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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   

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http://www.mousephenotype.org/impress

Contains standardized phenotyping protocols essential for the characterization of mouse phenotypes. IMPReSS holds definitions of the phenotyping Pipelines and mandatory and optional Procedures and Parameters carried out and data collected by international mouse clinics following the protocols defined. This allows data to be comparable and shareable and ontological annotations permit interspecies comparison which may help in the identification of phenotypic mouse-models of human diseases. The IMPC (International Mouse Phenotyping Consortium) core pipeline describes the phenotype pipeline that has been agreed by the research institutions. IMPReSS has a SOAP web service machine interface. The WSDL can be accessed here: http://www.mousephenotype.org/impress/soap/server?wsdl

Proper citation: Impress (RRID:SCR_006160) Copy   

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http://www.cafevariome.org/

Clearinghouse and exchange portal for gene variant (mutation) data produced by diagnostics laboratories, offering users a portal through which to announce, discover and acquire a comprehensive listing of observed neutral and disease-causing gene variants in patients and unaffected individuals. Cafe Variome is not a ''''database'''' for the hosting/display/release of data, but a shop window for finding data. As such, it holds only core info for each record, and uses this merely to enable holistic searching across resources. Diagnostics laboratories routinely assess DNA samples from patients with various inherited disorders, and so produce a great wealth of data on the genetic basis of disease. Unfortunately, those data are not usually shared with others. To address this gross deficiency, a novel system has been developed that aims to facilitate the automated transfer of diagnostic laboratory data to the wider community, via an internet based Cafe for routinely exchanging genetic variation data. The flow of research data concerning the genetic basis of health and disease is critical to understanding and developing treatments for a range of genetic diseases. Overall, the project aims to lower the barriers and provide incentives for a willing community to share data, and thereby facilitate the broader exploitation of diagnostic laboratory data. Cafe Variome aims to address the above data flow problems by: # Minimizing the effort required to publish variant data # Ensuring attribution for data creators working in diagnostic laboratories Key elements of the project strategy are: * Data publication will be automated by endowing standard analysis tools used by laboratories with an online data submission function. Submissions will be received by a central Internet depot, which will serve as a place where published datasets are advertised, and subsequently discovered by diverse 3rd parties. * Each dataset will be unambiguously linked with the data submitter''''s identity, and systems devised to facilitate citation of published variant datasets so they can be cited in the literature. Data creators will thus be credited for their contributions. Data submitters can use Cafe Variome to simply announce or publicize their data to the world. To enable this, only core, non-identifiable data is submitted to the central repository, enabling users to search and discover records of interest in the source repository. The data are not automatically handed on to the user (unless intended by the submitters). Hence, the concept is used to deal with the challenge of maximally sharing data whilst fully respecting ethico-legal considerations.

Proper citation: cafe variome (RRID:SCR_006162) Copy   

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http://www.patientcrossroads.com/

A trusted third-party gatekeeper of patient data from participants in a rare disease ecosystem, collecting and managing the information in a scalable, cost-effective manner. Each patient registry provides critical disease knowledge which makes that disease easier to study, increasing the probability a treatment can be developed. PatientCrossroads takes a network approach to patient registry programs. Unlike companies that merely sell registry software, we offer a full range of administration, management, and genetic curation services. What does this consolidated, patient-centric approach to patient registries mean? * Patients can more easily find registries and provide their valuable data (including locations of blood and tissue samples as well as reports of diagnoses, disease symptoms, treatment usage, and lifestyle activities) * Patients can be confident in the privacy of their de-identified data and the knowledge that PatientCrossroads does not sell patient data * Researchers and pharmaceutical companies have a larger, more easily accessible pool of potential patients for research studies and clinical trials targeting specific rare diseases * Pharmaceutical companies can collect post-market surveillance data in a more scalable and cost-effective manner * Rare disease advocacy and research foundations can more easily organize their global patient populations for inclusion in trials and studies

Proper citation: PatientCrossroads (RRID:SCR_006279) Copy   

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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   

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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://blogs.plos.org/mfenner/2011/02/01/epub-wordpress-plugin-released-today/

Martin Fenner''s blog is about a WordPress plugin that he created that automatically creates ePub files from blog posts - they are created in the background when you save a blog post. The plugin can be installed directly from your WordPress installation. For now the plugin, ePub Export, only stores the text and images, but the next version should allow embedding of all kinds of files, most importantly data. ePub is a very interesting document format for scholarly publishing and has several advantages over PDF, including: * ePub can be used for all steps in the creation of a scholarly document, including data collection, authoring, annotating and peer review. There is no need for time-consuming and expensive format conversions. Currently most manuscripts are submitted in Microsoft Word or LateX formats, and then converted first to XML and then to HTML and PDF. Metadata such as author identifiers, digital object identifiers and semantic information can be added early on and don''t get lost in a format conversion. * ePub makes it easy to include supplementary material, e.g. video and other multimedia content, the datasets used in the publication (particularly the data used for tables and figures), all cited references in BibTeX format, etc. * ePub is much better suited for reading on mobile devices, as the format allows reflowing of content. Most articles today are printed from the PDF and then read, but this behavior is rapidly changing.

