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Cambridge Structural Database

Cambridge Structural Database
Established in 1965, the CSD is the world’s repository for small-molecule organic and metal-organic crystal structures. Containing over 800,000 entries from x-ray and neutron diffraction analyses and more than 50,000 new structures added every year, this unique database of accurate 3D structures has become an essential crystallography resource to scientists around the world.

The UC Berkeley Libraries provides access to both the WebCSD (no downloads needed) and the complete CSDS client system (download here).

ProQuest and RefWorks downtime January 16

ProQuest will be unavailable from 7 p.m. on Saturday, January 16 until 3 a.m. on Sunday, January 17 due to scheduled maintenance. RefWorks will also be unavailable at that time.

This outage will affect a number of our databases including the following:

  • Agricola
  • Dissertations and Theses (Dissertation Abstracts)
  • Earthquake Engineering Abstracts
  • Environmental Sciences and Pollution Management
  • GeoRef
  • Historical Newspapers
  • PAIS International
  • PsycInfo
  • Sociological Abstracts

NCBI bioinformatics tools: An introduction

NCBI logo

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.

Date: Tuesday, Nov. 3
Time:
12 – 1 pm
Location:
Bioscience Library Training Room, 2189 VLSB

Add this workshop to my bCal

Open to all interested students and researchers; no registration is required.
Questions? Contact esmith@library.berkeley.edu

BIOBASE Proteome and HGMD

BIOBASE PROTEOME

BIOBASE Proteome includes tools for gene set analysis and pathway visualization:

  • search for individual gene, disease, and drug reports by name
  • browse for sets of genes, diseases, and drugs which share a desired set of characteristics
  • upload a list of genes and identify those characteristics which are statistically over-represented
  • export annotated characteristics for a gene list
  • build and visualize protein-protein networks, overlaid with disease and drug assignments
  • annotate custom sequences

BIOBASE HGMD provides data on inherited human gene mutations that:

  • are known to be associated with a particular gene or disease
  • disrupt a splice donor or acceptor site, or
  • result in a specific amino acid change.

Proteome/HGMD Workshops: Katherine Wendelsdorf, Ph.D., QIAGEN/BIOBASE Senior Scientist, will be presenting hands-on training workshops on Proteome and HGMD:

Date: Thursday, October 29, 2015
Time: 11:00 am – 12:00 pm (Proteome); 12:00 – 1:00 pm (HGMD)
Location: Bioscience Library Training Room, 2189 VLSB

The workshops are open to all interested researchers. If you are interested in attending, please let us know.

Questions? Please contact bios@library.berkeley.edu

New Database: GIDEON: the world’s premier Global Infectious Disease knowledge management tool

Gideon Logo

We are happy to announce that GIDEON (Global Infectious Diseases and Epidemiology Online Network) has been licensed for UCB use!

GIDEON’s Infectious diseases module facilitates diagnoses, and tracks information on Infectious Diseases from around the globe.

  • Include tabs on Diagnosis, Diseases, Travel, Drugs and Vaccines.
  • The Microbiology module, allows you to identify a taxon based on its phenotypic characteristics and view a list of the typical positive and negative reactions for a specified organism and compare the reactions of two or more species.

Gideon Screenshot

Check out the Video Tutorials, Tutorial, and GIDEON Cases, which provide examples of how you can use GIDEON.

Fall workshops

Spring workshops

The science and engineering libraries are holding a series of workshops during Fall Semester that can help you get the most out of freely available as well as Berkeley subscribed resources. Workshops include:

  • Citation management: EndNote, Evernote, Mendeley, and more
  • Productivity tools: Berkeley online tools for reading, writing, and collaborating more effectively
  • Intro to GIS tools and resources: an introduction to Geographic Information Systems and mapping tools
  • Data management: the best ways to create a data management plan, create, store, backup, and share your data
  • Publish for impact: This session gives tips on publishing your research for maximum impact and will cover open access, alternative publishing options, and promotion of your work

Check out the full schedule with locations and times on our Events Calendar. All workshops are drop-in – no registration required.

ADS gets a new interface

The Astrophysics Data System or ADS, a tool for finding astronomical and planetary science, has introduced a beta version of its new interface, Bumblebee. Bumblebee builds on the ADS “Classic” and ADS “2.0” interfaces, and introduces new filtering options and the ability to search full-text.

For the time being, the myADS notification service will remain unchanged, but look forward to a new custom notification service in the coming year.

For help constructing complex searches, visit: http://adsabs.github.io/help/search/

And for the hackers among you, visit github to check out Bumblebee’s publicly accessible code.

Connoisseur of Number Sequences: Q&A with Neil Sloane

Quanta Magazine last week published an article about the Online Encyclopedia of Integer Sequences (OEIS) along with a great interview with its creator, Neil Sloane. The OEIS “contains more than a quarter of a million different sequences of numbers that arise in different mathematical contexts.” Check out the interesting article and the OEIS itself!

Web of Science downtime July 26

Due to scheduled maintenance to install a new update, access to Web of Science may be intermittent during the maintenance window. This update will be installed between 6:00 a.m.?6:00 p.m. on Sunday, July 26, 2015.

DMPTool downtime Wednesday July 15

DMPTool2

The DMPTool will be unavailable from Wednesday July 15, 2015 at 5:00pm through Thursday, July 16 at 2:00am (PDT), due to scheduled maintenance. During this period users will not be able to log in or have access to their data management plans. We apologize for the inconvenience.

For questions about the DMPTool or about other data management tools and services available to UC Berkeley researchers, please see our page on Scientific Data Services or contact data-consult@lists.berkeley.edu.

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