Asterias: a parallelized web-based suite for the analysis of expression and aCGH data

Asterias (\url{http://www.asterias.info}) is an integrated collection of freely-accessible web tools for the analysis of gene expression and aCGH data. Most of the tools use parallel computing (via MPI). Most of our applications allow the user to obtain additional information for user-selected genes by using clickable links in tables and/or figures. Our tools include: normalization of expression and aCGH data; converting between different types of gene/clone and protein identifiers; filtering and imputation; finding differentially expressed genes related to patient class and survival data; searching for models of class prediction; using random forests to search for minimal models for class prediction or for large subsets of genes with predictive capacity; searching for molecular signatures and predictive genes with survival data; detecting regions of genomic DNA gain or loss. The capability to send results between different applications, access to additional functional information, and parallelized computation make our suite unique and exploit features only available to web-based applications.Comment: web based application; 3 figure

Improving the Computer Science in Bioinformatics Through Open Source Pedagogy

Bioinformatics relies more than ever on information technologies. This pressures scientists to keep up with software development best practices. However, traditional computer science curricula do not necessarily expose students to collaborative and long-lived software development. Using open source principles, practices, and tools forms an effective pedagogy for software development best practices. This paper reports on a bioinformatics teaching framework implemented through courses introducing computer science students to the field. The courses led to an initial product release consisting of software and an Escherichia coli K12 GenMAPP Gene Database, within a total incubation time of six months

Improving the Computer Science in Bioinformatics Through Open Source Pedagogy

Bioinformatics relies more than ever on information technologies. This pressures scientists to keep up with software development best practices. However, traditional computer science curricula do not necessarily expose students to collaborative and long-lived software development. Using open source principles, practices, and tools forms an effective pedagogy for software development best practices. This paper reports on a bioinformatics teaching framework implemented through courses introducing computer science students to the field. The courses led to an initial product release consisting of software and an Escherichia coli K12 GenMAPP Gene Database, within a total incubation time of six months

Why Are Computational Neuroscience and Systems Biology So Separate?

Despite similar computational approaches, there is surprisingly little interaction between the computational neuroscience and the systems biology research communities. In this review I reconstruct the history of the two disciplines and show that this may explain why they grew up apart. The separation is a pity, as both fields can learn quite a bit from each other. Several examples are given, covering sociological, software technical, and methodological aspects. Systems biology is a better organized community which is very effective at sharing resources, while computational neuroscience has more experience in multiscale modeling and the analysis of information processing by biological systems. Finally, I speculate about how the relationship between the two fields may evolve in the near future

Current practice in software development for computational neuroscience and how to improve it

Almost all research work in computational neuroscience involves software. As researchers try to understand ever more complex systems, there is a continual need for software with new capabilities. Because of the wide range of questions being investigated, new software is often developed rapidly by individuals or small groups. In these cases, it can be hard to demonstrate that the software gives the right results. Software developers are often open about the code they produce and willing to share it, but there is little appreciation among potential users of the great diversity of software development practices and end results, and how this affects the suitability of software tools for use in research projects. To help clarify these issues, we have reviewed a range of software tools and asked how the culture and practice of software development affects their validity and trustworthiness. We identified four key questions that can be used to categorize software projects and correlate them with the type of product that results. The first question addresses what is being produced. The other three concern why, how, and by whom the work is done. The answers to these questions show strong correlations with the nature of the software being produced, and its suitability for particular purposes. Based on our findings, we suggest ways in which current software development practice in computational neuroscience can be improved and propose checklists to help developers, reviewers and scientists to assess the quality whether particular pieces of software are ready for use in research

SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data

<p>Abstract</p> <p>Background</p> <p>Censored data are increasingly common in many microarray studies that attempt to relate gene expression to patient survival. Several new methods have been proposed in the last two years. Most of these methods, however, are not available to biomedical researchers, leading to many re-implementations from scratch of ad-hoc, and suboptimal, approaches with survival data.</p> <p>Results</p> <p>We have developed SignS (Signatures for Survival data), an open-source, freely-available, web-based tool and R package for gene selection, building molecular signatures, and prediction with survival data. SignS implements four methods which, according to existing reviews, perform well and, by being of a very different nature, offer complementary approaches. We use parallel computing via MPI, leading to large decreases in user waiting time. Cross-validation is used to asses predictive performance and stability of solutions, the latter an issue of increasing concern given that there are often several solutions with similar predictive performance. Biological interpretation of results is enhanced because genes and signatures in models can be sent to other freely-available on-line tools for examination of PubMed references, GO terms, and KEGG and Reactome pathways of selected genes.</p> <p>Conclusion</p> <p>SignS is the first web-based tool for survival analysis of expression data, and one of the very few with biomedical researchers as target users. SignS is also one of the few bioinformatics web-based applications to extensively use parallelization, including fault tolerance and crash recovery. Because of its combination of methods implemented, usage of parallel computing, code availability, and links to additional data bases, SignS is a unique tool, and will be of immediate relevance to biomedical researchers, biostatisticians and bioinformaticians.</p

Harmonizing CMMI-DEV 1.2 and XP Method to Improve The Software Development Processes in Small Software Development Firms

Most software development organizations are small firms, and they have realized the need to manage and improve their software development and management activities. Traditional Software Process Improvement (SPI) models and standards are not realistic for these firms because of high cost, limited resources and strict project deadlines. Therefore, these firms need a lightweight software development method and an appropriate SPI model to manage and improve their software development and management processes. This study aims to construct a suitable software development process improvement framework for Small Software Development Firms (SSDFs) based on eXtreme Programming (XP) method and Capability Maturity Model Integration for Development Version 1.2 (CMMI-Dev1.2) model. Four stages are involved in developing the framework: (1) aligning XP practices to the specific goals of CMMI-Dev1.2 Key Process Areas (KPAs); (2) developing the proposed software development process improvement framework based on extending XP method by adapting the Extension-Based Approach (EBA), CMMI-Dev1.2, and generic elements of the SPI framework; (3) verifying the compatibility of the proposed framework to the KPAs of CMMI-Dev1.2 by using focus group method coupled with Delphi technique; and (4) validating the modified framework by using CMMI-Dev1.2 questionnaire as a main item to validate the suitability of the modified framework for SSDFs, and conducting two case studies to validate the applicability and effectiveness of this framework for these firms. The result of aligning XP practices to the KPAs of CMMI-Dev1.2 shows that twelve KPAs are largely supported by XP practices, eight KPAs are partially supported by XP practices, and two KPAs are not-supported by XP practices. The main contributions of this study are: software development process improvement framework for SSDFs, elicit better understanding of how to construct the framework, and quality improvement of the software development processes. There are possible avenues for extending this research to fulfil the missing specific practices of several KPAs, examining other agile practices and using CMMI-Dev1.3 to improve the framework, and conducting more case studie