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http://medicine.yale.edu/index.aspx

Proper citation: Yale School of Medicine; Connecticut; USA (RRID:SCR_006339) Copy   

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http://www.physionet.org/physiobank/database/sleep-edf/

Sleep EEG dataset from 8 subjects in European Data Format (EDF) including original recordings and their hypnograms as described in B Kemp, AH Zwinderman, B Tuk, HAC Kamphuisen, JJL Obery��. Analysis of a sleep-dependent neuronal feedback loop: the slow-wave microcontinuity of the EEG. IEEE-BME 47(9):1185-1194 (2000). The recordings were obtained from Caucasian males and females (21 - 35 years old) without any medication; they contain horizontal EOG, FpzCz and PzOz EEG, each sampled at 100 Hz. The sc* recordings also contain the submental-EMG envelope, oro-nasal airflow, rectal body temperature and an event marker, all sampled at 1 Hz. The st* recordings contain submental EMG sampled at 100 Hz and an event marker sampled at 1 Hz. The 4 sc* recordings were obtained in 1989 from ambulatory healthy volunteers during 24 hours in their normal daily life, using a modified cassette tape recorder. The 4 st* recordings were obtained in 1994 from subjects who had mild difficulty falling asleep but were otherwise healthy, during a night in the hospital, using a miniature telemetry system with very good signal quality.

Proper citation: Sleep-EDF Database (RRID:SCR_006976) Copy   

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http://alchemy.sourceforge.net/

ALCHEMY is a genotype calling algorithm for Affymetrix and Illumina products which is not based on clustering methods. Features include explicit handling of reduced heterozygosity due to inbreeding and accurate results with small sample sizes. ALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods. It has been developed for and tested on Affymetrix GeneChip Arrays, Illumina GoldenGate, and Illumina Infinium based assays. Primary motivations for ALCHEMY''s development was the lack of available genotype calling methods which can perform well in the absence of heterozygous samples (due to panels of inbred lines being genotyped) or provide accurate calls with small sample batches. ALCHEMY differs from other genotype calling methods in that genotype inference is based on a parametric Bayesian model of the raw intensity data rather than a generalized clustering approach and the model incorporates population genetic principles such as Hardy-Weinberg equilibrium adjusted for inbreeding levels. ALCHEMY can simultaneously estimate individual sample inbreeding coefficients from the data and use them to improve statistical inference of diploid genotypes at individual SNPs. The main documentation for ALCHEMY is maintained on the sourceforge-hosted MediaWiki system. Features * Population genetic model based SNP genotype calling * Simultaneous estimation of per-sample inbreeding coefficients, allele frequencies, and genotypes * Bayesian model provides posterior probabilities of genotype correctness as quality measures * Growing number of scripts and supporting programs for validation of genotypes against control data and output reformating needs * Multithreaded program for parallel execution on multi-CPU/core systems * Non-clustering based methods can handle small sample sets for empirical optimization of sample preparation techniques and accurate calling of SNPs missing genotype classes ALCHEMY is written in C and developed on the GNU/Linux platform. It should compile on any current GNU/Linux distribution with the development packages for the GNU Scientific Library (gsl) and other development packages for standard system libraries. It may also compile and run on Mac OS X if gsl is installed.

Proper citation: ALCHEMY (RRID:SCR_005761) Copy   

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http://clinicaltrials.gov/ct2/show/NCT00248651

Multi-center, randomized, placebo-controlled trial evaluating the tricyclic antidepressant, amitriptyline and the selective serotonin reuptake inhibitor (SSRI), escitalopram to placebo in patients with functional dyspepsia. The purpose of this study is to determine whether amitriptyline and escitalopram are more efficacious than placebo in relief of the symptoms of functional dyspepsia, adjusting for psychological and psychiatric co-morbidities.

