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http://sourceforge.net/projects/baccontigeditor/

A simple sequence alignment editing tool, written in Java.

Proper citation: BACContigEditor (RRID:SCR_001617) Copy   

•   Source: SciCrunch Registry

http://www.bari2d.org/

A multicenter randomized clinical trial that aims to determine the best therapies for people with type 2 diabetes and moderately severe cardiovascular disease. 2368 participants were randomized at 49 sites in 6 countries. All subjects were given intensive medical therapy to control cholesterol and blood pressure and given counseling, if needed, to quit smoking and to lose weight. Beyond that, they compared whether prompt revascularization, either bypass surgery or angioplasty, e.g. stents, was more effective than medical therapy alone. At the same time, they also looked at which of two diabetes treatment strategies resulted in better outcomes����??insulin-providing versus insulin-sensitizing - that is, increasing the amount of insulin or making the insulin work better. Only patients with known type 2 diabetes and heart disease that could be treated appropriately with a revascularization OR medical therapy alone were eligible for the trial. Patients entered the study between January 2001 ����?? March 2005 and were followed for an average of five years. When a patient entered the study, physicians first decided whether that patient should receive stenting or bypass surgery. The patient then received their randomization assignment. All patients were treated in BARI 2D for both their diabetes and heart disease, as well as other risk factors that might effect those diseases, regardless of which group they were in. Diabetes-specific complications including retinopathy, nephropathy, neuropathy, and peripheral vascular disease were monitored regularly. Tests, blood samples, urine samples, and treatment cost data were obtained periodically through the trial and examined by experts at 7 central laboratories and other research partners. Experts on risk factors routinely oversaw treatments of all patients at 4 central management centers. A panel of independent experts reviewed data every six months to make sure that all patients were receiving safe care.

Proper citation: BARI 2D (RRID:SCR_001496) Copy   

•   Source: SciCrunch Registry

http://jdrf.org/

Global funder of type 1 diabetes (T1D) research that aims to progressively remove the impact of T1D from people's lives until a world without T1D is achieved. JDRF collaborates with a wide spectrum of partners and is the only organization with the scientific resources, regulatory influence, and a working plan to better treat, prevent, and eventually cure T1D. More than 80 percent of JDRF's expenditures directly support research and research-related education. In 2012 Forbes magazine named JDRF one of its five All-Star charities, citing the organization's efficiency and effectiveness. The organization awards research grants for laboratory and clinical investigations and sponsors a variety of career development and research training programs for new and established investigators. JDRF also sponsors international workshops and conferences for biomedical researchers. Individual chapters offer support groups and other activities for families affected by diabetes.

Proper citation: Juvenile Diabetes Research Foundation (RRID:SCR_001522) Copy   

•   Source: SciCrunch Registry

https://bioinformatics.ca/jobs

Job postings available to Bioinformatics.ca members. To become a member please sign up for an account. DISCLAMER: OICR and the Canadian Bioinformatics Workshops are not affiliated with and have not investigated the companies listing jobs on this site. OICR is not making any representations with respect to the positions and is not acting as an agent for the companies listed.

Proper citation: Bioinformatics Jobs Board (RRID:SCR_001484) Copy   

•   Source: SciCrunch Registry

http://www.ara.com/products/mppd.htm

Computational model that can be used for estimating human and rat airway particle dosimetry. The model is applicable to risk assessment, research, and education. The MPPD model calculates the deposition and clearance of monodisperse and polydisperse aerosols in the respiratory tracts of rats and human adults and children (deposition only) for particles ranging in size from ultrafine (0.01 micrometers) to coarse (20 micrometers). The models are based on single-path and multiple-path methods for tracking air flow and calculating aerosol deposition in the lung. The single-path method calculates deposition in a typical path per airway generation, while the multiple-path method calculates particle deposition in all airways of the lung and provides lobar-specific and airway-specific information. Within each airway, deposition is calculated using theoretically derived efficiencies for deposition by diffusion, sedimentation, and impaction within the airway or airway bifurcation. Filtration of aerosols by the nose and mouth is determined using empirical efficiency functions. The MPPD model includes calculations of particle clearance in the lung following deposition.

Proper citation: Multiple-Path Particle Dosimetry Model (RRID:SCR_001486) Copy   

•   Source: SciCrunch Registry

http://www.jaeb.org/

Freestanding, nonprofit coordinating center for multi-center clinical trials and epidemiologic research that focus on projects involving eye disorders or type 1 diabetes.

Proper citation: Jaeb Center for Health Research (RRID:SCR_001513) Copy   

•   Source: SciCrunch Registry

http://wordpress.org/

Web software which helps users create a website or blog. WordPress software can be downloaded and installed with an appropriate web host and minimum requirements. There is also a service called WordPress.com which allows users to get started with a new and free WordPress-based blog in seconds, though it varies in several ways and is less flexible than the self-installed WordPress. An array of plugins and themes are available to further customize a site.

