Browsing by Subject "Software tool"

Now showing 1 - 3 of 3

Open Access
In their words: Student feedback on an international project collaboration
(ACM, 2010) Chidanandan, A.; Russell-Dag, Lori; Laxer, C.; Ayfer, Reyyan
In this paper, we describe a collaborative course experience between students from universities in the USA and Turkey. Student teams worked together on a software engineering project for a non-profit organization based in Turkey. The students learned valuable skills in team-work, collaboration-facilitating software tools and working with peers from a different culture and a different time-zone. At the end of the course, in a focus group, students were asked for feedback regarding the course and its outcomes. In this paper, we describe the course from the student perspective. From this, and the instructor's experiences we provide a list of guidelines. Copyright 2010 ACM.
Open Access
Numerical methods and software tools for simulation, design, and resonant mode analysis of radio frequency birdcage coils used in MRI
(Wiley-Liss Inc., 2015) Gurler, N.; Ider, Y. Z.
Design of magnetic resonance imaging (MRI) radiofrequency (RF) coils using lumped circuit modeling based techniques begins to fail at high frequencies, and therefore more accurate models based on the electromagnetic field calculations must be used. Field calculations are also necessary to understand the interactions between the RF field and the subject inside the coil. Furthermore, observing the resonance behavior of the coil and the fields at the resonance frequencies have importance for design and analysis. In this study, finite element method (FEM) based methods have been proposed for accurate time-harmonic electromagnetic simulations, estimation of the tuning capacitors on the rungs or end rings, and the resonant mode analysis of the birdcage coils. Capacitance estimation was achieved by maximizing the magnitude of the port impedance at the desired frequency while simultaneously minimizing the variance of RF magnetic field in the region of interest. In order for the proposed methods to be conveniently applicable, two software tools, resonant mode and frequency domain analyzer (RM-FDA) and Optimum Capacitance Finder (OptiCF), were developed. Simulation results for the validation and verification of the software tools are provided for different cases including human head simulations. Additionally, two handmade birdcage coils (low-pass and high-pass) were built and resonance mode measurements were made. Results of the software tools are compared with the measurement results as well as with the results of the lumped circuit modeling based method. It has been shown that the proposed software tools can be used for accurate simulation and design of birdcage coils. © 2015 Wiley Periodicals, Inc.
Open Access
The systems biology graphical notation
(Nature Publishing Group, 2009-08) Le Novère, N.; Hucka, M.; Mi, H.; Moodie, S.; Schreiber, F.; Sorokin, A.; Demir, Emek; Wegner, K.; Aladjem, M. I.; Wimalaratne, S. M.; Bergman, F. T.; Gauges, R.; Ghazal, P.; Kawaji, H.; Li, L.; Matsuoka, Y.; Villéger, A.; Boyd, S. E.; Calzone, L.; Courtot, M.; Doğrusöz, Uğur; Freeman, T. C.; Funahashi, A.; Ghosh, S.; Jouraku, A.; Kim, S.; Kolpakov, F.; Luna, A.; Sahle, S.; Schmidt, E.; Watterson, S.; Wu, G.; Goryanin, I.; Kell, D. B.; Sander, C.; Sauro, H.; Snoep, J. L.; Kohn, K.; Kitano, H.
Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: process diagram, entity relationship diagram and activity flow diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling. © 2009 Nature America, Inc.