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http://ki.se/ki/jsp/polopoly.jsp?d=29328&a=31530&l=en

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Longitudinal Assessment of Clinical Course and BIOmarkers in severe Chronic AIRway Disease (BIOAIR) is a study within the European Network For Understanding Mechanisms Of Severe Asthma (ENFUMOSA). BIOAIR study involves studies of severe asthma. The 10% of all asthmatics who have the most difficult disease has a 5-year survival in level with severe cancer diseases, as well as account for half of the costs to society of asthma. Mechanisms for the development of severe asthma, however, is unknown. BIOAIR the project characterizes clinical Phenotype and biomarkers in a study involving 12 centers in nine European countries. In a longitudinal study comparing severe asthmatics with mild asthmatics and patients with COPD (Chronic obstructive pulmonary disease). Clinical data and medicine consumption are collected daily in over a year with the help of modern IT technology. Blood tests, urine samples, upphostningsprover and bronkialbiopsier are collected repeatedly and tested for a wide range of possible pathogenetic factors, including genotype.

Proper citation: BIOAIR - BIOmarkers in severe Chronic AIRway Disease (RRID:SCR_006007) Copy   

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http://ki.se/ki/jsp/polopoly.jsp?d=29328&a=31532&l=en

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Longitudinal studies that consist of more than 40 000 subjects that have been followed since 1986 to be used in studies on how hereditary factors influence the development and progression of Chronic Obstructive Pulmonary Disease (COPD). Its overall objective to find ??tg??rdbara determinants of especially asthma and COPD but also allergy and OSAS (obstructive sleep apnea syndrome). Research is carried out in two huvudforskningslinger; population studies among adults of asthma, allergies, COPD, chronic bronchitis and OSAS. The second main line of longitudinal studies on asthma and allergies among schoolchildren with measurement of incidence, remission and morbidity. The study followed annually all 3500 schoolchildren since 1996 when they went in first and second class in Kiruna, Lulea and Pitea. In addition to questionnaire studies contained in methods, as well as in the adult studies, mainly respiratory function, BMI, skin prick test and clinical interview. Main fragestallningen of risk factors for incident asthma and allergy.

Proper citation: OLIN - Obstructive Lung disease in Northern Sweden (RRID:SCR_006009) Copy   

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http://ki.se/ki/jsp/polopoly.jsp?d=29354&a=36389&l=en

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 2, 2016. The Swedish twin registry has recently examined all twins in Sweden born between 1959-1985. 25,000 individuals participated in the study. The twins had to implement a Web-based survey on the Internet or a telephone interview where we had to answer questions about, among other things, about the diseases they have, or have had, behaviors, eating and drinking habits, smoking habits, etc. The aim of the study is to extend the information in the Swedish twin registry. Our goal with twin studies are, inter alia, to study the relative importance of the heritage and environment for the emergence of various diseases. The responses from the study is currently the basis for a number of analyses regarding how inheritance and environment affects disease and tobacco habits. Currently third follow-up STAGE where 10,000 twins that had previously taken part are contacted again. The purpose of alteplase randomized controlled trials is to follow up the same individuals one year after the first and second questionnaire replies were received to see if anything has changed. The issues we are interested in the follow-up to include changes in general health, working and living situation, your weight, smoking habits, etc. Study Results The results we have so far come to and which we can present here are figures on the prevalence of certain diseases. The figures give a rough estimate of the incidence of these diseases will look for all individuals, born in Sweden in 1959-1985. The figures are based on the questions on the questionnaire which the twins themselves had to answer whether they have or have had various diseases.

Proper citation: KI Biobank - STAGE (RRID:SCR_006004) Copy   

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http://www.blast2go.com/b2ghome

An ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. Blast2GO (B2G) joins in one universal application similarity search based GO annotation and functional analysis. B2G offers the possibility of direct statistical analysis on gene function information and visualization of relevant functional features on a highlighted GO direct acyclic graph (DAG). Furthermore B2G includes various statistics charts summarizing the results obtained at BLASTing, GO-mapping, annotation and enrichment analysis (Fisher''''s Exact Test). All analysis process steps are configurable and data import and export are supported at any stage. The application also accepts pre-existing BLAST or annotation files and takes them to subsequent steps. The tool offers a very suitable platform for high throughput functional genomics research in non-model species. B2G is a species-independent, intuitive and interactive desktop application which allows monitoring and comprehending the whole annotation and analysis process supported by additional features like GO Slim integration, evidence code (EC) consideration, a Batch-Mode or GO-Multilevel-Pies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: Blast2GO (RRID:SCR_005828) Copy   

