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http://www.europeanlung.org/en/projects-and-research/projects/airprom/

Consortium focused on developing computer and physical models of the airway system for patients with asthma and chronic obstructive pulmonary disease (COPD). Developing accurate models will better predict how asthma and COPD develop, since current methods can only assess the severity of disease. They aim to bridge the gaps in clinical management of airways-based disease by providing reliable models that predict disease progression and the response to treatment for each person with asthma or COPD. A data management platform provides a secure and sustainable infrastructure that semantically integrates the clinical, physiological, genetic, and experimental data produced with existing biomedical knowledge from allied consortia and public databases. This resource will be available for analysis and modeling, and will facilitate sharing, collaboration and publication within AirPROM and with the broader community. Currently the AirPROM knowledge portal is only accessible by AirPROM partners.

Proper citation: AirPROM (RRID:SCR_003827) Copy   

•   Source: SciCrunch Registry

http://www.agedbrainsysbio.eu/

Consortium focused on identifying the foundational pathways responsible for the aging of the brain, with a focus on Late Onset Alzheimer's disease. They aim to identify the interactions through which the aging phenotype develops in normal and in disease conditions; modeling novel pathways and their evolutionary properties to design experiments that identify druggable targets. As early steps of neurodegenerative disorders are expected to impact synapse function the project will focus in particular on pre- or postsynaptic protein networks. The concept is to identify subsets of pathways with two unique druggable hallmarks, the validation of interactions occurring locally in subregions of neurons and a human and/or primate accelerated evolutionary signature. The consortium will do this through six approaches: * identification of interacting protein networks from recent Late-Onset Alzheimer Disease-Genome Wide Association Studies (LOAD-GWAS) data, * experimental validation of interconnected networks working in subregion of a neuron (such as dendrites and dendritic spines), * inclusion of these experimentally validated networks in larger networks obtained from available databases to extend possible protein interactions, * identification of human and/or primate positive selection either in coding or in regulatory gene sequences, * manipulation of these human and/or primate accelerated evolutionary interacting proteins in human neurons derived from induced Pluripotent Stem Cells (iPSCs) * modeling predictions in drosophila and novel mouse transgenic models * validation of new druggable targets and markers as a proof-of-concept towards the prevention and cure of aging cognitive defects. The scientists will share results and know-how on Late-Onset Alzheimer Disease-Genome Wide Association Studies (LOAD-GWAS) gene discovery, comparative functional genomics in mouse and drosophila models, in mouse transgenic approaches, research on human induced pluripotent stem cells (hiPSC) and their differentiation in vitro and modeling pathways with emphasis on comparative and evolutionary aspects. The four European small to medium size enterprises (SMEs) involved will bring their complementary expertise and will ensure translation of project results to clinical application.

Proper citation: AgedBrainSYSBIO (RRID:SCR_003825) Copy   

•   Source: SciCrunch Registry

https://www.bioshare.eu/

A consortium of leading biobanks and international researchers from all domains of biobanking science to ensure the development of harmonized measures and standardized computing infrastructures enabling the effective pooling of data and key measures of life-style, social circumstances and environment, as well as critical sub-components of the phenotypes associated with common complex diseases. The overall aim is to build upon tools and methods available to achieve solutions for researchers to use pooled data from different cohort and biobank studies. This, in order to obtain the very large sample sizes needed to investigate current questions in multifactorial diseases, notably on gene-environment interactions. This aim will be achieved through the development of harmonization and standardization tools, implementation of these tools and demonstration of their applicability. BioSHaRE researchers are collaborating with P3G, the Global Alliance for Genomics and Health, IRDiRC (International Rare Diseases Research Consortium), H3Africa and other organizations on the development of an International Code of Conduct for Genomic and Health-Related Data Sharing. A draft version is available for external review. Generic documents have been prepared covering areas of biobanking that are of major importance. SOPs have been finalized for blood withdrawal (SOPWP5001blood withdrawal), manual blood processing (SOPWP5002blood processing), shipping of biosamples (SOPWP5003shipping) and withdrawal, processing and storage of urine samples (SOPWP5004urine).

Proper citation: BioSHaRE (RRID:SCR_003811) Copy   

•   Source: SciCrunch Registry

http://www.evoio.org/wiki/MIAPA

Central hub for resources related to developing and deploying a Minimal Information for a Phylogenetic Analysis (MIAPA) standard.

