biology, Duke research, rstats

Surveying Our Researchers

Understanding library users’ research goals remains a key element of the Perkins Library’s Strategic Plan.  As part of the Library’s User Studies Initiative, Teddy Gray surveyed the Biology Department in the Fall of 2010 to discover what tools and resources departmental members use in their research, researchers’ data management needs, and the impact of the BES Library closing in 2009.

DATA AND DATA MANAGEMENT IN BIOLOGY
From the 18 interviews of faculty, graduate students, postdocs, and lab managers, we learned–not surprisingly–that nearly all the interviewees use data in their research, most of which they generate themselves. Half incorporate data from others into their work with nearly a third using sequence data from GenBank. Out of the 12 interviewees who generate data in their labs, two-thirds archive their data in existing repositories.

In addition to the interviews, this survey also examined research articles produced by Duke Biologists from 2009 in which we paid special attention to their methods sections and citation patterns. From analyzing departmental research articles, we found out the nearly 40% of the authors deposited their research data into either GenBank or a journal archive. Only one author deposited data into another existing scientific repository. Again nearly 40% of the authors used a general statistical package in their work (SAS and R being the most popular), while nearly half used a biology-specific statistical tool.

THE (RISE?) PREVALENCE of R
Almost everyone interviewed uses statistical tools in their research with over half now using R. Many also use biology-specific statistical programs.

PRINT VERSUS ELECTRONIC
All but one of the interviewees prefer the online versions of library material over the print. A third use image databases–primarily Google Images–in their teaching and presentations; however, only one interviewee knew of subject specific image databases such as the Biology Image Library. And while some interviewees missed the convenience of easy shelf browsing with the BES Library so close by, all are happy with the daily document delivery to the building.

FINAL THOUGHTS
We are grateful to the Biology Department for their support (and time) in conducting this survey and plan to use the results as the basis for library services.  Data and GIS Services is always interested in hearing more from Duke researchers about the nature of your research! Please let us know if you would like to discuss your research interest and/or library needs.

Data Visualization, GIS, Open Data

Wrangle, Refine, and Represent

Data visualization and data management represented the core themes of the 2011 Computer Assisted Reporting (CAR) Conference that met in Raleigh from February 24-27.  Bringing together journalists, computer scientists, and faculty, the conference united a number of communities that share a common interest in gathering and representing empirical evidence online (and in print).

While the conference featured luminaries in data visualization (Amanda Cox, David Huynh , Michal Migurski, Martin Wattenberg) who gave sage advice on how to best represent data online, web based data visualization tools provided a central focus for the conference.

Notable tools that may be of interest to the Duke research (and teaching) community include:

DataWrangler – An interactive data cleaning tool much like Google Refine (see below)

Google Fusion Tables – “manage large collections of tabular data in the cloud” – Fusion tables provides convenient access to google’s data visualization and mapping services.  The service also allows groups to annotate data online.

Google Refine – Refine is primarily a data cleaning tool that simplifies the process of cleaning data for further processing or analysis.  While users of existing data management tools may not be convinced to leave their current data management tool, Refine provides a rich suite of tools that will likely attract many new converts.

Many Eyes – One of the premier online visualization tools hosted by IBM.  Visualizations range from pie charts to digital maps to text analysis.  Many Eye’s versatility is one of its key strengths.

Polymaps – Billed as a “javascript library for image- and vector-tiled maps” – Polymaps allows the creating of custom lightweight map services on the web.

SIMILE Project (Semantic Interoperability of Metadata and Information in unLike Environments) – The SIMILE Project is a collection of different research projects designed to “enhance inter-operability” among digital assets.  At the conference, the Exhibit Project received particular attention for its ability to produce data rich visualization with very little coding required.

Timeflow –  Presented by Sarah Cohen and designed by Martin Wattenberg- Timeflow provides a convenient application for visualizing temporal data.

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!