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http://neuroscienceblueprint.nih.gov/

Collaborative framework that includes the NIH Office of the Director and the 14 NIH Institutes and Centers that support research on the nervous system. By pooling resources and expertise, the Blueprint identifies cross-cutting areas of research, and confronts challenges too large for any single Institute or Center. The Blueprint makes collaboration a day-to-day part of how the NIH does business in neuroscience, complementing the basic missions of Blueprint partners. During each fiscal year, the partners contribute a small percentage of their funds to a common pool. Since the Blueprint's inception in 2004, this pool has comprised less than 1 percent of the total neuroscience research budget of the partners. In 2009, the Blueprint Grand Challenges were launched to catalyze research with the potential to transform our basic understanding of the brain and our approaches to treating brain disorders. * The Human Connectome Project is an effort to map the connections within the healthy brain. It is expected to help answer questions about how genes influence brain connectivity, and how this in turn relates to mood, personality and behavior. The investigators will collect brain imaging data, plus genetic and behavioral data from 1,200 adults. They are working to optimize brain imaging techniques to see the brain's wiring in unprecedented detail. * The Grand Challenge on Pain supports research to understand the changes in the nervous system that cause acute, temporary pain to become chronic. The initiative is supporting multi-investigator projects to partner researchers in the pain field with researchers in the neuroplasticity field. * The Blueprint Neurotherapeutics Network is helping small labs develop new drugs for nervous system disorders. The Network provides research funding, plus access to millions of dollars worth of services and expertise to assist in every step of the drug development process, from laboratory studies to preparation for clinical trials. Project teams across the U.S. have received funding to pursue drugs for conditions from vision loss to neurodegenerative disease to depression. Since its inception in 2004, the Blueprint has supported the development of new resources, tools and opportunities for neuroscientists. For example, the Blueprint supports several training programs to help students pursue interdisciplinary areas of neuroscience, and to bring students from underrepresented groups into the neurosciences. The Blueprint also funds efforts to develop new approaches to teaching neuroscience through K-12 instruction, museum exhibits and web-based platforms. From fiscal years 2007 to 2009, the Blueprint focused on three major themes of neuroscience - neurodegeneration, neurodevelopment, and neuroplasticity. These efforts enabled unique funding opportunities and training programs, and helped establish new resources including the Blueprint Non-Human Primate Brain Atlas.

Proper citation: NIH Blueprint for Neuroscience Research (RRID:SCR_003670) Copy   

•   Source: SciCrunch Registry

http://vano.cellexplorer.org/

VANO is a Volume image object AnNOtation System for 3D multicolor image stacks, developed by Hanchuan Peng, Fuhui Long, and Gene Myers. VANO provides a well-coordinated way to annotate hundreds or thousands of 3D image objects. It combines 3D views of images and spread sheet neatly, and is just easy to manage 3D segmented image objects. It also lets you incorporate your segmentation priors, and lets you edit your segmentation results! This system has been used in building the first digital nuclei atlases of C. elegans at the post-embryonic stage (joint work with Stuart Kim lab, Stanford Univ), the single-neuron level fruit fly neuronal atlas of late embryos (with Chris Doe lab, Univ of Oregon, HHMI), and the compartment-level of digital map(s) of adult fruit fly brains (several labs at Janelia Farm, HHMI). VANO is cross-platform software. Currently the downloadable versions are for Windows (XP and Vista) and Mac (Intel-chip based, Leopard or Tiger OS). If you need VANO for different systems (such as 64bit or 32bit, Redhat Linux, Ubuntu, etc), you can either compile the software, or send an email to pengh (at) janelia.hhmi.org. VANO is Open-Source. You can download both the source code files and pre-complied versions at the Software Downloads page.

Proper citation: Volume image object AnNOtation System (RRID:SCR_003393) Copy   

•   Source: SciCrunch Registry

http://www.mindtouch.com/

A web based social authoring and publishing environment that adheres to open standards and RESTful design principals. It provides wiki-like ease of use with a sophisticated web services framework for rapid application development, creating flexible workflows and rapid integration. MindTouch creates a vibrant real-time information fabric by federating content from across enterprise silos, such as CRM, ERP, file servers, email, databases, web services and more.

Proper citation: Mindtouch DekiWiki (RRID:SCR_003425) Copy   

•   Source: SciCrunch Registry

http://www.addconsortium.org/

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   

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http://portal.ncibi.org/gateway/mimiplugin.html

The Cytoscape MiMI Plugin is an open source interactive visualization tool that you can use for analyzing protein interactions and their biological effects. The Cytoscape MiMI Plugin couples Cytoscape, a widely used software tool for analyzing bimolecular networks, with the MiMI database, a database that uses an intelligent deep-merging approach to integrate data from multiple well-known protein interaction databases. The MiMI database has data on 119,880 molecules, 330,153 interactions, and 579 complexes. By querying the MiMI database through Cytoscape you can access the integrated molecular data assembled in MiMI and retrieve interactive graphics that display protein interactions and details on related attributes and biological concepts. You can interact with the visualization by expanding networks to the next nearest neighbors and zooming and panning to relationships of interest. You also can perceptually encode nodes and links to show additional attributes through color, size and the visual cues. You can edit networks, link out to other resources and tools, and access information associated with interactions that has been mined and summarized from the research literature information through a biology natural language processing database (BioNLP) and a multi-document summarization system, MEAD. Additionally, you can choose sub-networks of interest and use SAGA, a graph matching tool, to match these sub-networks to biological pathways.

