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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   

•   Source: SciCrunch Registry

http://ugene.unipro.ru/

A multiplatform open-source software to assist molecular biologists without much expertise in bioinformatics to manage, analyze and visualize their data. UGENE integrates widely used bioinformatics tools within a common user interface. The toolkit supports multiple biological data formats and allows the retrieval of data from remote data sources. It provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees and 3D structures. Most of the integrated algorithms are tuned for maximum performance by the usage of multithreading and special processor instructions. UGENE includes a visual environment for creating reusable workflows that can be launched on local resources or in a High Performance Computing (HPC) environment. UGENE is written in C++ using the Qt framework. The built-in plugin system and structured UGENE API make it possible to extend the toolkit with new functionality.

Proper citation: Unipro UGENE (RRID:SCR_005579) 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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http://publications.nigms.nih.gov/computinglife/

An NIGMS magazine that showcases the exciting ways that scientists are using the power of computers to expand our knowledge of biology and medicine. From text messaging friends to navigating city streets with GPS technology, we''re all living the computing life. But as we''ve upgraded from snail mail and compasses, so too have scientists. Computer advances now let researchers quickly search through DNA sequences to find gene variations that could lead to disease, simulate how flu might spread through your school and design three-dimensional animations of molecules that rival any video game. By teaming computers and biology, scientists can answer new and old questions that could offer insights into the fundamental processes that keep us alive and make us sick. This booklet introduces you to just some of the ways that physicists, biologists and even artists are computing life. Each section focuses on a different research problem, offers examples of current scientific projects and acquaints you with the people conducting the work. You can follow the links for online extras and other opportunities to learn aboutand get involved inthis exciting new interdisciplinary field.

Proper citation: NIGMS Computing Life (RRID:SCR_005850) Copy   

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http://www.thomaskoenig.ch/Lester/ibaspm.htm

The aim of this work is to present a toolbox for structure segmentation of structural MRI images. All programs were developed in MATLAB based on a widely used fMRI, MRI software package, SPM99, SPM2, SPM5 (Wellcome Department of Cognitive Neurology, London, UK). Other previous works have developed a similar strategy for obtaining the segmentation of individual MRI image into different anatomical structures using a standardized Atlas. Have to be mentioned the one introduced by Montreal Neurological Institute (MNI) that merges the information coming from ANIMAL (algorithm that deforms one image (nonlinear registration) to match previously labelled) and INSECT (Cerebral Tissue Classification) programs for obtaining a suitable gross cortical structure segmentation (Collins et al, 1999). Here both, nonlinear registration and gray matter segmentation processes have been performed through SPM99, SPM2, SPM5 subroutines. Three principal elements for the labeling process are used: gray matter segmentation, normalization transform matrix (that maps voxels from individual space to standardized one) and MaxPro MNI Atlas. All three are combined to yield a good performance in segmenting gross cortical structures. The programs here can be used in general for any standardized Atlas and any MRI image modality. System Requirements: 1. The IBASPM graphical user interface (GUI) runs only under MATLAB 7.0 or higher. The non-graphical version runs under MATLAB 6.5 or higher. 2. Statistical Parametrical Mapping Software SPM2, SPM5 Main Functions: * Atlasing: Main function ( This file contains spm_select script from SPM5 toolbox and uigetdir script from MATLAB 7.0 ). * Auto_Labeling : Computes individual atlas. * Create_SPAMs : Constructs Statistical Probability Anatomy Maps (SPAMs). * Create_MaxProb : Creates Maximum Probability Atlas (MaxPro) using the SPAMs previously computed. * All_Brain_Vol : Computes whole brain volume masking the brain using the segmentation files (if the segmentation files does not exist it segments). * Struct_Vol : Computes the volume for different structures based on individual Atlas previously obtained by the atlasing process. * Vols_Stats : Computes mean and standard deviation for each structure in a group of individual atlases.

Proper citation: IBASPM: Individual Brain Atlases using Statistical Parametric Mapping Software (RRID:SCR_007110) Copy   

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http://www.birncommunity.org/tools-catalog/gradient-non-linearity-distortion-correction/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software tool to correct gradient non-linearity distortions in MR structural images. This correction improves test-retest reproducibility crucial for multi-site studies.

Proper citation: Gradient Non-linearity Distortion Correction (RRID:SCR_007350) Copy   

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http://ki.se/ki/jsp/polopoly.jsp?d=29358&a=31596&l=en

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. So far there is only limited knowledge about possible genetic influences in acute spinal cord injuries (SCI). In this project DNA is collected prospectively from persons with SCI admitted to the acute SCI rehabilitation unit of the Karolinska University Hospital. Trauma is the cause of injury in a majority of the patients. Other causes of injury are spinal abscesses, tumors or spinal infarctions. The aim of the project is to create a sufficiently large DNA biobank with samples from 200-400 individuals from clinically well characterized patients to allow for studies of association between candidate genes and clinical outcome parameters.

