Date: Tuesday, July 5, 2016
Time: 12:30pm – 1:30pm
Location: Street Level Conference Room
Showing 1 to 10 of 10 items tagged as open source
Provider: International Neuroinformatics Coordinating Facility
Descriptions: INCF develops and maintains database and computational infrastructure for neuroscientists. Software tools and standards for the international neuroinformatics community are developed through INCF programs that address infrastructural issues of high importance to the neuroscience community. INCF collects and makes available neuroinformatics tools in the INCF Software Center, where anyone can upload documentation, executables and related files, track use of their software, create a wiki, and establish development teams. Two of the most popular INCF products are Waxholm Space and MUSIC, which are direct outcomes of the INCF Program on Digital Atlasing and Multi-Scale Modeling, respectively. INCF also arranges Scientific Workshops and holds an annual neuroinformatics conference.
Keywords: biomedical research, brain, brain mapping, informatics, neuroscience, open access, open source, research
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.
Keywords: Baylor, biology, biomedical research, biotechnology, business, collaborative, drugs, engineering, environmental, genetics, information technology, medicine, multidisciplinary, nanotechnology, open source, research, scientist, software, technology
Provider: Center for History and New Media, George Mason University
Descriptions: Zotero is a free bibliographic citation manager available as a Firefox browser add-on. Hundreds of citation styles are available, and one can hover over the complete list to see examples of each. Zotero offers a number of handy features, including automatic recognition of bibliographic records within websites, collaborative file-sharing options, and much more. Documentation, FAQ's, tutorials and links to user forums are provided under the Support tab, and translations of these help pages in one or more of 14 other languages are posted with each- presumably this amenity is a work in progress. Zotero will not work with browsers other than Firefox.
Keywords: open source, research, software
Provider: Whole Brain project - UC-San Diego
Descriptions: The Whole Brain Catalog is the flagship project of the Whole Brain Project at the University of California - San Diego. It is an open source, downloadable, multi-scale virtual catalog of the mouse brain and its cellular components, providing zoomable 3D views of structures and their surroundings deep inside the mouse brain. The data is also brought to life with simulation and animation. "In providing open source and collaborative tools, the Whole Brain Project allows neuroscience researchers to make new connections with collaborators and newly discovered data. Combining previously unconnected databases across a single network make possible new and exciting insights about the brain."
Keywords: animal, animation, biomedical research, brain, life sciences, mouse, neurology, neuroscience, open access, open source, research, software
Provider: International DOI Foundation
Descriptions: DOI, or Digital Object Identifier, is a standardized system for providing actionable, persistent and interoperable links to "objects," the scope of which was originally limited to online documents, but which term is now applied in this context to online datasets, videos and other formats and types of information containers. Every resource relevant to DOI's is either present in or linked to from this website, for instance: FAQ's, a detailed handbook, fact sheets and white papers; links to DOI registration agencies like DataCite and CrossRef; and links to browser tools being developed to facilitate and expand the usefulness and applicability of the Digital Object Identifier.
Keywords: data, deep web, digital, DOI, informatics, information management, information science, links, ontology, open source, periodicals, portal, research, search, W4eb tools
Provider: National Institutes of Health/National Library of Medicine
Contents: Abstracts, archive, directory, index, open-source, summaries
Access Level: Free, Open Access
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.
Keywords: bioinformatics, biomedical research, collaborative, data-sharing, genetics, genomics, laboratory, life sciences, open source, repositories
Provider: Quertle, LLC
Descriptions: Developed by two experts in bioinformatics and data analysis, Quertle offers a uniquely effective way to execute a combined search of the biomedical literature in PubMed, the RePORTER grants database, TOXLINE, and a medical/life science news outlet. This tool also searches the full text of open-access material in BioMed Central and PubMed Central, as well as that of user-submitted scientific whitepapers and research posters. Quertle uses natural-language query constructs very like sentence structure and uses relationships to return relevant results. For details on how it works, see the FAQ tab. A handy brochure on searching and video/other tutorials are found under the Resources tab. Quertle also works with various bibliographic management tools, including RefWorks. Searches can be saved, and alerts service is available (these features require the user to set up a free account.)
Keywords: biomedical research, free, full text, news, NIH, open access, open source, search, search engine, Web tools
Provider: Neuroimaging Informatics Tools and Resources Clearinghouse
Descriptions: Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) is sponsored by the NIH Blueprint for Neuroscience Research. It offers the neuroscience community free databases and applications for imaging, a forum and a news feed. Researchers can look for applications based on their attributes and popularity, and can also compare similar utilities, check on software development stages, and submit their own databases and applications for sharing. Many links to related resources are also provided here.
Keywords: anatomy, biomedical research, brain, brain mapping, data, data analysis, informatics, medical imaging, networking, neuroimaging, neuroscience, news, NIH, ontology, open access, open source, research, software, U.S. Government, Web tools
Provider: Netherlands BioInformatics Centre
Descriptions: NBIC is engaged in bioinformatics research and education. Its website includes free software downloads, information on databases and projects, a journal and newsletter, and secondary-level education materials.
Keywords: biomedical research, blog, conference, data analysis, DNA, genes, genome, genomics, informatics, journal, news, open source, partial open access, pharmacogenomics, research, scientist, sequencing, software