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Showing 1 to 36 of 36 items tagged as collaborative


Neuro-Ophthalmology Virtual Education Library (NOVEL)

database

Provider: Spencer S. Eccles Health Sciences Library, University of Utah/North American Neuro-Ophthalmology Society (NANOS)
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Descriptions: A discipline-specific, open-access repository of digital materials (images, video, lectures, articles and animations), to be used for educational and research purposes by health care professionals, educators, patients, and students. Features include a patient-specific portal, an ophthalmology curriculum outline, a list of outside resources, and a guide to contributing materials to the site. Many articles from Journal of Neuro-Ophthalmology are available here. Initial funding was provided by the National Library of Medicine. Materials may be used with proper attribution, under a Creative Commons license. This resource is still very much in development, but contains much useful material.
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Structural Biology Knowledgebase

database

Provider: Nature.com and PSI (Protein Structure Initiative)
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Descriptions: The Structural Biology Knowledgebase (SBKB) is the product of a collaboration between the Protein Structure Initiative (PSI) and Nature Publishing Group (NPG.) The site offers an easy way of keeping up to date on the latest developments from the PSI, and more generally, in the fields of structural genomics and structural biology. Some areas of this site require a free registration involving affirmation of a statement declaring that one's purpose is strictly non-commercial and that one is an academic.
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Protein Data Bank: An Information Portal to Biological Macromolecular Structures

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Provider: RCSB (Research Collaboratory for Structural Bioinformatics)
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Descriptions:  "The RCSB (Research Collaboratory for Structural Bioinformatics) is dedicated to improving our understanding of the function of biological systems through the study of the 3-D structure of biological macromolecules. RCSB members work cooperatively and equally through joint grants and subsequently provide free public resources and publications to assist others and further the fields of bioinformatics and biology."  Protein Data Bank (PDB) curates and annotates data according to agreed-upon standards and is a member of the ww (world wide) PDB. Use this database to perform simple and advanced searches based on sequence, structure and function annotations, and to visualize, download, and analyze molecules. The database is primarily for researchers, but the site also includes an entire section (PDB101) of information quite accessible enough for educational purposes. Check out the "Molecule of the Month" feature. The extensive archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies.  As with many scientific databases, a personal log-in affords access to more features. The database is managed by Rutgers and University of California San Diego.
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Internet Archive

website

Provider: Internet Archive (nonprofit organization)
Descriptions: The Internet Archive, a digital library of Internet sites and other cultural artifacts, holds a great many free diversions, and many of these are educational-- full-text books, university lectures, music, films, photography and software. There is also the Wayback Machine, for viewing earlier versions of websites: "Browse through 85 billion web pages archived from 1996 to a few months ago." In collaboration with the National Federation of the Blind, Internet Archive now also provides free access to more than a million books for blind, sight-impaired and dyslexic readers.
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BioMedSearch.com

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Provider: BioMedSearch.com
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Descriptions: BioMedSearch combines Medline/PubMed citations with data from other sources- dissertations, theses, practice guidelines-  with the aim of creating the most comprehensive biomedical literature search available. Free registration gives the user access to advanced account features: saved searches, alerts, saving documents to portfolios, commentary and sharing of documents with other registered users. Registration is unnecessary for searching without advanced features. This search engine also provides grouped subject clusters and sub-clusters for refinement of results, and detailed syntax instructions and record field abbreviations for use in Advanced search mode. Browser plug-ins are supplied for Chrome, Firefox and Internet Explorer.
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iBridge Network

website

Provider: Kauffman Innovation Network, Inc.
Descriptions: "Linking ideas & innovation" is the motto of the iBridge organization. "While traditional search engines provide a means for looking for information, the iBridgeSM Network provides a public, centralized source for unbiased information about early stage technologies and inventions. Our objective is to drive transparency and access to university developed innovations that are available today as well as to field experts, ideas and information. Through the iBridgeSM Network, researchers and those seeking innovations can easily search for and obtain the resources they need." Non-members exploring this site can view the brief descriptions of inventions/innovations by subject or by organization, and see which of these organizations form special communities in iBridge. A free sign-up allows the user to e-mail for more information about the entries. Submissions include technologies that can be licensed, research opportunities, material transfer agreements, and laboratory and equipment availability. The provocative and informative blogs here are accessible to all who visit the site. iBridge is funded in large part by the Kauffman Foundation.
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Global Network for Neglected Tropical Diseases

