DOCSLIB.ORG

C Copyright by Nikita Agarwal May 2011

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
C Copyright by Nikita Agarwal May 2011 c Copyright by Nikita Agarwal May 2011 COUPLED CELL NETWORKS - INTERPLAY BETWEEN ARCHITECTURE & DYNAMICS A Dissertation Presented to the Faculty of the Department of Mathematics University of Houston In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy By Nikita Agarwal May 2011 COUPLED CELL NETWORKS - INTERPLAY BETWEEN ARCHITECTURE & DYNAMICS Nikita Agarwal Approved: Dr. Michael J. Field (Committee Chair) Department of Mathematics, University of Houston Committee Members: Dr. Matthew Nicol Department of Mathematics, University of Houston Dr. Andrew T¨or¨ok Department of Mathematics, University of Houston Dr. Jeff Moehlis Department of Mechanical Engineering, University of California, Santa Barbara, CA Dr. Mark A. Smith Dean, College of Natural Sciences and Mathematics University of Houston ii Acknowledgments First of all, I wish to thank my thesis advisor, Professor Michael Field, for his guidance, patience, generosity, and insight. I thank him for giving me freedom to explore on my own, and helping me through the difficulties in the process. I admire him for his down-to-earth attitude and simplicity. I feel fortunate to have him as my advisor. I feel immense gratitude for the academic and financial support that he provided me during my Ph.D. The research is supported by NSF Grants DMS-0600927 and DMS-0806321. I thank Dr. Matthew Nicol, Dr. Andrew T¨or¨ok, and Dr. Jeff Moehlis for being on my defense committee, reading my thesis and suggesting improvements. I thank Dr. Field for giving me the opportunity to visit University of War- wick; College of Engineering, Mathematics and Physical Sciences at University of Exeter; University of Porto; and Centre for Interdisciplinary Computational and Dynamical Analysis (CICADA) at University of Manchester, and collaborate with some great minds in the field of Dynamical Systems. These visits enhanced my knowledge and helped me in expanding my research scope through research talks and discussions. I also thank Dr. Ana Dias and Dr. Manuela Aguiar for proposing the problem discussed in Chapter 6 during my visit to Porto. I thank Dr. Peter Ashwin and Dr. David Broomhead for advising me during my visits to Exeter and Manchester, respectively. I also thank my friend and colleague Alexandre Ro- drigues (University of Porto) for insightful mathematical discussions. I hope to continue collaborating with them in future. I thank the Department of Mathematics at UH for giving me the opportu- nity to teach Honors Calculus which enhanced my mathematical knowledge and iii improved my teaching skills. My teaching supervisors, Dr. Matthew Nicol and Dr. Vern Paulsen for the encouragement. I thank the professors at UH, who have helped me in exploring various areas of Mathematics. I thank my teachers at Lady Shri Ram College, Delhi, India who laid strong mathematical background and motivated me to pursue a career in Mathematics. I thank graduate advisors, Ms. Pamela Draughn and Dr. Shanyu Ji, and other staff members for making the administrative work easier. On a personal note, I thank my family (my father Mr. Hem Prakash Agarwal, mother Mrs. Shashi Agarwal, my brothers Dr. Sidharth and Nishant, my sister- in-laws Jolly and Shweta) for their immense love and constant support, due to which I was able to write this thesis. I thank my little nephew and nieces, Manvi, Avni, Soumya, and Paras for their love; my uncle, Mr. Ramesh Agarwal for his encouragement. I am extremely fortunate to have my best friend, Ila Gupta, who has given me unconditional love and support throughout the past years. I thank her for having full faith in me even when I was hopeless, and showing me that there is light at the end of every tunnel. All these past years in the United States would have been impossible without her. I also thank my aunt, Mrs. Sarita Gupta for her encouragement and support. I thank my friend, Vandana Sharma for her cooperation. I thank all my friends and colleagues in the Mathematics department. I dedicate this thesis to my family and grandparents (Late Shri Jagdish Prasad, Late Smt Sarbati Devi, Late Shri Kashi Ram, and Smt Shakuntala Devi). iv COUPLED CELL NETWORKS - INTERPLAY BETWEEN ARCHITECTURE AND DYNAMICS An Abstract of a Dissertation Presented to the Faculty of the Department of Mathematics University of Houston In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy By Nikita Agarwal May 2011 v Abstract We are interested in studying the dynamics on coupled cell networks using the network topology or architecture. The original motivation of this work comes from the work by Aguiar et al. [4] on dynamics of coupled cell networks and Dias and Stewart [18] on equivalence of coupled cell networks with linear phase space. In this thesis, we give a necessary and sufficient condition for the dynamical equiv- alence of two coupled cell networks. The results are applicable to both continuous and discrete dynamical systems and are framed in terms of what we call input and output equivalence. We also give an