Scientific Software Development Research Articles

The Saccharomyces Genome Database: Advanced Searching Methods and Data Mining.

At the core of the Saccharomyces Genome Database (SGD) are chromosomal features that encode a product. These include protein-coding genes and major noncoding RNA genes, such as tRNA and rRNA genes. The basic entry point into SGD is a gene or open-reading frame name that leads directly to the locus summary information page. A keyword describing function, phenotype, selective condition, or text from abstracts will also provide a door into the SGD. A DNA or protein sequence can be used to identify a gene or a chromosomal region using BLAST. Protein and DNA sequence identifiers, PubMed and NCBI IDs, author names, and function terms are also valid entry points. The information in SGD has been gathered and is maintained by a group of scientific biocurators and software developers who are devoted to providing researchers with up-to-date information from the published literature, connections to all the major research resources, and tools that allow the data to be explored. All the collected information cannot be represented or summarized for every possible question; therefore, it is necessary to be able to search the structured data in the database. This protocol describes the YeastMine tool, which provides an advanced search capability via an interactive tool. The SGD also archives results from microarray expression experiments, and a strategy designed to explore these data using the SPELL (Serial Pattern of Expression Levels Locator) tool is provided.

Brittleness and Bureaucracy: Software as a Material for Science

Through examining a case study of a major fluids modelling code, this paper charts two key properties of software as a material for building models. Scientific software development is characterized by piecemeal growth, and as a code expands, it begins to manifest frustrating properties that provide an important axis of motivation in the laboratory. The first such feature is a tendency towards brittleness. The second is an accumulation of supporting technologies that sometimes cause scientists to express a frustration with the bureaucracy of highly regulated working practices. Both these features are important conditions for the pursuit of research through simulation.

Test-Driven Development in scientific software: a survey

Scientific software developers are increasingly employing various software engineering practices. Specifically, scientists are beginning to use Test-Driven Development (TDD). Even with this increasing use of TDD, the effect of TDD on scientific software development is not fully understood. To help scientific developers determine whether TDD is appropriate for their scientific projects, we surveyed scientific developers who use TDD to understand: (1) TDDs effectiveness, (2) the benefits and challenges of using TDD, and (3) the use of refactoring practices (an important part of the TDD process). Some key positive results include: (1) TDD helps scientific developers increase software quality, in particular functionality and reliability; and (2) TDD helps scientific developers reduce the number of problems in the early phase of projects. Conversely, some key challenges include: (1) TDD may not be effective for all types of scientific projects; and (2) Writing a good test is the most difficult task in TDD, particularly in a parallel computing environment. To summarize, TDD generally has a positive effect on the quality of scientific software, but it often requires a large effort investment. The results of this survey indicate the need for additional empirical evaluation of the use of TDD for the development of scientific software to help organizations make better decisions.

Claims about the use of software engineering practices in science: A systematic literature review

Context: Scientists have become increasingly reliant on software in order to perform research that is too time-intensive, expensive, or dangerous to perform physically. Because the results produced by the software drive important decisions, the software must be correct and developed efficiently. Various software engineering practices have been shown to increase correctness and efficiency in the development of traditional software. It is unclear whether these observations will hold in a scientific context.Objective: This paper evaluates claims from software engineers and scientific software developers about 12 different software engineering practices and their use in developing scientific software.Method: We performed a systematic literature review examining claims about how scientists develop software. Of the 189 papers originally identified, 43 are included in the literature review. These 43 papers contain 33 different claims about 12 software engineering practices.Results: The majority of the claims indicated that software engineering practices are useful for scientific software development. Every claim was supported by evidence (i.e. personal experience, interview/survey, or case study) with slightly over half supported by multiple forms of evidence. For those claims supported by only one type of evidence, interviews/surveys were the most common. The claims that received the most support were: “The effectiveness of the testing practices currently used by scientific software developers is limited” and “Version control software is necessary for research groups with more than one developer.” Additionally, many scientific software developers have unconsciously adopted an agile-like development methodology.Conclusion: Use of software engineering practices could increase the correctness of scientific software and the efficiency of its development. While there is still potential for increased use of these practices, scientific software developers have begun to embrace software engineering practices to improve their software. Additionally, software engineering practices still need to be tailored to better fit the needs of scientific software development.

