An Introduction to Programming for Bioscientists: A Python-based Primer

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a 'variable', the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables, numerous exercises, and 19 pages of Supporting Information; currently in press at PLOS Computational Biolog

Models in the Cloud: Exploring Next Generation Environmental Software Systems

There is growing interest in the application of the latest trends in computing and data science methods to improve environmental science. However we found the penetration of best practice from computing domains such as software engineering and cloud computing into supporting every day environmental science to be poor. We take from this work a real need to re-evaluate the complexity of software tools and bring these to the right level of abstraction for environmental scientists to be able to leverage the latest developments in computing. In the Models in the Cloud project, we look at the role of model driven engineering, software frameworks and cloud computing in achieving this abstraction. As a case study we deployed a complex weather model to the cloud and developed a collaborative notebook interface for orchestrating the deployment and analysis of results. We navigate relatively poor support for complex high performance computing in the cloud to develop abstractions from complexity in cloud deployment and model configuration. We found great potential in cloud computing to transform science by enabling models to leverage elastic, flexible computing infrastructure and support new ways to deliver collaborative and open science

(MU-CTL-01-12) Towards Model Driven Game Engineering in SimSYS: Requirements for the Agile Software Development Process Game

Software Engineering (SE) and Systems Engineering (Sys) are knowledge intensive, specialized, rapidly changing disciplines; their educational infrastructure faces significant challenges including the need to rapidly, widely, and cost effectively introduce new or revised course material; encourage the broad participation of students; address changing student motivations and attitudes; support undergraduate, graduate and lifelong learning; and incorporate the skills needed by industry. Games have a reputation for being fun and engaging; more importantly immersive, requiring deep thinking and complex problem solving. We believe educational games are essential in the next generation of e-learning tools. An extensible, freely available, engaging, problem-based game platform that provides students with an interactive simulated experience closely resembling the activities performed in a (real) industry development project would transform the SE/Sys education infrastructure. Our goal is to extend the state-of-the-art research in SE/Sys education by investigating a game development platform (GDP) from an interdisciplinary perspective (education, game research, and software/systems engineering). A meta-model has been proposed to provide a rigourous foundation that integrates the three disciplines. The GDP is intended to support the semi-automated development of collections of scripted games and their execution, where each game embodies a specific set of learning objectives. The games are scripted using a template based approach. The templates integrate three approaches: use cases; storyboards; and state machines (timed, concurrent, hierarchical state machines). The specification templates capture the structure of the game (Game, Acts, Scenes, Screens, Challenges), storyline, characters (player, non-player, external), graphics, music/sound effects, rules, and so on. The instantiated templates are (manually) transformed into XML game scripts that can be loaded into the SimSYS Game Play Engine. As a game is played, the game play events are logged; they are analyzed to automatically assess a player’s accomplishments and automatically adapt the game play script. Currently, we are manually defining a collection of games. The games are being used to ensure the GDP is flexible and reliable (i.e., the prototype can load and correctly run a variety of game scripts), the ontology is comprehensive, and the templates assist in defining well-organized, modular game scripts. In this report, we present the initial part of an Agile Software Development Process game (Act I, Scenes 1 and 2) that embodies learning objectives related to SE fundamentals (requirements, architecture, testing, process); planning with Gantt charts; working with budgets; and selecting a team for an agile development project. A student player is rewarded in the game by getting hired, scoring points, or getting promoted to lead a project. The game has a variety of settings including a classroom, job fair, and a work environment with meeting rooms, cubicles, and a water cooler station. The main non-player characters include a teacher, boss, and an evil peer. In the future, semi-automated support for creating new game scripts will be explored using a wizard interface. The templates will be formally defined, supporting automated transformation into XML game scripts that can be loaded into the SimSYS Game Engine. We also plan to explore transforming the requirements into a notation that can be imported into a commercial tool that supports Statechart simulation