basicsynbio and the BASIC SEVA collection: Software and vectors for an established DNA assembly method

Standardized DNA assembly methods utilizing modular components provide a powerful framework to explore design spaces and iterate through Design-Build-Test-Learn cycles. Biopart Assembly Standard for Idempotent Cloning (BASIC) DNA assembly uses modular parts and linkers, is highly accurate, easy to automate, free for academic and commercial use, while enabling simple hierarchical assemblies through an idempotent format. These attributes facilitate various applications including pathway engineering, ribosome binding site tuning, fusion protein synthesis and multiplex gRNA expression. In this work we present basicsynbio, an open-source software encompassing a Web App (https://basicsynbio.web.app/) and Python Package (https://github.com/LondonBiofoundry/basicsynbio). With basicsynbio, users can access commonly used BASIC parts and linkers while robustly designing new parts and assemblies with exception handling for common design errors. Furthermore, users can export sequence data and create build instructions for manual or automated workflows. The generation of build instructions relies on the BasicBuild Open Standard which is easily parsed for bespoke workflows and is serialised in Java Script Object Notation for transfer and storage. We demonstrate basicsynbio by assembling a collection of 30 BASIC-compatible vectors using various sequences including modules from the Standard European Vector Architecture (SEVA). The BASIC SEVA collection encompasses plasmids containing six antibiotic resistance markers and five origins of replication from different compatibility groups, including a temperature-sensitive variant. We deposit the collection on Addgene under an OpenMTA agreement, making them available. Furthermore, these sequences are accessible from within the basicsynbio application programming interface along with other collections of parts and linkers, providing an ideal environment to design BASIC DNA assemblies for bioengineering applications.

Integrated control of individual plasma scalars with simultaneous Neoclassical Tearing-Mode suppression

Simulations using the Control-Oriented Transport SIMulator (COTSIM) and DIII-D experiments have been carried out to demonstrate the performance of a novel integrated-control architecture for simultaneous regulation of individual-scalar magnitudes. The individual scalars considered in this work include kinetic variables, such as the thermal stored-energy or volume-average toroidal rotation, and magnetic variables such as the safety factor profile at different spatial locations. Separate control algorithms have been designed independently for each of these individual variables that use robust, nonlinear control techniques. In addition, the individual-scalar controllers have been integrated with Neoclassical Tearing-Mode (NTM) suppression algorithms, supervisory and exception handling algorithms, and an actuator manager, both within COTSIM and in the Plasma Control System (PCS) of the DIII-D tokamak. The resulting architecture has a high level of integration and some of the functionalities that will be required to fulfill the advanced-control requirements anticipated for ITER. Initial simulations using COTSIM suggest that the plasma performance and its Magneto-HydroDynamic (MHD) stability may be improved under integrated feedback control. These simulation results also show good qualitative agreement with DIII-D experimental results in the steady-state high-$q_{min}$ scenario, which is one of the candidates for steady-state operation in ITER. By means of individual-scalar feedback-control techniques in conjunction with NTM-suppression techniques, the confinement deterioration caused by NTMs in these scenarios may be significantly ameliorated.

Designing and implementing performance measurement systems based on enterprise engineering guidelines

PurposeThis conceptual paper presents a proposal for improving a performance measurement (PM) system implementation process based on enterprise engineering (EE) guidelines, which gives the process a sense of completeness.Design/methodology/approachThis paper analyzes a well-known process for PM systems implementation organized in two phases: identifying, designing and implementing the top-level performance measures; and cascading the top-level measures and identify appropriate lower-level performance measures. The proposed improvements to the studied process derive from the EE guidelines, which establish a basis for the structure of an organizational management system, the formalization and synchronization of processes, performance expectations, exception handling and change management.FindingsThe study reveals that not all EE guidelines are covered by the analyzed process, with four of them having no evidence of being adopted: involvement of people in process design and implementation; ensuring interoperability between different systems in the information structure; addressing of all possible exceptions; coherence and consistency of semantics across all processes.Originality/valueBy the lens of EE guidelines, this paper advances a how-to-guide. This paper can support managers and researchers on PM system design and implementation, given the importance and relevance of EE recommendations having a consistent and well-structured procedure.

Image Information Collection System Based on Python Web Crawler Technology

Collecting data from the Internet is the key to solve the problem of data sources. This paper studies the image information collection system based on Python web crawler technology.This paper studies and develops a data acquisition system based on Python web crawler technology, which realizes the automatic collection of subject data. In this paper, we use urllib, beautiful soup, threading library to design and develop a system model framework including data crawling, exception handling, robots protocol management and multithreading management modules. Through the application of specific cases, this paper introduces the data acquisition process. Experimental data show that compared with the traditional manual data acquisition, the proposed method greatly improves the work efficiency.

SECURE CODE DESIGN PADA PEMROGRAMAN BERORIENTASI OBJEK DENGAN PENANGANAN PENGECUALIAN

Proses pengembangan perangkat lunak harus mengikuti tahapan tertentu yang disebut dengan Software Development Life Cycle atau (SDLC). Pada pengembangan perangkat lunak, yang belum nampak secara eksplisit pada SDLC adalah aspek keamanan. Keamanan seharusnya hadir pada setiap tahapan SDLC. Keamanan perangkat lunak bisa dimulai dari security requirement, secure design, secure coding, hingga pengujian. Tahapan coding merupakakan implementasi dari desain dalam bentuk kode. Programmer harus berhati-hati agar tidak ada lubang keamanan pada saat perangkat lunak dikembangkan. Membuat perangkat lunak yang aman dengan desain memerlukan pertimbangan pada bagiamana cara menangani kesalahan, terutama pada tahapan coding. Bahasa pemrograman Java yang memiliki sifat mengurangi kemungkinan terjadinya kesalahan tipe data. Bahasa termasuk ke dalam pemrograman berorientasi objek. Pemrograman berorientasi objek merupakan teknik membuat suatu program berdasarkan objek dan hal yang bisa dilakukan oleh objek tersebut. Bahasa Java menyediakan fitur penanganan pengecualian, seperti pernyataan throw dan blok try-catch-finally. Pada bahasa ini terdapat exception handling yaitu mekanisme penangan error yang mungkin terjadi dalam suatu program