Scientific software development viewed as knowledge acquisition: Towards understanding the development of risk-averse scientific software

This paper presents a model of software development based on knowledge acquisition. The model was formulated from 10 years of studies of scientific software and scientists who develop software as part of their science. The model is used to examine assumptions behind software development models commonly described in software engineering literature, and compare these with the observed way scientists develop software. This paper also explains why a particular type of scientist, one who works in a highly risk-averse application domain, does not conform to the common characterization of all scientists as “end-user programmers”. We offer observations of how this type of scientist develops trustworthy software. We observe that these scientists work outside the ubiquitous method-based software development paradigms, using instead a knowledge acquisition-based approach to software development. We also observe that the scientist is an integral part of the software system and cannot be excluded from its consideration. We suggest that use of the knowledge acquisition software development model requires research into how to support acquisition of knowledge while developing software, how to satisfy oversight in regulated application domains, and how to successfully manage a scientific group using this model.

Lifting Industrial Ecology Modeling to a New Level of Quality and Transparency: A Call for More Transparent Publications and a Collaborative Open Source Software Framework

SummaryIndustrial ecology (IE) is a maturing scientific discipline. The field is becoming more data and computation intensive, which requires IE researchers to develop scientific software to tackle novel research questions. We review the current state of software programming and use in our field and find challenges regarding transparency, reproducibility, reusability, and ease of collaboration. Our response to that problem is fourfold: First, we propose how existing general principles for the development of good scientific software could be implemented in IE and related fields. Second, we argue that collaborating on open source software could make IE research more productive and increase its quality, and we present guidelines for the development and distribution of such software. Third, we call for stricter requirements regarding general access to the source code used to produce research results and scientific claims published in the IE literature. Fourth, we describe a set of open source modules for standard IE modeling tasks that represent our first attempt at turning our recommendations into practice. We introduce a Python toolbox for IE that includes the life cycle assessment (LCA) framework Brightway2, the ecospold2matrix module that parses unallocated data in ecospold format, the pySUT and pymrio modules for building and analyzing multiregion input‐output models and supply and use tables, and the dynamic_stock_model class for dynamic stock modeling. Widespread use of open access software can, at the same time, increase quality, transparency, and reproducibility of IE research.

On the Validation of a Specific Development Process for Scientific Software using the Inspection Technique DOI - 10.5752/P.2316-9451.2015v3n2p3

The increasing demand for software has generated greater need for software development processes. However, although the literature does not present processes for the development of scientific software, in previous studies, a Specific Development Process for Scientific Software ( SDPSS ) was proposed. SDPSS was conceived based on Humphrey’s Methodology, which defines that the execution of eight steps is necessary for the acquisition of a process. Having in mind that the first six steps have already been carried out, the current study considers the accomplishment of the seventh and eighth steps of the Methodology, which are the validation of the initial process and its later improvement. It is important to highlight the significance of these steps because a process must be tested and validated to ensure its efficiency. Hence, first, a webapp to automate and model the SDPSS was developed to aid in its implementation. Subsequently, SDPSS was applied in real environments of scientific software development to obtain results that were analyzed through a validation technique by inspection, known as VProcInsp. Despite some inconsistencies, it was concluded that SDPSS can really contribute to the development of academic scientific software.

Emergency Physicians' Perceptions and Decision-making Processes Regarding Patients Presenting with Palpitations

BackgroundPalpitations are a common emergency department (ED) complaint, yet relatively little research exists on this topic from an emergency care perspective. ObjectivesWe sought to describe the perceptions and clinical decision-making processes of emergency physicians (EP) surrounding patients with palpitations. MethodsWe conducted 21 semistructured interviews with a convenience sample of EPs. We recruited participants from academic and community practice settings from four regions of the United States. The transcribed interviews were analyzed using a combination of structural coding and grounded theory approaches with ATLAS.ti, a qualitative data analysis software program (version 7; Atlas.ti Scientific Software Development GmbH, Berlin, Germany). ResultsEPs perceive palpitations to be a common but generally benign chief complaint. EPs' clinical approach to palpitations, with regards to testing, treatment, and ED management, can be classified as relating to one or more of the following themes: 1) risk stratification, 2) diagnostic categorization, 3) algorithmic management, and 4) case-specific gestalt. With regard to disposition decisions, four main themes emerged: 1) presence of a serious diagnosis, 2) perceived need for further cardiac testing/monitoring, 3) presence of key associated symptoms, 4) request of other physician or patient desire. The interrater reliability exercise yielded a Fleiss' kappa measure of 0.69, indicating substantial agreement between coders. ConclusionEPs perceive palpitations to be a common but generally benign chief complaint. EPs rely on one or more of four main clinical approaches to manage these patients. These findings could help guide future efforts at developing risk-stratification tools and clinical algorithms for patients with palpitations.

