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Bioscience Library

Open Genomic Data Repositories & Analysis Resources workshop

This workshop will introduce you to the rich ecosystem of genomic data repositories and analysis tools available for discovery and utilization of open genomic data. We will focus on a handful of bioinformatics tools that are accessible to researchers without programming expertise. We will also review current publisher and funder data sharing policies to understand “open data” as it relates to genomic research.

We will spend the last 45 minutes of the workshop on a hands-on gene expression reanalysis use case that shows you how to:

  • Search the Gene Expression Omnibus for datasets of interest
  • Use GEO2R to analyze gene expression data and generate a list of differentially expressed genes
  • Use pathway and network tools to interpret that gene list in a biological context

Date: Wednesday, April 27, 2016

Time: 12 – 1:30 pm; this is a hands-on workshop, so please bring your own laptop

Location: D-Lab Conference Room, 371 Barrows Hall

Please register: http://dlab.berkeley.edu/register?field_training_uid=25457

(Space is limited, and registered and waitlisted attendees will have priority.)

Presenter: Dr. Megan Laurance is the Research Informationist at the UCSF Library where she uses her expertise in genomic data analysis and knowledge management to help researchers get up to speed on various bioinformatics methods, databases and software, and integrate those tools into their own data analysis and interpretation workflows. Prior to becoming the Research Informationist at UCSF in 2013, Dr. Laurance spent 12 years at a genomic software and database company, and spent 10 years at the bench as a researcher studying various topics including transplantation biology, transcription, and cancer.

Questions? Please contact bios@library.berkeley.edu

Laptop lending at the Bioscience Library

MacBook Air laptops are now available for lending at the Bioscience & Natural Resources Library. Students may check out laptops for one-day – long enough to finish that paper, use for a class presentation, or watch a few movies!

Laptops run Windows or OSX and are loaded with the following software: Microsoft Office Suite, Adobe Creative Suite, Java, Flash, RealPlayer, QuickTime, Silverlight. Technical details, circulation information, and the library’s device lending policies can be found on the Library FAQ.

NCBI Workshop: SRA and dbGaP

NCBI logo

On Wednesday, March 23 from 9 – 11 am PDT, NCBI staff will present a workshop for advanced users of SRA and dbGaP who are interested in using public datasets, and:

  • Use and move large genomic datasets,
  • Use cloud computing for analyzing genomic datasets,
  • Express an interest in doing parallel work on genomic datasets,
  • Or are well-versed in RNA-Seq, variant calling, or metagenomics.

The registration link lists the specific topics the workshop will cover. For a more general explanation of NCBI’s genomic resources, please visit NCBI Learn for webinars and factsheets pertaining to dbGaP, SRA, and more.

Reposted from NCBI News.

DMPTool downtime Wednesday Feb. 3

DMPTool2

The DMPTool will be unavailable on Wednesday Feb. 3, 2016 from 5:00 to 6:00pm (PST), 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 Research Data Management page or contact researchdata@berkeley.edu.

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, Jan. 26
Time:
12 – 1 pm
Location:
Bioscience Library Training Room, 2189 VLSB (inside the library)

Add this workshop to my bCal

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

Encyclopedia of Cell Biology

Encyclopedia of Cell Biology cover

The Encyclopedia of Cell Biology is a new online reference covering molecular, organizational, functional, and systems cell biology, with an emphasis on higher eukaryotes. Among the topics covered:

  • Nucleic acid and protein synthesis
  • Imaging
  • Cytoskeleton and motors
  • Cellular immunology
  • Stem cell biology
  • Omics
  • Computational cancer biology

The more than 280 articles include fully annotated figures and links to additional reading.

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

UC Publication Management System = OA upload-a-thons

Drop-in for assistance with the new publication management system & easy deposit of your articles into eScholarship.
This “harvesting” system is currently being implemented across the UC campuses in response to the Academic Senate’s call for an efficient mechanism for facilitating faculty participation in the UC Open Access policy. The initial focus is on supporting the Open Access Policy, the system has the ability to connect campus systems like faculty profile pages, offering the potential for streamlining additional publication reporting and management processes in the future.

Visit one of the Upload-a-thons for assistance with this new system.
http://blogs.lib.berkeley.edu/whats-new.php/uc-open-access-policy-upload

BIOBASE Proteome and HGMD workshops

BIOBASE PROTEOME

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.

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.

Questions? Please contact bios@library.berkeley.edu

NEW! Bioscience & Natural Resources Library website

Please visit our NEW website! It is one of many library homepages included in the UC Berkeley Library’s move to update and improve our information pages.  As we migrated the content of the “classic” Bioscience & Natural Resources Library website to the new format, we were careful to make sure that all of the special resources on the ‘classic’ website were included.

New website: Bioscience & Natural Resources Library.
If you don’t see links on the first page check the Bioscience & Natural Resources Library Subject Guides list, or contact us.

The Bioscience eJournal list has a new look but the same content.  Bioscience e-Journals List

Thank you!

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