Posts by Category: Biological Informatics

DNA Barcoding 101

May 25, 2016

DNA Barcoding 101
http://www.dnabarcoding101.org/

With a budget of 150 million dollars a year and a history dating back to 1890, Cold Spring Harbor (CSH) Laboratory is one of the nation’s most respected private, non-profit research institutions. Now, the Lab has given the world an excellent educational website on the topic of DNA Barcoding, a method that allows experts and non-experts alike to objectively identify species based on their unique pattern of DNA sequence. On the site, readers may like to start by scouting the Introduction page, which outlines the methods and applications of DNA Barcoding. From there, educators may want to download “Using DNA Barcodes to Identify and Classify Living Things,”the PDF document that outlines the experimental methods used to document species. Here readers will learn how to gather samples, use a smartphone to take photographs, drop a pin for location, use a field guide to identify the specimen to the degree possible, and then label and analyze the DNA. All the necessary equipment is listed in the document. This will be added to Biological Informatics Subject Tracer™. From The Scout Report, Copyright Internet Scout 1994-2016. https://www.scout.wisc.edu

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Bento Lab – Experience Genetics Everywhere

May 18, 2016

Bento Lab – Experience Genetics Everywhere
https://www.bento.bio/

Check out what their users are doing on their Stories page. Bento Lab allows you to copy DNA and do basic DNA analysis, for example to compare species or different versions of a gene like the PTC gene that relates to taste receptors. If you have never done DNA analysis before, get in touch as they are working on a Getting Started page. Bento Lab is geared towards both professional and science education. Their beta testers come from all different backgrounds. Their users are working with Bento Lab for everything from molecular fieldwork, to science outreach, to creating cool art. The CRISPR technique primarily relies on reagents (primers and plasmids) as well as equipment. The equipment required for CRISPR includes a thermocycler, which Bento Lab contains. You may also need an electroporator and an incubator. Over the years, we have benefitted immensely from the generosity and innovativeness of the Open Source, Open Science, DIYbio and Biocommons community. We stand on the shoulders of giants such as Hackteria, the fantastic OpenPCR project, the iGEM community, and many, many others. For them, accessibility is the priority. They want to document the project well, so they are giving themselves a runway. They are planning to release the firmware source code, the electronic specifications and CAD files of the functional device (more suitable for readily-available materials!) into the public domain by the end of 2016. This will be added to Biological Informatics Subject Tracer™.

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The CIPRES Science Gateway V. 3.3

May 17, 2016

The CIPRES Science Gateway V. 3.3
https://www.phylo.org/

The CIPRES Science Gateway V. 3.3 is a public resource for inference of large phylogenetic trees. It is designed to provide all researchers with access to NSF XSEDE’s large computational resources through a simple browser interface. You can now also access these same capabilities programatically with the CIPRES REST API. High Performance Parallel Codes for Large Tree Inference and Sequence Alignment on XSEDE:RAxML; MrBayes; BEAST; BEAST2; GARLI; MAFFT; DPPDIV; FastTree, jModelTest2, and Migrate-N. If you need access to PhyloBayes, please inquire. Serial Codes for Tree Inference: PAUP* (Inference by Parsimony); Poy (Alignment and Inference); Serial Codes for Sequence Alignment: ClustalW; Contralign; MUSCLE; PROBCONS; PROBALIGN. This will be added to Biological Informatics Subject Tracer™.

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PLOS: Pathogens

May 13, 2016

PLOS: Pathogens
http://journals.plos.org/plospathogens/

Most journals hide their peer-reviewed articles behind an expensive paywall, making it virtually impossible for the average educated citizen to access their content. In the same liberating tradition as other PLOS journals, PLOS: Pathogens, publishes its groundbreaking articles in an open access format, so that anyone with an interest in the latest research on infectious agents can gain uninterrupted knowledge on the topic. Recent articles have included a reflection about the process by which prions (a particular kind of infectious protein) went from being a “scientific curiosity” to “public enemy number one” in the course of half a year; an opinion article in which one researcher presents a theory about how a better understanding of defensive microbes will lead to more advanced disease control; and a fascinating article on advances in RNA Polymerization. Articles range in depth, from opinion pieces that can be understood by anyone with a passing interest in pathogens, to research articles best understood by fellow pathogen scholars. This will be added to Biological Informatics Subject Tracer™. This will be added to Healthcare Resources Subject Tracer™. From The Scout Report, Copyright Internet Scout 1994-2016. https://www.scout.wisc.edu

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bioRxiv – The Preprint Server for Biology

April 18, 2016

bioRxiv – The Preprint Server for Biology
http://biorxiv.org/

bioRxiv (pronounced “bio-archive”) is a free online archive and distribution service for unpublished preprints in the life sciences. It is operated by Cold Spring Harbor Laboratory, a not-for-profit research and educational institution. By posting preprints on bioRxiv, authors are able to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals. This will be added to Academic and Scholar Search Engines and Sources white paper. This will be added to the tools section of Research Resources Subject Tracer™. This will be added to Biological Informatics Subject Tracer™.

