Posts by Category: Biological Informatics

SmidgION – Nanopore Sensing for Use With Mobile Devices

April 04, 2018
 

SmidgION – Nanopore Sensing for Use With Mobile Devices
https://nanoporetech.com/products/smidgion

Nanopore sensing technology can uniquely be miniaturised for portable analysis of DNA and other biological molecules. The handheld MinION is already established for portable DNA sequencing. Oxford Nanopore has now started developing an even smaller device, SmidgION. he end-to-end process of sample preparation, measurement and analysis for nanopore technology is become increasingly simplified. For example, new kits allow ten minute library preparation, the VolTRAX will provide programmable hands-off sample preparation, and Oxford Nanopore provides analysis workflows such as ‘What’s in my Pot’ (WIMP). As end-to-end analysis becomes more accessible, the SmidgION is being designed to allow analyses by more people and in more locations. SmidgION uses the same core nanopore sensing technology as MinION and PromethION but will be designed for use with smartphones or other mobile, low power devices. It is designed to cater for a broad range of field-based analyses; potential applications may include remote monitoring of pathogens in a breakout or infectious disease; the on-site analysis of environmental samples such as water/metagenomics samples, real time species ID for analysis of food, timber, wildlife or even unknown samples; field-based analysis of agricultural environments, and much more. This will be added to Biological Informatics Subject Tracer™. This will be added to Business Intelligence Resources Subject Tracer™. This will be added to Entrepreneurial Resources Subject Tracer™. This will be added to the tools section of Research Resources Subject Tracer™.

 

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BEN Portal: BioSciEdNet

March 19, 2018

BEN Portal: BioSciEdNet
www.biosciednet.org/portal

Originally featured in the 01-18-2013 Scout Report, we’ve decided to re-feature the BEN Portal: a project of the American Association for the Advancement of Science (AAAS). For almost two decades the BEN Portal, which stands for BiosciEdNet, has sought to provide “seamless access to e-resources, but to also serve as a catalyst for strengthening teaching and learning in the biological sciences.” Today, the BEN Portal (which has also been affiliated with the National Science Digital Library since 2005) features publications from over thirty organizations, including the AAAS, the American Physiological Society, the Biotechnology Institute, the Howard Hughes Medical Institute, and much more. Visitors are invited to conduct a text search in this collection or browse materials by subject. In addition, educators can browse teaching strategies by classroom level (K-12 educators; college faculty). The BEN Portal features both free resources and resources that require a subscription: users have the option to limit search results to free resources. This will be added to Biological Informatics Subject Tracer™. This will be added to Healthcare Resources Subject Tracer™. This will be added to Business Intelligence Resources Subject Tracer™. This will be added to Entrepreneurial Resources Subject Tracer™. This will be added to the tools section of Research Resources Subject Tracer™. Copyright © 2017 Internet Scout Research Group – http://scout.wisc.edu

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The Kepler Project

March 13, 2018

The Kepler Project
https://kepler-project.org/

The Kepler Project is dedicated to furthering and supporting the capabilities, use, and awareness of the free and open source, scientific workflow application, Kepler. Kepler is designed to help scien­tists, analysts, and computer programmers create, execute, and share models and analyses across a broad range of scientific and engineering disciplines. Kepler can operate on data stored in a variety of formats, locally and over the internet, and is an effective environment for integrating disparate software components, such as merging “R” scripts with compiled “C” code, or facilitating remote, distributed execution of models. Using Kepler’s graphical user interface, users simply select and then connect pertinent analytical components and data sources to create a “scientific workflow”—an executable representation of the steps required to generate results. The Kepler software helps users share and reuse data, workflows, and compo­nents developed by the scientific community to address common needs. The Kepler software is developed and maintained by the cross-project Kepler collaboration, which is led by a team consisting of several of the key institutions that originated the project: UC Davis, UC Santa Barbara, and UC San Diego. Primary responsibility for achieving the goals of the Kepler Project reside with the Leadership Team, which works to assure the long-term technical and financial viability of Kepler by making strategic decisions on behalf of the Kepler user community, as well as providing an official and durable point-of-contact to articulate and represent the interests of the Kepler Project and the Kepler software application. Details about how to get more involved with the Kepler Project can be found in the developer section of this website. Kepler is a java-based application that is maintained for the Windows, OSX, and Linux operating systems. The Kepler Project supports the official code-base for Kepler development, as well as provides materials and mechanisms for learning how to use Kepler, sharing experiences with other workflow developers, reporting bugs, suggesting enhancements, etc. This will be added to Biological Informatics Subject Tracer™. This will be added to Healthcare Resources Subject Tracer™. This will be added to Business Intelligence Resources Subject Tracer™. This will be added to Entrepreneurial Resources Subject Tracer™. This will be added to the tools section of Research Resources Subject Tracer™.

