Science & Engineering Libraries
Cambridge Structural Database 2018 Available
The 2018 Cambridge Structural Database System (including ConQuest and Mercury) is available for downloading from the UC distribution site. The Cambridge Structural Database is crystal structure database, with over 900,000 entries for organic and organometallic compounds.
Downloading CSD:
- You must be on the campus network or wifi or using VPN to access the files on that page.
- Don’t forget the site and confirmation codes, which you can get by clicking Berkeley (UCB) link. You’ll need those codes during the CSDS installation.
- CSDS is available for Windows, OSX, and Linux/Unix. It is recommended that you uninstall CSDS 2017 before you start this installation.
- There’s an additional Windows application that can be downloaded separately. CrossMiner is a “novel tool that allows crystal structure databases such as the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB) to be searched in terms of pharmacophore queries.”
- You can also search the CSD structures through WebCSD, without installing any software.
CSDS Documentation:
- What’s new in the 2018 release.
- Information about CSDS, including links to the specific databases.
- Documentation for CSDS.
Please contact Kortney Rupp if you have questions about CSD.
Love Data Week 2018!
The University Library, Research IT, and Berkeley Institute for Data Science invite faculty, students, and staff to a series of events on February 12th-16th during Love Data Week 2018. Love Data Week is a nationwide campaign designed to raise awareness about data visualization, management, sharing, and preservation.
Please join us to learn about multiple data services that the campus provides and discover options for managing and publishing your data. Graduate students, researchers, librarians and data specialists are invited to attend these events to gain hands on experience, learn about resources, and engage in discussion around researchers’ data needs at different stages of their research process.
To register for these events and find out more, please visit: http://guides.lib.berkeley.edu/ldw2018guide
Schedule:
Intro to Scopus APIs – Learn about different types of APIs Scopus has to offer and how to get data from APIs. In the first hour, learn about the portal, what the API can do, and about different use cases. Following a short break, the instructor will take the group through live queries, show how to test code, provide tips and tricks, and will leave the group with sample code to work with. Attendees will be able to follow up with the instructor via webinar to troubleshoot and ask further questions about specific projects. Register from here.
01:00 – 03:00 p.m., Tuesday, February 13, Doe Library, Room 190 (BIDS)
Refreshments will be provided.
Data stories and Visualization Panel – Learn how data is being used in creative and compelling ways to tell stories. Researchers across disciplines will talk about their successes and failures in dealing with data.
1:00 – 02:45 p.m., Wednesday, February 14, Doe Library, Room 190 (BIDS)
Refreshments will be provided.
Planning for & Publishing your Research Data – Learn why and how to manage and publish your research data as well as how to prepare a data management plan for your research project.
01:00 – 02:00 p.m., Thursday, February 15, Doe Library, Room 190 (BIDS)
We hope to see you there!
For your consideration: Electronic Laboratory Notebooks
As a previous research chemist, I spent a lot of time populating laboratory notebooks during my undergraduate and graduate research. I used to pride myself in keeping what I thought to be a notebook in which the experiments could all be reproduced at any time (naive, I know). When I joined a research group in graduate school, my advisor told me we were going to use Microsoft OneNote as our group notebook. At first, I was confused and hesitant about making the switch. My natural my workflow and data organization had to dramatically change to adjust to the digital recordkeeping environment I now found myself in. I soon realized the transition would allow me to focus more on the science and less on the printing, pasting, and handwriting. As an atomic force microscopist, I found it quick and easy to import digital images, chemical structures and screenshots of methods directly from digital articles. Over time I developed new strategies for organization including color coding to tie together sample preparations with the corresponding AFM images. I also created file naming standards and table of content pages to allow my labmates and advisor to search my notebook easily. These strategies ultimately allowed me to conduct my work in a more efficient and easily reproducible way and I now cannot imagine a world in which I could conduct science using a paper notebook.
Adopting any new workflows into an already complicated, time-sensitive environment can seem overwhelming and possess a steep learning curve. Libraries and librarians at UC Berkeley are well positioned to help researchers improve their productivity, transparency, and reproducibility by adopting a digital recordkeeping system. To try and provide some insight into how to determine which ELN to use and a strategy to make the transition to ELNs, I have created a guide and am available to assist throughout the transition process.
