Model-Driven Approach for Realization of Data Collection Architectures for Cyber-Physical Systems of Systems to Lower Manual Implementation Efforts

Data collection from distributed automated production systems is one of the main prerequisites to leverage information gain from data analysis in the context of Industrie 4.0, e.g., for the optimization of product quality. However, the realization of data collection architectures is associated with immense implementation efforts due to the heterogeneity of systems, protocols, and interfaces, as well as the multitude of involved disciplines in such projects. Therefore, this paper contributes with an approach for the model-driven generation of data collection architectures to significantly lower manual implementation efforts. Via model transformations, the corresponding source code is automatically generated from formalized models that can be created using a graphical domain-specific language. The automatically generated architecture features support for various established IIoT protocols. In a lab-scale evaluation and a unique generalized extrapolation study, the significant effort savings compared to manual programming could be quantified. In conclusion, the proposed approach can successfully mitigate the current scientific and industrial challenges to enable wide-scale access to industrial data.

Seq: A High-Performance Language for Bioinformatics

The scope and scale of biological data are increasing at an exponential rate, as technologies like next-generation sequencing are becoming radically cheaper and more prevalent. Over the last two decades, the cost of sequencing a genome has dropped from $100 million to nearly $100-a factor of over 10⁶-and the amount of data to be analyzed has increased proportionally. Yet, as Moore's Law continues to slow, computational biologists can no longer rely on computing hardware to compensate for the ever-increasing size of biological datasets. In a field where many researchers are primarily focused on biological analysis over computational optimization, the unfortunate solution to this problem is often to simply buy larger and faster machines. Here, we introduce Seq, the first language tailored specifically to bioinformatics, which marries the ease and productivity of Python with C-like performance. Seq starts with a subset of Python-and is in many cases a drop-in replacement-yet also incorporates novel bioinformatics- and computational genomics-oriented data types, language constructs and optimizations. Seq enables users to write high-level, Pythonic code without having to worry about low-level or domain-specific optimizations, and allows for the seamless expression of the algorithms, idioms and patterns found in many genomics or bioinformatics applications. We evaluated Seq on several standard computational genomics tasks like reverse complementation, k-mer manipulation, sequence pattern matching and large genomic index queries. On equivalent CPython code, Seq attains a performance improvement of up to two orders of magnitude, and a 160× improvement once domain-specific language features and optimizations are used. With parallelism, we demonstrate up to a 650× improvement. Compared to optimized C++ code, which is already difficult for most biologists to produce, Seq frequently attains up to a 2× improvement, and with shorter, cleaner code. Thus, Seq opens the door to an age of democratization of highly-optimized bioinformatics software.