Bioscience, Natural Resources & Public Health Library

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

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.

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

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

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