Proper citation: WordPress (RRID:SCR_001518) Copy   

•   Source: SciCrunch Registry

http://www.trigr.org

International, randomized, double-blinded trial to determine whether weaning to a casein hydrolysate formula during the first 6-8 months of life in place of cow milk based formula reduces the incidence of autoimmunity and type 1 diabetes in genetically susceptible newborn infants. 2160 eligible infants were randomized to test or control formulas when mothers decide to wean from exclusive breastfeeding. The participants will be monitored up to the age of 10 years for the appearance of diabetes-predictive autoantibodies and clinical type 1 diabetes. The TRIGR trial will determine whether delayed exposure to intact food proteins will reduce the chances of developing type 1 diabetes later in life. All babies in the study received the recommendation to breastfeed for at least the first six months of life. If a mother was unable to exclusively breastfeed before the baby was 8 months of age, her child was randomly assigned to one of two groups. One group of these babies received a trial formula based on extensively hydrolyzed protein; the other group received another trial formula containing a smaller amount of hydrolyzed protein. In the hydrolyzed formula, the big protein molecules have been split into very small fragments to provide a source of nutritional amino acids, but the fragments are likely too small to stimulate the immune system. The TRIGR trial will also be able to analyze whether exclusive breastfeeding per se can reduce the risk of the children to develop type 1 diabetes.

Proper citation: TRIGR (RRID:SCR_001550) Copy   

•   Source: SciCrunch Registry

http://ki.se/?l=en

Medical university in Stockholm, Sweden that offers more than fifty disciplines of medicine for study.

Proper citation: Karolinska Institute; Stockholm; Sweden (RRID:SCR_001548) Copy   

•   Source: SciCrunch Registry

http://www.k-state.edu/

Public doctoral university located in Manhattan, Kansas that is involved with research, especially agricultural.

Proper citation: Kansas State University; Kansas; USA (RRID:SCR_001533) Copy   

•   Source: SciCrunch Registry

https://github.com/CollasLab/edd

A ChIP-seq peak caller for detection of megabase domains of enrichment.

Proper citation: Enriched Domain Detector (RRID:SCR_001693) Copy   

•   Source: SciCrunch Registry

http://www.clarklabs.org/

Geospatial software for monitoring and modeling the Earth system. Includes tools for GIS, image processing, surface analysis, vertical applications for land change analysis and earth trends exploration, and more.

Proper citation: IDRISI (RRID:SCR_001696) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/devel/bioc/html/CNVrd2.html

A software package that uses next-generation sequencing data to measure human gene copy number for multiple samples, indentify SNPs tagging copy number variants and detect copy number polymorphic genomic regions.

Proper citation: CNVrd2 (RRID:SCR_001723) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/2.13/bioc/html/sSeq.html

Software package to discover the genes that are differentially expressed between two conditions in RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation. The method of moment (MM) estimates for dispersion are shrunk towards an estimated target, which minimizes the average squared difference between the shrinkage estimates and the initial estimates. The exact per-gene probability under the NB model is calculated, and used to test the hypothesis that the expected expression of a gene in two conditions identically follow a NB distribution.

Proper citation: sSeq (RRID:SCR_001719) Copy   

•   Source: SciCrunch Registry

http://www.kcl.ac.uk/index.aspx

Public research university located in London, United Kingdom that offers undergraduate, graduate, and professional degree programs in medicine, economics, social sciences, etc.

Proper citation: King's College London; London; United Kingdom (RRID:SCR_001744) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.dreamhosters.com/?page_id=113#Genomic_Protein_Sequence_Analysis

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. An R software package for detecting and correcting biases in RNA-Sequencing data.

Proper citation: RNASeqBias (RRID:SCR_001739) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.med.yale.edu/group/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. An R code for Bayesian modeling of paired RNA-seq experiments.

Proper citation: pairedBayes (RRID:SCR_001738) Copy   

•   Source: SciCrunch Registry

http://www.yahrparkinson.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 28, 2017. Foundation that helps junior physicians and neuroscientists continue their research on Parkinson's Disease and related disorders, with financial support for professional and intellectual development. It promotes an international community of researchers, focusing on the young enthusiastic investigators and clinicians who might otherwise be forced to abandon their ideas and efforts.

Proper citation: Melvin Yahr International Parkinson's Disease Foundation (RRID:SCR_001652) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/dnaclust/

Software program for clustering large number of short similar DNA sequences. It was originally designed for clustering targeted 16S rRNA pyrosequencing reads.

Proper citation: DNACLUST (RRID:SCR_001771) Copy   

•   Source: SciCrunch Registry

http://intermine.github.io/intermine.org/

An open source data warehouse system built for the integration and analysis of complex biological data that enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding data. InterMine includes a user-friendly web interface that works "out of the box" and can be easily customized for specific needs, as well as a powerful, scriptable web-service API to allow programmatic access to data.

Proper citation: InterMine (RRID:SCR_001772) Copy   

•   Source: SciCrunch Registry