CAMP: a modular metagenomics analysis system for integrated multistep data exploration

Motivation:Computational analysis of large-scale metagenomics sequencing datasets have proven to be both incredibly valuable for extracting isolate-level taxonomic, and functional insights from complex microbial communities. However, due to an ever-expanding ecosystem of metagenomics-specific methods and file-formats, designing seamless and scalable end-to-end workflows, and exploring the massive amounts of output data have become studies unto themselves. One-click bioinformatics pipelines have helped to organize these tools into targeted workflows, but they suffer from general compatibility and maintainability issues, and preclude replication.Methods:To address the gap in easily extensible yet robustly distributable metagenomics workflows, we have developed a module-based metagenomics analysis system “Core Analysis Modular Pipeline” (CAMP), written in Snakemake, a popular workflow management system, along with a standardized module and working directory architecture. Each module can be run independently or conjointly with a series of others to produce the target data format (e.g. short-read preprocessing alone, or short-read preprocessing followed by de novo assembly), and outputs aggregated summary statistics reports and semi-guided Jupyter notebook-based visualizations.Results:We have applied CAMP to a set of ten metagenomics samples to demonstrate how a modular analysis system with built-in data visualization at intermediate steps facilitates rich and seamless inter-communication between output data from different analytic purposes.Availability:The CAMP ecosystem (module template and analysis modules) can be found https://github.com/Meta-CAMP.

Modular™ Systems At Work

As one of the standard electrophysiological signals in the human body, the photoplethysmography contains detailed information about the blood microcirculation and has been commonly used in various medical scenarios, where the accurate detection of the pulse waveform and quantification of its morphological characteristics are essential steps. In this paper, a modular pulse wave preprocessing and analysis system is developed based on the principles of design patterns. The system designs each part of the preprocessing and analysis process as independent functional modules to be compatible and reusable. In addition, the detection process of the pulse waveform is improved, and a new waveform detection algorithm composed of screening-checking-deciding is proposed. It is verified that the algorithm has a practical design for each module, high accuracy of waveform recognition and high anti-interference capability. The modular pulse wave preprocessing and analysis software system developed in this paper can meet the individual preprocessing requirements for various pulse wave application studies under different platforms. The proposed novel algorithm with high accuracy also provides a new idea for the pulse wave analysis process.

Proceedings of the 12th annual international conference companion on Aspect-oriented software development

The methodology, used in the Modular ECG Analysis System (MEANS) is described. MEANS consists of modules for signal analysis and diagnostic classification. The basic structure of the modular interpretation system remained intact over a period of 20 years, while all modules underwent many changes as a function of experience and insight, and the continuously changing information technology. The article describes the advantages of a modular approach to decision-support systems, the most important ones being easier maintenance of the software package and separate optimization and testing of each module. The overall evaluation of MEANS was done in the CSE study. Evaluation results for modules and for the entire system are presented.

Modular battery energy storage system design factors analysis to improve battery-pack reliability

Reddit is a major source of user-generated content filled with discussions, opinions, and emotions. However, analyzing this data is challenging due to slang, sarcasm, and informal text. This study intro- duces CrowdPulse, a modular Reddit analysis system that processes and visualizes discussions into meaningful insights. The system includes modules for data collection, text cleaning, sentiment analysis, and visualization, offering transparency, scalability, and interactivity for researchers and businesses.

Building software-based tools for the analysis and design of large-scale, wide area communication networks requires more than a judicial application of graph theory, optimization and queueing; it requires an effective systems engineered approach to managing real-world constraints and change throughout the life-cycle of competing networking technologies. This talk will examine the role of theory, realism, and process in roughly ten years work by the author and colleagues in developing tools for modeling, analysis, design of wide area networks. Starting with the philosophical and methodological underpinnings of the work, the talk will: ~ describe a range of real-world network analysis and design scenarios that arise in the life cycles of these networks, ~ characterize various design problems associated with these scenarios, ~ trace the development and continued evolution of a collection of tools for addressing the design problems, and ~ illustrate some new scenarios (e.g., ATM) driving current research. Of particular emphasis throughout this work is a philosophical bent towards realistic problem formulations and solution techniques which rapidly yield implementable results for large backbone networks employing distributed, adaptive routing. A principal product of the this research is a large scale software system known as M11DAS (Mod ular Information Infrastructure Design and Analysis System). M11DAS (and its UVa-developed ancestor, DESI) is used by the Center for Engineering, Defense Information Systems Agency as its principal data backbone design and analysis tool and is one of the key tools used in supporting planning for DISA's Defense Information System Network architecture. Recently, the tool has also been adapted under FAA sponsorship through MITRE's Center for Advanced Aviation System Development (CAASD) to support analysis and design of the FAA's NADIN 11 network.

