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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   

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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   

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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   

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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   

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http://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html

A microarray normalization software (SCAN) to facilitate personalized-medicine workflows with an extension (UPC) that estimates whether a given gene/transcript is active above background levels in a given sample. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration. A

Proper citation: SCAN.UPC (RRID:SCR_001334) Copy   

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http://neuroinformatics.kiv.zcu.cz/articles/read/eegerp-portal-eegbase-_2014-12-19

EEG base is a system for storage and management of EEG/ERP resources - data, metadata, tools and materials related to EEG/ERP experiments. EEG base advances electrophysiology research by enabling access to public data, tools and results of research groups. The system essentially offers the following set of features (the set of accessible features depends on a specific user role): * User authentication * Storage, update, and download of EEG/ERP data and metadata * Storage, update and download of EEG/ERP experimental design (experimental scenarios) * Storage, update and download of data related to testing subjects * Fulltext search * Sharing of knowledge and working in groups The system is based on tree layer architecture (MVC pattern) consisting of persistent layer (relational database), application layer (object oriented code, object relational mapping from persistence layer) and presentation layer (JSP). The persistence layer uses Hibernate framework; Oracle 11g database server is used to ensure the processing of large data files. Application and presentation layers are designed and implemented using Spring technology. This framework supports MVC architecture, Dependency injection and Aspect Oriented Programming. There were no significant difficulties with integration of both frameworks, Hibernate and Spring MVC. Spring Security framework is used to ensure management of authentication and user roles. Since the system is thought to be finally open to the whole EEG/ERP community it is necessary to protect EEG/ERP data and metadata, and especially personal data of testing subjects stored in the database from an unauthorized access. Then a restricted user policy is applied and user roles are introduced. The complete overview of the system features and user roles (use case diagram) is available in (Pergler 2009). Concerning the architectural layers there is a question which layer is more feasible for mapping of its structure into ontology. Currently we have studied two possibilities: * Mapping from the persistence layer (relational database) * Mapping from the application layer (object oriented code) The mapping from the application layer to an ontology includes the precedent object relational mapping provided by Hibernate framework.

Proper citation: EEGbase (RRID:SCR_001452) Copy   

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https://rdrr.io/bioc/betr/man/betr.html#heading-0

Software package that implements the Bayesian Estimation of Temporal Regulation algorithm to identify differentially expressed genes in microarray time-course data.

Proper citation: betr (RRID:SCR_001332) Copy   

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https://school.wakehealth.edu/departments/neurology

Department at the Wake Forest University's School of Medicine that hosts physicians who specialize in neurological topics such as neuromuscular disease, epilepsy, pediatric neurology, strokes, neuropsychology, neurosonology, and neurorehabilitaiton.

Proper citation: Wake Forest University School of Medicine: Department of Neurology (RRID:SCR_001453) Copy   

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http://www.roche.com/

A Swiss global health-care company that operates under two divisions: Pharmaceuticals and Diagnostics.

Proper citation: Roche (RRID:SCR_001326) Copy   

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https://bioconductor.org/packages//2.11/bioc/html/gprege.html

Software R package for Gaussian Process Ranking and Estimation of Gene Expression time-series. The software fits two Gaussian processes (GPs) with an radial basis function (RBF) (+ noise diagonal) kernel on each profile. One GP kernel is initialized wih a short lengthscale hyperparameter, signal variance as the observed variance and a zero noise variance. It is optimized via scaled conjugate gradients (netlab). A second GP has fixed hyperparameters: zero inverse-width, zero signal variance and noise variance as the observed variance. The log-ratio of marginal likelihoods of the two hypotheses acts as a score of differential expression for the profile. Comparison via receiver operating characteristic curves (ROC curves) is performed against Bayesian hierarchical model for the analysis of time-series (BATS) (Angelini et.al, 2007).

Proper citation: gprege (RRID:SCR_001324) Copy   

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https://www.bioconductor.org/packages//2.13/bioc/html/waveTiling.html

Software package to conduct transcriptome analysis for tiling arrays based on fast wavelet-based functional models.

Proper citation: waveTiling (RRID:SCR_001322) Copy   

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http://sourceforge.net/projects/kanalyze/

A Java toolkit designed to convert DNA and RNA sequences into k-mers.

Proper citation: KAnalyze (RRID:SCR_001323) Copy   

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http://www.bioconductor.org/packages/release/bioc/html/AffyExpress.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data.

Proper citation: AffyExpress (RRID:SCR_001321) Copy   

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http://www.px.nsls.bnl.gov/

Biomedical technology research center that creates optimal facilities and environments and support for macromolecular structure determination by synchrotron X-ray diffraction at the National Synchrotron Light Source for the benefit of outside and in-house investigators. The PXRR innovates new access modes such as Mail-in crystallography, builds new facilities, currently on the X25 undulator, advances automation, develops remote participation software, collaborates with outside groups, teaches novice users, and supports vising investigators with 7-day, 20-hours staff coverage.

Proper citation: Macromolecular Crystallography Research Resource (RRID:SCR_001442) Copy   

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