps corresponding to the two aspects of the protein sequence clustering domain. First, ADDA splits protein sequences into domains. The idea behind ADDA is in principle the application of Occam''s razor; the goal is to describe the diversity of protein sequences with a minimal set of protein domains. The algorithm behind ADDA approximates this minimal set. In practice ADDA works by looking at where BLAST alignments are located on the sequence and splits the sequences, so that as few as possible alignments are cut by domain boundaries and that as many alignments as possible stretch over complete domains. Secondly, ADDA takes all the domains and then arranges them in a minimum spanning tree, where the similarity between two domains is determined by their relative overlap given a BLAST alignment. Each link in the tree is then checked by a pairwise profile-profile comparison and links below a threshold are removed. The remaining connected components are then taken to represent protein domain families.

Proper citation: ADDA - Automatic Domain Decomposition Algorithm (RRID:SCR_007546) Copy   

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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   

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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   

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http://genotan.sourceforge.net/

A free software tool to identify length variation of microsatellites from short sequence reads.

Proper citation: GenoTan (RRID:SCR_007935) Copy   

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http://enhancer.lbl.gov/

Resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer marks. Central public database of experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to particular tissue, or download entire collections of enhancers with defined tissue specificity or conservation depth.

Proper citation: VISTA Enhancer Browser (RRID:SCR_007973) Copy   

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http://cor.physiol.ox.ac.uk/

Cellular Open Resource is a Microsoft Windows environment for cellular modeling that is built around CellML (except for reactions and metadata which are not supported). It offers, through CellML, an ''out of the box'' access to a large database of single cell models. COR was among the early adopters of this standard, eventually forming the first publicly available CellML-based modeling and collaboration environment. From the onset, COR was designed to provide an environment that could not only be used by experienced modelers, but also by experimentalists, teachers and students. It therefore tries to combine a user-friendly interface with a computationally efficient numerical engine. In this paper, we introduce the philosophy behind COR, explain its user interface and current functionality, including the editing and running of CellML files, highlight lessons learned from user feedback and problems experienced during the development of COR and conclude by exploring future development potential. Sponsors: This study has been supported by a grant from the UK Biotechnology and Biological Sciences Research Council (BB/E024955/1). Keyword: Cell, Model, Cellular, Modeling, Open resource, Microsoft, Environment, Database, Experimentalist, Teacher, Student, Modeler, Computationally, Development,

Proper citation: Cellular Open Resource (RRID:SCR_008022) Copy   

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