Public health is a broad, cross-disciplinary field of study. Drawing on information from primary medical research, disease surveillance, public policy, geography, and sociology (to name just a few), public health researchers and practitioners wade through copious amounts of data to answer their research questions. In addition to the major health information resources (think PubMed), many additional online tools exist to aid anyone interested in public … Continue reading Lesser-known Public Health Resources

Molecular biology is the study of biological macromolecules at the structural and functional level, particularly DNA and proteins. There are many free resources on the Internet to study various aspects of these primary constituents. The following is a list of some of these web-based tools and a brief description with some verbiage used from the native site. This is not a comprehensive list, but it … Continue reading Web-based Molecular Biology Tools

Re3data launched at the tail end of 2012 with the goal of registering all research data repositories. These research data repositories are collections of datasets usually associated with a particular discipline or a particular geographic region. Because of the way data repositories have cropped up on an as-needed basis over the past 50 years, these repositories are myriad and take a specialized knowledge to navigate … Continue reading re3data.org: Registry of Research Data Repositories

In light of the one year anniversary of engrXiv, and the recent creation of AgriXiv and PsyArXiv, we wanted to highlight the availability of preprint repositories for STEM disciplines.  Preprint services provide free, open access to research articles.  The goal of these sites include disseminating “knowledge quickly and efficiently” (1), “providing a free, open access outlet for new findings” (2), and making “research outputs …  immediately available … Continue reading STEM Preprint Repositories: Where Are They Now?

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 History, Harvard 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).”

Continue reading “The Encyclopedia of Life is 10 years old!”

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 “Index-Cat”

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?”

Continue reading “NCBI Bioinformatics Tools: Protein, BLAST, COBALT, and Cn3D Structure Viewer”

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

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).

Continue reading “Alleviating the high cost of science textbooks with Open Educational Resources”