Proper citation: KI Biobank - SCI (RRID:SCR_005849) Copy   

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http://www.bcgsc.ca/platform/bioinfo/software/alea

A computational software toolbox for allele-specific (AS) epigenomics analysis. It incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. It provides a customizable pipeline of command line tools for AS analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. ALEA takes advantage of the available genomic resources for human (The 1000 Genomes Project Consortium) and mouse (The Mouse Genome Project) to reconstruct diploid in-silico genomes for human or hybrid mice under study. Then, for each accompanying ChIP-seq or RNA-seq dataset, it generates two Wiggle track format (WIG) files from short reads aligned differentially to each haplotype.

Proper citation: ALEA (RRID:SCR_006417) Copy   

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http://www.incf.org/newsroom

Find all news and updates about INCF and neuroinformatics in the International Neuroinformatics Coordinating Facility (INCF) Newsroom.

Proper citation: INCF Newsroom (RRID:SCR_006493) Copy   

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http://www.vivo.colostate.edu/molkit/index.html

The Molecular Toolkit is a group of programs for analysis and manipulation of nucleic acid and protein sequence data. The programs are written in Java (1.0) and require that your browser support this language. Also, it''s best if your monitor supports a screen resolution of at least 800x600. Nucleic Acid Analysis and Manipulation Programs: *Dot Plots - Examine the similarity of two DNA (or RNA) sequences by production of a similarity matrix displayed as a dot plot. *Manipulate and Display Sequences - Perform simple manipulations on a DNA sequence (inverse, complement, inverse-complement, double-stranded etc). *Restriction Maps - Generate graphical and text-based maps for restriction endonuclease cleavage of DNA. *Translate - Translate a DNA or RNA sequence and obtain graphical and text depictions of the resulting protein sequences. Protein Analysis Programs *Reverse Translate - Reverse translate a protein sequence into DNA. *Protein Composition - Obtain the amino acid composition of a protein. *Hydrophobicity Plots - Plot hydrophobic and hydrophilic domains of a protein.

Proper citation: Molecular Toolkit (RRID:SCR_007068) Copy   

•   Source: SciCrunch Registry

http://ki.se/ki/jsp/polopoly.jsp?d=29332&a=103697&l=en

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. Recently it has been discovered that specific Single Nucleotide Polymorphisms (SNPs) may elevate the risk of developing prostate cancer. This study aims at investigating whether it is possible to use these SNPs in a clinical setting in order to sharpen the diagnostic tools when investigating if a man has prostate cancer. By collecting blood from men who have undergone a needle biopsy of the prostate and do a SNP analysis of their genes and compare this with the result of the biopsy and PSA result we hope to be able to develop a test that is more specific than the routine that is being used today. Sample types: * EDTA whole blood * DNA Number of sample donors: 5321 (June 2010)

Proper citation: SPSAC - Stockholm PSA Cohort (RRID:SCR_006042) Copy   

•   Source: SciCrunch Registry

http://ki.se/ki/jsp/polopoly.jsp?d=29346&a=103574&l=en

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 2, 2016. Cardiovascular disease and periodontitis are common diseases, causing considerable suffering and costs. Despite strong links between the two diseases it is unclear if periodontitis causes cardiovascular disease. The primary aims are to investigate whether periodontitis is a risk factor for the development of myocardial infarction and if periodontitis increases the risk for new cardiovascular events such as myocardial infarction, stroke and death in patients with a previous myocardial infarction. PAROKRANK is a case control study. Cases (n=1500) are patients with a first myocardial infarction and controls population derived people without cardiovascular disease(n=1500). Both groups are subjected to predefined dental examinations, analyses of a variety of risk factors and a biobank of blood and dental samples will be established. Information is collected from available registries (RIKS-HIA and SEPHIA) and study specific records.

Proper citation: KI Biobank - PAROKRANK (RRID:SCR_006045) Copy   

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http://www.sanger.ac.uk/Projects/D_rerio/zmp/

Create knockout alleles in protein coding genes in the zebrafish genome, using a combination of whole exome enrichment and Illumina next generation sequencing, with the aim to cover them all. Each allele created is analyzed for morphological differences and published on the ZMP site. Transcript counting is performed on alleles with a morphological phenotype. Alleles generated are archived and can be requested from this site through the Zebrafish International Resource Center (ZIRC). You may register to receive updates on genes of interest, or browse a complete list, or search by Ensembl ID, gene name or human and mouse orthologue.

Proper citation: ZMP (RRID:SCR_006161) Copy   

•   Source: SciCrunch Registry

http://www.addgene.org/vector-database/

Vector database is a digital collection of vector backbones assembled from publications and commercially available sources. This is a free resource for the scientific community that is compiled by Addgene. Only the plasmids deposited at Addgene are available for purchase through this website.

