Category Archives: Biology

Virtual Fly Brain

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Rating: Very Good

Strong Points: Easy to use, tutorials and demonstration videos are available

Weak Points: The new version of the website is still in beta testing

www.virtualflybrain.org

The common fruit fly, Drosophila melan­ogaster, is an important model organism, particularly in neuroscience research. The Virtual Fly Brain is an excellent resource for researchers who need to closely ex­amine the fly’s neuroanatomy. Users can select an area from an image of an adult fly brain to discover more information about it, including a detailed description of the area, any synonyms used to describe it, and links to references. There is also a search feature for users who know the name of their brain region of interest but not its location. Additionally, image and template data are available for download. The current website only includes information for the adult fly brain, but an updated version including larval information is currently in testing and available for users to peruse. The Virtual Fly Brain is an excellent resource for neuroscientists using Drosophila to interrogate the structure and function of the brain.

Source: GenEngNews, Jan. 2019, vol. 39 (1)  “Best of the Web”

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>

BenchSci, an antibody-finding search engine free to academics

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The Peter B. Lewis Library is pleased to present BenchSci to the Princeton research community.

Registration is free to all scientists with a princeton.edu or affiliated institutional emails at https://www.benchsci.com

BenchSci is a online platform designed to help scientists find antibodies from publications. Their proprietary machine-learning algorithm was trained by PhD-level scientists to identify and understand the usage of commercial antibodies in the research literature.

When searching for a specific protein target, BenchSci curates published data in the form of figures to simplify the literature search process. The figures can then be filtered by specific experimental contexts cited in the paper such as techniques, tissue, cell lines, and more, to help users pinpoint antibodies that have been published under experimental conditions matching their study interest.

For more information about BenchSci, please refer to this article: https://blog.benchsci.com/7-features-to-find-antibodies

To learn how to navigate BenchSci, please watch this short video: https://youtu.be/EFaDwTtqlv4

For further inquiries or feedback, contact Maurice Shen, PhD, the Head of Academic Relations at BenchSci, at maurice@benchsci.com

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

Human Anatomy Atlas 2018

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URL:http://apple.co/2De3BmW
  • Excellent (4 stars)
  • Great design and user interface (Strong points)
  • None (Weak points)
Platform: iPhone/iPad/Android (2017 version available)  
Cost:Free

“Human Anatomy Atlas 2018 is an excellent app that brings human anatomy to life. The app has beautifully rendered 3D images of the major anatomical systems that can be explored and dissected from the interface. However, the really interesting part of the app comes with the Augmented Reality feature. By allowing the app to use your phone’s camera, it finds a surface in your environment and places the anatomical model there, giving the impression that it is right in the room with you. This feature also allows the user to “dissect” the anatomical model, making this an incredibly useful accompaniment for anyone studying human anatomy. Human Anatomy Atlas 2018 is an incredibly designed and executed app that is not only informative but fascinating and fun to use, without the formaldehyde smell that typically permeates such an in-depth look at human anatomy.”

https://www.genengnews.com/best-science-apps/human-anatomy-atlas-2018/448

Genetic Engineering and Biotechnology News,  January 01, 2018 (Vol. 38, No. 1)

Best Science Apps

BioSciEdNet — the BEN Portal, catalyst for teaching & learning in the biosciences

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“
BEN Portal: BioSciEdNet Science
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. [MMB]

Source:  Scout Report, Dec. 1, 2017 (direct quote)

Springer Nature Experiments Database — an indexed searching tool

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German “Springer Nature launches Springer Nature Experiments – a free-to-use research solution for the life sciences – 12 Oct 2017

Springer Nature has launched a new, free-to-use research solution, Springer Nature Experiments, to help researchers in the life sciences advance discovery by accessing the most relevant protocols and methods to support their research projects.

Protocols are ‘recipes’ used in laboratory research to support the design and implementation of reproducible experiments. The step-by-step instructions help researchers recreate an experiment by typically including information on the materials required, equipment and set-up. Methods are new scientific procedures for solving existing problems. Together, these two different types of content are the cornerstone for scientists to successfully conduct their research.