algorithm that allows explicit construction of the cells in a system with a given network architecture in terms of the cells from an equivalent system with different network architecture. We provide a number of examples to illustrate the results we obtain. The dynamics of large coupled dynamical systems can be extremely difficult to analyze. One way of approaching the study of dynamics of networks is to start with a simple, well-understood but interesting small network and investigate how the simple network can be naturally embedded in a larger network in such a way that the dynamics of the small network appears in the dynamics of the larger network. This process is termed inflation, and was introduced by Aguiar et al. [4]. We give a necessary and sufficient condition for the existence of a strongly connected inflation. We also provide a simple algorithm to construct the inflation as a sequence of simple inflations. Finally, we give an example of a 3-cell coupled cell network having non-trivial syn- chrony subspaces that supports heteroclinic cycles with switching between them. vi Contents List of Figures x 1 Introduction 1 1.1 Overviewofthesis............................ 7 2 Background and Preliminaries 10 2.1 Generalities on coupled cell networks . .. 10 2.1.1 Structure of coupled cell networks: cells and connections . 11 2.1.2 Discrete and continuous coupled cell systems . .. 17 2.1.3 Passivecells........................... 21 2.1.4 Some special classes of coupled cell networks . .. 25 2.2 Generalitiesongraphs . 31 2.3 Synchronyclass ............................. 34 3 Dynamical Equivalence 37 4 Dynamical Equivalence : Networks with Asymmetric Inputs 41 4.1 Inputequivalence ............................ 41 4.2 Outputequivalence ........................... 47 vii 4.3 Examples ................................ 55 4.3.1 Systemswithtoralphasespace . 55 4.3.2 Systems with non-Abelian group as a phase space . 61 5 Dynamical Equivalence : General Networks 64 5.1 Outputequivalence ........................... 65 5.2 Inputequivalence ............................ 86 5.2.1 Splittings and connection matrices . 91 5.3 Examples ................................ 98 5.4 Universalnetwork. 100 6 Inflation of Strongly Connected Networks 106 6.1 Networks with a single input type . 117 6.1.1 Networkswithnoselfloops . 118 6.1.2 Networkswithselfloops . 126 6.2 Networks with multiple input types . 127 6.3 Examples ................................130 7 Switching in Heteroclinic Cycles 132 7.1 Introduction...............................132 7.2 Example.................................135 7.3 Switching in a heteroclinic network . 137 7.4 Forwardswitching. 143 7.5 Horseshoes................................145 8 Conclusions 147 viii Appendix 152 8.1 Relation between g and f inExample5.1.24 . 152 Bibliography 154 ix List of Figures 2.1 A cell with six inputs and one output. Inputs of the same type (for example the second and third input) can be permuted without affectingtheoutput. .......................... 11 2.2 Examples of coupled cells: (i) shows an incomplete network with an unfilled input cell A2, (ii) shows a three cell asymmetric input network;allinputsarefilled.. 13 2.3 Scalingcell ............................... 21 2.4 AddandAdd-Subtractcells . 22 2.5 Building new cells using Add, Add-Subtract cells . .... 23 2.6 Choose and pick cells C(a, b : u, v), C(1, 2:2, 2)........... 24 c1+d1 q d1 q 2.7 The lines l1 : v = u , l2 : v = u + , l3 : v = − c2+d2 − c2+d2 − d2 d2 α+β p β p u , l4 : v = u + , R1: feasibility region of (T ), R2: γ+δ − γ+δ δ δ feasibility region of (D)......................... 30 2.8 Two representations of the same directed graph . ... 32 4.1 input dominated by ........................ 42 M N 4.2 The system built using the cell from and an Add-Subtract cell. 43 G F x 4.3 The system built using 3 cells from and an Add-Subtract cell. 49 G F 4.4 Networks and differ in the first input to B ........... 55 M N 2 5.1 The cell D. The choose and pick cells are linear combinations of the vector field f modelling ...................... 79 F 5.2 The cell D, built from class C cells .................. 83 5.3 Universal network of 2 cells - (a) without self loops, (b) with self loopsallowed. ..............................103 5.4 Universal network of 3 cells. The network with edges labelled 1, , 4 ··· is a universal network without self loops; together with edges la- belled 5, 6 is a universal network with self loops allowed. 104 6.1 is a 2-fold simple inflation of ...................110 N M 6.2 Network architectures of , , . ................116 M0 ··· M9 6.3 is a strongly connected 3-fold simple inflation of ; is a N1 M N2 strongly connected 2-fold simple inflation of ............119 M 6.4 The composite of two simple inflations . 125 6.5 A strongly connected (4, 3, 2)-inflation , of (with symmetric M4 M inputs)..................................128 6.6 A strongly connected (4, 3, 2)-inflation , of (asymmetric inputs) 129 N M 7.1 The network .............................135 M 7.2 Plot shows the time evolution of x and the trajectories close to the cycles γ , i =1, , 4 projected on the (x , x )-plane.
