Software

About: Software is a research topic. Over the lifetime, 130577 publications have been published within this topic receiving 2028987 citations. The topic is also known as: computer software & computational tool.

GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations

Abstract: Genome annotations are often published as plain text files describing genomic features and their subcomponents by an implicit annotation graph. In this paper, we present the GenomeTools, a convenient and efficient software library and associated software tools for developing bioinformatics software intended to create, process or convert annotation graphs. The GenomeTools strictly follow the annotation graph approach, offering a unified graph-based representation. This gives the developer intuitive and immediate access to genomic features and tools for their manipulation. To process large annotation sets with low memory overhead, we have designed and implemented an efficient pull-based approach for sequential processing of annotations. This allows to handle even the largest annotation sets, such as a complete catalogue of human variations. Our object-oriented C-based software library enables a developer to conveniently implement their own functionality on annotation graphs and to integrate it into larger workflows, simultaneously accessing compressed sequence data if required. The careful C implementation of the GenomeTools does not only ensure a light-weight memory footprint while allowing full sequential as well as random access to the annotation graph, but also facilitates the creation of bindings to a variety of script programming languages (like Python and Ruby) sharing the same interface.

Identifying and qualifying reusable software components

Abstract: Identification and qualification of reusable software based on software models and metrics is explored. Software metrics provide a way to automate the extraction of reusable software components from existing systems, reducing the amount of code that experts must analyze. Also, models and metrics permit feedback and improvement to make the extraction process fit a variety of environments. Some case studies are described to validate the experimental approach. They deal with only the identification phase and use a very simple model of a reusable code component, but the results show that automated techniques can reduce the amount of code that a domain expert needs to evaluate to identify reusable parts. >

Arduino: a low-cost multipurpose lab equipment.

Abstract: Typical experiments in psychological and neurophysiological settings often require the accurate control of multiple input and output signals. These signals are often generated or recorded via computer software and/or external dedicated hardware. Dedicated hardware is usually very expensive and requires additional software to control its behavior. In the present article, I present some accuracy tests on a low-cost and open-source I/O board (Arduino family) that may be useful in many lab environments. One of the strengths of Arduinos is the possibility they afford to load the experimental script on the board’s memory and let it run without interfacing with computers or external software, thus granting complete independence, portability, and accuracy. Furthermore, a large community has arisen around the Arduino idea and offers many hardware add-ons and hundreds of free scripts for different projects. Accuracy tests show that Arduino boards may be an inexpensive tool for many psychological and neurophysiological labs.

Computer applications in second language acquisition

Abstract: Computer Applications in Second Language Acquisition explores computer applications in second language acquisition by reviewing and interpreting research and development in three areas: computer-assisted second language learning, computer-assisted second language assessment, and computer-assisted second language research – addressing issues such as effective use of software in language teaching, values and limitations of computer-assisted testing, and the study of second language development with interactive computer programs. It offers a unique view of the topic by examining computer applications through perspectives from applied linguistics; it identifies cross-disciplinary work relevant to software development, use, and evaluation; and it suggests critical research directions. This is the first single volume on computer applications in the field which includes issues in teaching, assessment, and SLA research, and which treats evaluation extensively.