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miniTUBA is a web-based modeling system that allows clinical and biomedical researchers to perform complex medical/clinical inference and prediction using dynamic Bayesian network analysis with temporal datasets. The software allows users to choose different analysis parameters (e.g. Markov lags and prior topology), and continuously update their data and refine their results. miniTUBA can make temporal predictions to suggest interventions based on an automated learning process pipeline using all data provided. Preliminary tests using synthetic data and laboratory research data indicate that miniTUBA accurately identifies regulatory network structures from temporal data. miniTUBA represents in a network view possible influences that occur between time varying variables in your dataset. For these networks of influence, miniTUBA predicts time courses of disease progression or response to therapies. minTUBA offers a probabilistic framework that is suitable for medical inference in datasets that are noisy. It conducts simulations and learning processes for predictive outcomes. The DBN analysis conducted by miniTUBA describes from variables that you specify how multiple measures at different time points in various variables influence each other. The DBN analysis then finds the probability of the model that best fits the data. A DBN analysis runs every combination of all the data; it examines a large space of possible relationships between variables, including linear, non-linear, and multi-state relationships; and it creates chains of causation, suggesting a sequence of events required to produce a particular outcome. Such chains of causation networks - are difficult to extract using other machine learning techniques. DBN then scores the resulting networks and ranks them in terms of how much structured information they contain compared to all possible models of the data. Models that fit well have higher scores. Output of a miniTUBA analysis provides the ten top-scoring networks of interacting influences that may be predictive of both disease progression and the impact of clinical interventions and probability tables for interpreting results. The DBN analysis that miniTUBA provides is especially good for biomedical experiments or clinical studies in which you collect data different time intervals. Applications of miniTUBA to biomedical problems include analyses of biomarkers and clinical datasets and other cases described on the miniTUBA website. To run a DBN with miniTUBA, you can set a number of parameters and constrain results by modifying structural priors (i.e. forcing or forbidding certain connections so that direction of influence reflects actual biological relationships). You can specify how to group variables into bins for analysis (called discretizing) and set the DBN execution time. You can also set and re-set the time lag to use in the analysis between the start of an event and the observation of its effect, and you can select to analyze only particular subsets of variables.
Proper citation: miniTUBA (RRID:SCR_003447) Copy
A biomedical ontology in the area of vaccine adverse events aimed to represent and analyze various vaccine-specific adverse events. OVAE is an extension of the Ontology of Adverse Events (OAE) and the Vaccine Ontology (VO).
Proper citation: Ontology of Vaccine Adverse Events (RRID:SCR_003442) Copy
https://code.google.com/p/proteomecommons-tranche/
A distributed file storage system that you can upload files to and download files from. All files uploaded to the repository are replicated several times to protect against their accidental loss. Files uploaded to the repository can be of any size, can be of any file type, and can be encrypted with a passphrase of your choosing. The Proteome Commons Tranche repository is the first instance of a Tranche repository. Tranche, was created so that anybody can take it and make their own Tranche repository. This is the first implementation of the Tranche software, and is useful as a test bed for the software. This repository relies on educational institutions to provide the hardware and facilities for Tranche servers. While we maintain a set of servers, the continued growth of this public resource will rely on the generosity of the institutions that use the repository most.