Load more

Recommended publications
  • September 2014
    LONDONLONDON MATHEMATICALMATHEMATICAL SOCIETYSOCIETY NEWSLETTER No. 439 September 2014 Society Meetings HIGHEST HONOUR FOR UK and Events MATHEMATICAN Professor Martin Hairer, FRS, 2014 University of Warwick, has become the ninth UK based Saturday mathematician to win the 6 September prestigious Fields Medal over Mathematics and the its 80 year history. The medal First World War recipients were announced Meeting, London on Wednesday 13 August in page 15 a ceremony at the four-year- ly International Congress for 1 Wednesday Mathematicians, which on this 24 September occasion was held in Seoul, South Korea. LMS Popular Lectures See page 4 for the full report. Birmingham page 12 Friday LMS ANNOUNCES SIMON TAVARÉ 14 November AS PRESIDENT-DESIGNATE LMS AGM © The University of Cambridge take over from the London current President, Professor Terry Wednesday Lyons, FRS, in 17 December November 2015. SW & South Wales Professor Tavaré is Meeting a versatile math- Plymouth ematician who has established a distinguished in- ternational career culminating in his current role as The London Mathematical Director of the Cancer Research Society is pleased to announce UK Cambridge Institute and Professor Simon Tavaré, Professor in DAMTP, where he NEWSLETTER FRS, FMedSci, University of brings his understanding of sto- ONLINE: Cambridge, as President-Des- chastic processes and expertise newsletter.lms.ac.uk ignate. Professor Tavaré will in the data science of DNA se- (Cont'd on page 3) LMS NEWSLETTER http://newsletter.lms.ac.uk Contents No. 439 September 2014 15 44 Awards Partial Differential Equations..........................37 Collingwood Memorial Prize..........................11 Valediction to Jeremy Gray..............................33 Calendar of Events.......................................50 News LMS Items European News.................................................16 HEA STEM Strategic Project...........................
    [Show full text]
  • The Eagle 2013 the EAGLE
    VOLUME 95 FOR MEMBERS OF ST JOHN’S COLLEGE The Eagle 2013 THE EAGLE Published in the United Kingdom in 2013 by St John’s College, Cambridge St John’s College Cambridge CB2 1TP johnian.joh.cam.ac.uk Telephone: 01223 338700 Fax: 01223 338727 Email: [email protected] Registered charity number 1137428 First published in the United Kingdom in 1858 by St John’s College, Cambridge Designed by Cameron Design (01284 725292, www.designcam.co.uk) Printed by Fisherprint (01733 341444, www.fisherprint.co.uk) Front cover: Divinity School by Ben Lister (www.benlister.com) The Eagle is published annually by St John’s College, Cambridge, and is sent free of charge to members of St John’s College and other interested parties. Page 2 www.joh.cam.ac.uk CONTENTS & MESSAGES CONTENTS & MESSAGES THE EAGLE Contents CONTENTS & MESSAGES Photography: John Kingsnorth Page 4 johnian.joh.cam.ac.uk Contents & messages THE EAGLE CONTENTS CONTENTS & MESSAGES Editorial..................................................................................................... 9 Message from the Master .......................................................................... 10 Articles Maggie Hartley: The best nursing job in the world ................................ 17 Esther-Miriam Wagner: Research at St John’s: A shared passion for learning......................................................................................... 20 Peter Leng: Living history .................................................................... 26 Frank Salmon: The conversion of Divinity
    [Show full text]
  • Carta Abierta Al Presidente Juan Manuel Santos Y Más De Mil
    Carta abierta al Presidente Juan Manuel Santos Estimado señor Presidente: Los abajo firmantes nos dirigimos a Ud. para solicitarle la libertad inmediata del académico colombiano Dr. Miguel Ángel Bettrén, El Dr. Beltrán ha estado encarcelado desde mayo de 2009 sin que se le haya probado delito alguno. Ha sido acusado de "rebelión" y tildado de terrorista por ei Estado colombiano; sin embargo, no se ha presentado ninguna prueba que respalde esas acusaciones. Nos preocupa seriamente el hecho de que, como tantos otros en Colombia, el Dr. Beltrán haya sido detenido por sus opiniones políticas antes que por algún delito, de que se le haya privado de su libertad con el fin de silenciarte y de amedrentar a quienes como él quisieran expresar oposición. Creemos que la