website

Provider: The Global Network for Neglected Tropical Diseases is an advocacy initiative dedicated to raising the awareness, political will, and funding necessary to control and eliminate the most common neglected tropical diseases (NTDs)--a group of disabling, disfiguring, and deadly diseases affecting more than 1.4 billion people worldwide who live on less than $1.25 a day.
Descriptions: The Global Network for Neglected Tropical Diseases is an advocacy initiative dedicated to raising the awareness, political will, and funding necessary to control and eliminate the most common neglected tropical diseases (NTDs)--a group of disabling, disfiguring, and deadly diseases affecting more than 1.4 billion people worldwide who live on less than $1.25 a day.
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Systematic Review Data Repository

database

Provider: AHRQ (Agency for Healthcare Research and Quality)
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Descriptions: In an effort to reduce the burden of conducting systematic reviews, the Evidence-based Practice Center (EPC) at Tufts Medical Center, with support from the Agency for Healthcare Research and Quality (AHRQ), developed a collaborative, web-based repository of systematic review data. This resource serves as both an archive and data extraction tool and is shared among organizations and individuals producing systematic reviews worldwide, enabling the creation of a central database of systematic review data which may be critiqued, updated, and augmented on an ongoing basis. This database is made freely accessible to facilitate evidence reviews, which in turn can improve and facilitate healthcare policy-making. To contribute comments or data, register for a free personal account.
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World Digital Library

website

Provider: Library of Congress and UNESCO (United Nations Education, Scientific and Cultural Organization)
Descriptions: Initiated as a joint project of the Library of Congress and UNESCO (United Nations Education, Scientific and Cultural Organization) and launched in 2009, the World Digital Library is a curated collection of a variety of digitized items- books, art, film, periodicals and more, many of them considered primary source materials- representing the cultural identities and histories of UNESCO's member nations through every branch of learning. In the initial exploration one can view thumbnails of content according to time, place, topic, item type or institution.
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Encyclopedia of Life

website

Provider: Encyclopedia of Life
Descriptions: The Encyclopedia of Life is a work in progress that aims to dynamically synthesize biodiversity knowledge about all known species: taxonomy, geographic distribution, genetics, evolutionary history, morphology, behavior, ecological relationships, and importance for human well being. As it becomes more complete, it may serve as the primary resource for scientists, natural resource managers, conservationists, teachers, and students around the world. The EOL's creators and contributors believe that "...its encompassing scope and innovation will have a major global impact in facilitating biodiversity research, conservation, and education." The EOL is staffed by both scientists and non-scientists working from museums and research institutions around the world.
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Diigo

website

Provider: Diigo.com
Descriptions: Diigo (said to stand for Digest of Internet Information, Groups and Other stuff) began as a simple, free bookmarking tool, but now includes features that enable sharing and collaboration, page archiving and public or private sticky-note style annotation. Mobile applications are available, along with browser toolbars. Educators can apply for free access to a premium version with features helpful in the classroom setting. Instructions for migrating from Delicious are posted on the site.
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OpenThesis

database

Provider: OpenThesis.org
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Descriptions: OpenThesis is primarily an international repository of free abstracts of theses, dissertations and other academic documents, enhanced by search, organization and collaboration tools. It also provides e-publishing and conventional publishing services for modest prices, including print-on-demand.
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NIH Data Sharing Repositories

database

Provider: National Institutes of Health/National Library of Medicine
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Descriptions: This is a portal with a sortable list of 45 NIH and outside entities' data repositories and data-sharing facilitation sites that offer open-source software. Links to submission and download policies and instructions are provided for each. Research areas include: genomics of the nematode, drosophila, zebrafish and rat; sequencing data; peptides and proteins; pathogens and vectors; the NCI cancer imaging repository; neuroscience, rare diseases, Parkinson's, autism, and more.
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Proteopedia: Life in 3-D