Supervisor continuity or co-location: which matters in residency education? Findings from a qualitative study of remote supervisor family physicians in Australia and Canada.

Changes to health care systems and working hours have fragmented residents' clinical experiences with potentially negative effects on their development as professionals. Investigation of off-site supervision, which has been implemented in isolated rural practice, could reveal important but less overt components of residency education. Insights from sociocultural learning theory and work-based learning provided a theoretical framework. In 2011-2012, 16 family physicians in Australia and Canada were asked in-depth how they remotely supervised residents' work and learning, and for their reflections on this experience. The verbatim interview transcripts and researchers' memos formed the data set. Template analysis produced a description and interpretation of remote supervision. Thirteen Australian family physicians from five states and one territory, and three Canadians from one province, participated. The main themes were how remoteness changed the dynamics of care and supervision; the importance of ongoing, holistic, nonhierarchical, supportive supervisory relationships; and that residents learned "clinical courage" through responsibility for patients' care over time. Distance required supervisors to articulate and pass on their expertise to residents but made monitoring difficult. Supervisory continuity encouraged residents to build on past experiences and confront deficiencies. Remote supervision enabled residents to develop as clinicians and professionals. This questions the supremacy of co-location as an organizing principle for residency education. Future specialists may benefit from programs that give them ongoing and increasing responsibility for a group of patients and supportive continuity of supervision as residents.

Factors influencing healthy lifestyle changes: a qualitative look at low-income families engaged in treatment for overweight children.

Childhood obesity disproportionately affects low-income minority populations, yet there is a paucity of literature about effective interventions in this population. This study sought to understand the experience of low-income majority Hispanic families engaged in obesity treatment. We conducted six focus groups (2=English, 4=Spanish) with families who completed a community-based, family-oriented obesity treatment program, using standard qualitative focus group interview methods. Transcripts were recorded, transcribed, and analyzed for thematic content. Two coders using the software program ATLAS.ti (v.7.0; Scientific Software Development GmbH, Berlin, Germany) coded each transcript independently; reflexive team analysis with three study team members was used to reach a consensus. Participants (n=37) indicated high program satisfaction. Parents reported buying less junk/fast food, increased consumption of fruits and vegetables, preparing and eating more meals as a family, and increasing their families' physical activity (PA). Four barrier and facilitator themes emerged. Barrier themes were time and financial cost, parent's lack of time and energy, influence of family members, and challenges regarding physical environment. Facilitator themes were skill building around healthy eating and parenting, family involvement, and long-term health concerns. Unanticipated findings, parents reported, were that changes resulted in children sleeping better, feeling happier, and less irritability. Despite low-income families experiencing barriers to lifestyle changes to manage obesity, they made positive dietary changes and increased PA by learning specific skills and including the whole family in those changes. Additionally, some unexpected benefits were noted, including improved sleep, less irritability, and children appearing happier. Future studies should consider using these parent-identified outcomes as secondary measures of program effectiveness.

Orchestrating high-throughput genomic analysis with Bioconductor.

Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors.

Enabling systematic, harmonised and large-scale biofilms data computation: The Biofilms Experiment Workbench

Background and objectiveBiofilms are receiving increasing attention from the biomedical community. Biofilm-like growth within human body is considered one of the key microbial strategies to augment resistance and persistence during infectious processes. The Biofilms Experiment Workbench is a novel software workbench for the operation and analysis of biofilms experimental data. The goal is to promote the interchange and comparison of data among laboratories, providing systematic, harmonised and large-scale data computation. MethodsThe workbench was developed with AIBench, an open-source Java desktop application framework for scientific software development in the domain of translational biomedicine. Implementation favours free and open-source third-parties, such as the R statistical package, and reaches for the Web services of the BiofOmics database to enable public experiment deposition. ResultsFirst, we summarise the novel, free, open, XML-based interchange format for encoding biofilms experimental data. Then, we describe the execution of common scenarios of operation with the new workbench, such as the creation of new experiments, the importation of data from Excel spreadsheets, the computation of analytical results, the on-demand and highly customised construction of Web publishable reports, and the comparison of results between laboratories. ConclusionsA considerable and varied amount of biofilms data is being generated, and there is a critical need to develop bioinformatics tools that expedite the interchange and comparison of microbiological and clinical results among laboratories. We propose a simple, open-source software infrastructure which is effective, extensible and easy to understand. The workbench is freely available for non-commercial use at http://sing.ei.uvigo.es/bew under LGPL license.