libertad académica y la libertad de expresión son derechos fundamentales, y que son los pilares de una sociedad democrática; pero la actual detención del Dr. Beltrán muestra que en Colombia no se está respetando ni la una ni la otra. Por lo tanto, le instamos a que ordene su libertad inmediata. Ei alto número de presos políticos en las cárceles colombianas - sean académicos, sindicalistas, dirigentes comunitarios u otros activistas de la sociedad civil • desmiente las declaraciones de que el Estado colombiano respeta los derechos humanos. >1 Le instamos a que ponga fin inmediato a esta situación vergonzosa. Atentamente, Professor Sir Richard Roberts, Nobel Prize Winner Professor Sir John Bali, Sedleian Professor of Natural Philosophy, University of Oxford Professor Dame Janet Nelson,
    [Show full text]
  • Advance Program Now Available
    Genetic and Evolutionary Computation Conference 2007 Conference Program Table of Contents GECCO is evolving! 1 Program Outline 2 Instructions for Paper and Poster Presenters 3 Organizers 4 Program Committee 6 Papers Nominated for Best Paper Awards 11 Human-Competitive Results Awards 14 Evolutionary Computation in Practice 15 Competitions 15 Tutorials and Workshops Schedule 16 Paper Presentation Sessions At-A-Glance 18 Monday Paper and Poster Presentations 20 Monday Keynote Debate 36 Tuesday Paper and Poster Presentations 40 Wednesday Paper Presentations 58 ACM and SIGEVO Membership 71 UCL Campus Maps and Directions 73—74 GECCO is sponsored by the Association for Computing Machinery Special Interest Group on Genetic and Evolutionary Computation (SIGEVO). SIG Services: 2 Penn Plaza, Suite 701, New York, NY, 10121, USA, 1-800-342-6626 (USA and Canada) or +212-626-0500 (Global). gc-cfp-wm-07x1 8 November 06 Sponsor and Supporters We gratefully acknowledge and thank our Supporters. ACM SIGEVO Association for Computing Machinery GECCO 2007 is Special Interest Group on Sponsored By: Genetic and Evolutionary Computation Conference Venue University College London Supporter: The Science Department Keynote Supporter: Of the Natural History Museum Competition Quantdesk Ltd Supporter: Student Travel Grant Supporters Tiger Mountain Scientific, Inc. GECCO is evolving! Welcome to GECCO 2007! I would like to take this opportunity to welcome you, thank all those who have participated to create the current GECCO, and tell you what’s new this year. This year represents a major transition in GECCO’s evolution. There has been a growing view that for GECCO to maintain its place as the leading conference in the field of evolutionary computation it should globalize and be held also outside the United States.
    [Show full text]
  • Conceptual Frameworks for Artificial Immune Systems
    Int. Journ. of Unconventional Computing, Vol. 1, pp. 00–00 © 2005 Old City Publishing, Inc. Reprints available directly from the publisher Published by license under the OCP Science imprint, Photocopying permitted by license only a member of the Old City Publishing Group Conceptual Frameworks for Artificial Immune Systems SUSAN STEPNEY1, ROBERT E. SMITH2, JONATHAN TIMMIS3, ANDY M. TYRRELL4, MARK J. NEAL5 AND ANDREW N. W. HONE6 1Dept. Computer Science, University of York, YO10 5DD, UK 2The Intelligent Computer Systems Centre, University of the West of England, Bristol, BS16 1QY, UK 3Computing Laboratory, University of Kent, Canterbury, CT2 7NF, UK 4Dept. Electronics, University of York, YO10 5DD, UK 5Dept. Computer Science, University of Wales Aberystwyth, SY23 2AX, UK 6Institute of Mathematics, Statistics and Actuarial Science, University of Kent, Canterbury, CT2 7NF, UK Received 16 December 2004; Accepted 4 February 2005 We propose that bio-inspired algorithms are best developed and analysed in the context of a multidisciplinary conceptual framework that provides for sophisticated biological models and well-founded analytical principles, and we outline such a framework here, in the context of Artificial Immune System (AIS) network models, and we discuss mathematical techniques for analysing the state dynamics of AIS. We further propose ways to unify several domains into a common meta-framework, in the context of AIS population models. We finally discuss a case study, and hint at the possibility of a novel instantiation of such a meta-framework, thereby allowing the building of a specific computational framework that is inspired by biology, but not restricted to any one particular biological domain.
