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http://www.scytek.com/

An Antibody supplier

Proper citation: ScyTek Laboratories (RRID:SCR_005919) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/MetaQC/

Software for quality control and diagnosis for microarray meta-analysis. Quantitative quality control measures include: (1) internal homogeneity of co-expression structure among studies (internal quality control; IQC); (2) external consistency of co-expression structure correlating with pathway database (external quality control; EQC); (3) accuracy of differentially expressed gene detection (accuracy quality control; AQCg) or pathway identification (AQCp); (4) consistency of differential expression ranking in genes (consistency quality control; CQCg) or pathways (CQCp). For each quality control index, the p-values from statistical hypothesis testing are minus log transformed and PCA biplots were applied to assist visualization and decision. Results generate systematic suggestions to exclude problematic studies in microarray meta-analysis and potentially can be extended to GWAS or other types of genomic meta-analysis. The identified problematic studies can be scrutinized to identify technical and biological causes (e.g. sample size, platform, tissue collection, preprocessing etc) of their bad quality or irreproducibility for final inclusion / exclusion decision.

Proper citation: MetaQC (RRID:SCR_006000) Copy   

•   Source: SciCrunch Registry

http://www.wf4ever-project.org/

Project to addresses challenges associated with the preservation of scientific experiments in data-intensive science, including: * The definition of models to describe, in a standard way, scientific experiments by means of workflow-centric Research Objects, which comprise scientific workflows, the provenance of their executions, interconnections between workflows and related resources (e.g., datasets, publications, etc.), and social aspects related to such scientific experiments. * The collection of best practices for the creation and management of Research Objects. * The analysis and management of decay in scientific workflows. To address these challenges they are creating an architecture and tooling for the access, manipulation, sharing, reuse and evolution of Research Objects in a range of disciplines. This will result into the next generation RO-enabled myExperiment.

Proper citation: Workflow4Ever (RRID:SCR_005939) Copy   

•   Source: SciCrunch Registry

http://www.ddcf.org/

The mission of the Doris Duke Charitable Foundation is to improve the quality of people''s lives through grants supporting the performing arts, environmental conservation, medical research and the prevention of child abuse, and through preservation of the cultural and environmental legacy of Doris Duke''s properties. Established in 1996, the foundation supports four national grant-making programs. It also supports three properties that were owned by Doris Duke in Hillsborough, New Jersey; Honolulu, Hawaii; and Newport, Rhode Island. The foundation is headquartered in New York and is governed by a board of 12 Trustees. DDCF''s activities are guided by the will of Doris Duke, who endowed the foundation with financial assets that totaled approximately $1.6 billion as of December 31, 2010. The foundation regularly evaluates and modifies its allocation of resources from the endowment to support the programs and properties and to respond to fluctuations in portfolio returns. The foundation awarded its first grants in 1997. As of December 31, 2011, the foundation has awarded grants totaling more than $1 billion. DDCF awards grants in four core program areas: * The Arts Program supports performing artists with the creation and public performance of their work. * The Environment Program supports efforts that enable communities to protect and manage wildlife habitat and create efficient built environments. * The Medical Research Program seeks to contribute to the prevention and cure of disease by supporting clinical research. * The Child Abuse Prevention Program seeks to protect children from abuse and neglect in order to promote their healthy development. In the fall of 2007, DDCF also launched the African Health Initiative, with the goal of strengthening health systems in sub-Saharan Africa. The Building Bridges Program, which seeks to increase public understanding of Islamic cultures through media and the arts, is funded through the Doris Duke Foundation for Islamic Art and is headquartered in DDCF''s offices in New York. The Properties In her will, Doris Duke requested that several operating foundations manage the properties listed below. She also expressed her wishes that the properties be opened for public visitation and used for educational programs. The operating foundations receive funding from the Doris Duke Charitable Foundation. * The Duke Farms Foundation manages a 2,700-acre property in Hillsborough, New Jersey, which is known as Duke Farms and has a mission of environmental stewardship. * The Doris Duke Foundation for Islamic Art manages Doris Duke''s home in Honolulu, Hawaii, which is known as Shangri La and serves as a center for the study of Islamic art and cultures. * The Newport Restoration Foundation preserves historic houses in Newport, Rhode Island, and operates Doris Duke''s home in Newport known as Rough Point, which is also a public museum.

Proper citation: Doris Duke Charitable Foundation (RRID:SCR_006012) Copy   

•   Source: SciCrunch Registry

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

Software package that provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs (single nucleotide variants).

