DOCSLIB.ORG

User's Manual

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
User's Manual FCModeler User’s Manual Version 1.0 September 2002 Written by Zach Cox Julie Dickerson Adam Tomjack Copyright Julie Dickerson, Iowa State University 2002 Table of Contents 1 Introduction to FCModeler .....................................................................................................1 2 Setting Up FCModeler............................................................................................................ 1 2.1 Setting up the FCModelerConfig File............................................................................. 1 2.2 Running FCModeler....................................................................................................... 1 3 Sources of Input ...................................................................................................................... 1 3.1 Graph XML Files............................................................................................................ 1 3.1.1 XML Format ........................................................................................................... 1 3.1.2 Example of a Complete XML File.......................................................................... 5 3.1.3 Opening a Graph XML File.................................................................................... 6 3.1.4 Saving a Graph XML File....................................................................................... 7 3.1.5 Saving a JPEG Image of the Graph ........................................................................ 8 3.2 MySQL Database............................................................................................................ 8 4 Graph Layout.......................................................................................................................... 8 4.1 Simple Dot Layout.......................................................................................................... 8 4.2 Rank-Cluster Dot Layout................................................................................................ 9 4.2.1 Layout XML File .................................................................................................... 9 4.3 GEM Layout(s)............................................................................................................. 10 5 Interacting with the Graph View........................................................................................... 12 5.1 Selecting Node and Edge Figures................................................................................. 12 5.2 Node Figures................................................................................................................. 13 5.2.1 Adding................................................................................................................... 13 5.2.2 Deleting................................................................................................................. 13 5.2.3 Moving.................................................................................................................. 13 5.3 Edge Figures................................................................................................................. 13 5.3.1 Adding................................................................................................................... 14 5.3.2 Modifying ............................................................................................................. 14 5.3.3 Deleting................................................................................................................. 14 5.3.4 Moving.................................................................................................................. 14 5.4 Zooming........................................................................................................................ 15 5.5 Panning ......................................................................................................................... 15 5.6 Finding a Particular Node ............................................................................................. 15 6 Mappings............................................................................................................................... 15 6.1 Node and Edge Properties............................................................................................. 15 6.1.1 Property Viewer.................................................................................................... 16 6.2 Visual Attributes of Node and Edge Figures ................................................................ 17 6.3 Using Visual Attributes to Visualize Properties ........................................................... 17 6.4 Creating Mappings Using the Mapping Editor............................................................. 18 7 Animation ............................................................................................................................. 19 7.1 XML File Format.......................................................................................................... 19 7.2 Controls......................................................................................................................... 21 8 Graph Theoretic Operations.................................................................................................. 21 8.1.1 Subgraph Creation................................................................................................ 21 8.1.2 Strongly Connected Components ......................................................................... 22 ii 8.1.3 Cycle Search......................................................................................................... 23 8.1.4 Cycle XML Files................................................................................................... 24 8.2 Alternate Paths between Nodes .................................................................................... 25 8.3 Clustering Cycles.......................................................................................................... 25 9 FCModeler and R.................................................................................................................. 28 10 References......................................................................................................................... 