Proper citation: Proteome Commons Tranche repository (RRID:SCR_003441) Copy
The Cancer Text Information Extraction System (caTIES) provides tools for de-identification and automated coding of free-text structured pathology reports. It also has a client that can be used to search these coded reports. The client also supports Tissue Banking and Honest Broker operations. caTIES focuses on two important challenges of bioinformatics * Information extraction (IE) from free text * Access to tissue. Regarding the first challenge, information from free-text pathology documents represents a vital and often underutilized source of data for cancer researchers. Typically, extracting useful data from these documents is a slow and laborious manual process requiring significant domain expertise. Application of automated methods for IE provides a method for radically increasing the speed and scope with which this data can be accessed. Regarding the second challenge, there is a pressing need in the cancer research community to gain access to tissue specific to certain experimental criteria. Presently, there are vast quantities of frozen tissue and paraffin embedded tissue throughout the country, due to lack of annotation or lack of access to annotation these tissues are often unavailable to individual researchers. caTIES has three goals designed to solve these problems: * Extract coded information from free text Surgical Pathology Reports (SPRs), using controlled terminologies to populate caBIG-compliant data structures. * Provide researchers with the ability to query, browse and create orders for annotated tissue data and physical material across a network of federated sources. With caTIES the SPR acts as a locator to tissue resources. * Pioneer research for distributed text information extraction within the context of caBIG. caTIES focuses on IE from SPRs because they represent a high-dividend target for automated analysis. There are millions of SPRs in each major hospital system, and SPRs contain important information for researchers. SPRs act as tissue locators by indicating the presence of tissue blocks, frozen tissue and other resources, and by identifying the relationship of the tissue block to significant landmarks such as tumor margins. At present, nearly all important data within SPRs are embedded within loosely-structured free-text. For these reasons, SPRs were chosen to be coded through caTIES because facilitating access to information contained in SPRs will have a powerful impact on cancer research. Once SPR information has been run through the caTIES Pipeline, the data may be queried and inspected by the researcher. The goal of this search may be to extract and analyze data or to acquire slides of tissue for further study. caTIES provides two query interfaces, a simple query dashboard and an advanced diagram query builder. Both of these interfaces are capable of NCI Metathesaurus, concept-based searching as well as string searching. Additionally, the diagram interface is capable of advanced searching functionalities. An important aspect of the interface is the ability to manage queries and case sets. Users are able to vet query results and save them to case sets which can then be edited at a later time. These can be submitted as tissue orders or used to derive data extracts. Queries can also be saved, and modified at a later time. caTIES provides the following web services by default: MMTx Service, TIES Coder Service
Proper citation: caTIES - Cancer Text Information Extraction System (RRID:SCR_003444) Copy
http://www.compgen.org/tools/metagen
Software program providing a method for meta-analysis of case-control genetic association studies using random-effects logistic regression.
Proper citation: metagen (RRID:SCR_003443) Copy
http://code.google.com/p/omrse/
An ontology covering the domain of social entities that are related to health care, such as demographic information (social entities for recording gender (but not sex) and marital status, for example) and the roles of various individuals and organizations (patient, hospital, etc.)
Proper citation: Ontology of Medically Related Social Entities (RRID:SCR_003439) Copy
MIT's Department of Brain and Cognitive Sciences stands at the nexus of neuroscience, biology and psychology. We combine these disciplines to study specific aspects of the brain and mind including: vision, movement systems, learning and memory, neural and cognitive development, language and reasoning. Together, MIT's Department of Brain and Cognitive Sciences offers extraordinary learning opportunities for undergraduate, graduate and postdoctoral students. Because the human brain is immensely complex in many different ways at once, we pursue every level of inquiry - from molecules to cells to circuits to the mystery of the mind itself. As we study its diseases and disorders, its development and daily feats, like vision, speech, movement and memory, we also integrate methods and insights from every area of brain research. This unusual diversity of expertise fosters an intensely creative atmosphere that sparks startling collaborations. Already known for remarkable contributions to the field, our faculty members continually stretch the limits of knowledge, and bring the same passion to educating our exceptional students. A key part of the BCS mission is to offer its graduate and undergraduate students an educational experience of the highest quality. Our graduate students benefit from the impressive range of our program, and from the ability to participate in research projects with faculty members who are leaders in their fields. The department's undergraduate program, which includes both neuroscience and cognitive science, is one of the fastest-growing majors at MIT.
