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http://www.vph-noe.eu/

The VPH NoE is a project which aims to help support and progress European research in biomedical modeling and simulation of the human body. This project will improve our ability to predict, diagnose and treat disease, and have a dramatic impact on the future of healthcare, the pharmaceutical and medical device industries. The VPH Network of Excellence (VPH NoE) is designed to foster, harmonize and integrate pan-European research in the field of i) patient-specific computer models for personalised and predictive healthcare and ii) ICT-based tools for modeling and simulation of human physiology and disease-related processes. The main objectives of the VPH Network of Excellence are to support the: :- Coordination of research portfolios of VPH NoE partners through initiation of Exemplar integrative research projects that encourage inter-institution and interdisciplinary VPH research; :- Integration of research infrastructures of VPH NoE partners through development of the VPH ToolKit: a shared and mutually accessible source of research equipment, managerial and research infrastructures, facilities and services; :- Development of a portfolio of interdisciplinary training activities including a formal consultation on, and assessment of, VPH careers; :- Establishment of a core set of VPH-related dissemination and networking activities which will engage everyone from partners within the VPH NoE/other VPH projects, to national policy makers, to the public at large; :- Creation of Industrial, Clinical and Scientific Advisory Boards that will jointly guide the direction of the VPH NoE and, through consultation, explore the practical and legal options for real and durable integration within the VPH research community; :- Implementation of key working groups that will pursue specific issues relating to VPH, notably integrating VPH research worldwide through international physiome initiatives. Finally, by involving clinical and industrial stakeholders, VPH NoE also plans to lay a reliable ground to support sustainable interactions and collaboration between research and healthcare communities. Virtual Physiological Human lists, as its main target outcome, patient-specific computer models for personalized and predictive healthcare and ICT-based tools for modeling and simulation of human physiology and disease-related processes. Collaborative projects (IPs and STREPs) within the call will meet specific objectives, addressing: patient-specific computational modeling and simulation of organs or systems data integration and new knowledge extraction and clinical applications and demonstration of tangible benefits of patient-specific computational models. The networking action outlined within the call - the VPH NoE - should serve to connect these efforts, and lay the foundations for the methodological and technical framework to support such research. It should also build on previous EC investment in this field, including the outcomes of VPH type' projects funded within the EU Sixth Framework Programme, and through other National and International initiatives. The Virtual Physiological Human Network of Excellence (VPH NoE) has been designed with "service to the community" of VPH researchers as its primary purpose. Its aims range from the development of a VPH ToolKit and associated infrastructural resources, through integration of models and data across the various relevant levels of physiological structure and functional organization, to VPH community building and support. The VPH NoE aims to foster the development of new and sustainable educational, training and career structures for those involved in VPH related science, technology and medicine. The VPH NoE constitutes a leading group of universities, institutes and organizations who will, by integrating their experience and ongoing activities in VPH research, promote the creation of an environment that actively supports and nurtures interdisciplinary research, education, training and strategic development. The VPH NoE will lead the coordination of diverse activities within the VPH Initiative to help deliver: new environments for predictive, patient-specific, evidence-based, more effective and safer healthcare; improved semantic interoperability of biomedical information and contribution to a common health information infrastructure; facile, on-demand access to distributed European computational infrastructure to support clinical decision making; and increased European multidisciplinary research excellence in biomedical informatics and molecular medicine by fostering closer cooperation between ICT, medical device, medical imaging, pharmaceutical and biotech companies. The VPH NoE will connect the diverse VPH Initiative projects, including not only those funded as part of the VPH initiative but also those of previous EC frameworks and national funding schemes, together with industry, healthcare providers, and international organizations, thereby ensuring that these impacts will be realized. VPH NoE work packages and project structure The VPH NoE activities are divided between five main work packages (follow the links at the top of the page for more information on each). In brief, the focus of each work package is as follows: -Work package 1: Network Management -Work package 2: VPH NoE Exemplar Projects -Work package 3: VPH NoE ToolKit development -Work package 4: VPH NoE Training and Career Development -Work package 5: Spreading Excellence within the VPH NoE and VPH-I In view of its role as the networking action for the VPH Initiative, all VPH NoE activities have been designed to serve and interconnect not only the VPH NoE core members, but also the projects funded within the VPH call (VPH-I) and the wider research community. Key activities which the VPH NoE will pursue, in support of the development of a research environment which facilitates integrative, interdisciplinary and multilevel VPH research, are: -Support for integrative research -Training and dissemination activities -Networking activities Sponsors: VPH NoE is supported by The Directorate-General Research (DG RTD) and The Directorate-General Information Society and Media (DG INFSO).

