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A collaborative network among university-led drug discovery centers and programs to allow scientists to exchange technical expertise on drug discovery and development strategies as well as form partnerships with each other, biopharma companies, and drug discovery-focused contract service organizations and consultants. The website will also serve as a repository for drug discovery events, educational material, job postings, and partnership opportunities. Through active member participation this website will become a valuable tool for every scientist working in the drug discovery arena. In addition, involvement of members will enable them to effectively advocate to the NIH and other funding agencies to increase the awareness of the growing number of academic drug discovery scientists and their success as well as their needs.
Proper citation: Academic Drug Discovery Consortium (RRID:SCR_003706) Copy
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
http://graphml.graphdrawing.org/
A file format for graphs that consists of a language core to describe the structural properties of a graph and a flexible extension mechanism to add application-specific data. It is based on XML and is ideally suited as a common denominator for all kinds of services generating, archiving, or processing graphs. Its main features include support of * directed, undirected, and mixed graphs, * hypergraphs, * hierarchical graphs, * graphical representations, * references to external data, * application-specific attribute data, and * light-weight parsers.
Proper citation: GraphML (RRID:SCR_003545) Copy
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
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
http://www.isi.edu/integration/karma/
An information integration software tool that enables users to integrate data from a variety of data sources including databases, spreadsheets, delimited text files, XML, JSON, KML and Web APIs. Users integrate information by modeling it according to an ontology of their choice using a graphical user interface that automates much of the process. Karma learns to recognize the mapping of data to ontology classes and then uses the ontology to propose a model that ties together these classes. Users then interact with the system to adjust the automatically generated model. During this process, users can transform the data as needed to normalize data expressed in different formats and to restructure it. Once the model is complete, users can publish the integrated data as RDF or store it in a database.
Proper citation: Karma (RRID:SCR_003732) Copy
Satellite facility that downlinks, processes, archives, and distributes remote-sensing data to scientific users around the world. Three major components: * Satellite Tracking Ground Station: Part of NASA?s Near Earth Network system of ground stations around the world. * Synthetic Aperture Radar Distributed Active Archive Center (SAR DAAC): ASF maintains the NASA archive of SAR data from a variety of satellites and aircraft, and provides these data and associated specialty support services to U.S. Government-approved researchers in support of NASA?s Earth Science Data and Information System project. * ASF Enterprise Center (ASFE): In support of UAF?s mission to be a student-centered research university, the ASF-E focuses on applications of remote-sensing data, specifically for UAF research. The ASF-E includes the GeoData Center (GDC), which provides data management and archive services for UAF principal investigators and maintains a variety of geophysical data collections in support of scientific research.
Proper citation: Alaska Satellite Facility (RRID:SCR_003610) Copy
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
https://github.com/alyssafrazee/polyester
An R package designed to simulate RNA sequencing experiments with differential transcript expression. Given a set of annotated transcripts, it will simulate the steps of an RNA-seq experiment (fragmentation, reverse-complementing, and sequencing) and produce files containing simulated RNA-seq reads. Simulated reads can be analyzed using a choice of downstream analysis tools. Polyester has a built-in wrapper function to simulate a case/control experiment with differential transcript expression and biological replicates. Users are able to set the levels of differential expression at transcripts of their choosing. This means they know which transcripts are differentially expressed in the simulated dataset, so accuracy of statistical methods for differential expression detection can be analyzed. Polyester offers several unique features: * Built-in functionality to simulate differential expression at the transcript level * Ability to explicitly set differential expression signal strength * Simulation of small datasets, since large RNA-seq datasets can require lots of time and computing resources to analyze * Generation of raw RNA-seq reads, as opposed to alignments or transcript-level abundance estimates * Transparency/open-source code
Proper citation: Polyester (RRID:SCR_003602) Copy
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
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
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
Cure Alzheimer's Fund is a 501(c)(3) public charity. At Cure Alzheimer's Fund, our mission is to fund research with the highest probability of slowing, stopping or reversing Alzheimer's disease. This topical portal has a lot of information including news and blog. Cure Alzheimer's Fund is governed by a board of directors; administered by a small, full-time staff; and guided scientifically by a Research Consortium. A Scientific Advisory Board audits the research program to make sure it is consistent with the objectives of the foundation. Cure Alzheimer's Fund is a doing business as name for the Alzheimer's Disease Research Foundation, federal tax ID # 52-2396428.
Proper citation: Cure Alzheimers Fund (RRID:SCR_003564) Copy
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
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
Consortium that brings together Europe's top industrial and academic experts to develop new tests that will help researchers detect potential liver toxicity issues much earlier in drug development, saving many patients from the trauma of liver failure. The team aims to deepen the understanding of the science behind drug-induced liver injury, and use that knowledge to overcome the many drawbacks of the tests currently used. A major focus will be on a systematic and evidence-based evaluation of both currently available and new laboratory test systems, including cultures of liver cells in one-dimensional and three dimensional configurations. The project will also develop models that take into account the natural differences between patients. This is important because factors such as certain genes, the liver's immune response, and viral infections have all been associated with an increased risk of DILI. The project will seek to address the current lack of human liver cells available to researchers by using induced pluripotent stem cells (iPSCs) generated from patients who are particularly sensitive to DILI. Another strand of the project will develop computer models to unravel the complex, often inter-related mechanisms behind DILI. Finally, the team will assess how accurate the results of laboratory tests are at predicting actual outcomes in patients.
Proper citation: MIP-DILI (RRID:SCR_003870) Copy
Data management platform and data repository based on the CKAN tool for managing and publishing collections of data. It enables the user to search for data, register published datasets, create and manage groups of datasets, and get updates from datasets and groups of interest.
Proper citation: Datahub (RRID:SCR_003996) Copy
A nonprofit, patient-focused, patient-run organization that provides non-medical services to those affected by chronic kidney disease (CKD). RSN strives to help patients develop their personal coping skills, special talents, and employability by educating and empowering them and their family members to take control of the course and management of the disease. RSN plays a vital role in providing lawmakers and policymakers with the patient''s perspective on the needs and capabilities of people with CKD.
Proper citation: Renal Support Network (RRID:SCR_004049) Copy
http://www.newmeds-europe.com/
Consortium that will develop new models and methods to enable novel treatments for schizophrenia and depression including three important missing tools that will facilitate the translation of scientific findings into benefits for patients. The project will focus on developing new animal models which use brain recording and behavioral tests to identify innovative and effective drugs for schizophrenia. The project will develop standardized paradigms, acquisition and analysis techniques to apply brain imaging, especially fMRI and PET imaging to drug development. It will examine how new genetic findings (duplication and deletion or changes in genes) influence the response to various drugs and whether this information can be used to choose the right drug for the right patient. And finally, it will try and develop new approaches for shorter and more efficient trials of new medication - trials that may require fewer patients and give faster results.
Proper citation: NEWMEDS (RRID:SCR_003872) Copy
Nonprofit organization committed exclusively to support research seeking the cause of the potentially debilitating kidney disease Focal Segmental Glomerulosclerosis (FSGS) and Nephrotic Syndrome, improve treatment and find a cure. NephCure Kidney International is: * Committed to funding research around the globe that will continue to move us closer to an improved treatment and a cure. * The primary source of information on Nephrotic Syndrome and FSGS. * Leading the charge for legislative action to provide more federal funding for research into Nephrotic Syndrome and FSGS. * Working to attract researchers to this field. * Educating the public and raising awareness about Nephrotic Syndrome and FSGS.
Proper citation: NephCure Kidney International (RRID:SCR_003993) Copy
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