Coloured Petri net models for automated manufacturing systems

In this paper, we propose an approach, using Coloured Petri Nets (CPN) for modelling flexible manufacturing systems. We illustrate our methodology for a Flexible Manufacturing Cell (FMC) with three machines and three robots. We also consider the analysis of the FMC for deadlocks using the invariant analysis of CPNs.

Active-contour-based automated image quantitation techniques for Western Blot analysis

Western Blot analysis is an analytical technique used in Molecular Biology, Biochemistry, Immunogenetics and other Molecular Biology studies to separate proteins by electrophoresis. The procedure results in images containing nearly rectangular-shaped blots. In this paper, we address the problem of quantitation of the blots using automated image processing techniques. We formulate a special active contour (or snake) called Oblong, which locks on to rectangular shaped objects. Oblongs depend on five free parameters, which is also the minimum number of parameters required for a unique characterization. Unlike many snake formulations, Oblongs do not require explicit gradient computations and therefore the optimization is carried out fast. The performance of Oblongs is assessed on synthesized data and Western Blot Analysis images.

A LSQR-type method provides a computationally efficient automated optimal choice of regularization parameter in diffuse optical tomography

Purpose: Developing a computationally efficient automated method for the optimal choice of regularization parameter in diffuse optical tomography. Methods: The least-squares QR (LSQR)-type method that uses Lanczos bidiagonalization is known to be computationally efficient in performing the reconstruction procedure in diffuse optical tomography. The same is effectively deployed via an optimization procedure that uses the simplex method to find the optimal regularization parameter. The proposed LSQR-type method is compared with the traditional methods such as L-curve, generalized cross-validation (GCV), and recently proposed minimal residual method (MRM)-based choice of regularization parameter using numerical and experimental phantom data. Results: The results indicate that the proposed LSQR-type and MRM-based methods performance in terms of reconstructed image quality is similar and superior compared to L-curve and GCV-based methods. The proposed method computational complexity is at least five times lower compared to MRM-based method, making it an optimal technique. Conclusions: The LSQR-type method was able to overcome the inherent limitation of computationally expensive nature of MRM-based automated way finding the optimal regularization parameter in diffuse optical tomographic imaging, making this method more suitable to be deployed in real-time. (C) 2013 American Association of Physicists in Medicine. http://dx.doi.org/10.1118/1.4792459]

An automated approach to network features of protein structure ensembles

Network theory applied to protein structures provides insights into numerous problems of biological relevance. The explosion in structural data available from PDB and simulations establishes a need to introduce a standalone-efficient program that assembles network concepts/parameters under one hood in an automated manner. Herein, we discuss the development/application of an exhaustive, user-friendly, standalone program package named PSN-Ensemble, which can handle structural ensembles generated through molecular dynamics (MD) simulation/NMR studies or from multiple X-ray structures. The novelty in network construction lies in the explicit consideration of side-chain interactions among amino acids. The program evaluates network parameters dealing with topological organization and long-range allosteric communication. The introduction of a flexible weighing scheme in terms of residue pairwise cross-correlation/interaction energy in PSN-Ensemble brings in dynamical/chemical knowledge into the network representation. Also, the results are mapped on a graphical display of the structure, allowing an easy access of network analysis to a general biological community. The potential of PSN-Ensemble toward examining structural ensemble is exemplified using MD trajectories of an ubiquitin-conjugating enzyme (UbcH5b). Furthermore, insights derived from network parameters evaluated using PSN-Ensemble for single-static structures of active/inactive states of 2-adrenergic receptor and the ternary tRNA complexes of tyrosyl tRNA synthetases (from organisms across kingdoms) are discussed. PSN-Ensemble is freely available from http://vishgraph.mbu.iisc.ernet.in/PSN-Ensemble/psn_index.html.

Quantifying Vocal Mimicry in the Greater Racket-Tailed Drongo: A Comparison of Automated Methods and Human Assessment

Objective identification and description of mimicked calls is a primary component of any study on avian vocal mimicry but few studies have adopted a quantitative approach. We used spectral feature representations commonly used in human speech analysis in combination with various distance metrics to distinguish between mimicked and non-mimicked calls of the greater racket-tailed drongo, Dicrurus paradiseus and cross-validated the results with human assessment of spectral similarity. We found that the automated method and human subjects performed similarly in terms of the overall number of correct matches of mimicked calls to putative model calls. However, the two methods also misclassified different subsets of calls and we achieved a maximum accuracy of ninety five per cent only when we combined the results of both the methods. This study is the first to use Mel-frequency Cepstral Coefficients and Relative Spectral Amplitude - filtered Linear Predictive Coding coefficients to quantify vocal mimicry. Our findings also suggest that in spite of several advances in automated methods of song analysis, corresponding cross-validation by humans remains essential.