Proper citation: Virtual Physiological Human Network of Excellence (RRID:SCR_002855) Copy   

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

Software package that provides an interface to simulate metabolic reconstruction from the BiGG database and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs.

Proper citation: BiGGR (RRID:SCR_002854) Copy   

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

An R package for predicting the activity of metabolic pathways based solely on a metabolomics data set containing a list of metabolites identified and their respective abundances in different biological samples. PAPi generates hypothesis that improves the final biological interpretation.

Proper citation: PAPi (RRID:SCR_002857) Copy   

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http://nbc.jhu.edu/

This center provides routine behavioral/cognitive testing of mice with phenotypes that are expressed as a consequence of alterations at the level of gene function, and that are relevant to basic neuroscience and to animal models of neurological and psychiatric disorders. Current Research Behavioral testing within the center involves a collaborative component in which mice provided by users are assessed for behavioral/cognitive functions. All research includes behavioral assessment of a variety of genetically altered mice provided by users. Services Provided The objective of the center is to provide a link between genetic and molecular analysis of neural function and the study of integrative systems and clinical conditions through behavioral assessment of animal models, and mouse behavioral phenotypes generated by genetic modification. Sponsors: This resource is supported by the National Center of Research Resources (Grant Number: P40 RR017688).

Proper citation: Neurogenetics and Behavior Center (RRID:SCR_002851) Copy   

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http://www.ambystoma.org/

Portal that supports Ambystoma-related research and educational efforts. It is composed of several resources: Salamander Genome Project, Ambystoma EST Database, Ambystoma Gene Collection, Ambystoma Map and Marker Collection, Ambystoma Genetic Stock Center, and Ambystoma Research Coordination Network.

Proper citation: Sal-Site (RRID:SCR_002850) Copy   

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http://www.nap.edu/

The National Academies Press (NAP) was created by the National Academies to publish the reports issued by the National Academy of Sciences, the National Academy of Engineering, the Institute of Medicine, and the National Research Council, all operating under a charter granted by the Congress of the United States. The NAP publishes more than 200 books a year on a wide range of topics in science, engineering, and health, capturing the most authoritative views on important issues in science and health policy. The institutions represented by the NAP are unique in that they attract the nation's leading experts in every field to serve on their award-winning panels and committees. This is the right place for definitive information on everything from space science to animal nutrition. Many books can be read on-line for free. NAP also offers many titles in electronic Adobe PDF format. Hundreds of these books can be downloaded for free by the chapter or the entire book, while others are available for purchase. Sponsors: This resource is supported by The National Academies.

Proper citation: National Academies Press (RRID:SCR_002844) Copy   

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http://www.ebi.ac.uk/arrayexpress/

International functional genomics data collection generated from microarray or next-generation sequencing (NGS) platforms. Repository of functional genomics data supporting publications. Provides genes expression data for reuse to the research community where they can be queried and downloaded. Integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. Data collected to MIAME and MINSEQE standards. Data are submitted by users or are imported directly from the NCBI Gene Expression Omnibus.

Proper citation: ArrayExpress (RRID:SCR_002964) Copy   

•   Source: SciCrunch Registry

http://www.uc.pt/en

Public university in Coimbra, Portugal that offers degree programs in a variety of fields including law, medicine, science and technology, pharmaceuticals, and sports sciences.

Proper citation: University of Coimbra; Coimbra; Portugal (RRID:SCR_002842) Copy   

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http://www.ncrr.nih.gov/clinical_research_resources/resource_directory/general_clinical_research_centers/program_information/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Through the General Clinical Research Centers (GCRC) program, NCRR funds a national network that provides settings for medical investigators to conduct safe, controlled, state-of-the-art, in-patient and out-patient studies of both children and adults. GCRCs also provide infrastructure and resources that support several career development opportunities.

Proper citation: General Clinical Research Centers Program (RRID:SCR_002847) Copy   

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http://www.mybiosoftware.com/population-genetics/332

A tool for SNP Search and downloading with local management. It also offers flanking sequence downloading and automatic SNP filtering. It requires Windows and .NET Framework.