Proper citation: Functional Dyspepsia Treatment Trial (RRID:SCR_006691) Copy   

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http://www.ifs.org.uk/ELSA

An interdisciplinary data resource on health, economic position and quality of life as people age. Longitudinal multidisciplinary data from a representative sample of the English population aged 50 and older have been collected. Both objective and subjective data are collected relating to health and disability, biological markers of disease, economic circumstance, social participation, networks and well-being. Participants are surveyed every two years to see how people''s health, economic and social circumstances may change over time. One of the study''s aims is to determine the relationships between functioning and health, social networks, resources and economic position as people plan for, move into and progress beyond retirement. It is patterned after the Health and Retirement Study, a similar study based in the United States. ELSA''s method of data collection includes face-to-face interview with respondents aged 50+; self-completion; and clinical, physical, and performance measurements (e.g., timed walk). Wave 2 added questions about quality of health care, literacy, and household consumption, and a visit by a nurse to obtain anthropometric, blood pressure, and lung function measurements, as well as saliva and blood samples, and to record results from tests of balance and muscle strength. Another new aspect of Wave 2 is the ''Exit Interview'' carried out with proxy informants to collect data about respondents who have died since Wave 1. This interview includes questions about the respondents'' physical and psychological health, the care and support they received, their memory and mood in the last year of their life, and details of what has happened to their finances after their death. Wave 3 data added questions related to mortgages and pensions. The intention is to conduct interviews every 2 years, and to have a nurse visit every 4 years. It also is envisioned that the ELSA data will ultimately be linked to available administrative data, such as death registry data, a cancer register, NHS hospital episodes data, National Insurance contributions, benefits, and tax credit records. The survey data are designed to be used for the investigation of a broad set of topics relevant to understanding the aging process. These include: * health trajectories, disability and healthy life expectancy; * the determinants of economic position in older age; * the links between economic position, physical health, cognition and mental health; * the nature and timing of retirement and post-retirement labour market activity; * household and family structure, social networks and social supports; * patterns, determinants and consequences of social, civic and cultural participation; * predictors of well-being. Current funding for ELSA will extend the panel to 12 years of study, giving significant potential for longitudinal analyses to examine causal processes. * Dates of Study: 2002-2007 * Study Features: Longitudinal, International, Anthropometric Measures * Sample Size: ** 2000-2003 (Wave 1): 12,100 ** 2004-2005 (Wave 2): 9,433 ** 2006-2007 (Wave 3): 9,771 ** 2008-2009 (Wave 4): underway Links * Economic and Social Data Service (ESDS): http://www.esds.ac.uk/longitudinal/about/overview.asp * ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00139#scope-of-study

Proper citation: English Longitudinal Study of Ageing (RRID:SCR_006727) Copy   

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http://www.unisa.it/english/index

Proper citation: University of Salerno; Salerno; Italy (RRID:SCR_007853) Copy   

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http://www.neuro.fsu.edu/

The Program in Neuroscience is an independent research and graduate training program at Florida State University, which is a Carnegie Research I university. The Program includes faculty from the departments of Biological Science, Biomedical Science, Mathematics, and Psychology. Its objective is to promote interdisciplinary basic research into neural processes, including the biological mechanisms underlying behavior, and to provide advanced graduate training leading to the Ph.D. degree in Neuroscience. The program maintains specialized research support services and personnel, and provides special courses and symposia on contemporary neuroscience issues. Each semester the program brings to Florida State prominent neuroscientists who give colloquia and hold informal discussions with graduate students and faculty. Neuroscience, the study of brain and nervous system function, encompasses many of the unanswered questions about the nature of humans and other species. It stakes out a territory along the frontier of human knowledge where research can make a real difference to understanding. Traditionally, the primary emphasis of the FSU program has been on sensory processes. This focus is now supplemented by research and instruction in the biophysics and electrophysiology of excitable cells, neurotransmitter and hormone action, neural development and plasticity, circadian rhythms, feeding and regulatory processes, and the genetic bases of neurobiology and behavior. Broad interdisciplinary training is emphasized in the early years so that students develop skills in approaching research problems with multiple levels of analysis, from molecular to behavioral.

Proper citation: Florida State University Program in Neuroscience (RRID:SCR_007451) Copy   

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http://omicsoft.com/osa/

A fast and accurate alignment tool for RNA-Seq data.

Proper citation: Omicsoft Sequence Aligner (RRID:SCR_005270) Copy   

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http://www.hunter.cuny.edu/

Proper citation: Hunter College; New York; USA (RRID:SCR_005707) Copy   

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http://bc02.iis.sinica.edu.tw/gobu/manual/index.html

Gene Ontology Browsing Utility (GOBU) (GOBU) is a Java-based software program for integrating biological annotation catalogs under an extendable software architecture. Users may interact with the Gene Ontology and user-defined hierarchy data of genes, and then use its plugins to (and not limited to) (1) browse the GO hierarchy with user defined data, (2) browse GO-oriented expression levels in the user data, (3) compute GO enrichment, and/or (4) customize data reporting. A set of classes and utility functions has been established so that a customized program can be made as a plugin or a command-line tool that programmically manipulate the Gene Ontology and specified user data. See the source code repository for examples. Reference Lin WD, Chen YC, Ho JM, Hsiao CD. GOBU: Toward an Integration Interface for Biological Objects. Journal of Information Science and Engineering. 2006 22(1):19-29. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: Gene Ontology Browsing Utility (GOBU) (RRID:SCR_005662) Copy   

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http://clinicaltrials.gov/show/NCT00237081

Clinical study that investigated several hundred families with two or more blood relatives with interstitial cystitis in order to understand the molecular genetic basis of this condition. The study sought to find changes in genes that are found far more commonly in family members who have interstitial cystitis than in those who do not have the disease. Identifying these genes should lead to a better understanding of the cause of interstitial cystitis. This is a national study which is conducted by telephone and mail, and in which participants could participate entirely from their home.

