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bioRxiv: a free open access archive for unpublished preprints in the life sciences

bioRxiv (pronounced “bio-archive”) is a free online archive and distribution service for unpublished preprints in the life sciences.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
  • bioRxiv logoGenomics
  • 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.

Conference Reflections: A Chemistry Librarian Discovers the Digital Humanities

Header image for LAUC-B 2017 conference

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.

Barack Obama Bust
3D Printed bust of President Barack Obama.

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.
A Crack in Creation

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

De Gruyter and Princeton Mathematics eBook Collection logo

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

Ingenuity Pathway Analysis

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)

Reaxys 2.0 Migration

 

Logo for Reaxys Database

Reaxys is a web-based tool for the retrieval of chemistry information and data from published literature, including journals and patents.Chemists at Berkeley are active users of Reaxys, doing 1000’s of searches/month!

Elsevier has rolled out a new version of Reaxys (Reaxys 2.0) that has a number of enhanced features, including:

  1.       An increasingly simple user interface.  The opening page has spaces to (a) type in the search query in a search bar or (b) type in the name of the structure or draw the structure.
  2.       Search functions using the querylets to increase the specificity of the search and reduces the time that the user has to filter the results post search.
  3.       Search functions that contain auto suggest. Similarly it also searches for singular/plural and synonyms
  4.       Using Boolean operators (obviously one of Elsevier’s strengths)
  5.       Listing hits in the initial screen (post search).  No secondary search needed.
  6.       A big increase in the number of searchable Asian patents

The migration is Reaxys 2.0 is ongoing, but migration should be completed by November 30, 2017. Soon UCB users will be directed to the new interface, but will continue to have the option to use the old interface for the foreseeable future.

JAMAevidence: Using Evidence to Improve Care

JAMAevidence

JAMAevidence helps clinical decision makers identify the best available evidence.

Check out their guides to the systematic consideration of the validity, importance, and applicability of claims about the assessment of health problems and the outcomes of health care.

Try it out!

Engineering Academic Challenge!

The Elsevier Engineering Academic Challenge is back! The team-based challenge lasts for five weeks and began on September 18. Register here to get started and win prizes!

 

quote about EAC

UPDATE: Elsevier Data Publishing Requirements

Last spring, we posted about data publishing requirements from Elsevier, Springer/Nature, and AAAS. At the time, Elsevier was the most lenient on their data publishing policies and used language that was suggestive and encouraging of data publishing. As of September 5th, 2017, that is no longer the case. Elsevier has signed on to the Transparency and Openness Guidelines (TOP) through the Center for Open Science. We talk and write a lot about transparency, openness, and sharing in science; however, there is a disconnect between the conversations and the daily workflows and practice of scientists. I was once told, after giving a workshop on data sharing, that I was an idealist trying to preach to realists. In order to close that gap, we need more publishers, like Elsevier, to make the ideal a reality, and enforce strict guidelines on data sharing and publishing.

Elsevier Logo

 

Let’s take a look at the 5 new data sharing requirements, which will be implemented for 1800 of Elsevier’s titles:

Option A:  you are encouraged to

  • deposit your research data in a relevant repository
  • cite this dataset in your article

Option B: you are encouraged to

  • deposit your research data in a relevant repository
  • cite this dataset in your article
  • link this dataset in your article
  • If you can’t do this, be prepared to explain why!

Option C: you are required to

  • deposit your research data in a relevant repository
  • cite this dataset in your article
  • link this dataset in your article
  • if you can’t do this, be prepared to explain why!

Option D: you are required to

  • deposit your research data in a relevant repository
  • cite this dataset in your article
  • link this dataset in your article

Option E: you are required to

  • deposit your research data in a relevant repository
  • cite this dataset in your article
  • link this dataset in your article
  • peer reviewers will review the data prior to publication

The new Elsevier policy is similar in nature to Springer/Nature with their tiered system of requirements. It’s important to check with your individual journal to see which option it falls under. Ideally, you will always follow option E, where you make your data openly available, cited, linked, and provide the proper amount of metadata to go through the peer review process or be reused by another researcher.

 

If you have any questions about how to enrich the metadata of your dataset, or where to deposit your research data, please email researchdata@berkeley.edu!

 

 

Workshops on Scopus for literature searching and research impact

Want to make the most of our subscription to Scopus to improve your literature searching or evaluate your research impact? Attend one of our upcoming Scopus workshops! The Library is hosting two back-to-back workshops on September 28 to provide tips on using this large abstract and citation database covering the peer-reviewed literature across disciplines.

Scopus banner image

Advanced Literature Searching with Scopus
September 28 | 2-3 p.m. | Bechtel Engineering Center, Kresge Engineering Library Training Room 110MD

Want to improve your literature searching and save yourself time? This workshop will cover advanced searching with Scopus, a large abstract and citation database covering the peer-reviewed literature: scholarly journals, books, and conference proceedings. The database covers publications in science, technology, medicine, social sciences, arts, and humanities. Come learn useful tips and techniques for finding relevant publications for your literature reviews.

Scopus Tools for Assessing Research Impact
September 28 | 3-4 p.m. | Bechtel Engineering Center, Kresge Engineering Library Training Room 110MD

This workshop will cover tools and techniques available in the citation database Scopus for maximizing and assessing your research impact. Topics to be covered include: citation analysis for authors, comparing journals with CiteScore, linking your Scopus Author ID to your ORCID ID, and using PlumX metrics in Scopus.

We encourage you to register online for these workshops but drop-ins will also be welcome as space allows.

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