Proper citation: deepSNV (RRID:SCR_006214) Copy   

•   Source: SciCrunch Registry

http://www.semantic-mediawiki.org/wiki/Semantic_MediaWiki

A free, open-source extension to MediaWiki - the wiki software that powers Wikipedia - that helps to search, organize, tag, browse, evaluate, and share the wiki''s content. While traditional wikis contain only text which computers can neither understand nor evaluate, SMW adds semantic annotations that allow a wiki to function as a collaborative database. Semantic MediaWiki introduces some additional markup into the wiki-text which allows users to add semantic annotations to the wiki. While this first appears to make things more complex, it can also greatly simplify the structure of the wiki, help users to find more information in less time, and improve the overall quality and consistency of the wiki. A large number of related extensions have been created that extend the ability to edit, display and browse through the data stored by SMW: the term Semantic MediaWiki is sometimes used to refer to this entire family of extensions.

Proper citation: Semantic MediaWiki (RRID:SCR_006246) Copy   

•   Source: SciCrunch Registry

https://github.com/RGLab/pepStat

Software for statistical analysis of peptide microarrays. It uses an integrated analytical method for analyzing peptide microarray antibody binding data, from normalization through subject-specific positivity calls and data integration and visualization.

Proper citation: pepStat (RRID:SCR_006240) Copy   

•   Source: SciCrunch Registry

http://pathogenseq.lshtm.ac.uk/estmoi

A per-based software to estimate multiplicity of infection (MOI) in parasite genomic sequence data. It is primarily developed to address the limitations of current laboratory (PCR) based estimates of multiplicity using high throughput sequence data. It requires a BAM (alignment output of short reads to the reference genome), VCF (a file with information on variant calls) and FASTA (reference genome) files. # Short reads are aligned to a reference genome using BWA, BOWTIE, SMALT or other short read aligners to generate a BAM file. # Single Nucleotide Polymorphisms (SNPs) are then identified using SAMTools/BCFtools and stored in the VCF format. # The reference FASTA file is expected to be indexed using ''samtools faidx'' to generate a *.fai file. estMOI generates files containing MOI estimates for each SNP combinations (file with name *.log) and a summary for all chromosomes (file with name *.txt).

Proper citation: estMOI (RRID:SCR_006192) Copy   

•   Source: SciCrunch Registry

https://www.rndsystems.com/

An Antibody supplier who also provides assay services and products.

Proper citation: R and D Systems (RRID:SCR_006140) Copy   

•   Source: SciCrunch Registry

http://www.ctf.org/

A non-profit dedicated to ending neurofibromatosis (NF) through research. It is the leading nonprofit funding source of NF research in the world. The mission of The Children''s Tumor Foundation is to: * Encourage and support research and the development of treatments and cures for neurofibromatosis types 1 and 2, schwannomatosis, and related disorders (hereafter collectively referred to as NF); * Support persons with NF, their families, and caregivers by providing thorough, accurate, current, and readily accessible information; * Assist in the development of clinical centers, best practices, and other patient support mechanisms (but not including direct medical care) to create better access to quality healthcare for affected individuals; and, * Expand public awareness of NF to promote earlier and accurate diagnoses by the medical community, increase the non-affected population''s understanding of the challenges facing people with NF, and encourage financial and other forms of support from public and private sources. Through the implementation of the Foundation''s research initiatives, progress is being made on all fronts and for all types of NF; from discovery studies understanding the molecular signaling deficits that cause the manifestations of NF to the growth of preclinical drug screening initiatives and the emergence of a growing number of clinical trials. The Foundation advances research through strategically integrated programs that speed therapies from the lab to the patient.

Proper citation: Childrens Tumor Foundation (RRID:SCR_006280) Copy   

•   Source: SciCrunch Registry

http://www.hybrow.org/

A prototype bioinformatics tool for designing hypotheses and evaluating them for consistency with existing knowledge. It consists of a modeling framework with the ability to accommodate diverse biological information sources, an event-based ontology for representing biological processes at different levels of detail, a database to query information in the ontology, and programs to perform hypothesis design and evaluation. There are five key components involved in making HyBrow work. # The Event-based ontology for representing biological knowledge # The Discreet Event Systems based conceptual framework which provides the theory that allows us to make statements in a context free formal language (made up of the ontology) and evaluate the statements for validity using constraints declared on existing data # The rule library that provides the steps to apply those constraints and decide support, contradiction or no comment. # The relational database that stores existing information structured into the ontology. # The user interface.

