Useful resources

BIOMODELS DATABASE

BioModels Database is a repository of computational models of biological processes. It hosts models described in peer-reviewed scientific literature and models generated automatically from pathway resources (Path2Models). A large number of models collected from literature are manually curated and semantically enriched with cross-references from external data resources (such as publications, databases of compounds and pathways, ontologies, etc.). The resource allows scientific community to store, search and retrieve mathematical models of their interest. In addition, features such as generation of sub-models, online simulation, conversion of models into different representational formats, and programmatic access via web services, are provided. All models are provided under the terms of the Creative Commons CC0 Public Domain Dedication, cf. its terms of use. This means that the models are available freely for use, modification and distribution, to all users. Users can browse and search the content of the repository, and download models in SBML format, as well as various other formats, such as XPP, VCML, SciLab, Octave, BioPAX, PNG, SVG, ... A human readable summary of each model is also available in PDF.

Link: ebi.ac.uk/biomodels-main

CARDIAC ATLAS PROJECT

The Cardiac Atlas Project seeks to establish a structural and functional atlas of the heart. This project is dedicated to combine cardiac modeling and biophysical analysis methods with a structural database for the comprehensive mapping of heart structure and function. The Cardiac Atlas Project has collected more than 2,500 de-identified cardiac patients along with their corresponding 3D finite element models. Researchers can therefore apply to access the cardiac data for specific research projects and clinicians are encouraged to contribute new cases.

Link: cardiacatlas.org

CARDIOVASCULAR AND PULMONARY MODEL REPOSITORY

This repository was constructed under the direction of the National Heart, Lung, and Blood Institute. The goal of this website is to maintain a library of computational models of normal and diseased human cardiovascular and pulmonary anatomy and input and output boundary conditions for various physiologic states. These models can be used to simulate cardiovascular and pulmonary solid and fluid mechanics and will provide spatially and temporally-resolved benchmark solutions that can be used by academic, government and industry researchers to verify their computational methods.

Link: vascularmodel.com/sandbox/doku.php?id=start

CELLDESIGNER.ORG

CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system proposed by Kitano, and are stored using the Systems Biology Markup Language (SBML), a standard for representing models of biochemical and gene-regulatory networks. Networks are able to link with simulation and other analysis packages through Systems Biology Workbench (SBW). CellDesigner supports simulation and parameter scan by an integration with SBML ODE Solver, SBML Simulation Core and Copasi. By using CellDesigner, one can browse and modify existing SBML models with references to existing databases, simulate and view the dynamics through an intuitive graphical interface.

Link: celldesigner.org

CELLML PROJECT

The CellML language is an open standard based on the XML markup language. CellML is being developed by the Auckland Bioengineering Institute at the University of Auckland and affiliated research groups. The purpose of CellML is to store and exchange computer-based mathematical models. CellML allows scientists to share models even if they are using different modelling tools. It also enables them to reuse components from one model in another, thus accelerating model development.

Link: cellml.org

COLOR ATLAS OF MEDICAL DISEASES

USIMD is a team of practicing healthcare professionals whose vision is to apply innovative and accessible technologies to enhance the relationship between patients and those who treat them. Utilizing new and proven Internet technologies, USIMD have created tools to facilitate access to healthcare information and services in a compelling and understandable format so that consumers can take more and better control of their own health needs. They also have built web-based tools for healthcare professionals to support and enhance the delivery of services to their patients, such as the Color Atlas of Medical Diseases.

Link: ecureme.com/atlas/version2001/atlas.asp

DDMORE

The Drug Disease Model Resources (DDMoRe) consortium builds and maintains a universally applicable, open source, model based framework, intended as the gold standard for future collaborative drug and disease Modelling & Simulation. Key Objectives:

• Enable efficient exchange and integration of modelling activities.
• Outputs across software tools, disciplines and departments within and among organizations.
• Provide standards applicable to all areas of Modelling and Simulation, appropriate for adoption and use by all relevant domain stakeholders.
• Development of an open, publicly available, free-to-use model repository, based on the developed standards, to promote the re-use of models.
• The model repository may evolve into a global reference for model-based efforts in the therapeutic areas Diabetes, Oncology and Other Diseases.
• Provide support for education and training in drug/disease Modelling and Simulation.

Link: ddmore.eu

ExPASy

ExPASy is the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. On this portal one can find resources from many different SIB groups as well as external institutions.

Link: expasy.org

MedPix®

MedPix® is a free online Medical Image Database and Radiology Portal, provided by the Departments of Radiology and Biomedical Informatics, Uniformed Services University, Bethesda, MD. MedPix® is a fully web-enabled cross-platform database, integrating images and textual information. Its primary target audience includes physicians and nurses, allied health professionals, medical students, graduate nursing students and other post-graduate trainees.

Link: rad.usuhs.edu/medpix/#pic

METAMODL

METAMODL is a web-based library of models, public source clinical outcome data and software tools to support strategic decision-making via model-based meta-analysis and disease progression models. METAMODL subscriptions are delivered via the web and feature a secure user-friendly interface to:

• Standardized public-source data for several therapeutic areas, primarily in the form of summary statistics for clinical outcomes as well as detailed descriptions of assigned treatments, the patient population and other trial characteristics. Publicly available individual data is included when possible.
• Mathematical models describing clinical outcomes or biomarkers as a function of treatment (typically drug and dose), time and patient characteristics.
• Computer scripts to implement and extend those models.
• Standard and premium subscribers have access to the data sets and models for all therapeutic areas.
• Limited subscriptions are also available for access to individual therapeutic areas.
• The target data deliverables for all therapeutic areas are model-ready data sets.
• The data sets and models are regularly updated (at least annually), so they are always kept relevant to the current marketplace.