Alice Fan, MD: New Cancer Therapies & Women in Science
The last Nanoscale Science and Engineering (NSE) seminar of the semester is scheduled for Friday, December 1st from 2:00 – 3:00 in 180 Tan Hall. Alice Fan, from the Stanford Medical School, will be speaking on new nanoimmunoassays that enable the isolation and analysis of tumor cells. Following her talk, the Graduate Women in Engineering (GradSWE) will host a coffee hour from 3:30-4:30 in 242 Sutardja Dai Hall.
bioRxiv: a free open access archive for unpublished preprints in the life sciences
bioRxiv (pronounced “bio-archive”) is a free online archive and distribution service for unpublished preprints in the life sciences. It is operated by Cold Spring Harbor Laboratory, a not-for-profit research and educational institution. By posting preprints on bioRxiv, authors are able to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals.
bioRxiv accepts preprints of articles covering all aspects of research in the life sciences. Categories include:
- Bioengineering
- Cancer biology
- Cell biology
- Ecology
- Epidemiology
Genomics- Molecular biology
- Neuroscience
- Pharmacology and toxicology
- Scientific Communication and Education
and more.
Readers may add public comments to articles on bioRxiv. Comments are moderated to ensure they conform to the standards of normal professional discourse.
Once an article is published in a journal, bioRxiv will automatically update the preprint with a link to the published version.
Life, gene editing, and rock ’n’ roll: 5 things we learned from Jennifer Doudna’s talk
When Jennifer Doudna was in high school, a guidance counselor called her into his office to talk to her about her career.
“What do you want to be when you grow up?” Doudna recalls him asking.
“I want to be a scientist,” Doudna said.
“Girls don’t do science,” she remembers him saying.
She has been proving him wrong ever since.
For one, the UC Berkeley professor co-invented CRISPR-Cas9 gene editing, hailed as the biggest biological breakthrough since the discovery of DNA’s molecular structure in the 1950s. The technology comes with the possibility of curing devastating diseases and improving lives but also raises ethical questions.
“If you have a tool that allowed precision changes to DNA to be made,” she said, “that provides a way that, in principle, one could alter human evolution by making changes that could become inherited by future generations.”
In the years that followed, Doudna has become instrumental in raising awareness and broadening understanding — within the scientific community and beyond — about the technology. It’s a duty Doudna doesn’t take lightly. “It’s something I feel deeply passionate about,” she said.
Doudna sat down in front of an audience Tuesday in the Bioscience & Natural Resources Library for a chat about her book (“A Crack in Creation” is out this year), her life, and her scientific breakthrough.
Here are five things we learned.
1. Her upbringing in Hawaii influenced her career path.
Growing up, Doudna lived in Hilo, a “small, rural town,” on the big island of Hawaii. It was living in Hawaii, surrounded by diverse wildlife (“blind cave spiders and all kinds of interesting plants,” she said) that sparked her lifelong love of science.
“When I think back on how I got interested in science and biology and chemistry,” she said, “it really, I think, stems from growing up in that island environment and wondering about how organisms can evolve to live in a setting like that.”
And in 10th grade, Doudna’s interest in science deepend, thanks to a chemistry teacher, Miss Wong, who “taught us kids that science was about solving puzzles — it was about asking questions and figuring out how to answer them.”
“I absolutely loved it,” she said. “It was fun, and I started imagining that it would be really great to grow up and have someone pay me to do what I thought was just kind of fun — playing around in a lab.”
2. Even bioscientists get the blues.
In her 40s — and well into her second decade of running her lab — she started to question whether her work was going to have an impact.
“I really almost had sort of a midlife crisis,” she said.
She took a leave of absence at Berkeley for an opportunity at a company — which, in retrospect, was the wrong move.
Although it was a great company, she began to realize, “It was just the wrong fit for me,” she said. “I felt it in my gut. This is not where I’m meant to be.”
“I realized that I just loved working with students. I loved being at a public university,” she said. “I really believed in that mission of having education available to anyone who can come and wants to learn and wants to work at this wonderful place that we have here.”
She asked her former colleagues at UC Berkeley if she could return.
“They took me back,” she said.
3. She didn’t like the name of her book at first.
Neither Doudna nor co-author Samuel Sternberg liked the title “A Crack in Creation,” which their editor suggested.
“It sounded very ominous, somehow,” she said.
Neither could think of a better title, and they were eventually won over.
“It does sort of convey this idea that … we’re sort of at a fork in the road, in a way, and it really does feel kind of profound at times to me,” she said. “We’re at a point where now we as a species have a tool that will allow us to control … who we are.”