Proper citation: HyBrow (Hypothesis Browser) (RRID:SCR_006272) Copy   

•   Source: SciCrunch Registry

http://www.gatesfoundation.org/

Foundation to help all people lead healthy, productive lives, this funding and job resource is focused on health, poverty, and opportunity. They work with partner organizations worldwide to tackle critical problems in four program areas. Their Global Development Division works to help the world''s poorest people lift themselves out of hunger and poverty. Their Global Health Division aims to harness advances in science and technology to save lives in developing countries. Their United States Division works to improve U.S. high school and postsecondary education and support vulnerable children and families in Washington State. And their Global Policy & Advocacy Division seeks to build strategic relationships and promote policies that will help advance their work. Our approach to grantmaking in all four areas emphasizes collaboration, innovation, risk-taking, and, most importantly, results. The foundation is unable to make grants directly to individuals. The majority of our funding is proactive and made to U.S. tax-exempt organizations that are independently identified by our staff.

Proper citation: Bill and Melinda Gates Foundation (RRID:SCR_006346) Copy   

•   Source: SciCrunch Registry

http://www.ivyfoundation.org/

Funds patient-focused research on gliomas to develop better diagnostics and treatments that lead to long-term survival and a high quality of life for patients with brain tumors. The goal is to decrease the suffering of patients with brain tumors. With an ultimate goal to cure brain cancer, their immediate goal is to improve diagnostics and treatment. They are dedicated to improving the lives of all patients with brain cancer by funding research that they hope will lead to the doubling of life expectancy of patients with brain cancer. Their goal is to do this within the next seven years. Since 2005 they''ve committed more than $50 million to research into brain tumors, with the expectation that this will lead to better diagnostics and therapies. They are dedicated to this search because funding leads to answers, and answers lead to hope.

Proper citation: Ben and Catherine Ivy Foundation (RRID:SCR_006333) Copy   

•   Source: SciCrunch Registry

http://vis.stanford.edu/wrangler/

Wrangler is an interactive tool for data cleaning and transformation. Spend less time formatting and more time analyzing your data. Why wrangle? * Too much time is spent manipulating data just to get analysis and visualization tools to read it. Wrangler is designed to accelerate this process: spend less time fighting with your data and more time learning from it. * Wrangler allows interactive transformation of messy, real-world data into the data tables analysis tools expect. Export data for use in Excel, R, Tableau, Protovis, ... * Want to learn more about Wrangler''s design? Take a look at our research paper. * Wrangler is still a work-in-progress. Please share your feedback and feature requests!

Proper citation: DataWrangler (RRID:SCR_006335) Copy   

•   Source: SciCrunch Registry

http://megasun.bch.umontreal.ca/People/lartillot/www/

A Bayesian Monte Carlo Markov Chain (MCMC) sampler software for phylogenetic reconstruction. Its main distinguishing feature is the underlying probabilistic model, CAT (Lartillot and Philippe, 2004). CAT is an infinite mixture model accounting for site-specific amino-acid or nucleotide preferences. It is well suited to phylogenomic studies using large multigene alignments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PhyloBayes (RRID:SCR_006402) Copy   

•   Source: SciCrunch Registry

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

Collegiate research university in Oxford, England. Teaching as early as 1096, making it the oldest university in English speaking world and world second oldest university in continuous operation.

Proper citation: University of Oxford; Oxford; United Kingdom (RRID:SCR_006361) Copy   

•   Source: SciCrunch Registry

http://www.uniovi.es/

Public university in Asturias. It is the only university in the region. It has three campus and research centres, located in Oviedo, Gijón and Mieres.

Proper citation: University of Oviedo; Oviedo; Spain (RRID:SCR_006359) Copy   

•   Source: SciCrunch Registry

http://snps.ccbr.utoronto.ca:8080/SNPdryad/

Service to predict deleterious non-synonymous human Single Nucleotide Polymorphisms (SNPs) using only orthologous protein sequences.

Proper citation: SNPdryad (RRID:SCR_006414) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/QCGWAS/

Software tools for (automated and manual) quality control of the results of Genome Wide Association Studies.

Proper citation: QCGWAS (RRID:SCR_006408) Copy   

•   Source: SciCrunch Registry

http://www.wpi.edu/

Private research university in Worcester, Massachusetts, focusing on the instruction and research of technical arts and applied sciences.

Proper citation: Worcester Polytechnic Institute; Massachusetts; USA (RRID:SCR_006328) Copy   

•   Source: SciCrunch Registry