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http://ki.se/en/meb/the-child-and-adolescent-twin-study-in-sweden-catss

Data and biomaterial from a study investigating how both genetic and environmental effects influence health and behavior in children and adolescents. In this study parents to all Swedish twins turning 9 or 12 years are asked to complete a telephone interview concerning the health and behavior of their twins. The interview screens for several different health (e.g., asthma, allergies, diabetes) and behavior (e.g., attention, social interaction) problems. Some of the families will be followed up with additional questionnaires, as well as with genotyping and clinical interviews. The response frequency of the telephone interview is 80%. By November 2008, 7408 interviews had taken place. Types of samples * Saliva alt. EDTA whole blood * DNA Number of sample donors: 10 721 (June 2010)

Proper citation: CATSS - Child and Adolescent Twin Study in Sweden (RRID:SCR_005945) Copy   

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http://ki.se/ki/jsp/polopoly.jsp?d=29354&a=66742&l=en

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 03, 2014. A study that is a follow-up of the CATSS study and includes 15-year old twins who have been identified with autism, ADHD, learning-, eating-, tics disorders, compulsion-, defiance-, conduct- or motor control problems. The study also includes the co-twin, controls and the parents. DNA will be collected from the twins and the parents. For the twins, both a saliva sample and capillary blood samples will be collected, and for the parents, a saliva sample will be collected. Types of samples * Saliva alt. capillary blood * DNA Number of sample donors: 764 (June 2010)

Proper citation: DOGSS (RRID:SCR_005946) Copy   

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http://code.google.com/

Developer tools, APIs and resources. Search developers.google.com and code.google.com.

Proper citation: Google Code (RRID:SCR_005786) Copy   

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http://ccr.coriell.org/Sections/Collections/HuREF/?SsId=78

The Human Reference Genetic Material Repository makes available DNA from a single individual, J. Craig Venter, whose genome has been sequenced and assembled. The DNA samples are prepared from a lymphoblastoid cell line established at Coriell Cell Repositories from a sample of peripheral blood. The DNA samples are available in 50 microgram aliquots. The lymphoblastoid cell line is not available for distribution. The human DNA sample provided is that of J. Craig Venter whose DNA from white blood cells and sperm was sequenced using Sanger chemistry (ABI Capillary Electrophoresis Platforms 3700 and 3730xl), assembled using the Celera Assembler and was published in PLoS Biology . J. Craig Venter, born on 14 October 1946, is a Caucasian male of self-reported European-American ancestry. The data available on this sample, whose genome assembly is referred to as HuRef, includes: * Whole Genome Shotgun Sequencing data * Sequence trace set deposited by JCVI in the NCBI trace archive * Human Genome Browser displaying sequence assembly, DNA variants and gene annotations Additional data sets from this study include: * Full set of Sanger reads used for genome assembly * SNP and insertion/deletion variant on the human genome sequence coordinates (NCBI version 36) * Affymetrix 500K GeneChip data * Illumina HumanHap650Y Genotyping BeadChip data Given the amount of data publicly available the genomic content of this sample, HuRef will be useful as a reference for many genetic studies.

Proper citation: Human Reference Genetic Material Repository (RRID:SCR_004693) Copy   

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http://www.sanger.ac.uk/resources/software/alien_hunter/

Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. An IVOM approach exploits compositional biases using variable order motif distributions and captures more reliably the local composition of a sequence compared to fixed-order methods. Optionally the predictions can be parsed into a 2-state 2nd order Hidden Markov Model (HMM), in a change-point detection framework, to optimize the localization of the boundaries of the predicted regions. The predictions (embl format) can be automatically loaded into the freely available Artemis genome viewer.

Proper citation: Alien hunter (RRID:SCR_004575) Copy   

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http://www.well.ox.ac.uk/platypus

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software tool designed for efficient and accurate variant detection in high throughput sequencing data. Haplotype based variant caller for next generation sequence data.