database

Provider: Weizmann Institute of Science
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Descriptions: Proteopedia is a free, collaborative (wiki) 3-D encyclopedia of proteins and other molecules. The images can be reduced and restored by component with a toggle, or caused to rotate from any starting angle. Contains an introduction to structural biology and features sections on biomolecules, enzymes, metabolism, gene expression/replication, diseases, immune system, and methods of determining and analyzing structure and sequence. Contains a table of contents and a detailed structure index
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NextBio Basic

database

Provider: NextBio
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Descriptions: NextBio Basic is a free web application for searching biomedical and genetic information. It provides access to a 'curated, correlated database' of public data into which NextBio integrates Medline literature, clinical trial information, and news. Its semantic framework is based on gene, tissue, disease and compound ontologies. Registered users (registration for this basic version is free) can personalize their experience, communicate, collaborate and share data with the rest of the NextBio community. For the registered user, a single search for a gene yields quick results arranged by category: an overview of the gene; a list of tissues in which the gene is expressed; diseases and compounds relating to the gene; a list of the top associated researchers and authors; literature, associated clinical trials, and more.
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Neuroscience Information Framework

database

Provider: National Institutes of Health
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Descriptions: The Neuroscience Information Framework is a dynamic inventory of web-based neuroscience resources: data, materials, and tools. An initiative of the NIH Blueprint for Neuroscience Research, NIF advances neuroscience research by enabling discovery and access to public research data and tools worldwide through an open source, networked environment. The NIF project is designed to serve the biomedical research community. The more participation from the community, the better the NIF... Collaborating institutions working on the current version of NIF include University of California, San Diego, California Institute of Technology, George Mason University, Yale University Medical College, and Washington University.
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Mendeley

database

Provider: Mendeley Ltd.
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Descriptions: Mendeley is an open-access reference management tool. Use drag-and-drop to add references to your list, or add via web import. Easily create bibliographies and insert citations into papers by adding a plug-in for your word processing program. Includes an integral pdf viewer that allows highlighting and annotation. Organize with list-sorting and by adding folders. Mendeley also provides for creation of one's own research profile and for setting up private and public groups for collaboration and sharing, with additional useful features for keeping everything clear and organized. A crowd-sourced catalog of citations provided in public groups can be viewed by subject area and individual citations may be downloaded to one's account. A subscription version of Mendeley provides expanded storage for groups and individuals, and technical support, space and flexible collaboration features for "Team" implementations. Note: The TMC Library does not provide particular support for this application.
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Atlas of Genetics and Cytogenetics in Oncology and Haematology

website

Provider: Jean-Loup Huret, Universite' de Poitiers
Descriptions: A contributory website- part database, part journal, according to the editors- meant for the use of clinicians and researchers in cytogenetics, molecular biology, oncology, hematology and pathology. Includes a portal to relevant websites and databases, a listing of scientific meetings and societies, and a section of university-level educational resources. Use of the contributors' original content is governed by terms of a Creative Commons license.
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STITCH (Search Tool for Interactions of Chemicals) 3.1: Chemical-Protein Interactions

website

Provider: University of Copenhagen, European Molecular Biology Laboratory, Swiss Institute of Bioinformatics, Technische Universitat Dresden, Universitat Zurich
Descriptions: STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature. STITCH contains interactions for over 74,000 small molecules and over 2.5 million proteins in 630 organisms." Search by single or multiple: name, chemical structure, or protein sequence; qualify by organism.
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Project Gutenberg – Online Catalog

website

Provider: Project Gutenberg
Descriptions: "Project Gutenberg is the place where you can download over 33,000 free ebooks to read on your PC, iPad, Kindle, Sony Reader, iPhone, Android or other portable device. We carry high quality items: Our books were previously published on paper by bona fide publishers and digitized by us with the help of thousands of volunteers. All our ebooks can be easily downloaded: Choose between ePub, Mobipocket, HTML and simple text formats. Our books are free in the United States because their copyright has expired. They may not be free of copyright in other countries. Readers outside of the United States must check the copyright laws of their countries before downloading or redistributing our ebooks."
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PHPartners

