Browsing by Subject "Alignment"

Now showing 1 - 3 of 3
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    An Automated Grid-Based Robotic Alignment System for Pick and Place Applications
    (2013-12) Bearden, Lukas R.; Razban, Ali; Wasfy, Tamer; Li, Lingxi; Anwar, Sohel
    This thesis proposes an automated grid-based alignment system utilizing lasers and an array of light-detecting photodiodes. The intent is to create an inexpensive and scalable alignment system for pick-and-place robotic systems. The system utilizes the transformation matrix, geometry, and trigonometry to determine the movements to align the robot with a grid-based array of photodiodes. The alignment system consists of a sending unit utilizing lasers, a receiving module consisting of photodiodes, a data acquisition unit, a computer-based control system, and the robot being aligned. The control system computes the robot movements needed to position the lasers based on the laser positions detected by the photodiodes. A transformation matrix converts movements from the coordinate system of the grid formed by the photodiodes to the coordinate system of the robot. The photodiode grid can detect a single laser spot and move it to any part of the grid, or it can detect up to four laser spots and use their relative positions to determine rotational misalignment of the robot. Testing the alignment consists of detecting the position of a single laser at individual points in a distinct pattern on the grid array of photodiodes, and running the entire alignment process multiple times starting with different misalignment cases. The first test provides a measure of the position detection accuracy of the system, while the second test demonstrates the alignment accuracy and repeatability of the system. The system detects the position of a single laser or multiple lasers by using a method similar to a center-of-gravity calculation. The intensity of each photodiode is multiplied by the X-position of that photodiode. The summed result from each photodiode intensity and position product is divided by the summed value of all of the photodiode intensities to get the X-position of the laser. The same thing is done with the Y-values to get the Y-position of the laser. Results show that with this method the system can read a single laser position value with a resolution of 0.1mm, and with a maximum X-error of 2.9mm and Y-error of 2.0mm. It takes approximately 1.5 seconds to process the reading. The alignment procedure calculates the initial misalignment between the robot and the grid of photodiodes by moving the robot to two distinct points along the robot’s X-axis so that only one laser is over the grid. Using these two detected points, a movement trajectory is generated to move that laser to the X = 0, Y = 0 position on the grid. In the process, this moves the other three lasers over the grid, allowing the system to detect the positions of four lasers and uses the positions to determine the rotational and translational offset needed to align the lasers to the grid of photodiodes. This step is run in a feedback loop to update the adjustment until it is within a permissible error value. The desired result for the complete alignment is a robot manipulator positioning within ±0.5mm along the X and Y-axes. The system shows a maximum error of 0.2mm in the X-direction and 0.5mm in the Y-direction with a run-time of approximately 4 to 5 minutes per alignment. If the permissible error value of the final alignment is tripled the alignment time goes down to 1 to 1.5 minutes and the maximum error goes up to 1.4mm in both the X and Y-directions. The run time of the alignment decreases because the system runs fewer alignment iterations.
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    Complex Proteoform Identification Using Top-Down Mass Spectrometry
    (2018-12) Kou, Qiang; Wu, Huanmei; Liu, Xiaowen; Liu, Yunlong; Al Hasan, Mohammad
    Proteoforms are distinct protein molecule forms created by variations in genes, gene expression, and other biological processes. Many proteoforms contain multiple primary structural alterations, including amino acid substitutions, terminal truncations, and posttranslational modifications. These primary structural alterations play a crucial role in determining protein functions: proteoforms from the same protein with different alterations may exhibit different functional behaviors. Because top-down mass spectrometry directly analyzes intact proteoforms and provides complete sequence information of proteoforms, it has become the method of choice for the identification of complex proteoforms. Although instruments and experimental protocols for top-down mass spectrometry have been advancing rapidly in the past several years, many computational problems in this area remain unsolved, and the development of software tools for analyzing such data is still at its very early stage. In this dissertation, we propose several novel algorithms for challenging computational problems in proteoform identification by top-down mass spectrometry. First, we present two approximate spectrum-based protein sequence filtering algorithms that quickly find a small number of candidate proteins from a large proteome database for a query mass spectrum. Second, we describe mass graph-based alignment algorithms that efficiently identify proteoforms with variable post-translational modifications and/or terminal truncations. Third, we propose a Markov chain Monte Carlo method for estimating the statistical signi ficance of identified proteoform spectrum matches. They are the first efficient algorithms that take into account three types of alterations: variable post-translational modifications, unexpected alterations, and terminal truncations in proteoform identification. As a result, they are more sensitive and powerful than other existing methods that consider only one or two of the three types of alterations. All the proposed algorithms have been incorporated into TopMG, a complete software pipeline for complex proteoform identification. Experimental results showed that TopMG significantly increases the number of identifications than other existing methods in proteome-level top-down mass spectrometry studies. TopMG will facilitate the applications of top-down mass spectrometry in many areas, such as the identification and quantification of clinically relevant proteoforms and the discovery of new proteoform biomarkers.
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    Improving alignment accuracy on homopolymer regions for semiconductor-based sequencing technologies
    (BioMed Central, 2016-08-22) Feng, Weixing; Zhao, Sen; Xue, Dingkai; Song, Fengfei; Li, Ziwei; Chao, Duojiao; He, Bo; Hao, Yangyang; Wang, Yadong; Liu, Yunlong; Department of Medical and Molecular Genetics, IU School of Medicine
    BACKGROUND: Ion Torrent and Ion Proton are semiconductor-based sequencing technologies that feature rapid sequencing speed and low upfront and operating costs, thanks to the avoidance of modified nucleotides and optical measurements. Despite of these advantages, however, Ion semiconductor sequencing technologies suffer much reduced sequencing accuracy at the genomic loci with homopolymer repeats of the same nucleotide. Such limitation significantly reduces its efficiency for the biological applications aiming at accurately identifying various genetic variants. RESULTS: In this study, we propose a Bayesian inference-based method that takes the advantage of the signal distributions of the electrical voltages that are measured for all the homopolymers of a fixed length. By cross-referencing the length of homopolymers in the reference genome and the voltage signal distribution derived from the experiment, the proposed integrated model significantly improves the alignment accuracy around the homopolymer regions. CONCLUSIONS: Besides improving alignment accuracy on homopolymer regions for semiconductor-based sequencing technologies with the proposed model, similar strategies can also be used on other high-throughput sequencing technologies that share similar limitations.