Category Archives: Genomics

CRISPR — HOW IT WORKS, an animation from HHMI

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Summary

Explore this dynamic interactive to learn the basic principles of how this revolutionary tool works and the many ways in which scientists are using it in their research.

Start Click & Learn

Since it was first described in 2012, CRISPR-Cas9 (often shortened to “CRISPR”) has generated much interest both for its exciting potential for treating genetic disease and potential ethical and safety concerns, such as by creating “designer babies” or “superhumans.” So far, CRISPR-based technologies are having the biggest impact in research laboratories where they are applied to a broad range of biological studies. These technologies are relatively cheap, easy to use, and allow researchers to ask new questions and get results faster than previously possible.

The CRISPR-Cas9: Mechanism & Applications interactive allows students to explore and learn about a biotechnology tool that is at the forefront of scientific research and hear directly from leading researchers about how they use CRISPR. It consists of a self-paced interactive animation and a series of short videos of different scientists who are using CRISPR-Cas9 technologies for basic research, medical, and agricultural applications.

In addition to the interactive, we’ve compiled a set of images, animations, and GIFs for use on social media, in the classroom, and for presentations to the public. Please credit HHMI BioInteractive when you use them.

Source: The BioInteractive Team <biointeractive@hhmi.org>

Data Management Plan Presentation – Wed., March 28th

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Data Management Plan Presentation

Wednesday, March 28, 12:00 – 1:00 pm

347 Lewis Science Library, Washington Road & Ivy Lane
[Lunch will be provided. RSVP here.]

This one-hour presentation by PU librarians, OIT and PICSciE/Research Computing staff is open to Princeton researchers, graduate students and grants personnel. Please share with those who may benefit from this presentation.

Topics

  • Why manage research data?
  • Elements of data management
  • How to write a data management plan
  • Common data management issues
  • Best practices for managing research data
  • Resources and support on campus

Best of the Web, GEN (Vol. 37, No. 8) SciPy PYTHON

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“Computer programming is becoming (or rather, already has become) an essential skill for modern-day life scientists. A popular programming language in many fields is Python, in large part due to its open-source development. As a result, there exist many free resources available to both experienced and novice Python users. A large collection of such resources can be found on SciPy.org, home of a number of scientific and computational software packages/libraries for Python. In addition to offering free downloads of those packages, the SciPy website also includes SciPy Central (a collection of useful Python code snippets), a blog, documentation for the various software packages, and a place for users to report bugs. Site visitors in search of even more information can browse the SciPy Cookbook, a collection of user-contributed “recipes” that span topics such as graphics, linear algebra, simple plotting, and differential equations.”

Genetic Engineering & Biotechnology News, April 15, 2017,  URL:scipy.org

Rated “Excellent”, free software downloads, good documentation

Viral Zone Best of the Web, Genetic Engng & Biotech News

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BestWeb_ViralZoneSource: | Best of the Web | GEN ViralZone |

Genetic Engineering & Biotechnology News//

Jun 15, 2016 (Vol. 36, No. 12)

“Do you know your DNA viruses from your RNA viruses, and can you spot a retrotranscribing virus when you see one? If not, the ViralZone from the Swiss Institute of Bioinformatics is a fantastic web resource for virologists and other scientists who use viral tools in their research. ViralZone includes description pages for over 500 viruses, and site visitors can access these pages either by a targeted search for a specific virus or by browsing the virus pages by a virus’ Baltimore classification, host, or virion. The website also includes a great deal of general information about viral molecular biology, including topics such as virus entry/exit, replication, and genome evolution. On the homepage, site visitors will find a news section (including a weekly podcast) so that they can keep up to date on the latest viral happenings.”

 

 

Scientists unveil a new Tree of Life

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TREEOFLIFE-blog427

“Bacteria dominate newly drawn tree of life
Scientists at the University of California at Berkeley and the University of Waterloo in Canada studied more than 3,000 species and pieced together bits of DNA to update the tree of life. The tree is dominated by bacteria, while all the eukaryotes are represented on a slender twig. The work is published in the journal Nature Microbiology.” The New York Times (free-article access for SmartBrief readers) (4/11)

By CARL ZIMMER,  APRIL 11, 2016

“A version of this article appears in print on April 12, 2016, on page D2 of the New York edition with the headline: The Tiniest Beings Writ Large.A version of this article appears in print on April 12, 2016, on page D2 of the New York edition with the headline: The Tiniest Beings Writ Large.”