28 10.1 Publications relating to FCModeler.............................................................................. 28 10.2 Open Source Code Used in FCModeler........................................................................ 28 List of Figures Figure 1. The open graph dialog box............................................................................................. 7 Figure 2. The save graph dialog box.............................................................................................. 7 Figure 3. Simple dot layout............................................................................................................ 8 Figure 4. Rank-cluster dot layout................................................................................................... 9 Figure 5: Example of a GEM layout............................................................................................. 11 Figure 6 shows the manipulation of node and edge objects in FCModeler.................................. 14 Figure 7 shows how to save graph coordinates using the save function under the File menu. .... 15 Figure 8. Property viewer showing property values of selected nodes and edges....................... 17 Figure 9. Mapping editor. ............................................................................................................ 18 Figure 10. Animation control....................................................................................................... 21 Figure 11. The subgraph creation dialog box. ............................................................................. 22 Figure 12 Example of selecting cycles and strongly connected components as subgraphs. ........ 23 Figure 13. The cycle search dialog box. ...................................................................................... 24 Figure 14. Map view showing results of the SOM algorithm. Each graph shows the model of the corresponding map unit, which is the generalized median of the cycles assigned to that map unit. ............................................................................................................................... 26 Figure 15. Full view of the bottom-left map unit, showing ten cycles clustered together........... 27 iii 1 Introduction to FCModeler FCModeler models and visualizes metabolic networks as graphs. Nodes of the graph represent specific biochemicals such as proteins, RNA, and small molecules, or stimuli, such as light, heat, or nutrients. Edges of the graph capture regulatory and metabolic relationships found in biological systems. FCModeler can dynamically display user-specified graphs and animate the results of different modeling algorithms on the graph. The fuzzy cognitive map modeling software is currently written in Matlab and interfaces with FCModeler via xml graph files. We plan to translate this software at a later date. 2 Setting Up FCModeler The FCModeler distribution is compatible with Windows 2000/XP and Linux machines. Download the file and unzip into your directory. This version is already compiled and the Java source code is included. If you make any improvements to the
Load more

Recommended publications
  • Modèle Document
    AVISO DT CorSSH and DT SLA Product Handbook Reference: CLS-DOS-NT-08.341 Nomenclature: - Issue: 2 rev 0 Date: October 2012 Aviso Altimetry 8-10 rue Hermès, 31520 Ramonville St Agne, France – [email protected] DT CorSSH and DT SLA Product Handbook CLS-DOS-NT-08.341 Iss :2.9 - date : 28/02/2012 - Nomenclature: - i.1 Chronology Issues: Issue: Date: Reason for change: 1.0 2005/07/18 1st issue 1.1 2005/11/08 Processing of ERS-2 data 1.2 2005/10/17 Processing of GFO data 1.3 2008/06/10 New standards for corrections and models for Jason-1 1.4 2008/08/07 New standards for corrections and models for Envisat after cycle 65. 1.5 2008/12/18 New standards for corrections and models for Jason-1 GDR-C. 1.6 2010/03/05 New standards for Jason-2 1.7 2010/06/08 New standards for corrections and/or models Processing of ERS-1 data 1.8 2011/04/14 Correction of table 2 1.9 2012/02/28 Specification of the reading routines for SLA files only 2.0 2012/10/16 New geodetic orbit for Jason-1 (c≥500) New version D for Jason-2 (c≥146) D : page deleted I : page inserted M : page modified DT CorSSH and DT SLA Product Handbook CLS-DOS-NT-08.341 Iss :2.9 - date : 28/02/2012 - Nomenclature: - i.2 List of Acronyms: ATP Along Track Product Aviso Archiving, Validation and Interpretation of Satellite Oceanographic data Cersat Centre ERS d’Archivage et de Traitement CLS Collecte, Localisation, Satellites CMA Centre Multimissions Altimetriques Cnes Centre National d’Etudes Spatiales CorSSH Corrected Sea Surface Height Doris Doppler Orbitography and Radiopositioning Integrated
    [Show full text]
  • USE and MAINTENANCE MANUAL
    USE and MAINTENANCE MANUAL -Steam sterilizer- FOREWORD This manual must be considered an integral part of the sterilizer, and must always be available to users. The manual must always accompany the sterilizer, even if it is sold to another user. All operators are responsible for reading this manual and for strictly complying with the instructions and information it provides. COMINOX is not liable for any damage to people, things, or the sterilizer itself in the event that the operator fails to comply with the conditions described in the manual. These instructions are confidential and the customer may not disclose any information to third parties. Further, this documentation and its attachments may not be tampered with or modified, copied, or ceded to third parties without authorization from COMINOX. 2 Table of contents TABLE OF CONTENTS TABLE OF CONTENTS ........................................................................................................................ 3 Reference index .............................................................................................................................. 6 Graphic representation of references Mod. 18 ......................................................................... 7 Graphic representation of references Mod. 24 ......................................................................... 8 INTRODUCTION .............................................................................................................................. 11 GENERAL SUPPLY CONDITIONS .......................................................................................................