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ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis

April 09, 2016

ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0149263

Bioinformatics analysis has become an integral part of research in biology. However, installation and use of scientific software can be difficult and often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces and documentation, or nonstandard input and output formats. In order to make bioinformatics software easily accessible to researchers, we here present a web-based platform. The Center for Bioinformatics Tuebingen (ZBIT) Bioinformatics Toolbox provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics and proteomics studies. All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service. The web platform is designed to facilitate the usage of the bioinformatics tools for researchers without advanced technical background. Users can combine tools for complex analyses or use predefined, customizable workflows. All results are stored persistently and reproducible. For each tool, we provide documentation, tutorials, and example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely available at https://webservices.cs.uni-tuebingen.de/. This will be added to Biological Informatics Subject Tracer™.

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The National Human Genome Research Institute: Fact Sheets

February 08, 2016

The National Human Genome Research Institute: Fact Sheets
http://www.genome.gov/10000202

The National Human Genome Research Institute (NHGRI) at the National Institute of Health (NIH) was established in 1989 for the express purpose of contributing to the International Human Genome Project – the multi-nation, decade-long project that successfully mapped the human genome. With such a rich pedigree it is no surprise that the NHGRI boasts a wonderfully informative website. Take, for instance, the Fact Sheets on Science, Research, Ethics and the Institute, featured here. Readers will find well over a dozen fact sheets, covering topics such as Comparative Genomics, Cloning, DNA Sequencing, and Genetic Mapping. For readers who are looking for clearly written, compendious treatments of all things related to genetics research, the NHGRI site will not disappoint. This will be added to Biological Informatics Subject Tracer™. From The Scout Report, Copyright Internet Scout 1994-2016. https://www.scout.wisc.edu

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Updated> Biological Informatics Subject Tracer White Paper Link Dataset Compilation

February 01, 2016

Updated> Biological Informatics 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 which is now a 36 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 (300KB) 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 1, 2016. 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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Awareness Watch Newsletter V14N2 February 2016

January 22, 2016

Awareness Watch Newsletter V14N2 February 2016
http://AwarenessWatch.VirtualPrivateLibrary.net/V14N2.pdf
Awareness Watch™ Newsletter Blog and Archives
http://www.AwarenessWatch.com/

The February 2016 V14N2 Awareness Watch Newsletter is a freely available 56 page .pdf document (432KB) from the above URL. This month’s featured report covers Biological Informatics 2016 and represents the latest World Wide Web resources for discovering new knowledge and understanding the latest happenings with regards to the rapidly changing and absolutely amazing area of biological informatics. The world is rapidly changing as transparency, big data and the ability to access data from new and now accessible databases becomes a reality! These resources are constantly updated by Subject Tracer™ Information Bots and the latest resources for biological informatics are available from the following URL: http://www.BiologicalInformatics.info/. This is one of the fastest growing and changing areas in science and these resources will help to keep you current and up to date within biological informatics. These resources will help you to discover the many pathways available to you through the Internet to find the latest health informatics, neuroinformatics, biodiversity informatics and biomolecular informatics sources and sites. The Awareness Watch Spotters cover many excellent and newly released annotated current awareness research sources and tools as well as the latest identified Internet happenings and resources including a number of neat and must-have tools! The Awareness Watch Article Review covers The Coup That Flopped: Facebook As a Platform for Emotional Protest by Jaroslav Švelch, Václav Štětka.

Subscribe to the monthly free Awareness Watch Newsletter by clicking here.

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eBiostatistics.com – Comprehensive, Open Access, Web Based Biostatistical Package

September 17, 2015

eBiostatistics.com – Comprehensive, Open Access, Web Based Biostatistical Package
http://www.draptis.com/ebiostat/

eBiostatistics.com (beta version) is the first comprehensive, open access, web-based, biostatistical package in the internet. It combines a menu-based GUI such as SPSS®, it is open access such as R, and exclusively online web-based such as OpenEpi. It offers a wide range of the most commonly used analytical applications. eBiostatistics.com is not dependent on different operating systems and internet browsers allowing additionally users from developing countries its use. This will be added to Biological Informatics Subject Tracer™.

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