Proper citation: MIAPA (RRID:SCR_003777) Copy   

•   Source: SciCrunch Registry

https://www.bigtencrc.org/

A consortium that aims to transform cancer research through collaborative oncology trials that leverage the scientific and clinical expertise of the Big Ten universities. The goal is to align the conduct of cancer research through collaborative, hypothesis-driven, highly translational oncology trials that leverage the scientific and clinical expertise. The clinical trials that will be developed will be linked to molecular diagnostics, enabling researchers to understand what drives the cancers to grow and what might be done to stop them from growing. The consortium also leverages geographical locations and existing relationships among the cancer centers. One of the consortium's goals is to harmonize contracts and scientific review processes to expedite clinical trials. The consortium will only focus on phase 0 to II trials because larger trials - even a randomized phase II trial - are difficult to conduct at a single cancer center.

Proper citation: Big Ten Cancer Research Consortium (RRID:SCR_004025) Copy   

•   Source: SciCrunch Registry

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

Consortium that created the capability to detect Adverse Drug Response (ADR) signals by creating the infrastructure for large-scale monitoring of drug safety using electronic health records (EHR). The platform leverages EHR''''s comprising demographics, drug use and clinical data of over 30 million patients from several European countries. Special attention was given to patient groups that are not routinely involved in clinical trials, for ethical or practical reasons (e.g. pregnant women, elderly people, people using many drugs simultaneously, and children). This project also studies and compares a number of different techniques that all aim to detect unexpected or disproportional rates of events. The algorithms that they studied originate not only from the field of (pharmaco)epidemiology, but also from fields such as bio-terrorism, machine learning, and classical signal detection. EU-ADR specific objectives are: To detect events, To relate these events to drugs, To develop hypothesis that explain adverse events, To detect adverse events earlier, and To avoid false positives. The web-based platform is available at https://bioinformatics.ua.pt/euadr/ EU-ADR has contributed to the ability to conduct better drug safety studies based on the re-use of healthcare data. By facilitating the early detection of adverse drug reactions, but also providing key information on populations at risk, potential drug interactions, potential underlying mechanisms and intervening pathways in adverse events, etc., the project will allow for improved and more complete information to be available for drug and healthcare delivery, leading to increased patient safety and its associated cost savings. The EU-ADR system can be considered as a complementary tool to already existing pharamcovigilance systems. Should the system be widespread in the long term, it has the potential to contribute to the development of future electronic health record systems, insofar as the expected benefits of these IT tools are only fully attainable when EHRs develop themselves in consistency, richness and formats that allow them to be subject of such tools. In anticipation, EU-ADR has been designed to be modular and scalable, so that different EHR databases (other than those participating in the Consortium) can be progressively enlisted in the future, adopt the software for data extraction and therefore become susceptible of exploitation by the system, for maximum global effect.

Proper citation: EU-ADR (RRID:SCR_004028) Copy   

•   Source: SciCrunch Registry

http://www.compact-research.org/

Consortium to reduce delivery and targeting bottlenecks for developing novel innovative biopharmaceutical based medicines. The project aims to shed new light on the obstacles biopharmaceuticals (medicines based on biological molecules such as proteins, peptides or nucleic acids) need to overcome to get to where they are needed in the body. The team will then use this information to develop and validate biopharmaceutical formulations to deliver these novel drugs to their targets. By finding more effective ways of administering these biopharmaceutical drugs, and improving their ability to travel through the body to where they are needed, COMPACT will allow more patients to benefit from biopharmaceuticals. Furthermore, designing less invasive administration routes and reducing the dose (and therefore the side effects) and frequency of administration will help to improve patient compliance with treatments.

Proper citation: COMPACT (RRID:SCR_003850) Copy   

•   Source: SciCrunch Registry

http://www.cihr.gc.ca/e/46475.html

Consortium that will be the premier research hub for all aspects of research involving neurodegenerative diseases that affect cognition in aging - including Alzheimer's disease. They will promote high impact, inter-institutional and interdisciplinary collaboration through a pan-Canadian approach, and will position Canadian researchers to lead and participate in a new wave of national and international initiatives with congruent goals. The consortium focuses research into the basic mechanisms of neurodegenerative diseases, accelerating the development of tools that can be used to assist in the diagnosis and treatment of the diseases. The intended outcome of these tools is to improve the quality of life and services patients with neurodegenerative diseases. As part of the Canadian contribution to the International Collaborative Research Strategy for Alzheimer's disease, the consortium brings together Canadian government agencies (federal and provincial), foundations, pharmaceutical companies, philanthropists and international stakeholders to identify if there are common causes and risk factors to neurodegenerative diseases. The consortium is focused on three themes: * Primary Prevention aimed at preventing the disease from developing * Secondary Prevention focused on delaying the clinical manifestations of the already developing disease * Quality of Life designed for helping individuals, caregivers and the health system in the context of a clinically developed disease.