Proper citation: Vector Database (RRID:SCR_005907) Copy   

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http://www.interpore.com/

Biomet and Interpore Cross are on the cutting edge of technology in the orthopedic biomaterials market. Our focus is developing and providing truly innovative products, which meet the rapidly expanding needs of orthopedic surgeons both today and in the future. Our Pro Osteon resorbable bone graft material is derived from an abundant non-decorative coral. Pro Osteon is available in a selection of fully resorbable sterile granules and blocks, in a variety of shapes and sizes. Our InterGro DBM products combine the osteoinductivity of DBM with a natural, non-soluble carrier that won''t wash away, delivering a unique bone graft that offers superior handling and performance characteristics. This highly-moldable composite graft can be easily formed to fit any shape fracture or defect.

Proper citation: Interpore Cross International (RRID:SCR_004776) Copy   

•   Source: SciCrunch Registry

http://ki.se/ki/jsp/polopoly.jsp?d=29332&a=103566&l=en

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd, 2023. The ICAP - Integrated analysis of prostate cancer study aims at identifying a set of biomarkers with high prognostic value for prostate cancer progression. These biomarkers will be used to customize treatment and to identify patients with high risk of recurrent disease. Sample types: * EDTA whole blood * DNA Number of sample donors: 505 (sample collection completed)

Proper citation: ICAP - Integrated analysis of prostate cancer (RRID:SCR_006035) Copy   

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http://ki.se/ki/jsp/polopoly.jsp?d=29332&a=103538&l=en

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Libro-1 is a study with the overall aim to identify prognostic factors for breast cancer. The study comprise women in the Stockholm-Gotland region that were diagnosed with breast cancer between the years 2001-2008. Register data (tumor characteristics and treatment), lifestyle factors and blood samples have been collected from the participants.

Proper citation: LIBRO-1: Individualized prediction and prevention of breast cancer (RRID:SCR_006036) Copy   

•   Source: SciCrunch Registry

http://cancer.case.edu/research/sharedresources/tissue/services/

A combined tissue bank and core facility which provides annotated human tissue samples for research purposes. The facility also offers high quality tissue procurement, tissue microarray, histology, immunohistochemistry, photomicroscopy, and laser capture microdissection services for both human and animal tissues to biomedical investigators conducting non-clinical research studies. The TPHC offers instruction to researchers on how to incorporate human tissue into research activities and how to work within the boundaries of patient confidentiality and other regulatory issues. The purpose of the TPHC is to provide tissue collection and processing services to intramural and extramural researchers studying cancer and other diseases. Normal, diseased, benign and malignant tissues are obtained, and matched normal adjacent tissues and tissues from different organ sites from the same donor can also be provided when available. Tissue samples are prepared according to user-specified protocols and can be fresh in a medium of choice, fixed in formalin, quick frozen in the vapor phase of liquid nitrogen or snap-frozen by plunging the sample into liquid nitrogen. Frozen tissues are held in the vapor phase of the liquid nitrogen. Tissues can also be embedded, cut and mounted on slides, and stained upon request. Tissue Microarray (TMA) services are offered for the design and construction of TMAs meeting specific project needs. Basic demographic data (age, race, gender) and histopathologic data from Surgical Pathology Reports are provided by the TPHC with the tissues.

Proper citation: Case Western Reserve Tissue Procurement and Histology Core Facility (RRID:SCR_005344) Copy   

•   Source: SciCrunch Registry

http://www.mousephenotype.org/

Center that produces knockout mice and carries out high-throughput phenotyping of each line in order to determine function of every gene in mouse genome. These mice will be preserved in repositories and made available to scientific community representing valuable resource for basic scientific research as well as generating new models for human diseases.

Proper citation: International Mouse Phenotyping Consortium (IMPC) (RRID:SCR_006158) Copy   

•   Source: SciCrunch Registry

http://www.procap.ki.se/procap_studie_info.htm

PROCAP is a study of the importance of lifestyle and genetic factors in the progression of localized cancer of the prostate. Our study hypothesis is that the likelihood of disease recurrence of prostate cancer is modified or determined by genetic variation in the human genome and/or lifestyle factors. To be able to test our hypothesis, we are using a large, population-based cohort of men with localized prostate cancer in Sweden, recruited in 1997-2002, from which detailed clinical information and data on progression already have been collected. From this cohort, we are collecting lifestyle data and blood samples from 8,500 men. If men with progressive prostate cancer could be identified on their genetic make-up, they could be given additional therapies targeted specifically at prostate cancer progression or monitored even more frequently so that progressions could be treated even earlier. If lifestyle factors are important, these results have an impact on recommendations given to men with newly diagnosed prostate cancer. In the study, we are asking the study persons to fill in an Internet-based questionnaire focusing on diet and physical activity and we ask them to leave 2 test tubes of blood at their local urologist/health care center. The pilot study has recently been completed and evaluated and the remaining 7,500 men in the cohort will be included during 2007 and 2008. So far, we have a response rate of approximately 85% on the blood samples. The response rate for the questionnaire is approximately 80% (both in the web based and paper based versions combined). Genotyping and analysis will begin in the fall of 2008. Sample types: * EDTA whole blood * Plasma * DNA Number of sample donors: 5492 (sample collection completed)

Proper citation: KI Biobank - PROCAP (RRID:SCR_006038) Copy   

•   Source: SciCrunch Registry