    [Show full text]
  • Thema4 Process Controller - No
    FEDEGARI STERILIZER FOAF NA1343AN Doc. no. 147854-3 FUNCTIONAL DESIGN SPECIFICATION Page 2 of 26 CONTENTS 1. Scope of Supply ........................................................................................................4 2. Operational ................................................................................................................5 3. Utilities Required demands ......................................................................................6 3.1 Environmental Conditions Requested for Installation............................................................................6 3.2 Others ....................................................................................................................................................6 4. Process Description..................................................................................................7 4.1 Saturated Steam Cycles........................................................................................................................8 4.2 Air-over-steam cycles ..........................................................................................................................10 4.3 Programs Included in Delivery.............................................................................................................11 4.4 Autoclave Performances .....................................................................................................................12 5. Mechanical Construction........................................................................................13
    [Show full text]
  • Theory, Synthesis, and Application of Adiabatic and Reversible Logic
    University of South Florida Scholar Commons Graduate Theses and Dissertations Graduate School 11-23-2013 Theory, Synthesis, and Application of Adiabatic and Reversible Logic Circuits For Security Applications Matthew Arthur Morrison University of South Florida, [email protected] Follow this and additional works at: https://scholarcommons.usf.edu/etd Part of the Computer Engineering Commons Scholar Commons Citation Morrison, Matthew Arthur, "Theory, Synthesis, and Application of Adiabatic and Reversible Logic Circuits For Security Applications" (2013). Graduate Theses and Dissertations. https://scholarcommons.usf.edu/etd/5082 This Dissertation is brought to you for free and open access by the Graduate School at Scholar Commons. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Scholar Commons. For more information, please contact [email protected]. Theory, Synthesis, and Application of Adiabatic and Reversible Logic Circuits For Security Applications by Matthew A. Morrison A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Computer Science and Engineering College of Engineering University of South Florida Major Professor: Nagarajan Ranganathan, Ph.D. Sanjukta Bhanja, Ph.D. Srinivas Katkoori, Ph.D. Jay Ligatti, Ph.D. Kandethody Ramachandran, Ph.D. Hao Zheng, Ph.D. Date of Approval: November 22, 2013 Keywords: Charge Based Computing, DPA Attacks, Encryption, Memory, Power Copyright © 2014, Matthew A. Morrison DEDICATION To my parents, Alfred and Kathleen Morrison, and to my grandparents, Arthur and Betty Kempf, and Alfred and Dorothy Morrison, for making all the opportunities I have possible. ACKNOWLEDGMENTS I would like to thank my advisor, Dr.
    [Show full text]
  • Being a Potential Waveform As an Experiential Choice
    Alternative view of segmented documents via Kairos 17 September 2013 | Draft Being a Waveform of Potential as an Experiential Choice Emergent dynamic qualities of identity and integrity -- / -- Introduction Exploring physical waves by playing analogy leapfrog Metaphorical waves with psychosocial implications Social implications of waves Eliciting psychosocial creativity through analogy Psychosocial potential of analogy detection Beyond explanations of whatever sophistication Waves and consciousness Being a waveform Attraction to curved forms as a vital clue Identification with waves of embodied movement Social initiatives as unrecognized waveforms Animations variously suggestive of "being a waveform" References The argument here is developed further in a second part (Encountering Otherness as a Waveform: in the light of a wave theory of being, 2013) and in an uncompleted third part (Clues to Comprehension through Wave Language: evoking Homo undulans, 2013) Introduction The variety of disciplines and beliefs suggest a multiplicity of ways through which an individual may choose to be framed and identified - - or have experience of life defined. Many take the form of assertions by authorities which deprecate and scorn ways calling their particular belief into question. This dynamic context does little for those born into it and faced with the confusion of how to live a meaningful life. The challenge can itself be variously discussed, as explored separately (Self-reflexive Challenges of Integrative Futures, 2008; Living as an Imaginal Bridge between Worlds, 2011; Paradoxes of Engaging with the Ultimate in any Guise, 2012). With the explosion of variously available knowledge to which it is only minimally possible to attend, incomprehension and uncertainty become ever more significant experientially (Living with Incomprehension and Uncertainty, 2012; Towards the Dynamic Art of Partial Comprehension, 2012).