Proper citation: Massachusetts Institute of Technology; Department of Brain and Cognitive Sciences (RRID:SCR_003437) Copy
http://www.physiol.ucl.ac.uk/research/silver_a/nclamp/
Data acquisition software that runs in conjunction with neuromatic. configured to work with Igor Pro on PC or Mac, instrutech or national instrument acquisition devices. Funded by The Medical Research Council (UK) Compatibility with WaveMetrics Igor Pro 5 and 6. Compatibility with Mac or PC. NIDAQ interfacing multifunction DAQ boards from National Instruments. Requires Igor NIDAQ Tools MX. ITC interfacing - data acquisition systems from InstruTech / Heka. Requires Igor ITC XOPs. Episodic acquisition (stim and sample). Continuous acquisition (currently for ITC users only). Online analysis, with ability to create your own analysis functions. Notes and Log Files which can be displayed within a table or notebook. Automatic saving of data and log folders to your hard drive. Flexible stimulus pulse generator with ability to use your own pulse waveforms. Instant accessibility to all of NeuroMatics and Igor Pros pre-existing data analysis functions.
Proper citation: Nclamp - data acquisition software for electrophysiology (RRID:SCR_003750) Copy
Initiative to improve health by speeding up the development of, and patient access to, innovative medicines, particularly in areas where there is an unmet medical or social need. It does this by initiating and managing consortia composed of the key players involved in healthcare research, including universities, the pharmaceutical and other industries, small and medium-sized enterprises (SMEs), patient organizations, and medicines regulators. IMI is a public-private partnership between the European Union and the European pharmaceutical industry, represented by the European Federation of Pharmaceutical Industries and Associations (EFPIA), with a timeframe separated into two phases (2008-2013, 2014-2024) that are each defined by unique research agendas. The first phase (2008 2013) had four pillars that defined the focus of its research agenda: * Predicting safety: evaluating the safety of a compound during the pre-clinical phase of the development process and the later phases in clinical development. * Predicting efficacy: improving the ability to predict how a drug will interact in humans and how it may produce a change in function. * Knowledge management: utilization of information and data for predicting safety and efficacy. * Education and training: closing existing training gaps in the drug development process. Some of the consortia managed under IMI focused on specific health issues while others focused on broader challenges in drug development. Additionally, IMI launched a number of education and training projects during its first phases. The goal of the second phase (IMI2, 2014-2024) is to develop next generation vaccines and drugs. The focus is on delivering the right prevention and treatment for the right patient at the right time. There is a strong focus on the development of new medicines with an emphasis on tools and methods that accelerate patient access to new medicines. IMI2's agenda can be defined by four axes of research: * target validation and biomarker research (efficacy and safety) * adoption of innovative clinical trial paradigms * innovative medicines * patient-tailored adherence programs As part of its distinct goals, IMI2 aims to deliver: * 30% better success rate in clinical trials of priority medicines identified by the WHO; clinical proof of concept in immunological, respiratory, neurological and neurodegenerative diseases in five years; * new and approved diagnostic markers for four of these diseases and at least two new medicines which could either be new antibiotics or new therapies for Alzheimer's disease.
Proper citation: Innovative Medicines Initiative (RRID:SCR_003754) Copy
A consortium that focuses their efforts on discovering and developing new pharmaceutical drugs, vaccines (both preventive and therapeutic) and diagnostics against the infectious diseases that are prevalent in developing countries. The initial targets are those disorders designated by WHO as neglected tropical diseases prevalent in developing nations. The consortium aims to facilitate international partnerships that enable Japanese technology, innovations, and insights to play a more direct role in improving global health. Another goal of GHIT is to develop a new drug-discovery screening platform to assist the screening of compound libraries housed within Japanese companies and academic institutions. The vision is to have Japanese research organizations donate compounds, with the Fund reimbursing screening costs and leveraging screening programs of existing product-development partners.
