NCBI bioinformatics tools: An introduction

NCBI-Logo_sm

A hands-on workshop introducing NCBI bioinformatics tools such as PubMed, Gene, Protein, Nucleotide, and BLAST:

  • Starting with a disease, syndrome, or process, identify the genes/proteins involved
  • Starting with an organism and a protein, find the protein sequence and gene coding region
  • Starting with a sequence, identify the gene/protein and source

The workshop will cover selecting the proper tools for your question, navigating through the interlinked NCBI databases, and saving your results. It will be offered twice:

  • Dates: Tuesday August 29 (add to bCal) and Wednesday August 30 (add to bCal)
  • Time: 12 – 1 pm
  • Location: Bioscience Library Training Room, 2101 VLSB

Open to all interested students and researchers; no registration is required.

Questions? Contact esmith@library.berkeley.edu

For additional workshops on citation managers, searching PubMed and Scopus, writing and collaboration tools, data visualization, productivity tools and techniques, and other topics, please see the Science Libraries Events Calendar.

Summer Reading: Silent Spring

Silent Spring

Silent Spring
Rachel Carson
Boston: Houghton Mifflin, 2002

Originally published in 1962, Silent Spring is credited with advancing the concepts of environmentalism that led to the founding of the United States Environmental Protection Agency, and existing laws that protect the air and water. Currently the agency, the Clean Air Act, the Safe Drinking Water Act, and the Clean Water Act are threatened. Gaining knowledge of the basis for the creation of the Agency and these environmental regulations allows one to articulate a position for maintaining and strengthening them.

This book is part of the 2017 Berkeley Summer Reading List. Stay tuned for more weekly posts!

From the University Librarian: Welcome to Fall 2017!

students gather on memorial glade

Students gather for Golden Bear Orientation on Memorial Glade this week. (Photo by Cade Johnson for the University Library)

On Tuesday, incoming freshman gathered outside Doe Library as they began the official start of their college career, an eight-day orientation to Berkeley and its tremendous resources. Today, as I look outside my office window, students enjoy lunch from multi-ethnic food trucks beside the Campanile. The campus is bursting with new energy and enthusiasm, and the Library is excited to be at the heart of it.

University Librarian

University Librarian Jeffrey MacKie-Mason

This semester, we are launching Level Up, a new program designed to empower all students to acquire 21st-century information skills. Level Up will offer a menu of skill-building workshops and online resources on topics such as fake news, social media for social good, and advanced data analysis.

We’ve launched a new initiative to help address the high and ever-increasing cost of education to students and their families, as state support continues to decline. We are leading a campus-wide collaboration on two pilot programs to improve course content affordability. We expect students to save hundreds of thousands of dollars in just the first year of this new program.

Our halls are filled with materials from our unique and diverse collections, including a gallery devoted to recent acquisitions by The Bancroft Library, and exhibits on the world-famous Summer of Love, the history of Syrian culture, and the team of female mathematicians featured in Hidden Figures.

It’s an incredible time to be at Berkeley and the Library, where we are passionate about our mission to “help current and future users find, evaluate, use, and create knowledge to better the world.” From incoming students to esteemed scholars, the Library welcomes you.

— Jeffrey MacKie-Mason, University Librarian

5 things you didn’t know about solar eclipses

Total solar eclipse (CC via Flickr)

By Tor Haugan

It’s bird! It’s a plane! It’s — an eclipse?

On Monday, the moon will completely cover the sun and cast a shadow across the country, marking the first total solar eclipse visible in the United States since Feb. 26, 1979 — and the first one whose path has traveled from one American coast to the next in 99 years.

Although the forthcoming solar spectacle will be fully visible only from a 70-mile-wide, 3,000-mile-long band — “the path of totality” — which stretches from Oregon to South Carolina, you won’t have to travel far to get your eclipse fix.

Earth and physical sciences librarian Sam Teplitzky, who recently chose the items for a Cal Day eclipse extravaganza in the Physics Library and a Maps and More pop-up event at the Earth Sciences Library, says she has noticed a surge in interest in the topic.

“We’ve had several patrons use the eclipse-related maps to help chart their own eclipse-chasing plans,” she says, “and the new books I purchased related to next week’s eclipse have been checked out all summer.”

Those who can’t make it to the path of totality to witness the full-on phenomenon in person can check out the eclipse-centric displays here on campus. One, on view until Oct. 1, is outside of the Earth Sciences & Map Library (open weekdays from 9 to 5 p.m.), in the lower level of the lobby of McCone Hall. The other, which will be up through the end of the month, is at the main reading room of the Physics-Astronomy Library (open weekdays from 1 to 5 p.m.).

