biology, Biostats, Uncategorized

What’s hot in molecular biology databases

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The journal Nucleic Acids Research has just published its 18th annual database issue. The current issue summarizes 96 new and 83 previously reviewed molecular biology databases, including GenBank, ENA, DDBJ, and GEO. Also included in the issue is an editorial advocating the creation of a “community-defined, uniform, generic description of the core attributes of biological databases,” which would be known as the BioDBCore checklist. Such a checklist would benefit both database users and provides: users would have a much easier time finding the appropriate resource and providers would be able to highlight specialized resources and the lesser known functionality of established databases.

Besides the databases reviewed in the current issue, Nucleic Acids Research maintains a select list of 1330 molecular biology databases that have been profiled in various database issues over the past 18 years.

economics, GIS, public policy

SimplyMap! – Census and business data made easier

Online mapping and data access has become even easier with the launch of SimplyMap 2.0.  A long time favorite of Economics and Public Policy courses (and faculty) at Duke, this program provides a straight forward interface for web-based mapping and data extraction application that lets users create thematic maps and reports using US census, business, and marketing data.

Screenshot
SimplyMap 2.0 map interface

Version 2.0 includes improvements designed to make it easier to find and analyze data and create professional looking GIS-style thematic maps.

Significant changes include:

  • A new multi-tab interface to allow you to easily switch between your projects
  • Interactive wizards to guide you through making maps and reports
  • Can choose to automatically select the geographic unit displayed on a map based on the zoom level
  • Easier searching and browsing to choose data variables
  • Assign keyword tags to organize your maps and reports
  • Share your work with other users of SimplyMap (send a URL that lets them open a copy of your map or report)
  • Data filters (greater than, less than, etc.) can now be applied to both maps and reports
  • More export options: Data: Excel, DBF, CSV;  Maps: GIF, PDF, Shapefiles (boundaries only, no attributes)
  • Faster performance

Give SimplyMap 2.0 a try and let us know what you think.  Support is always available in Perkins Data and GIS.

economics, GIS, policy, public policy

Policy Paradox: Mapping Residential Restrictions

Do residential restrictions placed on convicted sex offenders serve to protect the public?  Duke Economics Ph.D. candidate Songman Kang, has been using the analytical capabilities of geographic information software to help determine the extent to which the restrictions affect residential locations of sex offenders: computing the area covered by a restriction and determining which offenders had to relocate due to a restriction.

According to Kang, the residential restrictions are designed to reduce recidivism among sex offenders and prevent their presence near places where children regularly congregate.  Neither of these claims has been found consistent with empirical evidence though, and it is unclear whether the restrictions have been successful in reducing the rates of repeat sex offenses.  On the other hand, the restrictions severely limit residential location choices, and may force offenders to relocate away from employment opportunities and supportive networks of family and friends.  As a result of the deteriorated economic conditions, the offenders who had to relocate may become more likely to commit non-sex offenses.

The following maps illustrate some of the restricted zones in Miami and in the Triangle area of North Carolina studied by Mr. Kang.

Figure 1: Residential Restricted Zones in Miami

Figure 2: Triangle Restricted Residences

rstats, Statistics

Rolling with R in 2011

Interest in the open source statistical package R has grown over the last few years as researchers discover its powerful graphic capabilities, a suite of packages that extend its functionality, and its data import capabilities.  While several courses use R to teach introductory statistics, most researchers arrive at R with some statistical experience.  The following selected resources represent a growing number of books and websites designed to help orient users to the capabilities of R.

Quick-R Homepagequick_r
This website tries to provide a quick overview of basic data management and statistical capabilities of R for current SAS, SPSS, Stata, and Systat users.  The stress is on providing a brief overview of R commands for common data analysis needs.

R for Stata UsersR for Stata
A comprehensive guide for getting started in R using Stata as point of reference.

R for SAS and SPSS Users (not pictured)
Similar concept as R for Stata users.

Using R for Introductory Statistics
John Verzani’s R for Introductory Statistics is one of several introductions to using R for basic statistics. Examples are available as an R package.

Do you have other sources that you like for R?  Let us know in the comments.

GIS

Making Data Flow

As water quality and questions of water supply have grown more salient in the Triangle, Duke researchers have tried to contribute to the growing debate over water quality using the latest digital mapping (GIS) tools.  In the fall of 2009, Data and GIS Services in Perkins Library provided GIS analysis support for a stream and watershed assessment project that developed strategies to reverse the impact of poor urban stormwater management, degraded water quality, and the loss of natural habitats on the Duke campus.

Data/GIS helped the researchers access critical spatial data for the characterization of the contributing watershed’s current land use patterns.  This data enabled the students to analyze the watershed’s area of impervious surface and hydrologic flow paths, and helped inform the understanding of the water quality issues faced at the stream site.

The GIS map below illustrates how digital mapping tools can be used to summarize a large amount of complex data into a compelling presentation.

Special thanks to the interdisciplinary team of environmental and civil engineers, biology and environmental science majors, and a Nicholas MEM student who shared their project results: Alicia Burtner, Matt Ball, Nari Sohn, Avni Patel, Will Bierbower, Adam Nathan, Mike Schallmo, Justine Jackson-Ricketts, and Jai Singh.

Uncategorized

Welcome!

Welcome to the Perkins Data and GIS blog!  Our goal is to highlight Duke research, collections, policies, and tools surrounding empirical
data and digital maps of interest to the research community.  We hope that this blog will serve as a catalyst to link researchers and resources across the Duke community and beyond!