    [Show full text]
  • Preface, Tables of Content, Front Matter
    This PDF is a selection from an out-of-print volume from the National Bureau of Economic Research Volume Title: Measuring Business Cycles Volume Author/Editor: Arthur F. Burns and Wesley C. Mitchell Volume Publisher: NBER Volume ISBN: 0-870-14085-X Volume URL: http://www.nber.org/books/burn46-1 Publication Date: 1946 Chapter Title: Preface, tables of content, front matter Chapter Author: Arthur F. Burns, Wesley C. Mitchell Chapter URL: http://www.nber.org/chapters/c2979 Chapter pages in book: (p. -27 - 0) NATIONAL BUREAU OF ECONOMIC RESEARCH Studies in Business Cycles No.2 MEASURING BUSINESS CYCLES I NATIONAL BUREAU OF ECONOMIC RESEARCH 1964 OFFICERS Albert J. Hettinger. Jr., Chairman Arthur F. Burns, President Frank W. Fetter, Vice.President Donald B. Woodward, Treasurer Solomon Fabricant, Director of Research Geoffrey H. Moore, Associate Director of Research Hal B. Lary, Associate Director of Research William J. Carson, Executive Director DIRECrORS ATLARGE 1. RobertB. Anderson, New York City present Wallace J. Campbell, Nationwide insurance inhparti Erwin D. Canham, Christian Science Monitor Solomon Fabricant, New York Unwersity that th Marion B. Folsom. Eastman Kodak Company 2. Crawford H. Grecnewalt. E. I. du Pont de Nemours & Company Gabriel Hauge, Manufacturers Hanover Trust Cosnpany 3. A. J. Hayes. international Association of Machinists or to it Albert J. Hettinger. Jr.. Lazard Frères and Company Nicholas Kelley. Keltey Diye New/salt Maginnes & Warren H. W. Laidler. League for Industrial Democracy 4. Charles G. Mortimer, General Foods Corporation submjti George B. Roberts, Larch,nont. New York their u Harry Schernsan. Itook.of.the.Month Club Boris Shishkin.
    [Show full text]
  • UC San Diego Electronic Theses and Dissertations
    UC San Diego UC San Diego Electronic Theses and Dissertations Title Using Blinking to Mitigate Passive Side Channel Attacks and Fault Attacks Permalink https://escholarship.org/uc/item/8md473kk Author Blackstone, Jeremy Publication Date 2021 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA SAN DIEGO Using Blinking to Mitigate Passive Side Channel Attacks and Fault Attacks A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Computer Science by Jeremy Blackstone Committee in charge: Professor Ryan Kastner, Chair Professor Sean Gao Professor Truong Nguyen Professor Lawrence Saul Professor Geoff Voelker 2021 Copyright Jeremy Blackstone, 2021 All rights reserved. The Dissertation of Jeremy Blackstone is approved, and it is acceptable in quality and form for publication on microfilm and electronically. University of California San Diego 2021 iii DEDICATION To my wife Abigail Blackstone for reading and giving feedback on research papers regarding topics she is unfamiliar with and being the inspiration to finish them. iv EPIGRAPH Failure is simply the opportunity to begin again, this time more intelligently. Henry Ford v TABLE OF CONTENTS Dissertation Approval Page . iii Dedication . iv Epigraph . v Table of Contents . vi List of Figures . ix List of Tables . xi Acknowledgements . xii Vita........................................................................ xiii Abstract of the Dissertation . xiv Chapter 1 Background . 1 1.1 Cryptographic Algorithms . 1 1.1.1 AES . 2 1.1.2 PRESENT . 4 1.2 Passive Side Channel Attacks. 6 1.2.1 Power Analysis . 6 1.2.2 Electromagnetic Analysis Attacks . 10 1.3 Fault Analysis Attacks .