Proper citation: Platypus (RRID:SCR_005389) Copy   

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http://www.uthouston.edu/uth-big/Projects/BioBank.htm

The University of Texas Health Science Center at Houston (UTHealth) Clinical and Translational Sciences (CCTS) BioBank employs a federated rather than a centralized model which encourages participation by sample owners who are concerned about guaranteeing their ownership of samples and sample information about patients, samples and related clinical data. In a federated model, individual sites agree on shared policies and procedures for data and sample sharing and oversight. Samples remain with and are governed by the contributing principal investigator at each site. The contributing investigator has final authority whether or not to collaborate or to release samples to qualified researchers. The goal of SLED (Sample Location and Enhanced Distribution) is to help researchers overcome two of the biggest obstacles preventing their research from beginning: 1) location of samples and related data, and 2) requesting of samples and related data. Prior to SLED''s inception the existing system was limited to providing links to samples and data and relying on phone calls to sample owners to facilitate sharing. Collaboration between the CTSA Biobank Consortium and the informatics team at the University of Texas School of Biomedical Informatics is ongoing during this effort. The initial design was constructed using best practices offered by NIH, NCI, and other biobank industry leaders to support and to improve synergy and interaction among various research efforts. Through SLED, researchers will be able to search for samples using a variety of criteria including availability, clinical data, consent criteria, patient demographics, patient diagnoses, study data, and sample type at local and national biobank sites.

Proper citation: UTHealth BioBank (RRID:SCR_004570) Copy   

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http://www.spaintechnology.com/biotech/news/hiv-biobank.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 15, 2011. The Spanish HIV BioBank was created with the objectives of processing, storing and providing distinct samples from HIV/AIDS patients, categorized according to strictly defined characteristics, free of charge to research projects. Strict compliance to ethical norms is always guaranteed. HIV BioBank possesses nearly 50,000 vials containing different prospective longitudinal study sample types. More than 1,700 of these samples are now used in 19 national and international research projects. (2009) The HIV BioBank represents a novel approach to HIV research that might be of general interest not only for basic and clinical research teams working on HIV, but also for those groups trying to establish large networks focused on research on specific clinical problems. It also represents a model to stimulate cooperative research among large numbers of research groups working as a network on specific clinical problems. The HIV BioBank is able to very efficiently release samples to different research project not only in Spain but also in other countries.

Proper citation: HIV Biobank (RRID:SCR_004691) Copy   

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http://www.uni-bonn.de/~umt70e/soft.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5th,2023. Software application that calculates the sample size required for obtaining a prescribed power against a specified alternative for TDT. (entry from Genetic Analysis Software)

Proper citation: TDTPOWER (RRID:SCR_005021) Copy   

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http://www.gotaxexplorer.de/

The Functional Similarity Search Tool (FSST) has been implemented for comparing user defined sets of annotated entities. FSST supports the computation of functional similarity scores based on an individual ontology and of combined scores. Its multi-threaded Java implementation takes advantage of symmetric multi-processing computers, decreasing runtime considerably. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: FSST - Functional Similarity Search Tool (RRID:SCR_005819) Copy   

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http://www.mssm.edu/research/institutes/institute-for-personalized-medicine/biobank

The Mount Sinai Biobank is a large collection of DNA and plasma samples that are stored in a way that protects patients'' privacy while allowing research to be performed on de-identified clinical information from Mount Sinai''s data warehouse system. The Biobank''s goal is to acquire samples from a total of 100,000 donors over a period of several years. Mount Sinai is one of only a handful of places nationwide establishing biobanks on such a large scale. Funded by the Charles R. Bronfman Institute for Personalized Medicine, the Biobank project is a research project that is approved by the Mount Sinai Institutional Review Board and is continuously reviewed. Biobank Facts: * 17947 donors between 18 and 89 years of age have already participated in Biobank. * 194111 aliquots of DNA and * 212005 aliquots of plasma are available for future research.

Proper citation: Mount Sinai Biobank (RRID:SCR_004845) Copy   

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http://ki.se/ki/jsp/polopoly.jsp?d=29354&a=31618&l=en

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The aim of the study is to estimate the importance of genetic (primary) and environmental factors for economic behavior by conducting a series of standard behavioral economics experiments on a sample of twins from the Swedish Twin Registry.