Proper citation: SNPHunter (RRID:SCR_002968) Copy   

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http://www.jax.org/smsr/index.html

Resource of special strains of mice that are valuable tools for genetic analysis of complex diseases. They include panels of recombinant inbred (RI) and chromosome substitution (CS) strains.

Proper citation: Special Mouse Strains Resource (RRID:SCR_002885) Copy   

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http://berkeleybop.org/pkb/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This interface is for exploring data collected as part of the NIF Neurodegenerative Disease Ontology project. Not generally intended for public consumption yet, but people are welcome to look - large caveat emptor applies. Sponsors: This resource is part of the NIF project.

Proper citation: OBD-PKB Interface (RRID:SCR_002882) Copy   

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http://abel.ee.ucla.edu/cvxopt

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Software package for convex optimization based on the Python programming language. It can be used with the interactive Python interpreter, on the command line by executing Python scripts, or integrated in other software via Python extension modules. Its main purpose is to make the development of software for convex optimization applications straightforward by building on Pythons extensive standard library and on the strengths of Python as a high-level programming language. Current version includes the following features: * efficient Python classes for dense and sparse matrices (real and complex), with Python indexing and slicing and overloaded operations for matrix arithmetic * an interface to most of the double-precision real and complex BLAS * an interface to LAPACK routines for solving linear equations and least-squares problems, matrix factorizations (LU, Cholesky, LDLT and QR), symmetric eigenvalue and singular value decomposition, and Schur factorization * an interface to the fast Fourier transform routines from FFTW * interfaces to the sparse LU and Cholesky solvers from UMFPACK and CHOLMOD * routines for linear, second-order cone, and semidefinite programming problems * routines for nonlinear convex optimization * interfaces to the linear programming solver in GLPK, the semidefinite programming solver in DSDP5, and the linear, quadratic and second-order cone programming solvers in MOSEK * a modeling tool for specifying convex piecewise-linear optimization problems. A platform-independent source package and a binary Windows installer are available from the Download section. CVXOPT is also available precompiled for the major platforms: * Debian Linux * Ubuntu Linux * Fedora Linux * Python(x,y) for Microsoft Windows CVXOPT is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.

Proper citation: CVXOPT - Python Software for Convex Optimization (RRID:SCR_002918) Copy   

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http://www.neurogems.org/neosim/

Simulation software that includes a parallel discrete event simulation kernel for running models of spiking neurons on a cluster of workstations. Models are specified using NeuroML, and visualized using Java2D. Simulation components are distributed across a parallel machine or network and communicate using timestamped events. The successor NEOSIM2 project under the NeuroGems umbrella at Edinburgh University (http://www.neurogems.org) continues to distribute the software, http://www.neurogems.org/neosim2/ The NEOSIM project includes: * a parallel discrete event simulation kernel for running models of spiking neural networks on clusters of machines. * a modules kit for extending the behavior of neurons and connectivity patterns. * a user interface for building and running simulations. OS: Linux, MS-Windows

Proper citation: Neural Open Simulation (RRID:SCR_002916) Copy   

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http://cbio.mskcc.org/

Computational biology research at Memorial Sloan-Kettering Cancer Center (MSKCC) pursues computational biology research projects and the development of bioinformatics resources in the areas of: sequence-structure analysis; gene regulation; molecular pathways and networks, and diagnostic and prognostic indicators. The mission of cBio is to move the theoretical methods and genome-scale data resources of computational biology into everyday laboratory practice and use, and is reflected in the organization of cBio into research and service components ~ the intention being that new computational methods created through the process of scientific inquiry should be generalized and supported as open-source and shared community resources. Faculty from cBio participate in graduate training provided through the following graduate programs: * Gerstner Sloan-Kettering Graduate School of Biomedical Sciences * Graduate Training Program in Computational Biology and Medicine Integral to much of the research and service work performed by cBio is the creation and use of software tools and data resources. The tools that we have created and utilize provide evidence of our involvement in the following areas: * Cancer Genomics * Data Repositories * iPhone & iPod Touch * microRNAs * Pathways * Protein Function * Text Analysis * Transcription Profiling

Proper citation: Computational Biology Center (RRID:SCR_002877) Copy   

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http://www.mct.gov.br/index.php/content/view/323883.html