Proper citation: Wordpress ePub Plugin (RRID:SCR_006342) Copy   

•   Source: SciCrunch Registry

http://www.sdbonline.org

Non-profit professional society dedicated to advancement of the field of developmental biology. Excellence in research and education in developmental biology is fostered; advice and resources on careers in developmental biology is provided; and information for the public on relevant topics in developmental biology is provided. Perhaps most importantly, a communication hub for all developmental biologists is provided. The SDB is associated with the journal Developmental Biology; the SDB organizes scientific meetings that focus on developmental biology; the SDB has established programs to interface with the international community of developmental biologists; and the SDB maintains this society web site that covers all aspects of developmental biology. Membership includes developmental biologists at all stages of their careers from around the world.

Proper citation: Society for Developmental Biology (RRID:SCR_006299) Copy   

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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   

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http://www.biogrid.org.au

A federated data sharing platform and infrastructure that provides access to real-time clinical, imaging and biospecimen data across jurisdictions, institutions and diseases. The web-based platform provides a secure infrastructure that advances health research by linking privacy-protected and ethically approved data among a wide network of health collaborators. Access to de-identified health records data is granted to authorized researchers after an application process so patient privacy and intellectual property are protected. BioGrid Australia''s approved researchers are provided access to multiple institutional databases, via the BioGrid interface, preventing gaps in patient records and research analysis. This legal and ethical arrangement with participating collaborators allows BioGrid to connect data through a common platform where data governance and access is managed by a highly skilled team. Data governance, security and ethics are at the core of BioGrid''s federated data sharing platform that securely links patient level clinical, biospecimen, genetic and imaging data sets across multiple sites and diseases for the purpose of medical research. BioGrid''s infrastructure and data management strategies address the increasing need by authorized researchers to dynamically extract and analyze data from multiple sources whilst protecting patient privacy. BioGrid has the capability to link data with other datasets, produce tailored reports for auditing and reporting and provide statistical analysis tools to conduct more advanced research analysis. In the health sector, BioGrid is a trusted independent virtual real-time data repository. Government investment in BioGrid has facilitated a combination of technology, collaboration and ethics approval processes for data sharing that exist nowhere else in the world.

Proper citation: BioGrid Australia (RRID:SCR_006334) 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   

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http://embryo.soad.umich.edu/

Complete three-dimensional data set of reference magnetic resonance microscopy (MRM) images of the human embryo representing 10 stages of development for each of 18 human embryos representing Carnegie stages 10 through 23, a critical embryonic time period for organogenesis. The users of the collection are able to manipulate the data on their own personal computers to view any slice from any plane of sectioning. Dynamic rotational views of whole embryos and time-lapse views of the growing embryo are accessible. Each embryo was imaged with three magnetic resonance pulse sequences to obtain fully-registered T1-weighted, T2-weighted, and diffusion-weighted image datasets. A complete set of coronal, sagittal, and axial images were produced from each image data set. Several major organs were isolated from each T1-weighted embryo data set using image segmentation methods and separate image data sets were created to represent each of these organs. Additionally, each embryo was optically photographed under a low-power microscope. The formalin-fixed specimens came from the highly respected Carnegie Collection of Human Embryos. This is the first distributable work to document in three dimensions the anatomy of the human embryonic time period. Pseudo- time-lapse movies were created using morphing software to represent the fourth dimension (time). Carnegie stages are a system used by embryologists to describe the apparent maturity of embryos. An embryo is assigned a Carnegie stage (numbered from 1 to 23) based on its external features. This staging system is not dependent on the chronological age nor the size of the embryo. The stages, are in a sense, arbitrary levels of maturity based on multiple physical features. Embryos that might have different ages or sizes can be assigned the same Carnegie stage based on their external appearance because of the natural variation which occurs between individuals. Postovulatory age is frequently used by clinicians to describe the maturity of an embryo. It refers to the length of time since the last ovulation before pregnancy. Postovulatory age is a good indication of embryonic age because the time of ovulation can be determined and fertilization must occur close to the time of ovulation. The terms gestation, pregnancy, and conception are usually avoided in describing embryonic age because fertilization is not universally accepted as the commencement of development (some consider implantation as the beginning of development). MRM was performed at the Center for In-vivo Microscopy at Duke University. Image processing and data managment was performed at the School of Art and Design, University of Michigan.