An automated pipette puller for fabrication of glass micropipettes

Glass micropipettes are versatile probing tools for performing micro-and nano-manipulation tasks. This paper presents the design and development of an automated pipette puller system for fabrication of glass micropipettes. The pipette puller employs a new strategy for fabrication of micropipettes that enables achieving independent control of their taper, tip diameter, and bend-angle, and also facilitates theoretical derivation of simple, approximate relationships between the pipette shape and the pulling parameters. Subsequently, the design and fabrication of the pipette puller is described, which include that of the pipette heating system, the mechanical motion stages, and the control electronics of the pipette puller. The fabricated pipette puller is experimentally evaluated to demonstrate control of the taper, tip diameter, and the bend-angle of the micropipette. Further, the dependence of the taper and tip diameter on the pulling parameters is evaluated and is shown to be in alignment with the proposed theoretical relationships. (C) 2014 AIP Publishing LLC.

Evaluating FuncSION: A software for automated synthesis of design solutions for stimulating ideation during mechanical conceptual design

The goal of the work reported in this paper is to use automated, combinatorial synthesis to generate alternative solutions to be used as stimuli by designers for ideation. FuncSION, a computational synthesis tool that can automatically synthesize solution concepts for mechanical devices by combining building blocks from a library, is used for this purpose. The objectives of FuncSION are to help generate a variety of functional requirements for a given problem and a variety of concepts to fulfill these functions. A distinctive feature of FuncSION is its focus on automated generation of spatial configurations, an aspect rarely addressed by other computational synthesis programs. This paper provides an overview of FuncSION in terms of representation of design problems, representation of building blocks, and rules with which building blocks are combined to generate concepts at three levels of abstraction: topological, spatial, and physical. The paper then provides a detailed account of evaluating FuncSION for its effectiveness in providing stimuli for enhanced ideation.

Design of an Automated Dispenser Unit

This paper presents our work on developing an automated micro positioner and a low cost disposable dispenser module having a disposable dispenser core. The dispenser core is made up of Polydimethylsiloxane (PDMS). Once the user specifies the dispensing location in the Graphical User Interface (GUI), the movement of the micropositioner is automatic. The design, fabrication and characterization results of the dispenser module are also presented. The dispensing experiments are performed with Di-Ethanol Amine as the working reagent. The minimum dispensed volume achieved is about 4 nL.

Automated cell viability assessment using a microfluidics based portable imaging flow analyzer

In this work, we report a system-level integration of portable microscopy and microfluidics for the realization of optofluidic imaging flow analyzer with a throughput of 450 cells/s. With the use of a cellphone augmented with off-the-shelf optical components and custom designed microfluidics, we demonstrate a portable optofluidic imaging flow analyzer. A multiple microfluidic channel geometry was employed to demonstrate the enhancement of throughput in the context of low frame-rate imaging systems. Using the cell-phone based digital imaging flow analyzer, we have imaged yeast cells present in a suspension. By digitally processing the recorded videos of the flow stream on the cellphone, we demonstrated an automated cell viability assessment of the yeast cell population. In addition, we also demonstrate the suitability of the system for blood cell counting. (C) 2015 AIP Publishing LLC.

A semi-automated, field-portable microscopy platform for clinical diagnostic applications

Clinical microscopy is a versatile diagnostic platform used for diagnosis of a multitude of diseases. In the recent past, many microfluidics based point-of-care diagnostic devices have been developed, which serve as alternatives to microscopy. However, these point-of-care devices are not as multi-functional and versatile as clinical microscopy. With the use of custom designed optics and microfluidics, we have developed a versatile microscopy-based cellular diagnostic platform, which can be used at the point of care. The microscopy platform presented here is capable of detecting infections of very low parasitemia level (in a very small quantity of sample), without the use of any additional computational hardware. Such a cost-effective and portable diagnostic device, would greatly impact the quality of health care available to people living in rural locations of the world. Apart from clinical diagnostics, it's applicability to field research in environmental microbiology has also been outlined. (C) 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.

Development of an automated ultrasonic spray pyrolysis system and the growth of Cu2ZnSnS4 thin films

An automated ultrasonic spray pyrolysis system is fabricated for the growth of thin films. The system is equipped with x-y movement and enables film deposition in different patterns and spray rates. Cu-2(Zn,Sn)S-4 (CZTS) films are deposited using this setup. The substrate temperature (T-s) is varied from 240 to 490 degrees C. Kesterite CZTS phase is observed in all the films together with binary phases. The films prepared at T-s <340 degrees C showed SnxSy phase and those at T-s >340 degrees C showed Cu2S phase. Sulfur incorporation is maximum (40%) at 440 degrees C and the films showed better morphology. The Cu and S concentrations are varied to remove binary phases. Depth wise elemental analysis confirmed the existence of single phase CZTS. p-Type CZTS films of resistivity in the range of 10(2)-10(3) Omega cm are obtained. (C) 2015 Elsevier B.V. All rights reserved.