The widespread use of modular construction in the electronic equipment industry has resulted in the development of standard electronic modules (SEMs). These units are an extension of the original modular partitioning concept, and are designed for universal use, being interchangeable between different items of SEM equipment. They are highly reliable functional modules which may be discarded on failure, and are designed to be independent of manufacturer or technology level. As a consequence of their development, this paper describes the use of life cycle cost modelling in the design and evaluation of competing SEM/non-SEM modular systems.

Proceedings of the 13th international conference on Modularity

MODULAR ANALYTICS (Roche Diagnostics) (MODULARANALYTICS, Elecsys and Cobas Integra are trademarks of a member of the Roche Group) represents a new approach to automation for the clinical chemistry laboratory. It consists of a control unit, a core unit with a bidirectional multitrack racktransportation system, and three distinct kinds of analytical modules: an ISE module, a P800 module (44 photometric tests, throughput of up to 800 tests/h), and a D2400 module (16 photometric tests, throughput up to 2400 tests/h). MODULAR ANALYTICS allows customised configurations for various laboratory workloads. The performance and practicability of MODULAR ANALYTICS were evaluated in an international multicentre study at 16 sites. Studies included precision, accuracy, analytical range, carry-over, and workflow assessment. More than 700 000 results were obtained during the course of the study. Median between-day CVs were typically lessthan 3% for clinical chemistries and less than 6% for homogeneous immunoassays. Median recoveries for nearly all standardised reference materials were within 5% of assigned values. Method comparisons versus current existing routineinstrumentation were clinically acceptable in all cases. During the workflow studies, the work from three to four single workstations was transferred to MODULAR ANALYTICS, which offered over 100 possible methods, with reduction in samplesplitting, handling errors, and turnaround time. Typical sample processing time on MODULAR ANALYTICS was less than 30 minutes, an improvement from the current laboratory systems. By combining multiple analytic units in flexible ways, MODULAR ANALYTICS met diverse laboratory needs and offeredimprovement in workflow over current laboratory situations. It increased overall efficiency while maintaining (or improving) quality.

This paper introduces an enhanced method for developing video analysis tools, in the context of engineering research applications. It aims to expand the usual boundaries for design of image analysis systems to include explicitly ease of use, maintenance and upgradeability by researchers who have little or no background in image analysis. This challenge moves the emphasis away from the design of optimally efficient (but esoteric) tools for the processing of video- and image-based data, and shifts it towards the development of tools that perform satisfactorily, while being easy to understand, maintain and develop. In the proposed design methodology, this balance is struck using popular commercial software that has a thoroughly tried and tested user interface and yet supports modular expansion through the use of 'plug-ins'. This approach eliminates the need to deal with the vast majority of image analysis infrastructure, while focusing attention on the development of the code at the core of the required image analysis functionality. The development of this core code is then simplified through the selection of a plug-in creator tool that opts for visual programming 'in lieu' of procedural programming as far as possible. In order to evaluate the effectiveness of this proposed new system design approach, a case study is investigated that involves developing a solution to a real image analysis problem faced by research colleagues at the University of Brighton. This concerns a study of the air-side fouling phenomenon of compact heat exchangers by large particles. The implemented system delivers close monitoring of a radiator's surface so as to track the clogging mechanism during the execution of a series of wind-tunnel experiments, which attempt to replicate the fouling phenomenon realistically. The data extracted are presented in the form of several graphs, which describe the progress of these experiments, and have made a definite contribution to the work of the primary researchers. Primary researchers report that they have found the system easy to use, and have adapted it to suit their needs better.

Performance of an electrochemical microanalysis system

A unified analytical examination of the products of microwave oil shale has been completed. A sample of subituminous Colorado coal was also included. Analysis systems have been planned, constructed and placed into operation so as to provide a definitive profile of the composition of gases, oil, and water released by the microwave heated oil shale and coal samples. In a previous NSF study, it was reported that microwave retorted oil shale produced large quantities of high BTU content gas. In the data presented in this report, using a modular microcoulometric analysis system, a definitive profile of the composition of the gases, oil, and water, released by the microwave retorted oil shale and coal show that the previous results are confirmed.

This paper introduces the Assur Groups with cam pairs in order to apply modular analysis while investigating cam mechanisms. Modular analysis for linkages has been studied for a period of time. By decomposing the overall linkage into individual modules for independent analysis, the analysis of linkages is no longer so complicated. Under the same concept, this paper provides some cam-related modules. By studying its geometric and kinematics features, those modules can mixed with the linkage modules and analyze more complicated cam-modulated linkages. This paper demonstrated the process of developing the Assur Group with cam pairs and provided a classification system for those new Assur Groups. In the meantime, we deeply investigate the most basic Assur Group with a cam pair, which is class 1 order 2 RC module. It can conduct a forward geometric analysis to generate a cam profile while given the position of the cams and the external roller. This module can also conduct inverse kinematic analysis to acquire the follower angle while give the prescribed cam profile. The numerical example provided in the final section shows the convenience and efficiency of using modular analysis to analyze cam-modulated linkages. By developing those cam modules, it can simplify the cam analysis, thereby improving the implementation of cam mechanisms in industries.