Proper citation: Canadian Consortium on Neurodegeneration in Aging (RRID:SCR_003846) Copy   

•   Source: SciCrunch Registry

https://www.aakp.org/

Association of kidney patients focused on patient-centered education, advocacy and community. They share educational pieces covering every level of kidney disease, advocate for improved access to high-quality health care through regulatory and legislative reform at the federal level, and make an effort to bring kidney patients together to promote community, conversations and to seek out services that help maximize patients'' everyday lives.

Proper citation: American Association of Kidney Patients (RRID:SCR_003965) Copy   

•   Source: SciCrunch Registry

http://clinicaltrials.gov/show/NCT01211678

A consortium evaluating a new biomarker screening test that might help identify patients with rheumatoid arthritis (RA) who are unlikely to benefit from anti-tumor necrosis factor-alpha (TNFalpha) medications. BATTER-UP will enroll around 1,000 patients being treated by one of several marketed anti-TNF RA drugs: Enbrel, Remicade, Humira, Simponi, or Cimzia. Through data analyses and predictive response modeling, the consortium aims to better understand which patients with RA will derive the greatest benefit from TNF inhibitors. The investigators in this observational study will attempt to validate an 8-gene biomarker set based on work by Biogen Idec researchers as likely to predict anti-TNF responsiveness in patients with RA. In preliminary results, the 8-gene biomarker set predicted with 89% accuracy individuals who did not reach European League Against Rheumatism (EULAR) Disease Activity Score (DAS)-28 good response after 14 weeks of treatment. The 8 genes included in the screen are CLTB, MXRA7, CXorf52, COL4A3BP, YIPF6, FAM44A, SFRS2, and PGK1. Biological samples and clinical outcome information will be used to confirm and extend the utility of previously published biomarkers that can predict response to anti-TNF agents. These data may also generate new hypotheses for further testing. The BATTER-UP samples and data will be established as a reference set for investigation of personalized medicine in RA. The study will be a resource of DNA and other biological materials that can be investigated for biomarkers in the future as new technologies arise.

Proper citation: Biomarkers of Anti-TNF Treatment Efficacy in Rheumatoid Arthritis - Unresponsive Populations (RRID:SCR_004019) Copy   

•   Source: SciCrunch Registry

https://www.projectdatasphere.org/

Initiative to advance oncology research by enabling collaborative sharing of historical oncology clinical trial data through a universal platform (database). The initiative aims to network all stakeholders in the cancer community researchers, industry, academia, advocacy, and other organizations to share insights and collaborate on issues that could not be solved individually. To do this, they have made efforts to address issues of data privacy, security, intellectual property, resources, and incentives as part of its effort to maximize participation. Data contributions include control arms of clinical trials, and the platform uses data-security precautions and analytics to pool multiple studies associated with the same diagnosis in a manner that seeks to protect the privacy of patients and the security of the data contributed.

Proper citation: Project Data Sphere (RRID:SCR_003726) Copy   

•   Source: SciCrunch Registry

http://www.themmrf.org/research-programs/commpass-study/

A personalized medicine initiative to discover biomarkers that can better define the biological basis of multiple myeloma to help stratify patients. This effort hopes to obtain samples from approximately 1,000 multiple myeloma patients and follow them over time to identify how a patient's genetic profile is related to clinical progression and treatment response. As a partnership between 17 academic centers, 5 pharmaceuticals and the Department of Veterans Affairs, the goal of this eight year study is to create a database that can accelerate future clinical trials and personalized treatment strategies. MMRF's CoMMpass Study has the following goals: * Create a guide to which treatments work best for specific patient subgroups. * Share data with researchers to accelerate drug development for specific subtypes of multiple myeloma patients. In order to facilitate discoveries and development related to targeted therapies, the comprehensive data from CoMMpass is placed in an open-access research portal. The data will be part of the Multiple Myeloma Research Foundation's (MMRF) Personalized Medicine Platform combines CoMMpass data with those collected from MMRF's Genomics Initiative. It is hoped that the longitudinal data, combined with the annotated bio-specimens will help provide insights that can accelerate personalized therapies.