Social practices on the right to protection in childhood for boys, girls, teenagers, parental figures and teachers

This paper presents the results of formative research on the design, implementation, and assessment of a strategy to transform the social practices regarding the right to childhood protection in the Colombian Caribbean region. To characterize the social practices regarding the right to childhood protection as well as the cognitions and social norms that support them, on the part of the boys, girls, teenagers, parental figures and teachers in the Atlantic region.The study used focus groups with boys, girls, teenagers, parental figures, and teachers to identify both the social practices linked to this right and the cognitions and social norms that support these practices. The information was processed by performing a content analysis with Atlas.ti software (version 7, Scientific Software Development GmbH, Berlin, Germany).The results obtained for all populations indicate that there are social conventions that underpin the social practices that jeopardize the right to childhood protection. For this reason, educational and communication strategies should question the cognitions and social norms linked to childhood, upbringing, care, and protection when modeling new practices based on other meanings and the inclusion of other agents.

Facilitators and barriers to adherence in the initiation phase of Disease-modifying Antirheumatic Drug (DMARD) use in patients with arthritis who recently started their first DMARD treatment.

To explore themes associated with adherence in the initiation phase for first-time use of disease-modifying antirheumatic drugs (DMARD) in patients with inflammatory arthritis using focus groups and individual interviews. Thirty-three patients were interviewed in focus groups and individual interviews. Interviews were transcribed verbatim and imported into ATLAS.ti software (Scientific Software Development GmbH). Responses that included reasons for adherence or nonadherence in the initiation phase were extracted and coded by 2 coders separately. The 2 coders conferred until consensus on the codes was achieved. Codes were classified into overarching themes. Five themes emerged: (1) symptom severity, (2) experiences with medication, (3) perceptions about medication and the illness, (4) information about medication, and (5) communication style and trust in the rheumatologist. Perceptions about medication and the communication style with, and trust in, the rheumatologist were mentioned the most in relation to starting DMARD. The rheumatologist plays a crucial role in influencing adherence behavior by addressing perceptions about medication, providing information, and establishing trust in the treatment plan.

Collective empowerment: A comparative study of community work in Mumbai and Stockholm

Mumbai and Stockholm are worlds apart in terms of public services, infrastructures and standard of living. However, both cities have known common problems of social exclusion and marginalisation related to neo‐liberal globalisation. Social workers are facing similar challenges regarding collective empowerment as a strategy for community work. This comparative study explored how collective empowerment is undertaken by community workers. The research participants were 13 informants from community‐work organisations in the two settings. Semi‐structured interviews were used and were analysed with the help of Atlas‐ti 6.2 (ATLAS.ti Scientific Software Development GmbH D‐10623 Berlin Germany). Social work in Mumbai is in a context of extreme poverty and mainly within the informal sector, whereas in Stockholm most social work is done in relation to a public welfare model. In Stockholm, interventions are aimed towards strengthening social networks, without direct aim at social change. In Mumbai, community workers organise people for collective empowerment to strengthen marginalised groups and achieve social change.

An ethnographic study of communication challenges in maternity care for immigrant women in rural Alberta

Backgroundmany immigrant and ethno-cultural groups in Canada face substantial barriers to accessing health care including language barriers. The negative consequences of miscommunication in health care settings are well documented although there has been little research on communication barriers facing immigrant women seeking maternity care in Canada. This study identified the nature of communication difficulties in maternity services from the perspectives of immigrant women, health care providers and social service providers in a small city in southern Alberta, Canada. Methodsa focused ethnography was undertaken incorporating interviews with 31 participants recruited using purposive and snowball sampling. A community liaison and several gatekeepers within the community assisted with recruitment and interpretation where needed (n=1). All interviews were recorded and audio files were transcribed verbatim by a professional transcriptionist. The data was analysed drawing upon principles expounded by Roper and Shapira (2000) for the analysis of ethnographic data, because of (1) the relevance to ethnographic data, (2) the clarity and transparency of the approach, (3) the systematic approach to analysis, and (4) the compatibility of the approach with computer-assisted qualitative analysis software programs such as Atlas.ti (ATLAS.ti Scientific Software Development GmbH, Germany). This process included (1) coding for descriptive labels, (2) sorting for patterns, (3) identification of outliers, (4) generation of themes, (5) generalising to generate constructs and theories, and (6) memoing including researcher reflections. Findingsfour main themes were identified including verbal communication, unshared meaning, non-verbal communication to build relationships, and trauma, culture and open communication. Communication difficulties extended beyond matters of language competency to those encompassing non-verbal communication and its relation to shared meaning as well as the interplay of underlying pre-migration history and cultural factors which affect open communication, accessible health care and perhaps also maternal outcomes. Conclusionthis study provided insights regarding maternity health care communication. Communication challenges may be experienced by all parties, yet the onus remains for health care providers and for those within health care management and professional bodies to ensure that providers are equipped with the skills necessary to facilitate culturally appropriate care.