Proper citation: MiMI Plugin for Cytoscape (RRID:SCR_003424) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://edoctoring.ncl.ac.uk/Public_site/

Online educational tool that brings challenging clinical practice to your computer, providing medical education that is engaging, challenging and interactive. While there is no substitute for real-life direct contact with patients or colleagues, research has shown that interactive online education can be a highly effective and enjoyable method of learning many components of clinical medicine, including ethics, clinical management, epidemiology and communication skills. eDoctoring offers 25 simulated clinical cases, 15 interactive tutorials and a virtual library containing numerous articles, fast facts and video clips. Their learning material is arranged in the following content areas: * Ethical, Legal and Social Implications of Genetic Testing * Palliative and End-of-Life Care * Prostate Cancer Screening and Shared Decision-Making

Proper citation: eDoctoring (RRID:SCR_003336) Copy   

•   Source: SciCrunch Registry

http://rgd.mcw.edu/tools/ontology/ont_search.cgi

Ontology that defines hierarchical display of different rat strains as derived from parental strains. Ontology Browser allows to retrieve all genes, QTLs, strains and homologs annotated to particular term. Covers all types of biological pathways including altered and disease pathways, and to capture relationships between them within hierarchical structure. Five nodes of ontology include classic metabolic, regulatory, signaling, drug and disease pathways. Ontology allows for standardized annotation of rat. Serves as vehicle to connect between genes and ontology reports, between reports and interactive pathway diagrams, between pathways that directly connect to one another within diagram or between pathways that in some fashion are globally related in pathway suites and suite networks.

Proper citation: Rat Strain Ontology (RRID:SCR_003449) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.curealzfund.org/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.mip-dili.eu/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.k4dd.eu/

Project whose goal is to improve understanding of how potential drugs bind with their target, and develop methods and tools to allow researchers to study drug-target interactions with greater ease. These tools would help researchers to determine whether a drug candidate is likely to be safe and effective much earlier in the drug development process. The first goal of the team is to enhance understanding of binding kinetics; exactly how do small molecules interact with their targets? Ultimately, the project aims to develop a range of robust techniques, methods and models that could be easily incorporated into the drug development pathway and enable scientists and drug designers worldwide to reliably predict a molecule's kinetic properties (its "kinotype"). This information will allow drug developers to more easily determine the safety and efficacy of a molecule and will weed out ineffective or unsafe molecules earlier in the drug development process. Eventually, the project also hopes to raise awareness of the importance of considering the kinetic aspects of drug-target interactions throughout drug development.

Proper citation: Kinetics for Drug Discovery (RRID:SCR_003868) Copy   

•   Source: SciCrunch Registry

http://www.biovacsafe.eu/

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   

•   Source: SciCrunch Registry

http://dialysispatients.org/

A nationwide, non-profit, patient-led organization with membership open only to dialysis and pre-dialysis patients and their families working to improve the quality of life for all dialysis patients through education and advocacy. They are dedicated to developing awareness of dialysis issues, advocating for dialysis patients, promoting favorable public policy and improving the partnership between patients and caregivers. Their policies and their mission are guided solely by their membership.

Proper citation: Dialysis Patient Citizens (RRID:SCR_003981) Copy   

•   Source: SciCrunch Registry

http://www.aditecproject.eu/

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   

•   Source: SciCrunch Registry

http://www.abirisk.eu/

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   

•   Source: SciCrunch Registry

http://www.imi.europa.eu/content/eu-aims

Consortium aiming to generate tools that will enhance understanding of autism spectrum disorders (ASD) and pave the way for the development of new, safe and effective treatments for use in both children and adults. For example, the team will gather samples from people bearing certain mutations associated with ASD; this will pave the way for the generation of cell lines that can be used to test treatments. Elsewhere, the researchers will advance the use of brain scans as a tool to boost ASD drug discovery and also identify which people with ASD might respond best to a given drug. The project will also create a pan-European network of clinical sites. As well as making it easier to run clinical trials, this network will create an interactive platform for those with ASD and professionals. By the end of the 5 year project they expect to provide novel validated cellular assays, animal models, new fMRI methods with dedicated analysis techniques, new PET radioligands, as well as new genetic and proteomic biomarkers for patient-segmentation or individual response prediction. They will provide a research network that can rapidly test new treatments in man. These tools should provide their EFPIA partners with an added competitive advantage in developing new drugs for ASD.

Proper citation: EU-AIMS (RRID:SCR_003861) Copy   

•   Source: SciCrunch Registry

http://www.era-edta.org/

An association of European kidney specialists whose objective is advancement of medical science and of clinical work in nephrology, dialysis, renal transplantation, hypertension and related subjects. They aim at providing up-to-date knowledge, exclusively based on scientific data, independent from governments'' policies and from any influence of the industry. It is registered in England and Wales, but its area of activity mainly covers Europe and the Mediterranean area.

Proper citation: ERA-EDTA (RRID:SCR_003982) Copy   

•   Source: SciCrunch Registry