Proper citation: MMRF CoMMpass Study (RRID:SCR_003721) Copy   

•   Source: SciCrunch Registry

http://www.biomarcare.eu/

EU funded consortium including over 30 partner from academia and industry. BiomarCaRE aims to determine the value of established and emerging biomarkers to improve risk estimation of cardiovascular disease in Europe. BiomarCaRE relies on an exceptional resource of large scale epidemiological cohorts with long term follow-up and available bio specimens based on the population of the MORGAM Project as well as several cardiovascular disease cohorts and clinical trials.

Proper citation: BiomarCaRE (RRID:SCR_003841) Copy   

•   Source: SciCrunch Registry

http://www.alz.org/research/alzheimers_grants/biomarkers-across.asp

Consortium that launched a Request for Applications (RFA) to stimulate analyses across the Alzheimer's disease (AD) and Parkinson's disease (PD) research enterprises to engage in further data analysis of existing cohorts, including, but not limited to, biomarker discovery, standardization of assays, genetic profiles, and imaging modalities. The RFA aims to build on existing momentum to leverage similar activities and increase impact across the neurodegenerative disease spectrum. It also builds on recent evidence suggesting substantial overlap between AD, PD, and other neurodegenerative diseases pathologically, but also potentially biologically. The RFA is designed to enable preliminary pilot research or proof-of-principle studies utilizing data and/or samples from two large biomarker studies, the Alzheimer's Disease Neuroimaging Initiative (ADNI) and the Parkinson's Progression Markers Initiative (PPMI), in order to garner further research support from other funding agencies. Application Deadline: March 19, 2014. Efforts under BAND include studies that: * analyze datasets to test hypotheses related to aging and neurodegenerative disorders; * seek to identify panels or pathways that may play a role in disease mechanisms, such as around inflammation; * pursue shared or disparate biochemical markers of disease risk, onset or progression; * assess potential commonalities across the disease spectrum, including around other neurological disorders such as Lewy body dementia. Recent data reported at the 2013 Alzheimer's Association's International Conference stimulated discussion in the research community about the possible cross talk between AD and PD. For example, underlying pathologies / biomarkers, such as cerebrospinal fluid (CSF) alpha-synuclein, have been measured in the sample sets collected for both diseases to help understand similarities and differences in these diseases. Furthermore, similar imaging modalities, such as MRI and PET, are being employed to interrogate changes that occur with disease progression. As therapeutic approaches are developed that may be disease-modifying for several neurodegenerative diseases, stratification of clinical trial populations based on biomarker profiles may increase the probability of success in demonstrating a beneficial effect.

Proper citation: Biomarkers Across Neurodegenerative Diseases (RRID:SCR_004015) Copy   

•   Source: SciCrunch Registry

http://betabat.ulb.ac.be/

Project that aims to develop new treatment strategies based on knowledge of cellular dysfunction in diabetes. They will perform a detailed organelle diagnosis based on both focused and systems biology approaches, which will provide the scientific rationale for the design of specific interventions to boost the capacity of beta cells and brown adipocytes to regain homeostatic control. They propose that only by understanding the complex molecular mechanisms triggering cellular dysfunction in diabetes, and by integrating this knowledge at the systems level, will it be possible to develop interventional therapies that protect and restore beta cell and (Brown adipose tissue) BAT function. The ultimate goal is to offer individual therapeutic choices based on both genetic information and organelle diagnosis.

