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


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


Identifying Transgender and Other Gender Minority Respondents on Population-Based Surveys

Currently, most federally-supported population-based surveys do not include measures to identify transgender and other gender minority respondents, according to a report released by the Williams Institute on behalf of the Gender Identity in U.S. Surveillance (GenIUSS) group. The report entitled, "Best Practices for Asking Questions to Identify Transgender and Other Gender Minority Respondents on Population-Based Surveys," assesses current practices in sex and gender-related population research and offers strategies for establishing consistent, scientifically rigorous procedures for gathering information relevant to the needs and experiences of transgender people and other gender minorities.

The American Community Survey, the Current Population Survey, the Survey of Income and Program Participation, the National Crime Victimization Survey, the National Health Interview Survey, and the National Survey of Veterans are among the federally-supported population-based surveys that currently do not include measures to identify gender minority respondents. These are top-priority surveys for including recommended sex and gender-related measures.

"Research tells us that transgender people and other gender minorities face discrimination that impacts their health and well-being," says Jody L. Herman, who served as editor for the report and leads Williams Institute transgender research efforts. “Having representative data on the social, economic, and health status of gender minorities is key to guiding efforts by government and nonprofit agencies to address disparities."

The report recommends various promising measures and measurement approaches for identifying respondents as gender minorities in general population surveys. Among the most effective is the "two step" approach, which includes measures of self-reported assigned sex at birth (the sex recorded on one?s original birth certificate) and gender identity at the time of the survey.

Related to this post:

Creating Authentic Spaces: A Gender Identity and Gender Expression Toolkit: This toolkit provides constructive and tangible steps on how to implement anti-discrimination policies around gender identity and gender expression, as well as strategies and suggestions on creating affirming spaces for people who identify as trans and gender non-conforming.


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


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 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


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


Free Open Access Options for Berkeley Authors

UC Berkeley authors have several free options to publish their article in open access journals. Listed below are three rapid dissemination OA journals where articles are peer reviewed in which Berkeley authors can publish without paying an article processing charge (APC).

PeerJ logoPeerJ: publishes original research in the biological, medical and health sciences. Due to a partnership with the Berkeley Library, there is no cost for Berkeley authors to publish in PeerJ.

SAGE Open: publishes original research and review articles in humanities, social and behavioral sciences. The Library underwrites Berkeley authors’ publishing costs. This also includes AERA Open and some other OA journals hosted by SAGE.  

SAGE Open logo

 

 

 

eLife: publishes original research in life sciences and biomedicine. It is free to publish in eLife while the journal is being established though there are plans to institute article processing charges for authors in the future. eLife logo

More information on open access at UC Berkeley is available from this guide. Information on the UC Open Access Policy is here.


The Most Distinctive Causes of Death by State, 2001-2010

Online article from Preventing Chronic Disease:

Boscoe FP, Pradhan E. The Most Distinctive Causes of Death by State, 2001-2010. Prev Chronic Dis 2015;12:140395. DOI: http://dx.doi.org/10.5888/pcd12.140395

The map depicts a variety of distinctive causes of death based on a wide range of number of deaths, using the International Classification of Diseases, 10th Revision (ICD-10), List of 113 Selected Causes of Death file to present a nuanced view of mortality variation within the United States.


Vital Signs: Core Metrics for Health and Health Care Progress

"Thousands of measures are in use today to assess health and health care in the United States. Although many of these measures provide useful information, their sheer number, as well as their lack of focus, consistency, and organization, limits their overall effectiveness in improving performance of the health system. To achieve better health at lower cost, all stakeholders – including health profes­sionals, payers, policy makers, and members of the public – must be alert to the measures that matter most. What are the core measures that will yield the clearest understanding and focus on better health and well-being for Americans?"

In this Institute of Medicine report, with accompanying infographics, video, and briefs, a set of 15 standardized mea­sures is recommended. It is hoped that these could provide consistent benchmarks for health progress across the nation and improve system performance in the highest-priority areas.

What do you think?