Eclipse exhibit

Eclipse resources are on display at the Earth Sciences & Map Library until Oct. 1. (Photo by Cade Johnson for the University Library)

Eclipse books on display

The main reading room of the Physics-Astronomy Library will feature eclipse materials through August. (Photo by Cade Johnson for the University Library)

Bonita Dyess, circulation supervisor at the Earth Sciences & Map Library, was instrumental in putting together the eclipse displays.

“I hope people gain a different outlook on our science libraries from looking at our displays,” she says. “I also hope they gain a better understanding of what a total eclipse truly is and how rare this extraordinary event occurs, especially in the U.S.”

We pored over many of the eclipse-related offerings at the Library, full of little-known tidbits and fun facts. Here are just a few things we learned.

1. Eclipse chasing is old.
Heading to Oregon in time for the big event? You’re not alone. Many eclipse enthusiasts are making their way the path of totality — from Boiler Bay in Oregon to Charleston, South Carolina — for primo viewing. But eclipse chasing isn’t new: It is said to have started in 1715. In fact, that year, Sir Isaac Newton created diagrams of the eclipse in England for the public, according to “Total Solar Eclipses and How to Observe Them.”

Interested in the history of eclipse chasing? Rebecca Joslin’s “Chasing Eclipses: The Total Solar Eclipses of 1905, 1914, 1925” tackles the subject, and its beautiful imagery makes it one of librarian Teplitzky’s top eclipse-related picks at the Library.

2. Eclipses come with their own weather.
Like a neighborhood in San Francisco, eclipses are said to come with their own microclimates. Solar eclipses are associated with a drop in temperature — the moon is blocking the sun, after all. Tracking software, however, isn’t sophisticated enough to predict the the weather changes they trigger, according to “Total Solar Eclipses.”

But rapidly fluctuating weather? That’s something all of us in the Bay Area are used to.

3. According to legend, a dragon (or frog or vampire or werewolf or dog) ate the sun.
Eclipses have been explained throughout the years in legends and lore, which vary from culture to culture. The Chinese and Indonesians, for example, historically held that the eclipse is caused by a giant dragon eating the sun, accounting for its apparent disappearance. In fact, the Mandarin word for eclipse is “shi,” which means “eat.

Eclipse myths involving creatures eating the sun are not uncommon, although the beast ingesting the planets can vary depending on the stories’ origins. In Bolivia, it was a huge dog; in Vietnam, a ginormous frog; a werewolf in Serbia; and a vampire in Siberia, according to the fascinating tome “Total Eclipses: Science, Observations, Myths and Legends.”

4. Eclipses have appeared in many books throughout history — including maybe the Bible.
Eclipses are featured in some of the most highly regarded works in history, including those by Shakespeare (“King Lear”) and Mark Twain (“A Connecticut Yankee in King Arthur’s Court”). Even one of the “Twilight” books is called “Eclipse.”

Most notably, though, is that the Scriptures may depict a solar eclipse. The Bible mentions three hours of darkness in the daytime during Jesus’ crucifixion, according to “Total Eclipses.” But whether this was a religious miracle or a normal (albeit rare) astronomical occurrence — or something else entirely — remains up for debate.

5. Someday, solar eclipses will no longer be visible.
The moon is drifting away from the Earth at a rate of 38 mm per year — which is the thickness of about five iPhones stacked on top of one another. Someday, the moon will appear so small in the sky, it will be unable to obscure the sun, according to “Total Solar Eclipses.”

But don’t worry, chasers — it won’t happen anytime soon.

How to see the eclipse

If you do want to see the eclipse but are stuck in the Bay Area on Monday, fear not: Although the region doesn’t lie on the path of totality, we can catch a glimpse of a partial (or about 75 percent) eclipse — that is, if Karl the Fog is cooperative.

Set your alarm to 10:15 a.m. — or a few minutes earlier, for some wiggle room — so you don’t miss it.

If you don’t end up seeing it in person, of course, there’s the Eclipse Megamovie Project, a crowdsourced venture spearheaded by UC Berkeley and Google, which pulls together volunteer-submitted images of the eclipse from across the country. So, like the sun come Monday, you’ll be covered.

Librarian Teplitzky says, if the weather allows, she’ll likely step outside to look at the eclipse — “with my eclipse glasses,” she adds, referring to the protective eyewear that filters out harmful rays.

You’ll want to nab a pair, even if you’re watching from the Bay Area. After all, you wouldn’t want to risk your eyesight for when the next total solar eclipse is visible in the United States — in 2024.