Springer Nature publishes the largest available collection of protocols and methods for the life sciences with content from SpringerProtocols, Nature Methods, Nature Protocols and Protocol Exchange – the free repository for scientists to share their protocols with the scientific community. Springer Nature Experiments provides access to all of these through a single easy-to-use platform, designed to save researchers’ time.

The platform uses advanced knowledge models to categorise content based on techniques and organisms – the two most commonly used search categories identified in user research. With the help of cutting-edge artificial intelligence and text mining technologies, these terms are recognised and extracted from the content, enabling users to perform searches and narrow down their results quickly and easily.

In addition, users can evaluate and compare protocols prior to accessing the full-text with the help of protocol landing pages. These summarize key information such as the keywords mentioned, article history and citations which gives an indication of whether the protocol has been used successfully in other research projects.

Springer Nature Experiments is accessible online at https://experiments.springernature.com. Springer Nature will officially launch the new research solution at the Frankfurt Book Fair 2017.”

Source:  Knowledgespeak Newsletter

Encyclopedia of Life — now 10 years old!

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STS Science Resources

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).”

 From https://en.wikinews.org/wiki/Scientists_to_bring_all_species_together_in_Encyclopedia_of_Life

There is also a Wikipedia article about the EOL: https://en.wikipedia.org/wiki/Encyclopedia_of_Life

Efforts began with plants, animals and fungi.  It appears now that microorganisms have been added, as they’d hoped.  If one searches for tuberculosis, there are many hits,  but many are not very productive.  Searching on the Genus is the key – Mycobacterium.   The site provides the NCBI ( National Center for Biotechnology Information) taxonomy for these organisms.  There are many  entries on Staphylococcus species.  Not all hits will be productive, and they urge inquirers to request information.

There are tabs for:  Overview, Detail, Data, Media (including some videos), Maps, Names, Communities (which include related EOL groups, e.g. “Birds of America”), Collections (on-line databases), Resources, Literature and Updates.  These headings also serve as filters or limits.

I tried cardinal, but Cardinalis cardinalis — the scientific name, Genus and species — works  best, if you are looking for our most common red bird.

There are data which indicate species to species interactions, from this site:  http://www.globalbioticinteractions.org/  There are many links to many collections.

I looked up cedar and from starting to browse through <6400 entries, I soon (within the first page of 25) came upon Cedrus libani, and found much information, including a video about the restoration of the “Cedars of Lebanon”.   The page steers one to many “traits” including the IUCN (International Union for Conservation of Nature) status, which is “vulnerable” for this tree:   Its populations are declining.   Searching can be a bit tricky.  Scientific name works best.

 

UK Medical Heritage Library

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UK” The UK Medical Heritage Library now available online for free – 10 May 2017

A £1m project to digitise more than 15 million pages of 19th century medical texts has been completed and the material is now available online for free. It has taken three years to convert these historic published works for use in the 21st century by learners, teachers and researchers.

Covering much more than just medical sciences, this enormous library of text and images encompasses consumer health, sport and fitness, diet and nutrition, along with some weird and wonderful historical medical practices such as phrenology and hydrotherapy.

The project was jointly funded by education technology solutions not-for-profit, Jisc, and Wellcome Library, which contributed its entire 19th century collection, along with content from nine partner institutions: Royal College of Physicians of London, Royal College of Physicians of Edinburgh, Royal College of Surgeons of England, University College London, University of Leeds, University of Glasgow, London School of Hygiene and Tropical Medicine, King’s College London and the University of Bristol. As a collective, this will make a valuable resource for the exploration of medical humanities.

The aim has been to create a comprehensive online resource for the history of medicine and related sciences, which significantly increases the availability of digitised text for teaching, learning and research.

The collection, called the UK Medical Heritage Library, is completely open and can now be accessed for free via Jisc’s Historical Texts resource or via the Wellcome Library’s website.

Brought to you by Scope e-Knowledge Center, a world-leading provider of Abstracting & Indexing (A&I) Services, Knowledge Modeling Services (Taxonomies, Thesauri and Ontologies), Metadata Enrichment & Entity Extraction Services.”

Click here

Source:  Knowledgespeak Newsletter

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