Proper citation: Brazilian Ministry of Science Technology and Innovation (RRID:SCR_002876) Copy   

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https://github.com/nichtich/marginalia/wiki/Support-of-PDF-annotations

Wiki that provides a listing (and associated links) of various formats to store and export annotations. Apparently everyone uses his own proprietary format to store and export annotations. The FDF format (or better its XML variant XFDF) is or was used by Acrobat to store form values and annotations, but third-party implementations focus on the forms-part of FDF instead of the annotations-part. * XML Forms Data Format Specification (XFDF) 2.0 (2007). * iText classes (no full FDF/XFDF implementation) ** FdfReader ** FdfWriter ** XfdfReader * The commercial software Adobe Digital Editions explicitly supports external annotations. The FAQ says Digital Editions supports bookmarks, highlights, and text notes via its bookmarks panel. These annotations are stored in an open XML format separately from publications to enable seamless annotation across PDF- and EPUB-based publications. They will set the stage for future social networking features (such as sharing annotations within a community of readers). * Okular has its own annotation exchange format, similar to PDF annotation (comparison is needed) ** internal API documentation ** There is no file format documentation, but the source code is mainly in the methods AnnotationUtils storeAnnotation and Annotation store * Xournal is open source and allows some annotation, but its PDF reading ability is very limited. It also uses its own format to store annotations * Mendeley supports annotations, which can be synced independent from the PDF files they refer to, and exported together with PDFs. There is no documentation of the API and format they use to exchange annotations. * Evernote is worth a view. But proprietary and no Linux client. * iAnnotate seems to be popular on the iPad - can it export and import annotations? In which format? There is a good article by Scott McLeod with screenshots about his use of iAnnotate and Evernote to take notes (June 15, 2010). http://blogs.edweek.org/edweek/LeaderTalk/2010/06/tools_for_school_digital_docum.html

Proper citation: Support-of-PDF-annotations (RRID:SCR_002871) Copy   

•   Source: SciCrunch Registry

http://www.iscos.org.uk

ISCoS promotes the highest standard of care in the practice of spinal cord injury for men, women and children throughout the world. Through its medical and multi disciplinary team of Professionals ISCoS endeavours to foster education, research and clinical excellence. ISCoS has a membership of over 1,000 Clinicians and Scientists from 87 countries. They regularly update their knowledge at the Annual Scientific Meeting held in a different country each year. Goals of ISCoS: :- Serve as an international impartial, non-political and non-profit making association whose purpose is to study all problems relating to traumatic and non-traumatic lesions of the spinal cord. This includes causes, prevention, basic and clinical research, medical and surgical management, clinical practice, education, rehabilitation and social reintegration. This society will function in close collaboration with other national and international bodies, thereby encouraging the most efficient use of available resources. :- Provide a scientific exchange among its members and others by collecting and disseminating information through publications, correspondence, exhibits, regional and international seminars, symposia, conferences and otherwise. :- Advise, encourage, promote and when requested, assist in efforts to co-ordinate or guide research, development and evaluation activities related to spinal cord lesions throughout the world. :- Advise, encourage, guide and support the efforts of those responsible for the care of patients involved and when requested, correlate these activities throughout the world. :- Advise, encourage, guide and support the efforts of those responsible for the education and training of medical professionals and professionals allied to medicine and when requested, correlate these activities throughout the world.

Proper citation: International Spinal Cord Society (RRID:SCR_002908) Copy   

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http://www.ncbi.nlm.nih.gov/lovd/home.php?select_db=OCRL

The Lowe Syndrome Mutation Database is now being maintained by the National Center for Biotechnology Information (NCBI) at the National Institutes of Health. A database of mutations causing Lowe syndrome. Information on new mutations may be submitted online. Lowe oculocerebrorenal syndrome is an X-linked disorder caused by mutations in the OCRL1 gene, which encodes a 105-kDa Golgi protein with phosphatidylinositol (4,5) bisphosphate 5-phosphatase activity. genetics

Proper citation: Lowes Syndrome Mutation Database (RRID:SCR_002907) Copy   

•   Source: SciCrunch Registry

http://www.bhf.org.uk/

British charity and fundraiser for cardiovascular research.

Proper citation: British Heart Foundation (RRID:SCR_002905) Copy   

•   Source: SciCrunch Registry