4. She has a complicated relationship with the spotlight.
“People have called me the public face of CRISPR, and I’m sort of shocked by it,” she said.
But with glare of the spotlight comes the opportunity to raise awareness and educate the public.
“I feel sort of a sense of honor that I’ve been sort of thrust into this position of being a spokesperson for science, and it’s something that I feel deeply passionate about,” she said.
5. She had a brush with rock royalty.
With her profile having reached new heights come opportunities that she had never previously imagined.
“I was at a thing in London not long ago, and I turned around, and behind me was (rock guitarist) Jimmy Page,” she said. “We just struck up a conversation. We started talking about science, and about guitars, and Led Zeppelin.
“And I said to him, ‘I’m such a fangirl. I mean, I listened to your music growing up. Would you mind if I took a picture with you?’
“And (now) I have a picture with Jimmy Page.”
Conference Reflections: A Chemistry Librarian Discovers the Digital Humanities
Every year librarians from across the UC System come together to learn about emerging trends in library and information science at the LAUC-B conference. The 2017 theme was, “Focus on the visual: Digital Humanities and Libraries.” As the Chemical Information Librarian at UC Berkeley some people might wonder, what do I have in common with the digital humanities? I am an experienced chemist, but am a new librarian at UCB and have a lot to learn about the amazing work being done by my colleagues. The UC system supports many departments at the top of their field, so as you can imagine, the librarians for those departments and the entire system are often passionate and talented individuals.
As a subject liaison, I feel strongly that interdisciplinary and collaborative projects are leading to some incredible outcomes, spanning across the humanities and sciences. My favorite talk of the day came from the Associate Vice Provost and Executive Director of the California Digital Library (CDL), Günter Waibel, who delivered the opening keynote and outlined his work doing the first ever 3D printed bust of a sitting President, which had a great societal response. As librarians we always hope our work will touch people in powerful ways, it’s still unclear to me what my contribution to the field will be. As long as I can attend events like the LAUC-B conference, I am sure to find a great idea.
Author Event with Dr. Jennifer Doudna
Tuesday, November 14, 2017. 4:30-6:00pm.
Bioscience & Natural Resources Library, 2101 VLSB.
Dr. Jennifer A. Doudna, Professor of Molecular and Cell Biology and Chemistry, UC Berkeley and Investigator, Howard Hughes Medical Institute, will discuss her new book, A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution, a fascinating chronicle of the discovery of CRISPR and the ethical questions to come.
Sponsored by: University Library, Life & Health Sciences Division.
The Library attempts to offer programs in accessible, barrier-free settings. If you think you may require disability-related accommodations, please contact the event sponsor, Susan Koskinen, skoskine@berkeley.edu, as soon as possible.
De Gruyter and Princeton Mathematics eBook Collection
The Library recently purchased the De Gruyter and Princeton Mathematics eBook Collection. This collection consists of titles from nine well-known series published by Princeton University Press and De Gruyter – including books from the very respected series Annals of Mathematics Studies back to 1940! These series include highly-cited works from influential mathematicians such as Church, Halmos, Milnor, Polya, and Weyl, among many others.
The nine series are:
- Annals of mathematics studies
- De Gruyter expositions in mathematics
- De Gruyter series in nonlinear analysis and applications
- De Gruyter studies in mathematical physics
- De Gruyter studies in mathematics
- Mathematical notes
- Princeton mathematical series
- Princeton series in applied mathematics
- Radon series on computational and applied mathematics
Ingenuity Pathway Analysis (IPA) workshop
A representative from Qiagen will offer a hands-on training workshop on using IPA to interpret expression data (including RNA-seq).
Date: Thursday, Nov. 9
Time: 1:30-4:30 pm
Location: Bioscience Library Training Room, 2101 Valley Life Sciences Building
You are invited to participate in this free training, and are encouraged to bring your own laptop or use the computer workstations in our training room.
Please register if you are interested in attending.
The workshop will cover how to:
- Format, upload your data, and launch an analysis
- Identify likely pathways that are expressed
- Find causal regulators and their directional effect on gene functions and diseases
- Build pathways, make connections between entities, and overlay multiple datasets on a pathway or network
- Understand the affected biological processes
- Perform a comparison analysis: utilize a heat map to easily visualize trends across multiple time points or samples
Questions? Please contact Elliott Smith (esmith@library.berkeley.edu)