    [Show full text]
  • Online Card Management Administration Guide
    CentreSuite Online Card Management Administration Guide Purpose and Audience This guide is intended for Bank Administrators. This guide describes card management features and provides procedures for setting up and managing accounts, users, sites, and system settings. NOTE: Not all sections of this guide are applicable to Regions clients using the CentreSuite online card management platform. Online Card Management Administration Guide ii Copyright ©2018, Total System Services, Inc. All rights reserved worldwide. The information in this document is confidential and proprietary and is distributed to TSYS clients for their exclusive use in operating TSYS applications. It may not be reproduced in any form without prior written permission from TSYS, One TSYS Way, Columbus, GA 31901-4222. Total System Services, Inc.® and TSYS® are federally registered service marks of Total System Services, Inc. in the United States. Total System Services, Inc. owns a number of service marks which are registered in the United States and in other countries. All other products and company names are trademarks or registered trademarks of their respective companies. DRAFT Table of Contents iii About this guide . 1- 1 What is Online Card Management? . 1- 1 Using this guide with your Online Card Management application . 1- 1 Who should read this guide? . 1- 1 What is an administrator? . 1- 2 Using online help to find information . 1- 3 Log On and Self-Register . 2- 1 Log on to Online Card Management . 2- 1 Register to use Online Card Management . 2- 3 Change your password . 2-10 Edit your personal information . 2-12 Unlock your account or reset your password .
    [Show full text]
  • United States
    Hanoi 191208 Wikipedia SyHung2020 United States From Wikipedia, the free encyclopedia For other uses of terms redirecting here, see US (disambiguation), USA (disambiguation), and United States (disambiguation) The United States of America (commonly referred to as the United States, the U.S., the USA, or America) is a federal constitutional republic comprising fifty states and a federal district. The country is situated mostly in central North America, where its forty-eight contiguous states and Washington, D.C., the capital district, lie between the Pacific and Atlantic Oceans, bordered by Canada to the north and Mexico to the south. The state of Alaska is in the northwest of the continent, with Canada to its east and Russia to the west across the Bering Strait. The state of Hawaii is an archipelago in the mid-Pacific. The country also possesses several territories, or insular areas, scattered around the Caribbean and Pacific. At 3.79 million square miles (9.83 million km²) and with about 305 million people, the United States is the third or fourth largest country by total area, and third largest by land area and by population. The United States is one of the world's most ethnically diverse and multicultural nations, the product of large-scale immigration from many countries.[7] The U.S. economy is the largest national economy in the world, with an estimated 2008 gross domestic product (GDP) of US$14.3 trillion (23% of the world total based on nominal GDP and almost 21% at purchasing power parity).[4][8] .. The nation was founded by thirteen colonies of Great Britain located along the Atlantic seaboard.
    [Show full text]
  • UNIVERSITY of CALIFORNIA SAN DIEGO Using Blinking to Mitigate
    UNIVERSITY OF CALIFORNIA SAN DIEGO Using Blinking to Mitigate Passive Side Channel Attacks and Fault Attacks A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Computer Science by Jeremy Blackstone Committee in charge: Professor Ryan Kastner, Chair Professor Sean Gao Professor Truong Nguyen Professor Lawrence Saul Professor Geoff Voelker 2021 Copyright Jeremy Blackstone, 2021 All rights reserved. The Dissertation of Jeremy Blackstone is approved, and it is acceptable in quality and form for publication on microfilm and electronically. University of California San Diego 2021 iii DEDICATION To my wife Abigail Blackstone for reading and giving feedback on research papers regarding topics she is unfamiliar with and being the inspiration to finish them. iv EPIGRAPH Failure is simply the opportunity to begin again, this time more intelligently. Henry Ford v TABLE OF CONTENTS Dissertation Approval Page . iii Dedication . iv Epigraph . v Table of Contents . vi List of Figures . ix List of Tables . xi Acknowledgements . xii Vita........................................................................ xiii Abstract of the Dissertation . xiv Chapter 1 Background . 1 1.1 Cryptographic Algorithms . 1 1.1.1 AES . 2 1.1.2 PRESENT . 4 1.2 Passive Side Channel Attacks. 6 1.2.1 Power Analysis . 6 1.2.2 Electromagnetic Analysis Attacks . 10 1.3 Fault Analysis Attacks . 12 1.3.1 Differential Fault Analysis . 12 1.3.2 Fault Sensitivity Analysis . 23 1.3.3 Biased Fault Analysis . 26 1.3.4 Combined Fault Analysis . 28 1.4 Threat Model . 29 1.5 Passive Side Channel Countermeasures . 30 1.6 Fault Analysis Countermeasures . 30 1.6.1 Masking .
