Parametric Alignment of Drosophila Genomes

The classic algorithms of Needleman--Wunsch and Smith--Waterman find a maximum a posteriori probability alignment for a pair hidden Markov model (PHMM). In order to process large genomes that have undergone complex genome rearrangements, almost all existing whole genome alignment methods apply fast heuristics to divide genomes into small pieces which are suitable for Needleman--Wunsch alignment. In these alignment methods, it is standard practice to fix the parameters and to produce a single alignment for subsequent analysis by biologists. Our main result is the construction of a whole genome parametric alignment of Drosophila melanogaster and Drosophila pseudoobscura. Parametric alignment resolves the issue of robustness to changes in parameters by finding all optimal alignments for all possible parameters in a PHMM. Our alignment draws on existing heuristics for dividing whole genomes into small pieces for alignment, and it relies on advances we have made in computing convex polytopes that allow us to parametrically align non-coding regions using biologically realistic models. We demonstrate the utility of our parametric alignment for biological inference by showing that cis-regulatory elements are more conserved between Drosophila melanogaster and Drosophila pseudoobscura than previously thought. We also show how whole genome parametric alignment can be used to quantitatively assess the dependence of branch length estimates on alignment parameters. The alignment polytopes, software, and supplementary material can be downloaded at http://bio.math.berkeley.edu/parametric/.Comment: 19 pages, 3 figure

A Toolset for Supporting UML Static and Dynamic Model Checking

The Unified Modeling Language has become widely accepted as a standard in software development. Several tools have been produced to support UML model validation. However, most of them support either static or dynamic model checking; and no tools support to check both static and dynamic aspects of a UML model . But a UML model should include the static and dynamic aspects of a software system. Furthermore, these UML tools translate a UML model into a validation language such as PROMELA. But they have some shortcomings: there is no proof of correctness (with respect to the UML semantics) for these tools. In order to overcome these shortcomings, we present a toolset which can validate both static and dynamic aspects of a model; and this toolset is based on the semantic model using Abstract State Machines. Since the toolset is derived from the semantic model, the toolset is correct with respect to the semantic model

It Seemed Like a Good Idea at the Time (Hindsight is 2020)

Charles Kettering reportedly quipped: “99% of success is built on failure”. Yet, those failures rarely see the light of day, as publications naturally focus on successful innovations rather than the many failures that preceded them. The academic community is poorer as a result, as we are all left to re-create the same failures independently, rather than learning from one another. In this panel, we offer an opportunity to “celebrate failure”, by presenting four separate case studies of computing education initiatives that “seemed like a good idea at the time”, but ended up being spectacular failures. The presenters will discuss their “good ideas”, the disappointing results, and (most importantly) the lessons learned! Our goal is to foster a supportive community where failure is celebrated rather than criticized. We hope to laugh and learn together from these experience reports

ABET Accreditation in Colombian Higher Education Institutions: Opportunities and Barriers

Accreditation is a contemporary issue in engineering education. There are varying opinions about the opportunities and barriers of this process within the Colombian context. This study compared the advantages and disadvantages of various experiences published in the literature about ABET accreditation. The findings show the ABET accreditation promotes the adoption and implementation of a continuous improvement system and quality culture in engineering education. Additionally, the continuous improvement process aligns the institutional mission, program educational objectives, curricula, and student outcomes. On the contrary, the main concern is the high cost associated with preparing and adapting programs to meet the ABET requirements. Accreditation takes time and effort to be meaningful, which can sometimes lead to increased workloads and time requirements, inadequate training, and lack of faculty commitment. The compilation of experiences with the ABET accreditation process is a significant contribution to engineering programs of public universities in Colombia seeking international accreditation.La acreditación es un tema contemporáneo en la educación superior, particularmente en ingeniería. Existen variedad de opiniones sobre las oportunidades y barreras para emprender este proceso dentro del contexto colombiano. Este estudio comparó las ventajas y desventajas de varias experiencias publicadas en la literatura sobre la acreditación internacional ABET. Dentro de la ventaja se identificaron la formalización de una cultura de mejora continua y calidad en la educación, como también, la integración entre la misión institucional, los objetivos educativos del programa, los planes de estudio y los resultados de aprendizaje. Por el contrario, dentro de las barreras se identificaron los altos costos asociados en el desarrollo de la acreditación, así como la adaptación de los programas a nivel curricular y reglamentario para cumplir con los requisitos. La recopilación de experiencias sobre el proceso de acreditación ABET es una contribución significativa a los programas de universidades públicas en Colombia que buscan la acreditación internacional

Interactive radio’s promising role in climate information services: Farm Radio International concept paper

This paper focuses on how interactive radio programming can increase the reach of weather and seasonal climate information and related advisory services. In doing so, they can enhance small-scale farmers’ capacity to make optimal decisions and manage risks based on a better understanding of probabilistic seasonal forecasts. The objective is to outline strategy that could vastly and affordably expand the number of small-scale farmers that are reached by and benefit from weather and climate information and related advisory services. Building on Farm Radio International’s (FRI) pioneering African Farm Radio Research Initiative (AFRRI), we assess the opportunities for interactive radio to provide integrated climate and advisory information while increasing farmers’ equitable access to salient and legitimate programming. We describe a number of practical strategies that can be used to make radio-based climate communication interactive, outline elements of a successful interactive radio service targeting rural communities, and discuss costs and other issues required for sustainability

