ImageJ2: ImageJ for the next generation of scientific image data

ImageJ is an image analysis program extensively used in the biological sciences and beyond. Due to its ease of use, recordable macro language, and extensible plug-in architecture, ImageJ enjoys contributions from non-programmers, amateur programmers, and professional developers alike. Enabling such a diversity of contributors has resulted in a large community that spans the biological and physical sciences. However, a rapidly growing user base, diverging plugin suites, and technical limitations have revealed a clear need for a concerted software engineering effort to support emerging imaging paradigms, to ensure the software's ability to handle the requirements of modern science. Due to these new and emerging challenges in scientific imaging, ImageJ is at a critical development crossroads. We present ImageJ2, a total redesign of ImageJ offering a host of new functionality. It separates concerns, fully decoupling the data model from the user interface. It emphasizes integration with external applications to maximize interoperability. Its robust new plugin framework allows everything from image formats, to scripting languages, to visualization to be extended by the community. The redesigned data model supports arbitrarily large, N-dimensional datasets, which are increasingly common in modern image acquisition. Despite the scope of these changes, backwards compatibility is maintained such that this new functionality can be seamlessly integrated with the classic ImageJ interface, allowing users and developers to migrate to these new methods at their own pace. ImageJ2 provides a framework engineered for flexibility, intended to support these requirements as well as accommodate future needs

The Immune System: the ultimate fractionated cyber-physical system

In this little vision paper we analyze the human immune system from a computer science point of view with the aim of understanding the architecture and features that allow robust, effective behavior to emerge from local sensing and actions. We then recall the notion of fractionated cyber-physical systems, and compare and contrast this to the immune system. We conclude with some challenges.Comment: In Proceedings Festschrift for Dave Schmidt, arXiv:1309.455

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

Theoretical Engineering and Satellite Comlink of a PTVD-SHAM System

This paper focuses on super helical memory system's design, 'Engineering, Architectural and Satellite Communications' as a theoretical approach of an invention-model to 'store time-data'. The current release entails three concepts: 1- an in-depth theoretical physics engineering of the chip including its, 2- architectural concept based on VLSI methods, and 3- the time-data versus data-time algorithm. The 'Parallel Time Varying & Data Super-helical Access Memory' (PTVD-SHAM), possesses a waterfall effect in its architecture dealing with the process of voltage output-switch into diverse logic and quantum states described as 'Boolean logic & image-logic', respectively. Quantum dot computational methods are explained by utilizing coiled carbon nanotubes (CCNTs) and CNT field effect transistors (CNFETs) in the chip's architecture. Quantum confinement, categorized quantum well substrate, and B-field flux involvements are discussed in theory. Multi-access of coherent sequences of 'qubit addressing' in any magnitude, gained as pre-defined, here e.g., the 'big O notation' asymptotically confined into singularity while possessing a magnitude of 'infinity' for the orientation of array displacement. Gaussian curvature of k(k<0) is debated in aim of specifying the 2D electron gas characteristics, data storage system for defining short and long time cycles for different CCNT diameters where space-time continuum is folded by chance for the particle. Precise pre/post data timing for, e.g., seismic waves before earthquake mantle-reach event occurrence, including time varying self-clocking devices in diverse geographic locations for radar systems is illustrated in the Subsections of the paper. The theoretical fabrication process, electromigration between chip's components is discussed as well.Comment: 50 pages, 10 figures (3 multi-figures), 2 tables. v.1: 1 postulate entailing hypothetical ideas, design and model on future technological advances of PTVD-SHAM. The results of the previous paper [arXiv:0707.1151v6], are extended in order to prove some introductory conjectures in theoretical engineering advanced to architectural analysi