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UK Biobank – Improving the Health of Future Generations

March 12, 2018

UK Biobank – Improving the Health of Future Generations
http://www.ukbiobank.ac.uk/

UK Biobank is a national and international health resource with unparalleled research opportunities, open to all bona fide health researchers. UK Biobank aims to improve the prevention, diagnosis and treatment of a wide range of serious and life-threatening illnesses – including cancer, heart diseases, stroke, diabetes, arthritis, osteoporosis, eye disorders, depression and forms of dementia. It is following the health and well-being of 500,000 volunteer participants and provides health information, which does not identify them, to approved researchers in the UK and overseas, from academia and industry. Scientists, please ensure you read the background materials before registering. To our participants, we say thank you for supporting this important resource to improve health. Without you, none of the research featured on this website would be possible. This will be added to Biological Informatics Subject Tracer™. This will be added to Healthcare Resources Subject Tracer™. This will be added to Business Intelligence Resources Subject Tracer™. This will be added to Entrepreneurial Resources Subject Tracer™. This will be added to the tools section of Research Resources Subject Tracer™.

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Updated> Biological Informatics 2018 Subject Tracer White Paper Link Dataset Compilation

February 22, 2018

Updated> Biological Informatics 2018 Subject Tracer White Paper Link Dataset Compilation
http://www.BiologicalInformatics.info/

I have just updated my Subject Tracer™ Information Blog white paper link dataset compilation titled Biological Informatics 2018 which is now a 39 page paper listing selected resources both new and existing that will help anyone who is attempting to find the latest information about biological informatics that are available over the Internet. It is freely available as a .pdf file (309KB) at the above link from the Virtual Private Library™ and authored by Marcus P. Zillman, M.S., A.M.H.A. It was completely updated including link validation and new links added on February 22, 2018. Other white papers are available by clicking here.

This research is powered by Subject Tracer Bots™ available from the Virtual Private Library™.

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BIOZ – Best Way To Find Scientific Data

February 07, 2018

BIOZ – Best Way To Find Scientific Data
https://www.bioz.com/

Traditional life-sciences search tools focus on identifying research papers, but they don’t perform the difficult work of analyzing, aggregating and structuring data within and between papers. As a result, traditional tools are limited to providing a list of papers to read, and miss answering even the simplest research questions. Bioz goes further, much further, by combining the latest advances in computer science with in-house life-sciences expertise to help researchers plan experiments, write papers and apply for grants. Bioz’s unique engine mines hundreds of millions of pages of complex, dense and unstructured life-sciences papers, and then uses Natural Language Processing and Machine Learning to clean, tag and structure the data. The newly structured data forms the core of the Bioz platform, and places unprecedented scientific data at your fingertips. Insights focus on experimentation and include never before available objective recommendations, ratings and insights for hundreds of millions of reagents, lab equipment, assays, protocols and researchers. This will be added to Healthcare Resources Subject Tracer™. This will be added to Biological Informatics Subject Tracer™. This will be added to Academic and Scholar Search Engines and Sources white paper. This will be added to Business Intelligence Resources Subject Tracer™. This will be added to Entrepreneurial Resources Subject Tracer™. This will be added to the tools section of Research Resources Subject Tracer™

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arXiv.org – Open Access e-Prints

January 27, 2018

arXiv.org – Open Access e-Prints
https://arxiv.org/

Open access to 1,330,210 e-prints in Physics, Mathematics, Computer Science, Quantitative Biology, Quantitative Finance, Statistics, Electrical Engineering and Systems Science, and Economics. Started in August 1991, arXiv.org (formerly xxx.lanl.gov) is a highly-automated electronic archive and distribution server for research articles. Covered areas include physics, mathematics, computer science, nonlinear sciences, quantitative biology, quantitative finance, statistics, electrical engineering and systems science, and economics. arXiv is maintained and operated by the Cornell University Library with guidance from the arXiv Scientific Advisory Board and the arXiv Member Advisory Board, and with the help of numerous subject moderators. Users can retrieve papers from arXiv via the web interface. Registered authors may use our web interface to submit their articles to arXiv. Authors can also update their submissions if they choose, though previous versions remain available.  Listings of newly submitted articles in areas of interest are available via the web interface, via RSS feeds, and by subscription to automatic email alerts. This will be added to Healthcare Resources Subject Tracer™. This will be added to Biological Informatics Subject Tracer™. This will be added to Journalism Resources Subject Tracer™. This will be added to Business Intelligence Resources Subject Tracer™. This will be added to Entrepreneurial Resources Subject Tracer™. This will be added to the tools section of Research Resources Subject Tracer™. This will be added to Reference Resources Subject Tracer™. This will be added to New Economy Resources Subject Tracer™.

