Software Engineering as Instrumentation for the Long Tail of Scientific Software

The vast majority of the long tail of scientific software, the myriads of tools that implement the many analysis and visualization methods for different scientific fields, is highly specialized, purpose-built for a research project, and has to rely on community uptake and reuse for its continued development and maintenance. Although uptake cannot be controlled over even guaranteed, some of the key factors that influence whether new users or developers decide to adopt an existing tool or start a new one are about how easy or difficult it is to use or enhance a tool for a purpose for which it was not originally designed. The science of software engineering has produced techniques and practices that would reduce or remove a variety of barriers to community uptake of software, but for a variety of reasons employing trained software engineers as part of the development of long tail scientific software has proven to be challenging. As a consequence, community uptake of long tail tools is often far more difficult than it would need to be, even though opportunities for reuse abound. We discuss likely reasons why employing software engineering in the long tail is challenging, and propose that many of those obstacles could be addressed in the form of a cross-cutting non-profit center of excellence that makes software engineering broadly accessible as a shared service, conceptually and in its effect similar to shared instrumentation.Comment: 4 page

Does Global Warming Increase Establishment Rates of Invasive Alien Species? A Centurial Time Series Analysis

BACKGROUND: The establishment rate of invasive alien insect species has been increasing worldwide during the past century. This trend has been widely attributed to increased rates of international trade and associated species introductions, but rarely linked to environmental change. To better understand and manage the bioinvasion process, it is crucial to understand the relationship between global warming and establishment rate of invasive alien species, especially for poikilothermic invaders such as insects. METHODOLOGY/PRINCIPAL FINDINGS: We present data that demonstrate a significant positive relationship between the change in average annual surface air temperature and the establishment rate of invasive alien insects in mainland China during 1900-2005. This relationship was modeled by regression analysis, and indicated that a 1 °C increase in average annual surface temperature in mainland China was associated with an increase in the establishment rate of invasive alien insects of about 0.5 species year⁻¹. The relationship between rising surface air temperature and increasing establishment rate remained significant even after accounting for increases in international trade during the period 1950-2005. Moreover, similar relationships were detected using additional data from the United Kingdom and the contiguous United States. CONCLUSIONS/SIGNIFICANCE: These findings suggest that the perceived increase in establishments of invasive alien insects can be explained only in part by an increase in introduction rate or propagule pressure. Besides increasing propagule pressure, global warming is another driver that could favor worldwide bioinvasions. Our study highlights the need to consider global warming when designing strategies and policies to deal with bioinvasions

Data from: Relationships in the Lupinus albifrons species complex (Fabaceae) based on two highly variable chloroplast regions

The perennial lupines of western North America, previously suggested to be monophyletic, comprise an apparently rapid and recent species radiation concentrated in the California Floristic Province. The Lupinus albifrons species complex consists of a number of closely related yet morphologically variable taxa within the larger group of perennial lupines. We used sequence data from two rapidly evolving noncoding chloroplast regions to analyze relationships in the perennial lupines, with special emphasis on the Lupinus albifrons species complex. Sampling from throughout the ranges of species thought to be closely related to Lupinus albifrons, we found that this group is characterized by high genetic diversity not only between species, but also within species and even within populations. The results of this study call into question the monophyly of the western North American perennials. Only two taxa clearly emerge as deserving recognition at the species or subspecies level based on the molecular data: Lupinus paynei from Simi Valley, California, and Lupinus excubitus from eastern California and the San Gabriel Mountains. Although some taxonomic conclusions can be extrapolated from this study, overall, these results warn against undersampling in phylogenetic studies of recently evolved groups

Data from: Relationships in the Lupinus albifrons species complex (Fabaceae) based on two highly variable chloroplast regions

The perennial lupines of western North America, previously suggested to be monophyletic, comprise an apparently rapid and recent species radiation concentrated in the California Floristic Province. The Lupinus albifrons species complex consists of a number of closely related yet morphologically variable taxa within the larger group of perennial lupines. We used sequence data from two rapidly evolving noncoding chloroplast regions to analyze relationships in the perennial lupines, with special emphasis on the Lupinus albifrons species complex. Sampling from throughout the ranges of species thought to be closely related to Lupinus albifrons, we found that this group is characterized by high genetic diversity not only between species, but also within species and even within populations. The results of this study call into question the monophyly of the western North American perennials. Only two taxa clearly emerge as deserving recognition at the species or subspecies level based on the molecular data: Lupinus paynei from Simi Valley, California, and Lupinus excubitus from eastern California and the San Gabriel Mountains. Although some taxonomic conclusions can be extrapolated from this study, overall, these results warn against undersampling in phylogenetic studies of recently evolved groups

Illumina paired-end adapter schematic

<p>I made this to help myself understand how Illumina adapters work. This diagram includes the actual sequences of the adapters and how they align to each other.</p

Phylogenetic and population genetic investigations into the systematics of the Lupinus albifrons complex (Fabaceae) and the perennial lupines of western North America

<p>My PhD dissertation from Claremont Graduate University, 2010.</p

How Git works: a cartoon

<p>A cartoon of what Git looks like within one local repository.</p

Data from: Relationships in the Lupinus albifrons species complex (Fabaceae) based on two highly variable chloroplast regions

The perennial lupines of western North America, previously suggested to be monophyletic, comprise an apparently rapid and recent species radiation concentrated in the California Floristic Province. The Lupinus albifrons species complex consists of a number of closely related yet morphologically variable taxa within the larger group of perennial lupines. We used sequence data from two rapidly evolving noncoding chloroplast regions to analyze relationships in the perennial lupines, with special emphasis on the Lupinus albifrons species complex. Sampling from throughout the ranges of species thought to be closely related to Lupinus albifrons, we found that this group is characterized by high genetic diversity not only between species, but also within species and even within populations. The results of this study call into question the monophyly of the western North American perennials. Only two taxa clearly emerge as deserving recognition at the species or subspecies level based on the molecular data: Lupinus paynei from Simi Valley, California, and Lupinus excubitus from eastern California and the San Gabriel Mountains. Although some taxonomic conclusions can be extrapolated from this study, overall, these results warn against undersampling in phylogenetic studies of recently evolved groups