Proper citation: BetaBat (RRID:SCR_003834) Copy   

•   Source: SciCrunch Registry

http://www.basisproject.eu/

Consortium to generate complete catalogs of somatic mutations in 500 breast cancers, of the ER+ve HER2- subclass, under the International Cancer Genome Consortium model by high coverage, shotgun genome sequencing of both tumor and normal DNA. The strategy is to collect, store, review, quality control and extract DNA and RNA from breast cancer and normal tissues from 500 ER+, HER2- breast cancer cases which will be subjected to a coordinated series of genomic analyses including whole genome shotgun sequencing, genome-wide copy number analysis, mRNA expression analysis, miRNA expression analysis and genome-wide methylation analysis. A comprehensive catalogue of somatic mutations will be generated from each cancer. Somatic mutation catalogues from the 500 cancers will be analysed and integrated with expression and methylation data to identify novel cancer genes, characterize subverted biological pathways that are operative, describe patterns of somatic mutation and explore early translational applications of personalized somatic genomic data for patients with ER+, HER2- breast cancer. The results will impact the understanding of the causes and biology of breast cancer and will lead to major advances in detection, prevention and treatment in one of the most common diseases and causes of death in the developed world. The Consortium has completed a number of investigative exercises into the experimental protocols and technological practices relating to whole genome sequencing, epigenetics and transcriptomics including: * Completion of extensive testing of current RNA-seq protocol. * Designed and implemented a new, improved RNA-seq protocol which utilizes RNA samples regardless of their RNA Integrity Number. * Completed pilot testing of the Infinium 450k array and associated bi-sulfite sequencing. * Refined the whole genome sequencing library production protocols to produce more robust libraries. * Improved the primary variant-calling algorithms (for substitutions, insertions / deletions and rearrangements) * Developed new analytical algorithms to explore the resulting high-quality variants. As such, variant calling of whole genome sequencing data and secondary downstream analysis can begin in earnest in a trackable and automated fashion.

Proper citation: Breast Cancer Somatic Genetics Study (RRID:SCR_003832) Copy   

•   Source: SciCrunch Registry

http://kongress.mh-hannover.de/biohybrid/

Consortium with the goal of repairing damaged nerve trunks that will engage in the preclinical development of an artificial biohybrid nerve device for the regenerative treatment of traumatic injuries of peripheral nerves. Based on the extensive basic and clinical experience within this consortium the artificial nerve device will be developed together with standardized application and evaluation parameters. A key objective of this study is to generate a protocol that serves as a template for future clinical trials in the regenerative therapy of damaged peripheral nerves. The results of the multidisciplinary research will feed into the establishment of artificial biohybrid devices as stand alone alternatives to accepted standard procedures and tools. Furthermore, standardized application guidelines and evaluation parameters will be set up to enable continuous progress and evaluation of the outcome of clinical application.

Proper citation: BIOHYBRID (RRID:SCR_003838) Copy   

•   Source: SciCrunch Registry

http://sing.ei.uvigo.es/GC/

Tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification. While the user can work with different gene set collections and several microarray data files to configure specific classification experiments, the tool is able to run several tests in parallel. It is able to render valuable information for diagnostic analyses and clinical management decisions based on systematically evaluating custom hypothesis over different data sets using complementary classifiers, a key aspect in clinical research.

Proper citation: GeneCommittee (RRID:SCR_004168) Copy   

•   Source: SciCrunch Registry

http://www.wardwiki.com/w/Main_Page

Wardwiki is a wiki designed to give free advice to foundation doctors (also know as interns) to help with practical issues as they arise on hospital wards. Despite the proliferation of medical websites and expensive courses there remains a large gap in provision of practical, experience based guidance to help foundation doctors survive the first two years on the wards. You may search for topics of interest but there are also sections including Popular Topics, Popular Categories, Top 25 articles, and Featured article. It is the responsibility of each foundation doctor to ensure their actions, referrals and prescriptions are accurate. These pages are written and maintained to the best ability of the contributing authors. We encourage any contributions be well founded, accurate, in good faith, without endorsement of medical products or opinions, and not to breach existing copyright. WardWiki cannot accept liability for adverse events that may arise directly or indirectly from advice given.

Proper citation: WardWiki (RRID:SCR_004323) Copy   

•   Source: SciCrunch Registry

http://iubio.bio.indiana.edu/webapps/SeWeR/

Sequence analysis using Web Resources (SeWeR) is an integrated, Dynamic HTML (DHTML) interface to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser. It doesn''t require any server to host itself. The goal of SeWeR is to turn your web-browser into a powerful sequence-analysis tool. It is written entirely in JavaScript1.2. SeWeR can be downloaded and mirrored freely. The whole package is just around 300K. You can even run it from a floppy. SeWeR is not compatible with Netscape 6. SeWeR now generates graphics. Savvy is a plasmid drawing software that generates plasmid map in the revolutionary Scalable Vector Graphics format from W3C.

Proper citation: SeWeR - SEquence analysis using WEb Resources (RRID:SCR_004167) Copy   

•   Source: SciCrunch Registry