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The Winnower – Open Access Online Scholarly Publishing Platform

January 27, 2018

The Winnower – Open Access Online Scholarly Publishing Platform
https://thewinnower.com/

The Winnower is an open access online scholarly publishing platform that employs open post-publication peer review. You guessed it! They think transparency from start to finish is critical in scientific communication. Their aim is to revolutionize science by breaking down the barriers to scientific communication through cost-effective and transparent publishing for scholars. This will be added to Healthcare Resources Subject Tracer™. This will be added to Biological Informatics Subject Tracer™. This will be added to Journalism Resources Subject Tracer™. This will be added to Business Intelligence Resources Subject Tracer™. This will be added to Entrepreneurial Resources Subject Tracer™. This will be added to the tools section of Research Resources Subject Tracer™. This will be added to Reference Resources Subject Tracer™.

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GigaScience Journal

January 25, 2018

GigaScience Journal
https://academic.oup.com/gigascience

GigaScience aims to revolutionize publishing by promoting reproducibility of analyses and data dissemination, organization, understanding, and use. As an open access and open-data journal, we publish ALL research objects (data, software tools and workflows) from ‘big data’ studies across the entire spectrum of life and biomedical sciences. These resources are managed using the FAIR Principles for scientific data management and stewardship that state that research data should be Findable, Accessible, Interoperable and Reusable. To achieve our goals, the journal has a novel publication format: one that links standard manuscript publication with an extensive database that hosts all associated data and provides data analysis tools and cloud-computing resources. GigaDB provides a direct link between the published manuscript and the relevant supporting data. We have also built GigaGalaxy, a Galaxy-based data analysis platform to host computational methods and workflows, maximizing use of the data, tools and workflows in our papers in a more accessible and reproducible environment. Our scope covers not just ‘omic’ type data and the fields of high-throughput biology currently serviced by large public repositories, but also the growing range of more difficult-to-access data, such as imaging, neuroscience, ecology, cohort data, systems biology and other new types of large-scale sharable data. All articles and content (including blogs and peer reviews) published by GigaScience are made freely and permanently accessible online immediately upon publication, without subscription charges or registration barriers. All software is published under Open Source Initiative (OSI)-approved open source licences, and supporting data presented under a public domain CC0 waiver. Further information about our open access policies and our article processing charges to support these efforts can be found here. This will be added to Biological Informatics Subject Tracer™. This will be added to Healthcare Resources Subject Tracer™. This will be added to Business Intelligence Resources Subject Tracer™. This will be added to Entrepreneurial Resources Subject Tracer™. This will be added to the tools section of Research Resources Subject Tracer™. This will be added to Reference Resources Subject Tracer™.

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eLIFE – Open-access Journal That Publishes Promising Research in the Life and Biomedical Sciences

January 25, 2018

eLIFE – Open-access Journal That Publishes Promising Research in the Life and Biomedical Sciences
https://elifesciences.org/

eLife is a non-profit organisation inspired by research funders and led by scientists. Our mission is to help scientists accelerate discovery by operating a platform for research communication that encourages and recognises the most responsible behaviours in science. eLife publishes important research in all areas of the life and biomedical sciences. The research is selected and evaluated by working scientists and is made freely available to all readers without delay. eLife also invests in innovation through open-source tool development to accelerate research communication and discovery. Our work is guided by the communities we serve. eLife was founded in 2011 by the Howard Hughes Medical Institute, the Max Planck Society and the Wellcome Trust, who provide financial support and strategic guidance. In 2017, eLife introduced publication fees to cover some of our core publishing costs. Annual reports and financial statements are openly available. This will be added to Biological Informatics Subject Tracer™. This will be added to Healthcare Resources Subject Tracer™. This will be added to Business Intelligence Resources Subject Tracer™. This will be added to Entrepreneurial Resources Subject Tracer™. This will be added to the tools section of Research Resources Subject Tracer™. This will be added to Reference Resources Subject Tracer™.

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