The Blind Men and the Elephant: Towards an Empirical Evaluation Framework for Software Sustainability

Software sustainability has been identified as one of the key challenges in the development of scientific and engineering software as we move towards new paradigms of research and computing infrastructures. However, it is suggested that sustainability is not well understood within the software engineering community, which can led to ineffective and inefficient efforts to address the concept or result in its complete omission from the software system. This paper proposes a definition of software sustainability and considers how it can be measured empirically in the design and engineering process of software systems.

Continuous Integration for Concurrent Computational Framework and Application Development

Development of scientific software relies on specialized knowledge from a broad range of diverse disciplines including computer science, mathematics, engineering, and the natural sciences. Since it is rare for a given practitioner to simultaneously be an expert in each of the aforementioned fields, teamwork and collaboration are now the norm for scientific software development. This short paper discusses specific software development conventions that have led to the success of the MOOSE multiphysics framework at Idaho National Laboratory (INL), and ongoing plans to bring MOOSE to a wider community of developers as an open source project on GitHub.

A Scientist’s Perspective on Sustainable Scientific Software

Software underpins most of our daily activities, from banking and finance to interactions with the internet, to weather forecasts and reports. Software also impacts individuals, groups, and societies through policy implementation, since information for decision and policy making is frequently derived from software ranging from climate and weather models to financial forecasting systems. One way to gauge the extent to which specific software needs to be sustainable, accessible, and transparent essentially hinges on the degree to which scientific analysis software, models, and model output are used to help inform and guide policy. Climate models and related scientific results are perhaps the most obvious example of the need for sustainable and transparent software, due in part to the public forum in which the results are scrutinized and the implications on environmental management policy. Without almost ubiquitous adoption of best practices for scientific software development, maintenance, and use, the credibility of scientific results and of ourselves as scientists is substantially at risk; sustainable and transparent research processes are thus at the heart of maintaining and increasing our collective reputations. [The authors want to make clear that, by using climate models as an example of software with policy impacts, we are not claiming that these models, are written with little “best practices” in mind, nor that they are inherently unsustainable as software.]

A mixed-methods study on factors influencing prenatal weight gain in ethnic-minority women.

Gaining too much weight in pregnancy is associated with perinatal complications and increases the risks of future obesity for both women and their infants. Unfortunately, women enrolled in intervention trials have seen little improvement in adherence to prenatal weight gain recommendations compared to women receiving standard prenatal care. Therefore, the purpose of this descriptive mixed-methods study was to explore factors related to excessive weight gain in pregnancy. Nonpregnant nulliparous women, currently pregnant women, and postpartum women (N = 43) were recruited from a health center serving an inner-city minority community. Women completed questionnaires on knowledge, self-efficacy, and behaviors related to nutrition, exercise, and prenatal weight gain. Fifteen of these women participated in focus groups. Focus group data were analyzed using ATLAS.ti (Scientific Software Development GmbH, Berlin, Germany). Codes were created, themes were identified, and consensus was reached through multiple iterations of the analysis by study personnel. Excessive weight gain was common. Nutritional knowledge was poor and significantly lower among nonpregnant nulliparous women. Women felt sure that they could engage in healthy behaviors, but few did so. Participants in focus groups identified multiple barriers to healthy behaviors in pregnancy and made suggestions on how to help women more readily make improvements in these behaviors. Strategies identified in this study such as providing focused education directed at nonpregnant nulliparous women, stressing portion control, helping women better manage their cravings, and providing more pragmatic support and resources need to be explored in future research.