Proper citation: KI Biobank - Economical Behavior (RRID:SCR_005934) Copy   

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http://od1n.sourceforge.net

A C++ software framework to develop, simulate and run magnetic resonance sequences on different platforms.

Proper citation: Object-Oriented Development Interface for NMR (RRID:SCR_005974) Copy   

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https://eyegene.nih.gov

National network of research laboratories for genetic testing of eye disease. They offer testing for affected individuals coupled to registry of clinical information available through patient registry. Large data set for investigators to identify additional genetic risk factors and to explore relationship between genetic disease (genotype) and its clinical manifestation (phenotype).

Proper citation: eyeGENE (RRID:SCR_004523) Copy   

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http://www.biological-networks.org/p/outliers/

Software that performs a morphology-based approach for the automatic identification of outlier neurons based on neuronal tree structures. This tool was used by Zawadzki et al. (2012), who reported on and its application to the NeuroMorpho database. For the analysis, each neuron is represented by a feature vector composed of 20 measurements, which are projected into lower dimensional space with PCA. Bivariate kernel density estimation is then used to obtain a probability distribution for cells. Cells with high probabilities are understood as archetypes, while those with the small probabilities are classified as outliers. Further details about the method and its application in other domains can be found in Costa et al. (2009) and Echtermeyer et al. (2011). This version requires Matlab (Mathworks Inc, Natick, USA) and allows the user to apply the workflow using a graphical user interface.

Proper citation: DONE: Detection of Outlier NEurons (RRID:SCR_005299) Copy   

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http://www.rand.org/labor/FLS/IFLS.html

A dataset of an on-going multi-level longitudinal survey in Indonesia that collects extensive information on socio-economic and demographic characteristics of respondents, as well as extremely comprehensive interviews with local leaders about community services and facilities. The survey is ideally suited for research on topics related to important dynamic aging processes such as the transition from self-sufficiency to dependency, the decline from robust health to frailty, labor force and earning dynamics, wealth accumulation and decumulation, living arrangements and intergenerational transfers. The first wave of IFLS was fielded in 1993 and collected information on over 30,000 individuals living in 7,200 households. The sample covers 321 communities in 13 provinces in Indonesia and is representative of about 83% of the population. These households were revisited in 1997 (IFLS2), 2000 (IFLS3), and 2007-8 (IFLS4). A 25% sub-sample of households was re-interviewed in 1998 (IFLS2+). Special attention is paid to the measurement of health, including the measurement of anthropometry, blood pressure, lung capacity, a mobility test and collection of dry blood spots by a nurse or doctor. In addition to comprehensive life history data on education, work, migration, marriage and child bearing, the survey collects very detailed information on economic status of individuals and households. Links with non co-resident family members are spelled out in conjunction with information on borrowing and transfers. Information is gathered on participation in community activities and in public assistance programs. Measurement of health is a major focus of the survey. In addition to detailed information about use of private and public health services along with insurance status, respondents provide a self-reported assessment of health status. Detailed information on the local economy and prices of goods and services are also collected. These data may be matched with the individual and household-level data. Considerable attention has been placed on minimizing attrition in IFLS. In each re-survey, about 95% of households have been re-contacted. Around 10-15% of respondents have moved from the location in which they were interviewed in the previous wave. In addition, individuals who split-off from the original households have been followed. They have added around 1,000 households to the sample in 1997 and about 3,000 households in 2000. Data Availability: IFLS1 data are available through ICPSR as study number 6706. Data from subsequent waves of the IFLS can be accessed from the RAND project Website. * Dates of Study: 1993-2008 * Study Features: Longitudinal, International, Anthropometric Measures, Biomarkers * Sample Size: ** 1993: 22,000 (IFLS1) ** 1997: 33,000 (IFLS2) ** 1998: 10,000 (IFLS2+) ** 2000: 37,000 (IFLS3) ** 2008: 44,103 (IFLS4) Links: * IFLS1 ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/06706 * IFLS ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00184

Proper citation: Indonesia Family Life Survey (RRID:SCR_005695) Copy   

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