Link: metamodl.com

Open Repository

Open Repository is a hosted solution from BioMed Central that builds and maintains customized DSpace repositories on behalf of institutions and organizations. This allows an institution to preserve and showcase its intellectual output to a larger and unrestricted audience. Whilst built using open source DSpace software, the Open Repository service offers a number of additional benefits to users over the alternative of building an in-house solution. As well as providing stable and transparent pricing, Open Repository provides a range of extra features and support not available with the standard software. This includes full customization, backup and advanced download statistics.

Link: openrepository.com

Open Science Repository

The Open Science Repository publishes original research papers under open access. All papers in the Open Science Repository are open-access papers, readers do not need to pay to get access to full research content. Researchers from all fields of science can publish original papers and other scholarly communications through the sections of the Open Science Repository.

Link: open-science-repository.com

OpenSim

OpenSim is an open source software system for biomechanical modeling, simulation and analysis. Its purpose is to provide free and widely accessible tools for conducting biomechanics research and motor control science. OpenSim enables a wide range of studies, including analysis of walking dynamics, studies of sports performance, simulations of surgical procedures, analysis of joint loads, design of medical devices, and animation of human and animal movement. The software performs inverse dynamics analysis and forward dynamics simulations. OpenSim is used in hundreds of biomechanics laboratories around the world to study movement and has a community of software developers contributing new features. OpenSim is one of the flagship applications from Simbios, a NIH Center for Biomedical Computation at Stanford University.

Link: opensim.stanford.edu

OrthopaedicsOne

OrthopaedicsOne is the collaborative orthopaedic knowledge network for orthopaedic surgeons and musculoskeletal health care professionals - a repository of educational materials and a professional network for the exchange of information. All members can add or edit information throughout the workspace and all content is protected by a Creative Commons License to improve knowledge translation. OrthopaedicsOne has Managing Editors, Editors, Content Partners, an Advisory Board, Participating Groups, and Sponsoring Organizations but it belongs to the Community of Practice for orthopaedics and musculoskeletal health.

Link: orthopaedicsone.com/display/Main/Home

PATIENT CONTRIBUTED IMAGE REPOSITORY (PCIR)

The purpose of the PCIR is to allow patients to directly contribute their own medical images to the public domain for re-use for research, software development and education. From this website, researcher have at their disposal medical images and reports that have been de-identified and anonymized. There are no restrictions on their use. Anyone may download them. There is no data use agreement required to be signed. No login is necessary. The available images are packaged as bzip'd tar files containing one or more studies and their accompanying documentation. Mostly commonly, these packaged sets contain a single study in DICOM format files, and may or may not contain accompanying report documents. The latter, if present, will most commonly be DICOM secondary capture files if they were provided as scanned paper documents by the contributor.

Link: pcir.org

PhysiomeSpace

PhysiomeSpace is the digital library service designed to help researchers to share their biomedical data and models. PhysiomeSpace is accessible via the browser, and it allows managing the access permissions to own resources and searching for data made available by others. To facilitate discovery all data published into the repository have their metadata information public, but the access to the data itself is completely under the control of the data owner. To upload and download data to/from the repository a client application is made available, which allows to structure and visualize data, and to annotate them with the necessary metadata information. The system is free to use but it requires registration with a professional identity.

Link: physiomespace.com

VPH-Share

VPH-Share is a 4-year Integrated Project co-funded under the European Community's 7th Framework Programme aiming at building a safe, online facility in which medical simulation developers can produce workflows - chains of processing tasks - to allow raw medical data to be refined into meaningful diagnostic and therapeutic information. Via an easy to use graphical interface, all the functions needed by workflow developers are provided, including design, construction, data-access and storage, and high-speed computations. By allowing users to work collaboratively, and concentrate only on the actual workflow design process, we estimate that over half the tasks usually associated with workflow project construction can be avoided. The services are currently in beta release and accessible via a web application. The access is free but it requires registration.

Link: portal.vph-share.eu

P-MEDICINE PORTAL

“p-medicine - From data sharing and integration via VPH models to personalized medicine” is a 4-year Integrated Project co-funded under the European Community's 7th Framework Programme aiming at developing new tools, IT infrastructure and VPH models to accelerate personalized medicine for the benefit of the patient. The p-medicine portal provides clinicians, patients and researchers a platform to collaborate, share data and expertise, and use tools and services to improve personalized treatments of patients. The p-medicine portal is a single web-based environment from which most of the p-medicine applications can run. These applications are integrated together in a consistent and systematic way in the form of a web-based user interface. Access to the portal will be given after registration.

Link: pmedportal.ibmt.fraunhofer.de/workbench

Veterinary Support Personnel Network (VSPN)

The Veterinary Support Personnel Network supports the advancement of veterinary medicine by providing a worldwide community for veterinary support staff complete with message boards, resources, continual education, and interactive sessions in an encouraging, collaborative and sharing environment.

Link: vspn.org

Virtual Metabolic Human

The Virtual Metabolic Human is a freely available database that includes three resources:

• The most recent version of the human metabolic reconstruction (Recon2, Thiele et al., Nat Biotech, 2013)
• A collection of semi-curated metabolic reconstructions of human gut microbes. Having the metabolism of microbes and the human host combined in one database will allow more comprehensive scientific questions, such as metabolites unique to the microbiota, reactions/enzymes unique to the human providing potential microbial specific drug targets.
• A manually assembled compendium of inherited metabolic disease (Sahoo, Franzson et al. Molecular BioSystems., 2012). The database permits to connect the knowledge about clinical phenotypes, affected organs, and disease associated genes with the broader context of human metabolism.

The resources in the VMH database will be continuously updated and extended. We will add more human metabolic content and more gut microbial reconstructions in the near future.

Link: vmh.uni.lu