Sources: ABC Channel 7, American Astronomical Society, “Chasing Eclipses: The Total Solar Eclipses of 1905, 1914, 1925,” NASA, “Total Eclipses: Science, Observations, Myths and Legends”, “Total Solar Eclipses and How to Observe Them,” Washington Post

Two upcoming Free Speech events

 

Free Speech Movement CaféAlice Waters
Thursday September 7
6:00 p.m. – 7:30 p.m.
FSM Café

The Bay Area luminary and world-renowned founder and owner of Chez Panisse will read from her new memoir, Coming to My Senses: The Making of a Counterculture Cook. In her book, Alice Waters ” . . . retraces the events that led her to 1517 Shattuck Avenue and the tumultuous times that emboldened her to find her own voice as a cook when the prevailing food culture was embracing convenience and uniformity.” (Penguin Random House)

The Free Speech Movement (FSM) Café, centrally located at the south entrance to Moffitt Library on Floor 3, is a casual place to gather, study, or take a break with friends and colleagues. The Café honors Mario Savio, who played a key role in the struggle for free speech at UC, and commemorates the events of the Free Speech Movement at UC Berkeley. Indoor and terrace seating is provided.

Erwin Chemerinsky,  Dean of Berkeley Law

Note: This day/time are currently under review. Check back for an update.

Tuesday, September 26
6:00 p.m – 7:30 p.m.
Morrison Room, Doe Library

Erwin Chemerinsky became the 13th Dean of Berkeley Law on July 1, 2017, when he joined the faculty as the Jesse H. Choper Distinguished Professor of Law. He will be discussing his new book, Free Speech on Campus, which ” . . . provides the background necessary to understanding the importance of free speech on campus and offers clear prescriptions for what colleges can and can’t do when dealing with free speech controversies.” (Yale University Press)

 

Fall Workshops in the Sciences Libraries – Drop in and Learn!

This fall there is once again a packed schedule of drop-in workshops in the Science and Engineering Libraries! Topics include Citation Management, Literature Searching, Geographic Information Systems (GIS), Data Management, Data Visualization, NCBI tools, LaTeX, and more. Please check the Science Libraries Events Calendar for times, dates, locations, and class descriptions.

Welcome back! Art History/Classics Library Fall Hours Begin 8/23

Welcome back students and faculty! Fall hours for the Art History/Classics Library begin August 23rd.

hours

Learn Citation Management Tools

Over the course of the past decade a number of free software tools and apps—including Mendeley, Zotero, and RefWorks—have cropped up to help you to create, format and manage your citations. The Library has arranged this series of Fall 2017 drop-in workshops to help you get started (or dig deeper) with the citation management software of your choice:

Writing and Citing Tools: What are your options?

Citation Management: Best Practices

  • September 7, 12-1pm, Bioscience Library Training Room (VLSB)

LaTeX: Creating Tables, Figures, and Bibliographies

  • September 7, 4-5pm, Kresge Engineering Library Training Room

Mendeley Citation Management Workshop

  • September 12, 4-5pm, Bioscience Library Training Room (VLSB)

EndNote: Basics to Advanced

  • September 13, 12-1pm, Bioscience Library Training Room (VLSB)

Refworks: Citation Management with Google Docs

  • October 4, 12-1pm, Bioscience Library Training Room (VLSB)

Introduction to Zotero 5.0

  • October 10, 4:30-5:30pm, Moffitt Library Room 405

Advanced Zotero 5.0

  • October 17, 4:30-5:30pm, Moffitt Library Room 405

For more help managing your citations check out these library guides:

Summer Reading: Where Song Began

Where Song Began

Where Song Began: Australia’s Birds and How They Changed the World
Tim Low
New Haven: Yale University Press, 2016

Low’s book challenges expectations that all species originated from similar areas of the globe, instead arguing that most birds around the world today originated in Australia–and that they have influenced the world, including humans, to sing. He provides interesting insights into the size and aggressiveness of Australian birds, as well as odd and rare species, such as those with poisonous feathers.

This book is part of the 2017 Berkeley Summer Reading List. Stay tuned for more weekly posts!

Wiley Spectra Lab: Search the world’s largest NMR spectral collection

Do you need a fast, easy way to access spectra and identify an unknown compound?

Wiley Spectra Lab has acquired spectral data from Wiley, Wiley-VCH, Bio-Rad Sadtler and others to present the world’s largest collection of curated spectral data. Current licensing includes C-NMR, H-NMR and X-NMR spectroscopies.

You can search Wiley Spectra Lab in OskiCat or access it through the Chemistry and Chemical Engineering Library Guide under Properties and Data. Contact the Chemical Information Librarian, Kortney Rupp with any issues or questions.

An infographic describing Wiley Spectra Lab

Infographic for Wiley Spectra Lab

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We pored over many of the eclipse-related offerings at the Library, full of little-known tidbits and fun facts.... t.co/RbNU0t1mPB

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An exciting new resource for Berkeley scholars! t.co/SIqimadVkL

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Sharing knowledge is our goal here at the UC Berkeley Library. Check out our spaces and the students and staff... t.co/8DEHvKqt0W

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Check out this video tour of our Hargrove Music Library! t.co/2Xo36E5dCA