The Encyclopedia of Life is 10 years old!

The Encyclopedia of Life is 10 years old!  It is freely available on the web.  From their statistics, as of May 11, 2017, they have 5.5 million pages.  Responsibilities are shared by interested groups and individuals.  “The founding partners of the project include the Field Museum of Natural HistoryHarvard University, the Marine Biological Laboratory, the Smithsonian Institution, and the Biodiversity Heritage Library.  The Missouri Botanical Garden later joined, and negotiations are ongoing with the Atlas of Living Australia.  Other partners are the American Museum of Natural History (New York), Natural History Museum (London), New York Botanical Garden, and the Royal Botanic Gardens (Kew).”

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The Surgeon General’s Office in the United States Army started an index of all holdings in its library in 1880. The various volumes were printed until 1961. Because the Army Medical Library became the largest medical library in the world in the late 1890s, the Index-Catalogue of the Library of the Surgeon-General’s Office, 1880-1961, can be considered an almost complete compilation of the medical literature. Continue reading

NCBI Bioinformatics Tools: Protein, BLAST, COBALT, and Cn3D Structure Viewer

This tutorial is a step-by-step guide for searching for motifs for the SET domain, which I have taught for epigenetics students.

“For example, a protein called Clr4 from S. pombe contains the SET domain. How could you find mammalian homologous of Clr4? Let’s assume that you find 8 proteins in human database containing SET domain. How close are they? Can we draw a tree out of it? Can we align all these protein sequences together and compare their similarity, and find the most conserved motif (like GXGNA) shared with all these proteins? If I would like to know where this motif located in 3D structure, can we look at it on the published protein structure database?”

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Data in the Time of Cholerics: Where to Find Preserved Federal Data

During the recent change in federal government, researchers and librarians were concerned about loss of access to federal data, particularly in the area of environmental science where the new administration’s policies appeared to contradict scientific consensus. Early indications suggested that federal datasets and scientific information would be removed from the web entirely, or at least restricted in access.

In response to these concerns, a number academic institutions and other organizations began to organize data preservation efforts to ensure continued public access to endangered datasets. While websites of specific federal agencies continue to serve as the primary repositories of public data, this post focuses on a few public websites that aggregate and preserve federal datasets and provides a brief description of each. Continue reading

Alleviating the high cost of science textbooks with Open Educational Resources

OER Global Logo by Jonathas Mello is licensed under a Creative Commons Attribution Unported 3.0 License

Academic institutions are searching for ways to alleviate the financial burden that the increasing cost of textbooks places on their students. The average student spends $1200 annually for books and supplies, according to the Open Textbook Network.  Science textbooks are especially expensive, but OERs, or Open Educational Resources, are gaining acceptance as alternatives to traditional textbooks (Open Textbook Network, 2017).

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Apps: What are engineering students using?

one smartphone with colorful application icons (3d render)A survey conducted by the Pew Research Center in the fall of 2016 reports that 80% of US adults with some college and 89% of US college graduate own a smartphone.   (Pew Research Center, January 11, 2017).  Not surprising as the smartphone is the go-to for recent news, connecting with friends and family, and learning new things.  We know that smartphones are popular with the college population but how are college students using them in support of their study, in particular engineering students?

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MathSciNet is the premier index and reviews database for mathematics and related literature. It contains and continues from Mathematical Reviews (print), published from 1940 to 2012.  Produced by the American Mathematical Society, MathSciNet is international in scope, covering over 1800 current journals with more than 3.3 million publications ranging from 1810 to the current day.  Over 20,000 expert reviewers produce more than 80,000 reviews each year for MathSciNet.  These add tremendous value to the more than 100,000 new citations added annually.

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NGMBD, The National Geologic Map Database, a resource for everyone

In October, 2012, the U.S. Geological Survey (USGS) announced a new generation of the National Geologic Map Database, the index to United States maps.  It has resulted from a partnership between the USGS and the AASG, the Association of American Geologists.  Its antecedent directed searchers to regional map depositories, but now many maps and publications are freely available for downloading.  Some maps must still be purchased or otherwise obtained.

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