website

Provider: PHPartners Editorial Board
Descriptions: Partners in Information Access for the Public Health Workforce is a collaboration of U.S. government agencies, public health organizations, and health sciences libraries which provides timely, convenient access to selected public health resources on the Internet. Collaborating organizations include: the American Public Health Association, Agency for Healthcare Research and Quality, Centers for Disease Control and Prevention, Medical Library Association, National Library of Medicine, and the Public Health Foundation. The site serves as a portal for information compiled with the intention of helping the public health workforce find and use information effectively to the end of improving and protecting the public's health. The site provides links to information in several categories, including: health promotion and education; literature and guidelines; health data tools and statistics; grants and funding; and education and training.
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PharmGKB: Pharmacogenomics Knowledge Base

website

Provider: U.S. Department of Health and Human Services/Stanford University
Descriptions: PharmGKB's mission is "to collect, encode, and disseminate knowledge about the impact of human genetic variations on drug response. We curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways."
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Open WetWare

website

Provider: MIT (Massachusetts Institute of Technology)
Descriptions: "OpenWetWare is an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering. OWW provides a place for labs, individuals, and groups to organize their own information and collaborate with others easily and efficiently. In the process, we hope that OWW will not only lead to greater collaboration between member groups, but also provide a useful information portal to our colleagues, and ultimately the rest of the world."
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KEGG (Kyoto Encyclopedia of Genes and Genomics)

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Provider: Kanehisa Laboratories, Japan
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Descriptions: KEGG is a resource purposed to facilitate understanding of the functions and utilities of the biological system--  cells, organisms and ultimately the ecosystem--  based on genomic and molecular-level information. It is a computer representation of the biological system, consisting of the molecular building blocks-- genes, proteins and chemical substances, integrated with molecular wiring diagrams of interaction, reaction and relational networks. Extensive data is available to view; ftp downloading requires a subscription. KEGG was developed in collaboration with the Bioinformatics Center, Institute for Chemical Research, Kyoto University and the Human Genome Center, Institute of Medical Science, University of Tokyo.
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NextBio

website

Provider: NextBio
Descriptions: NextBio Basic is a free web application providing access to a 'curated, correlated database' of public data which also integrates literature, clinical trials and scientific news. Its semantic framework is based on gene, tissue, disease and compound ontologies. A single search for information on a gene yields results categorically arranged on a single page: an overview of the gene's functions; a list of tissues in which the gene is expressed; diseases and compounds relating to the gene; a list of the top topic-associated researchers and authors; literature, associated clinical trials, and more. Registered users of this application (registration for this basic version is free) can personalize their experience, communicate, collaborate and share data with the rest of the NextBio community.
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Neuroscience Online: an electronic textbook for the neurosciences

website

Provider: Dept. of Neurobiology and Anatomy, UT Medical School, Houston
Descriptions: "This online, interactive courseware for the study of neuroscience is provided by the Department of Neurobiology and Anatomy at The University of Texas Medical School at Houston. The project is being developed under the direction of the Department Chair and Editor, John H. Byrne." Due to its largely multimedia presentation, the text cannot be downloaded-- it must be experienced online. The preface to this absorbing resource indicates that it is meant primarily as a course for the first-year medical student, but is also useful for more advanced students. Includes end-of-chapter review questions.
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Nature.com Open Innovation Pavilion

website

Provider: Nature.com and InnoCentive
Descriptions: "NPG [Nature Publishing Group] has partnered with InnoCentive to launch the nature.com open innovation pavilion. By giving readers the opportunity to participate in research and development challenges, the nature.com open innovation pavilion aims to facilitate greater scientific collaboration... Companies and not-for-profit organizations (known as Seekers) can post Challenges in life sciences, physical sciences and clinical medicine on the nature.com open innovation pavilion. As Solvers, users can apply their expertise to important problems, stretch their creative boundaries, and win cash awards."
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GigaDB

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Provider: GigaScience and BGI
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Descriptions: GigaDB is an open repository of datasets that support the research published in the open access BioMed Central bioinformatics journal, GigaScience. GigaDB provides a place from which to download supporting data and tools associated with papers published in GigaScience, thus facilitating the reproducibility of research. DataCite DOIs are assigned to these accompanying datasets, an identification device which serves to facilitate tracking and discoverability, and to provide additional credit to the authors who make their data publicly available.
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Gene Ontology

