Tools   Select Another Resource Report Type

http://healthresearchfunding.org/

Health Research Funding is designed to bring researchers with peer-reviewed, worthwhile, unfunded projects together with patient advocacy organizations and other funding sources. Working together, we hope to foster the funding of new research that will provide hope to millions of people in this country with chronic diseases and disabilities. * We invite researchers with promising projects that have been scored but not funded by the NIH to submit their abstracts. By registering, you will be able to search for information about organizations that fund research and their requests for abstracts. * Researchers with proposals that have been peer-reviewed but not funded by a NHC member patient advocacy organization may also register. The National Health Council (NHC) developed this site with input from the National Institutes of Health (NIH), the nation''s medical research agency.

Proper citation: Health Research Funding (RRID:SCR_007790) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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

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

Proper citation: HighSSR (RRID:SCR_007949) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.med.upenn.edu/nscience/

The Department of Neuroscience is located in the School of Medicine at the University of Pennsylvania. Founded in 1992 to recognize the growing importance of neuroscience as a scientific discipline, the Department laboratories pursue a wide variety of research interests reflecting the entire range of modern neuroscience. The Department lies at the heart of the campus-wide Mahoney Institute of Neurological Sciences, the first research organization to receive NIH funding for training in the neurosciences.

Proper citation: University of Pennsylvania Medical Center Neuroscience (RRID:SCR_007978) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://smithlab.usc.edu/histone/rseg/

Software package aimed to analyze ChIP-Seq data, especially for identifying genomic regions and their boundaries marked by diffusive histone modification markers, such as H3K36me3 and H3K27me3.

Proper citation: RSEG (RRID:SCR_007695) Copy   

•   Source: SciCrunch Registry

http://www.buzsakilab.com/

Lab interested in understanding how neuronal circuitries of the brain support its cognitive capacities. Its goal is to provide rational, mechanistic explanations of cognitive functions at a descriptive level. In the lab''s view, the most promising area of cognitive faculties for scientific inquiry is memory, since it is a well-circumscribed term, can be studied in animals and substantial knowledge has accumulated on the molecular mechanisms of synaptic plasticity. Available software: * NeuroScope: NeuroScope can display local field potentials (EEG), neuronal spikes, behavioral events, as well as the position of the animal in the environment. It also features limited editing capabilities. * Klusters: Klusters is a powerful and easy-to-use cluster cutting application designed to help neurophysiologists sort action potentials from multiple neurons on groups of electrodes (e.g., tetrodes or multisite silicon probes). * KlustaKwik: KlustaKwik is a program for automatic cluster analysis, specifically designed to run fast on large data sets. * MATLAB m-files: A selection of MATLAB files developed in the lab., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Buzsaki Lab (RRID:SCR_008020) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/SOY

Growth, trait and development ontology for soybean

Proper citation: Soy Ontology (RRID:SCR_007847) Copy   

•   Source: SciCrunch Registry

http://www.hpid.org

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   

•   Source: SciCrunch Registry

http://www.alzheimers.org.au/

A website which provides in-depth fact sheets on aspects of dementia and dementia care. It provides information on member organizations in each state, support and respite services as well as counseling and education available through Alzheimer's Australia. This organization's vision is for a society committed to the prevention of dementia, while valuing and supporting people living with dementia. Alzheimer's Australia manages a wide range of innovative National Programs which provide information, support, counseling, training and education to people with dementia, their families and carers as well as to professionals working in the dementia field.

Proper citation: Alzheimer's Australia: Living with Dementia (RRID:SCR_008015) Copy   

•   Source: SciCrunch Registry

https://www.har.mrc.ac.uk

UK’s national facility for mouse genetics and use of mouse models for preclinical study of human disease.Offers services to researchers around the world. Services include free archiving of mouse lines to protect them for future use, distribution of mouse lines from the Archive, breeding and phenotyping of genetically altered mice, and genome engineering services to generate new mouse models.Offers archiving and distribution of mouse lines to safeguard germplasm collected from unique strains and make it readily available to the scientific community.

Proper citation: Medical Research Council Harwell: An International Centre for Mouse Genetics (RRID:SCR_008013) Copy   

•   Source: SciCrunch Registry

http://www-bird.jst.go.jp/index_e.html

BIRD''s mission is to aid the progress of bioinformatics and promote creation of new biology, which has computational, deductive, predictive, and theoretical features. (most of this site is in Japanese) To carry out its responsibilities, BIRD: * Promotes appropriate development of bioinformatics research and development, such as what kinds of databases and analysis software should be developed and what kind of computer facilities are needed for that development. * Maintains the computer environment and network and functions as a funding agency to further promotion plans. * Develops basic databases: genome sequence database, protein 3D structure database, gene expression profile database, molecular interaction database, etc. * Conducts and coordinates integration, enhancement, and standardization of the basic databases. * Develops computing tools for analyzing various kinds of biological and experimental data, data mining from databases, computer simulation of living systems and so on. * Develops ontologies necessary for data and knowledge description of databases storing biological functions and integration of the basic databases. * Conducts and coordinates research and development of innovative and creative technologies and theories which move toward understanding life as an information system, especially approaches by collaboration of computer scientists and experimental scientists. * Provides computer facilities for developing databases and software and making them publicly available. * Sets up training courses for teaching utilization of databases and tools for novices in bioinformatics and sponsors scientific meetings. * Provides community space with high performance computing facilities where innovative ideas are cultivated by free discussion and "trial and error" with the computer in order to promote development of young scientists who will create new biological discoveries based on bioinfomatics and become leaders in the field.

Proper citation: BIRD - Bio Info R and D (RRID:SCR_008010) Copy   

•   Source: SciCrunch Registry

http://t1dbase.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 26,2019. In October 2016, T1DBase has merged with its sister site ImmunoBase (https://immunobase.org). Documented on March 2020, ImmunoBase ownership has been transferred to Open Targets (https://www.opentargets.org). Results for all studies can be explored using Open Targets Genetics (https://genetics.opentargets.org). Database focused on genetics and genomics of type 1 diabetes susceptibility providing a curated and integrated set of datasets and tools, across multiple species, to support and promote research in this area. The current data scope includes annotated genomic sequences for suspected T1D susceptibility regions; genetic data; microarray data; and global datasets, generally from the literature, that are useful for genetics and systems biology studies. The site also includes software tools for analyzing the data.

Proper citation: T1DBase (RRID:SCR_007959) Copy   

•   Source: SciCrunch Registry