The development of a program analysis environment for Ada

A unit level, Ada software module testing system, called Query Utility Environment for Software Testing of Ada (QUEST/Ada), is described. The project calls for the design and development of a prototype system. QUEST/Ada design began with a definition of the overall system structure and a description of component dependencies. The project team was divided into three groups to resolve the preliminary designs of the parser/scanner: the test data generator, and the test coverage analyzer. The Phase 1 report is a working document from which the system documentation will evolve. It provides history, a guide to report sections, a literature review, the definition of the system structure and high level interfaces, descriptions of the prototype scope, the three major components, and the plan for the remainder of the project. The appendices include specifications, statistics, two papers derived from the current research, a preliminary users' manual, and the proposal and work plan for Phase 2

Delivering climate services for farmers and pastoralists through interactive radio

A scoping study to assess demand, opportunities and potential for the use of interactive radio to deliver climate services at scale for farmers and pastoralists was conducted by CCAFS in partnership with Farm Radio International in Tanzania, and Farm Radio Trust in Malawi in late 2014. Over 1280 individuals were interviewed in an audience research activity, while a desk survey, key informant interviews and knowledge partner engagement activities were undertaken to validate audience research and assess the wider context. The study reveals that for both Malawi and Tanzania, there is clear demand for climate information services via radio and mobile phone. Both radio and mobile phones are in common use, and are rated by farmers and pastoralists to have great potential as effective and trusted channels where they can access various climate information services. Surveyed farmers and pastoralists noted that radio programs, backed up by ICT services, would serve them best. Rainfall patterns, temperature data and forecasting services – both weekly and daily – were mentioned as particular needs. In general, farmers would trust climate information received via their preferred radio stations, and would use it in decision-making on their farms. Women and men differed in time spent listening to radio, in mobile phone airtime purchased, and in Malawi, phone ownership; but larger location differences masked any gender differences in preferences about information content, delivery channels, or expectations about user and benefit. As a response to farmer articulated demand, Farm Radio International and Farm Radio Trust propose working with key institutions and radio station partners to develop interactive programming for rural climate services as part of their implementation of the GFCS Adaptation Programme in Africa. Interactive climate services radio programming would respond to farmers’ ongoing climate information needs, and will engage them in program design, broadcast, monitoring and evaluation – together with partner radio stations. Interactive climate services radio programming will consist of short weekly radio programs, with the option of daily forecasts or interpretations, and will be complemented with ICT services via mobile phone. Programs will be continuously monitored and assessed by audiences and project staff to ensure relevance, usefulness, level of use and accuracy

Expectancies regarding the interaction between smoking and substance use in alcohol-dependent smokers in early recovery.

The purpose of this study was to investigate expectancies regarding the interaction between cigarette smoking and use of alcohol among alcohol-dependent smokers in early recovery, using the Nicotine and Other Substances Interaction Expectancies Questionnaire (NOSIE). Participants were 162 veterans, 97% male, with a mean age of 50 years, enrolled in a clinical trial aimed at determining the efficacy of an intensive smoking cessation intervention versus usual care. At baseline, participants were assessed on measures of smoking behavior, abstinence thoughts about alcohol and tobacco use, symptoms of depression, and smoking-substance use interaction expectancies. In addition, biologically verified abstinence from tobacco and alcohol was assessed at 26 weeks. Participants reported that they expected smoking to have less of an impact on substance use than substance use has on smoking (p < .001). Severity of depressive symptoms was significantly associated with the expectancy that smoking provides a way of coping with the urge to use other substances (p < .01). The expectation that smoking increases substance urges/use was predictive of prospectively measured and biologically verified abstinence from smoking at 26 weeks (p < .03). The results add to our knowledge of smoking-substance use interaction expectancies among alcohol-dependent smokers in early recovery and will inform the development of more effective counseling interventions for concurrent alcohol and tobacco use disorders

Advancing inclusive innovation policy in the UK’s second-tier city-regions

The UK exhibits stark regional economic divides which have been a long running concern for policymakers. With the levelling up agenda taking shape, city-regions in the UK are developing innovation and business support policies in seeking to deliver on a range of goals from traditional productivity concerns to wider social and environmental imperatives. Drawing on interviews with key actors in the city-regions of Cardiff, Manchester and Glasgow, this paper points to an emerging directional change in innovation policy, yet we show that capacities to articulate and implement an inclusive innovation approach vary widely. The uneven landscape for innovation policy within each of the city-regions, in terms of the location of innovation assets but also the varied institutional and social legacies shaping innovation policy, is also brought into view. Central to the reshaping of innovation policy in all cases, however, are agents working in networks, fashioning narratives and marshalling data in efforts to mobilise new ways of practicing innovation policy within what remains a centralised approach to sub-national economic development