Proper citation: Global Health Innovative Technology Fund (RRID:SCR_003753) Copy
http://www.stjohns.edu/academics/schools-and-colleges/college-pharmacy-and-health-sciences
The College of Pharmacy and Allied Health Professions equips students with the education, training and support they need to meet the present and future demands professionals encounter as pharmacists, physician assistants, clinical laboratory scientists, toxicologists and radiologic technologists. The College is committed to helping students: * Focus on the responsibilities of public health and service * Appreciate the ever-changing character of the health professions * Enjoy a broad, general education * Pursue graduate study in specialized fields of interest Facilities Laboratory facilities in the College of Pharmacy and Allied Health Professions include state-of-the-art equipment used in pharmacology/toxicology, medicinal chemistry, industrial pharmacy and drug information. Our facilities include: GC-mass spectrophotometers; transmission and scanning electron microscopes; Mrs.; capillary GCs; preparative and analytical HPLCs; liquid scintillation and gamma counters; luminometers; dissolution apparatus; membrane potentiometers; atomic absorption spectrophotometers; polygraphs; high-speed and ultracentrifuges. In addition, we have sophisticated tissue-cultures laboratories, molecular pharmacology and molecular biology laboratories, as well as an AAALAC accredited animal facility. In addition to the main University computer, a fully equipped microcomputer laboratory is located adjacent to the main science complex.
Proper citation: St. John's College of Pharmacy and Allied Health Professions (RRID:SCR_003752) Copy
http://purl.bioontology.org/ontology/MEDDRA
Ontology of Medical Dictionary for Regulatory Activities Terminology (MedDRA)
Proper citation: Medical Dictionary for Regulatory Activities (RRID:SCR_003751) Copy
http://bejerano.stanford.edu/phenotree/
Web server to search for genes involved in given phenotypic difference between mammalian species. The mouse-referenced multiple alignment data files used to perform the forward genomics screen is also available. The webserver implements one strategy of a Forward Genomics approach aiming at matching phenotype to genotype. Forward genomics matches a given pattern of phenotypic differences between species to genomic differences using a genome-wide screen. In the implementation, the divergence of the coding region of genes in mammals is measured. Given an ancestral phenotypic trait that is lost in independent mammalian lineages, it is shown that searching for genes that are more diverged in all trait-loss species can discover genes that are involved in the given phenotype.
Proper citation: Phenotree (RRID:SCR_003591) Copy
https://services.healthtech.dtu.dk/
Center for Biological Sequence Analysis of the Technical University of Denmark conducts basic research in the field of bioinformatics and systems biology and directs its research primarily towards topics related to the elucidation of the functional aspects of complex biological mechanisms. A large number of computational methods have been produced, which are offered to others via WWW servers. Several data sets are also available. The center also has experimental efforts in gene expression analysis using DNA chips and data generation in relation to the physical and structural properties of DNA. The on-line prediction services at CBS are available as interactive input forms. Most of the servers are also available as stand-alone software packages with the same functionality. In addition, for some servers, programmatic access is provided in the form of SOAP-based Web Services. The center also educates engineering students in biotechnology and systems biology and offers a wide range of courses in bioinformatics, systems biology, human health, microbiology and nutrigenomics.
Proper citation: DTU Center for Biological Sequence Analysis (RRID:SCR_003590) Copy
A three-year consortium that brings together insurers and health care providers to share information from approximately 9 million patients, with a goal that insights from the data will bring down healthcare costs and improve outcomes. It aims to be one of the largest health information exchanges in the country, with the goal of better connecting the vast, often disparate healthcare landscape across California. The database that will house patient data will be overseen by Orion Health, an independent eHealth software company. The information will only be used for clinical purposes. Academic research institutions can apply to use the Cal INDEX de-identified data for research to benefit the public good, such as population health initiatives. Cal INDEX has five main goals: * Improve the quality of care by providing clinicians with a unified statewide source of integrated patient information * Provide patients with a seamless transition between health plans or across various healthcare professionals and hospitals * Improve efficiency and reduce the cost of healthcare * Encourage healthcare technology innovation * Improve public health by providing de-identified data for medical research. Cal INDEX plans to launch at the end of 2014 with approximately 9 million health information records from combined members of Dignity Health and Blue Shield of California and Anthem Blue Cross. Cal INDEX is open to any health data contributor. Cal INDEX will establish a bi-directional data interface with providers to exchange data with EMRs and other hospital and office-based systems.