From FBR SmartBrief <fbr@smartbrief.com> Wed., April 13, 2016

GenBank has reached 200 billion base pairs from > 350,000 spp.

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“Almost the number of stars in the Milky Way.” Through this stellar comparison, the National Institutes of Health proudly announced in 2005 that the content of their computerized collection of DNA sequences called GenBank had reached 50 billion bases or units of DNA. Today, it contains far more, over 200 billion bases from over 350,000 different species, making it one of the largest scientific database in the world.

Here is the announcement of the availability of the Nirenberg papers: “GenBank & The Early Years of “Big Data”

http://circulatingnow.nlm.nih.gov/2016/03/03/genbank-the-early-years-of-big-data/

“Deciphering the Genetic Code: A 50 Year Anniversary” January, 2015

Marshall Nirenberg in the lab in early 1960’s, when he completed the first summary document of the genetic code — how triplets (DNA sequences) direct amino acids to form proteins.  Pictures of the group and more about the papers are here:

http://circulatingnow.nlm.nih.gov/2015/01/21/deciphering-the-genetic-code-a-50-year-anniversary/

A young man in a lab coat and plastic gloves holds up a glass tube in a laboratory.

MEDLINE ANNUAL CHANGES/UPDATES

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National Library of Medicine Technical Bulletin

This article collects the notable data changes made to MEDLINE during annual National Library of Medicine (NLM) maintenance known as Year-End Processing (YEP) for 2016:

MEDLINE Data Changes — 2016

Tybaert S. NLM Tech Bull. 2015 Nov-Dec;(407):e8.

2015 December 08 [posted]

Brand new concepts include: Autism Spectrum Disorder, Human Embryonic Stem Cells, Olive Oil, Origin of Life, Open Access Publishing, War-Related Injuries, RNAi Therapeutics, and many more terms.  Medline thesaurus terms are remapped when changes occur, so as to include articles under former headings.

Medical Subject Headings for 2016 are now available online

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NLM [National Library of Medicine] New files for Nov 10, 2015

*NLM Technical Bulletin, Nov-Dec 2015, 2016 Medical Subject Headings Available for Download  http://www.nlm.nih.gov/pubs/techbull/nd15/nd15_2016_mesh_avail.html

NLM Technical Bulletin, Sep-Oct 2015, 2016 MeSH Headings Available in the MeSH Browser [Editor’s note added November 10, 2015]  http://www.nlm.nih.gov/pubs/techbull/so15/so15_2016_mesh_browser.html

Directory of Open Access Journals — DOAJ

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This directory of OA journals is hosted by Lund University Libraries in Sweden.  From their homepage: http://www.doaj.org:

“DOAJ is an online directory that indexes and provides access to high quality, open access, peer-reviewed journals.”   One can search by keywords or browse through broader and narrower subject headings.

These stats are from their website, accessed Sept. 28, 2015:

  • 10,569 Journals
  • 6,464 searchable at Article level
  • 134 Countries
  • 2,091,552 Articles

Seen in “Outstanding Websites of 2014”, Choice, Sept. 2015, p. 33

ProQuest full text of scholarly journal content soon indexed by Google Scholar

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By Kurt Sanford, CEO

“ProQuest is enabling the full text of its scholarly journal content to be indexed in Google Scholar, improving discovery and research outcomes. Our goal is that by the third quarter of 2015, users starting their research in Google Scholar will be able to access full text via ProQuest.”

http://www.proquest.com/blog/pqblog/2015/Why-ProQuest-is-working-with-Google.html

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Tuesday, 18th August 2015

ProQuest Scholarly Content Now Discoverable in Google Scholar

By Africa S. Hands

From No Shelf Required:

ProQuest has marked another milestone in ease of access to its rich research content. The full text of its scholarly content – including journals and working papers – is now indexed in Google Scholar, enabling Google Scholar users to seamlessly discover and access their library’s ProQuest collections. Efficiency and productivity for both ProQuest and Google Scholar users is improved, while libraries benefit from increased usage for their subscribed collections.

Full story >>

http://www.libraries.wright.edu/noshelfrequired/2015/08/12/proquest-scholarly-content-now-discoverable-in-google-scholar/

Source via: ResourceShelf Newsletter – 8th September 2015

[ResourceShelf] Newsletter 643