Determinants of quality, latency, and amount of Stack Overflow answers about recent Android APIs.

Stack Overflow is a popular crowdsourced question and answer website for programming-related issues. It is an invaluable resource for software developers; on average, questions posted there get answered in minutes to an hour. Questions about well established topics, e.g., the coercion operator in C++, or the difference between canonical and class names in Java, get asked often in one form or another, and answered very quickly. On the other hand, questions on previously unseen or niche topics take a while to get a good answer. This is particularly the case with questions about current updates to or the introduction of new application programming interfaces (APIs). In a hyper-competitive online market, getting good answers to current programming questions sooner could increase the chances of an app getting released and used. So, can developers anyhow, e.g., hasten the speed to good answers to questions about new APIs? Here, we empirically study Stack Overflow questions pertaining to new Android APIs and their associated answers. We contrast the interest in these questions, their answer quality, and timeliness of their answers to questions about old APIs. We find that Stack Overflow answerers in general prioritize with respect to currentness: questions about new APIs do get more answers, but good quality answers take longer. We also find that incentives in terms of question bounties, if used appropriately, can significantly shorten the time and increase answer quality. Interestingly, no operationalization of bounty amount shows significance in our models. In practice, our findings confirm the value of bounties in enhancing expert participation. In addition, they show that the Stack Overflow style of crowdsourcing, for all its glory in providing answers about established programming knowledge, is less effective with new API questions

Strong associations between microbe phenotypes and their network architecture

Understanding the dependence and interplay between architecture and function in biological networks has great relevance to disease progression, biological fabrication and biological systems in general. We propose methods to assess the association of various microbe characteristics and phenotypes with the topology of their networks. We adopt an automated approach to characterize metabolic networks of 32 microbial species using 11 topological metrics from complex networks. Clustering allows us to extract the indispensable, independent and informative metrics. Using hierarchical linear modeling, we identify relevant subgroups of these metrics and establish that they associate with microbial phenotypes surprisingly well. This work can serve as a stepping stone to cataloging biologically relevant topological properties of networks and towards better modeling of phenotypes. The methods we use can also be applied to networks from other disciplines.Comment: Replaced by the version scheduled to appear in Phys. Rev. E (Rapid Comm.

Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees.

BackgroundOne of the great advantages of next generation sequencing is the ability to generate large genomic datasets for virtually all species, including non-model organisms. It should be possible, in turn, to apply advanced computational approaches to these datasets to develop models of biological processes. In a practical sense, working with non-model organisms presents unique challenges. In this paper we discuss some of these challenges for ChIP-seq and RNA-seq experiments using the undomesticated tree species of the genus Populus.ResultsWe describe specific challenges associated with experimental design in Populus, including selection of optimal genotypes for different technical approaches and development of antibodies against Populus transcription factors. Execution of the experimental design included the generation and analysis of Chromatin immunoprecipitation-sequencing (ChIP-seq) data for RNA polymerase II and transcription factors involved in wood formation. We discuss criteria for analyzing the resulting datasets, determination of appropriate control sequencing libraries, evaluation of sequencing coverage needs, and optimization of parameters. We also describe the evaluation of ChIP-seq data from Populus, and discuss the comparison between ChIP-seq and RNA-seq data and biological interpretations of these comparisons.ConclusionsThese and other "lessons learned" highlight the challenges but also the potential insights to be gained from extending next generation sequencing-supported network analyses to undomesticated non-model species

Statistical Mutation Calling from Sequenced Overlapping DNA Pools in TILLING Experiments

<p>Abstract</p> <p>Background</p> <p>TILLING (Targeting induced local lesions IN genomes) is an efficient reverse genetics approach for detecting induced mutations in pools of individuals. Combined with the high-throughput of next-generation sequencing technologies, and the resolving power of overlapping pool design, TILLING provides an efficient and economical platform for functional genomics across thousands of organisms.</p> <p>Results</p> <p>We propose a probabilistic method for calling TILLING-induced mutations, and their carriers, from high throughput sequencing data of overlapping population pools, where each individual occurs in two pools. We assign a probability score to each sequence position by applying Bayes' Theorem to a simplified binomial model of sequencing error and expected mutations, taking into account the coverage level. We test the performance of our method on variable quality, high-throughput sequences from wheat and rice mutagenized populations.</p> <p>Conclusions</p> <p>We show that our method effectively discovers mutations in large populations with sensitivity of 92.5% and specificity of 99.8%. It also outperforms existing SNP detection methods in detecting real mutations, especially at higher levels of coverage variability across sequenced pools, and in lower quality short reads sequence data. The implementation of our method is available from: <url>http://www.cs.ucdavis.edu/filkov/CAMBa/</url>.</p

Do We Run How We Say We Run? Formalization and Practice of Governance in OSS Communities

Open Source Software (OSS) communities often resist regulation typical of traditional organizations. Yet formal governance systems are being increasingly adopted among communities, particularly through non-profit mentor foundations. Our study looks at the Apache Software Foundation Incubator program and 208 projects it supports. We assemble a scalable, semantic pipeline to discover and analyze the governance behavior of projects from their mailing lists. We then investigate the reception of formal policies among communities, through their own governance priorities and internalization of the policies. Our findings indicate that while communities observe formal requirements and policies as extensively as they are defined, their day-to-day governance focus does not dwell on topics that see most formal policy-making. Moreover formalization, be it dedicating governance focus or adopting policy, has limited association with project sustenance

Improvement of firebrand tracking and detection software

Burning and glowing firebrands generated by wildland and urban fires may lead to the initiation of spot fnes and the ignition of structures. One of the ways to obtain this infonnation is to process tliennal video files. Earlier, a number of algorithms were developed for the analysis of the characteristics of fu'ebrands under field conditions. However, they had certain disadvantages. In this regard, this work is devoted to the development of new algorithms and their testing