    [Show full text]
  • Monophonic Piano Music Transcription
    ISSN (Print) : 0974-6846 Indian Journal of Science and Technology, Vol 9(28), DOI: 10.17485/ijst/2016/v9i28/97359, July 2016 ISSN (Online) : 0974-5645 Monophonic Piano Music Transcription Yong Yee Zien* and Yap Fa Toh School of Computer Sciences, Universiti Sains Malaysia, Penang - 11800, Malaysia; [email protected], [email protected] Abstract This paper proposes a method for computational monophonic piano music transcription, which detects the pitches of piano music and thus to identify the corresponding musical notations. This computational music transcription method consists of two main algorithms, which are Onset Detection Algorithm and Pitch Detection Algorithm. The Onset Detection methodAlgorithm and involves they are sound built wavebased filtering on the observation and sound waveof characteristics segmentation. of pianoAnd the sound Pitch signal. Detection The programAlgorithm is involvesfast and simpleperiod determination, frequency computation and musical notation identification. These proposed algorithms adopt time- domain input only, that is the monophonic piano music with slow or average speed up to 120 crotchet beats per minute. It is becauseto use, and the able performances to output result of the with algorithms 88% accuracy. are dependent However, on this the musicthreshold transcription values set method in the program. is limited Therefore, to specific further sound investigation and research have to be carried out in order to improve the performance of the program. Keywords: Automatic Music Transcription, Onset Detection Algorithm, Pitch Detection Algorithm 1. Introduction is only able to transcribe monophonic music, which is less complex if compared to polyphonic music. Music transcription is a process of writing musical The current work focuses on the monophonic piano notations based solely on a recording of music.
    [Show full text]
  • This PDF Is a Selection from an Out-Of-Print Volume from the National Bureau of Economic Research
    This PDF is a selection from an out-of-print volume from the National Bureau of Economic Research Volume Title: Measuring Business Cycles Volume Author/Editor: Arthur F. Burns and Wesley C. Mitchell Volume Publisher: NBER Volume ISBN: 0-870-14085-X Volume URL: http://www.nber.org/books/burn46-1 Publication Date: 1946 Chapter Title: Dating Specific and Business Cycles Chapter Author: Arthur F. Burns, Wesley C. Mitchell Chapter URL: http://www.nber.org/chapters/c2983 Chapter pages in book: (p. 56 - 114) fluctuatjo movemen movemen toward hi long in re tions of r Contour' C H A PT E R 4 characterj termed Oscillation Dating Specific and Business Cycles defined rn to trough years. to ten or ti of the sarni OccaSii NCE A TIME series has been adjusted for seasonal variations, it is ready cycles lasti forQ analysis on the plan sketched in Chapter 2. That plan, it will be re- of buildin called, consists of two parts. Each series is broken into segments con-c- full list of sponding in time to successive business cycles in the country to which imposed u the series relates, and the principal characteristics of these segments are same princ measured. Next, the series is broken into segments corresponding to its them, but own specific cycles, and their characteristics are measured. But before The ta the two sets of measurements can be made, the specific and business cycles cult accorc must be identified and their turning points dated. This chapter is con- those of ci cerned with the technical problem of dating cyclical fluctuations.
    [Show full text]