Proper citation: California Integrated Data Exchange (RRID:SCR_003747) Copy
Project focused on developing cutting edge tools to speed up and improve the testing and monitoring of vaccine safety, both before and after release to the market. The three specific objectives of the project are: * the characterization of early inflammation induced by vaccines currently on the market and the identification and validation of biomarkers of early inflammation and allergic responses; * the identification and validation of early biomarkers of autoimmunity and their use to help identifying population at risk of developing autoimmunity; * the analysis of the incidence and epidemiology of autoimmune disease in the general population and the link to genetic background or previous events in the life of patients, including severe effects, such as anaphylactic shock.
Proper citation: BioVacSafe (RRID:SCR_003745) Copy
http://www.coca-colacompany.com/
An American multinational beverage corporation and manufacturer, retailer and marketer of nonalcoholic beverage concentrates and syrups, which is headquartered in Atlanta, Georgia. (Wikipedia) It is the world's largest beverage company, refreshing consumers with more than 500 sparkling and still brands.
Proper citation: Coca-Cola Company (RRID:SCR_003749) Copy
http://www.sevenhillsbioreagents.com/
An Antibody supplier
Proper citation: Seven Hills Bioreagents (RRID:SCR_003748) Copy
A consortium that aims to accelerate the development of immunization technologies for the next generation of human vaccines. The goals are to characterize the mode of action and conduct comparative effectiveness studies of: adjuvants, vectors, formulations, delivery devices, routes of immunization, homologous and heterologous primeboost schedules, on vaccine efficacy. As part of these clinical trials, the consortium will also investigate the impact of host factors such as age, gender, genetics and pathologies. The consortium hopes to use insights gained from their projects to advance the development of next-generation vaccines, using tools such as standardized animal models to select promising immunization technologies. The intended outcome of this partnership is to improve the vaccine development process by advancing: basic research, new technology development, and clinical trial methods. Scientific objectives: # Development of adjuvants, vectors, formulations, and delivery devices # Selection of candidates, routes of immunization, and prime-boost combinations in animal models # Assessment of the impact of host factors in response to vaccination # Development of concepts and tools from human immunization # Development of concepts and tools to address regulatory and ethical issues posed by novel immunization technologies # Creation of an internationally recognized training program for translational immunology and vaccinology. Data is shared across the research partners within and between the different workstreams. Additionally, the consortium has plans to create a clinical database that combines phenotypic and clinical information to study the immune response to influenza vaccination at a population level, in an effort to advance studies into the effects of genetic background, gender, and disease on vaccine response.
Proper citation: Advanced Immunization Technologies (RRID:SCR_003741) Copy
A consortium that seeks to provide an integrated approach to anti-drug immunization by evaluating immunogenicity in hemophilia A, multiple sclerosis, and inflammatory diseases, and exploring new tools for protein drug immunogenicity. The data collected will be pooled in a single immunogenicity databank and will be standardized and used to develop models of anti-drug antibodies. By examining the correlation between patient and clinical factors and the incidence of immunogenicity, it hopes to reduce the regulatory and resource burdens of immunogenicity testing. The objectives of the consortium are: # Access to large cohorts of patients treated with marketed biopharmaceutical products # Complementary expertise for anti-drug antibodies (ADA) assays; standardization and characterization of ADA # Novel integrated approaches to characterize anti-drug lymphocyte responses # Development and validation of innovative prediction tools # Collection and integration of immunogenicity-related data and clinical relevance of ADA ABIRISK is grouped into five working projects, which communicate with one another and provide each other with results and data for analysis. The five working projects are: ADA assay development and validation and cohort management; cellular characterization and mechanisms of the AD immune response; evaluation and development of technologies for predicting immunogenicity; establishment of database, data analyses and integration; and project management and communication.
Proper citation: ABIRISK (RRID:SCR_003740) Copy
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