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Provider: Gene Ontology Project
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Descriptions: "The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. The project provides a controlled vocabulary of terms for describing gene product characteristics and gene product annotation data from GO Consortium members, as well as tools to access and process this data."  The Ontologies describe three aspects of molecular biology- biological processes, cellular components, and molecular functions. Gene Ontology's collected tools list includes hundreds from all over the world: specialized browsers, search engines, statistical analysis and visualization tools, and many other kinds. This project began as a collaboration between three model organism databases, FlyBase (Drosophila), the Saccharomyces Genome Database  and the Mouse Genome Database  in 1998. Since then, the GO Consortium has grown to include many other databases, including several of the world's major repositories for plant, animal and microbial genomes. See the GO Consortium page for a full list of member organizations.
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NanoHub.org

website

Provider: Network for Computational Nanotechnology
Descriptions: Supported by the National Science Foundation, this site is designed for and by the nanotech research community, providing tools and support for nanotech theory, modeling and simulation, and a forum in which to share knowledge within and between different nanotech research areas. This site is also a good resource for teachers, supplying curriculum items in the form of images, videos and learning modules.
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Medical Product Safety Network (MEDSUN)

website

Provider: U.S. Food and Drug Administration
Descriptions: MEDSUN "...is an adverse event reporting program launched in 2002 by the U.S. Food and Drug Administration’s Center for Devices and Radiological Health (CDRH). The primary goal for MedSun is to work collaboratively with the clinical community to identify, understand, and solve problems with the use of medical devices. Over 350 health care facilities, primarily hospitals, participate in the entire MedSun network." There are MEDSUN sub-networks for various conditions and clinical settings in which medical devices are commonly used: HeartNet, HomeNet, KidNet (neonates), LabNet, SightNet and TissueNet.
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DBGET search

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Provider: Kyoto University Bioinformatics Center
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Descriptions: DBGET is an integrated database retrieval system for accessing a web of molecular biology databases within GenomeNet and KEGG (Kyoto Encyclopedia of Genes and Genomes.)
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Cell, the: An Image Libary

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Provider: American Society for Cell Biology
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Descriptions: Supported by an award from National Institute of General Medical Sciences (NIGMS) and NIH, this is a peer-reviewed repository of thousands of often stunning microscopic images of cell types, processes and components. Most are free to use or under Creative Commons license by the authors, rather than restricted by publisher copyright. Free sign-in gives the user the ability to save images in a folder. Broader features like multiple public and private folders, sharing and annotation are in development. Many videos are also posted. Researchers are urged to contribute from their own work and experiments. For more information on the intent and the many current as well as future features of the database, read more at Leica Science Lab.
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BioMed Experts

database

Provider: Elsevier
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Descriptions: BioMed Experts is a professional networking platform that allows scientists and researchers around the world to establish new contacts, share data and collaborate. Profiles in BME are generated by extracting and assigning the biomedical concepts from an article to the authors and co-authors of the published article.  Unpublished professionals can also join, but no personal profile will be provided to them. One can still build a contact list from the list of 450,000 registered members. Free registration is required.
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BioMart Bio Portal

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Provider: BioMart
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Descriptions: The BioMart project provides free software and data services to the international scientific community in order to foster scientific collaboration and facilitate the scientific discovery process. The project adheres to the open source philosophy of promoting collaboration and code reuse. The majority of the contributed databases are of plant or human genomics-oriented data. Under Community, view the linked database list with descriptions and contributor names. Databases originate from the UK, USA, France, Spain, China and other countries. There are three separate portal websites-- the central "Bio" portal, a cancer portal, and one for mouse data.  Unfortunately, no link back to BioMart is provided once the user accesses one of the other portals.
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Alzforum (Alzheimer Research Forum)

website

Provider: Alzheimer Research Forum
Descriptions: This site contains and links to a huge number of resources for the Alzheimer researcher. Features include: a live discussion forum; citations to the latest papers (linking to PubMed); an international listing of institutes and laboratories; separate links for news on drugs, conferences and research; clinics information for the consumer; and more items too numerous to list here. It also provides links to the AlzSWAN Knowledge Base (see separate website listing) and its tutorials, and a collection of special seminars, on-line journal club discussions, recorded talks and other presentations that describe a variety of scientific hypotheses about the pathogenesis of Alzheimer's disease.
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