Proper citation: Maryland Genetics of Interstitial Cystitis (RRID:SCR_006992) Copy   

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http://bioinformatics.udel.edu/Research/skategenomeproject

Core facility provides a model for collaborative approaches to use specialized resources and expertise in an integrated process. Core builds on the expertise and resources provided by the Bioinformatics Cores of the five northeastern states that form NECC. The Skate Genome Annotation Workshops and Jamborees offer training and opportunities for faculty and students to work with and annotate genome sequences. Workshops include lectures, tutorials and exercises annotating the genome of the little skate, Leucoraja erinacea.

Proper citation: University of Delaware Skate Genome Project (RRID:SCR_005300) Copy   

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http://www.timelogic.com/catalog/799/velocimapper

Accelerated alignment tool for mapping data from next-generation DNA sequencing systems. It runs on TimeLogic''s newest FPGA-based DeCypher J-Series Similarity Search Engine Accelerator to provide fast and reliable results that significantly outperform software-only or GPU-accelerated alternatives.

Proper citation: VelociMapper (RRID:SCR_005262) Copy   

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http://www.sgn.cornell.edu/bulk/input.pl?modeunigene

Allows users to download Unigene or BAC information using a list of identifiers or complete datasets with FTP., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Sol Genomics Network - Bulk download (RRID:SCR_007161) Copy   

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http://www.nd.edu/

Proper citation: University of Notre Dame; Indiana; USA (RRID:SCR_006191) Copy   

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http://krasnow1.gmu.edu/cn3/L-Neuron/database/

A database of virtually generated anatomically plausible neurons for several morphological classes, including cerebellar Purkinje cells, hippocampal pyramidal and granule cells, and spinal cord motoneurons. It presently contains 542 cells. In the trade neurons collection the database contains an amaral cell archive, neuron morpho reconstructions, and mouse alpha motoneurons. Their collection of generated neurons include motoneurons, Purkinje cells, and hippocampal pyramidal cells.

Proper citation: Virtual NeuroMorphology Electronic Database (RRID:SCR_007118) Copy   

•   Source: SciCrunch Registry

http://owlapi.sourceforge.net/

The OWL API is a Java API and reference implementation for creating, manipulating and serializing OWL Ontologies. The latest version of the API is focused towards OWL 2. The OWLAPI underpins ontology browsing and editing tools and platforms such as SWOOP and Protege4. Note that this API, or any other OWL-based API, can be used without an integrated OWL parser if you download a pre-converted OWL file generated from OBO. See OBO Ontologies List for all OBO ontologies converted to OWL (we do not list the full complement of OWL-based APIs here, only those of direct relevance to GO). The OWL API includes the following components: * An API for OWL 2 and an efficient in-memory reference implementation * RDF/XML parser and writer * OWL/XML parser and writer * OWL Functional Syntax parser and writer * Turtle parser and writer * KRSS parser * OBO Flat file format parser * Reasoner interfaces for working with reasoners such as FaCT++, HermiT, Pellet and Racer Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: OWL API (RRID:SCR_005734) Copy   

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http://eagle-i.ea.vanderbilt.edu/i/00000139-c61a-a13e-b341-4bb480000000

Core facility that provides the following services: Energy Expenditure Assessment, Body Composition Assessment, Physical Activity Assessment. This component of the core utilizes existing institutional resources for measurement of energy balance and provides personnel support that permit assessment of research in energy balance and nutrition assessment.

Proper citation: Vanderbilt Energy Balance Core Laboratory (RRID:SCR_006665) Copy   

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http://linux1.softberry.com/spldb/SpliceDB.html

Database of canonical and non-canonical mammalian splice sites. The information about verified splice site sequences for canonical and non-canonical sites is presented with the supporting evidence. Weight matrices were built for the major splice groups, which can be incorporated into gene prediction programs.

Proper citation: SpliceDB (RRID:SCR_006262) Copy   

•   Source: SciCrunch Registry

http://neurofitter.sourceforge.net

Neurofitter is software for parameter tuning of electrophysiological neuron models. It automatically searches for sets of parameters of neuron models that best fit available experimental data, and therefore acts as an interface between neuron simulators, like Neuron or Genesis, and optimization algorithms, like Particle Swarm Optimization, Evolutionary Strategies, etc.

Proper citation: Neurofitter (RRID:SCR_005843) Copy   

•   Source: SciCrunch Registry