Proper citation: Multi-Dimensional Human Embryo (RRID:SCR_006296) Copy   

•   Source: SciCrunch Registry

https://syllabus.med.unc.edu/courseware/embryo_images/

Tutorial that uses scanning electron micrographs (SEMs) as the primary resource to teach mammalian embryology. The 3-D like quality of the micrographs coupled with selected line drawings and minimal text allow relatively easy understanding of the complex morphological changes that occur in utero. Because early human embryos are not readily available and because embryogenesis is very similar across mammalian species, the majority of micrographs that are utilized in this tutorial are of mouse embryos. The remainder are human. This tutorial is divided into units that may be studied in any order. All of the images have a legend that indicates the age of the embryo. If it is a mouse embryo, the approximate equivalent human age is indicated. To minimize labeling, color-coding is widely used. To view the micrographs without color, the cursor may be placed on the image. The SEMs used in this tutorial are from the Kathleen K. Sulik collection. The line drawings have been used with permission from Lippincott Williams & Wilkins and are from the 6th and 7th editions of Langman''s Medical Embryology by T.W. Sadler.

Proper citation: Embryo Images Normal and Abnormal Mammalian Development (RRID:SCR_006297) Copy   

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http://buridan.sourceforge.net/

Open source software written in R that tracks a single animal walking in a homogenous environment (Buritrack) and analyzes its trajectory. It extracts eleven metrics and includes correlation analyses and a Principal Components Analysis (PCA). It was designed to be easily customized to personal requirements. In combination with inexpensive hardware, these tools can readily be used for teaching and research purposes. Buritrack is a program to track individual Drosophila fruit flies online with any camera as they walk in Buridan's paradigm. The program extracts the coordinate locations of the fly and stores them in a text file.

Proper citation: Centroid Trajectory Analysis (RRID:SCR_006331) Copy   

•   Source: SciCrunch Registry

http://www.crowdlabs.org/

A social visualization repository for the scientific workflow management system VisTrails providing a platform for sharing and executing computational tasks. It adopts the model used by social Web sites and that integrates a set of usable tools and a scalable infrastructure to provide an environment for scientists to collaboratively analyze and visualize data. crowdLabs aims to foster collaboration but was specifically designed to support the needs of computational scientists, including the ability to access high-performance computers and manipulate large volumes of data. By providing mechanisms that simplify the publishing and use of analysis pipelines, it allows IT personnel and end users to collaboratively construct and refine portals. This lowers the barriers for the use of scientific analyses and enables broader audiences to contribute insights to the scientific exploration process, without the high costs incurred by traditional portals. In addition, it supports a more dynamic environment where new exploratory analyses can be added on-the-fly.

Proper citation: crowdLabs (RRID:SCR_006294) 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.animalgenome.org/pig/genome/db/

Database facilitating information integration and mining within the pig and across species of all genomics / genetics research results accumulated over the years including pig gene expression, quantitative trait loci (QTL), candidate gene, and whole genome association study (WGAS) results. The key functions developed so far include pig gene pages (a centralized gene search tool), a local copy of Biomart (for customizable genome information queries), genome feature alignment tools (Pig QTLdb and Gbrowse), integrated gene expression information (ANEXDB and ESTdb), a dedicated pig genome and gene set BLAST server, and virtual comparative map database and tools (VCmap). By developing the PGD, it is our aim to collaboratively utilize existing databases and tools via networked functions, such as web services, database API, etc., to maximize the potential of all related databases through the PGD implementation.

Proper citation: Pig Genome Database (RRID:SCR_006367) Copy   

•   Source: SciCrunch Registry

http://www.fmriconsulting.com/brodmann/

An atlas that facilitates fMRI analysis understanding by providing access to all of the functions that have been associated with each of the 52 Brodmann's areas or corresponding gyri. Links to main publications supporting the findings are provided in PubMed ID format. Brodmann's areas with similar functions and locations have been collapsed into a single page. The word left or right has been added indicating a lateralized function. All the abstracts published on PubMed on fMRI and brain PET studies in which the Brodmann's area or its anatomical correlate were mentioned have been reviewed up to August 2008. Abstracts with poorly described experimental methods or findings clearly conflicting with established knowledge provided by the clinical model were excluded. Studies on patients were also excluded.

Proper citation: Brodmann's Interactive Atlas (RRID:SCR_006368) 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.chemspider.com/

Collection of chemical structures. Provides access to structures, properties and associated information from hundreds of data sources to find compounds of interest and provides services to improve this data by curation and annotation and to integrate it with users applications.

Proper citation: ChemSpider (RRID:SCR_006360) Copy   

•   Source: SciCrunch Registry