    [Show full text]
  • UC San Diego UC San Diego Electronic Theses and Dissertations
    UC San Diego UC San Diego Electronic Theses and Dissertations Title Comparative Systems Biology Analysis of Microbial Pathogens Permalink https://escholarship.org/uc/item/0qn486q4 Author Monk, Jonathan Mayock Publication Date 2015 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO Comparative Systems Biology Analysis of Microbial Pathogens A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Chemical Engineering by Jonathan Mayock Monk Committee in charge: Professor Bernhard Ø. Palsson, Chair Professor Michael Heller, Co-Chair Professor Guarav Arya Professor Victor Nizet Professor Milton Saier 2015 Copyright Jonathan Mayock Monk, 2015 All rights reserved Signature Page The dissertation of Jonathan Mayock Monk is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Co- Chair Chair University of California, San Diego 2015 iii DEDICATION Dedication This work is dedicated to my parents, for the love and support they have given me that has enabled me to achieve this milestone. iv EPIGRAPH Epigraph The true delight is in the finding out rather than in the knowing. - Isaac Asimov v TABLE OF CONTENTS Table of Contents Signature Page ............................................................................................................... iii Dedication .....................................................................................................................
    [Show full text]
  • Conceptual Frameworks for Artificial Immune Systems
    Conceptual Frameworks for Artificial Immune Systems SUSAN STEPNEY1,ROBERT E. SMITH2,JONATHAN TIMMIS3, ANDY M. TYRRELL4,MARK J. NEAL5,ANDREW N. W. HONE6 1 Dept. Computer Science, University of York, YO10 5DD, UK 2 The Intelligent Computer Systems Centre, University of the West of England, Bristol, BS16 1QY, UK 3 Computing Laboratory, University of Kent, Canterbury, CT2 7NF, UK 4 Dept. Electronics, University of York, YO10 5DD, UK 5 Dept. Computer Science, University of Wales Aberystwyth, SY23 2AX, UK 6 Institute of Mathematics, Statistics and Actuarial Science, University of Kent, Canterbury, CT2 7NF, UK Received 16 December 2004; Accepted 4 February 2005 We propose that bio-inspired algorithms are best developed and analysed in the context of a multidisciplinary conceptual frame- work that provides for sophisticated biological models and well- founded analytical principles, and we outline such a framework here, in the context of Artificial Immune System (AIS) network models, and we discuss mathematical techniques for analysing the state dynamics of AIS. We further propose ways to unify several domains into a common meta-framework, in the context of AIS population models. We finally discuss a case study, and hint at the possibility of a novel instantiation of such a meta- framework, thereby allowing the building of a specific computa- tional framework that is inspired by biology, but not restricted to any one particular biological domain. 1 INTRODUCTION The idea of biological inspiration for computing is as old as computing itself. It is implicit in the writings of von Neumann and Turing, despite the fact that 1 modelling probes, observations, simplifying experiments analytical abstract framework/ representation principle biological system bio-inspired algorithms FIGURE 1 An outline conceptual framework for a bio-inspired computational domain these two fathers of computing are now more associated with the standard, distinctly non-biological computational models.
    [Show full text]
  • David S. Broomhead, Matemática Aplicada, Dinámica No Lineal Y Caos
    David S. Broomhead, Matemática aplicada, dinámica no lineal y caos David Broomhead nació en una familia de clase trabajadora. A continuación mostramos sus propias indicaciones sobre los antecedentes de su familia. Después de asistir a la escuela primaria, tomó su examen de más de once años y, dado que tuvo una buena actuación en este examen, pudo ingresar a la Escuela de Gramática de Aireborough, situada en el límite de Yeadon-Guiseley en Aireborough, West Yorkshire. Esta escuela primaria solo aceptaba alumnos que se hubieran desempeñado bien en el examen de más de once años. Completó su educación secundaria en esta escuela primaria en 1969 y luego pasó un año en Uganda, donde estudió y enseñó en una escuela. Citemos ahora la propia descripción que hace David Broomhead de su familia y educación recibida, que escribió en diciembre de 2007 [Referencia 2]: Como muchos de mis compañeros, me crié en una familia donde la clase social era un problema tangible. Sin embargo, dado el estado volátil del sistema de clases, la sociedad estaba plagada de contradicciones que se reflejaban en nuestras vidas. Éramos de clase trabajadora y, por lo tanto, socialistas, pero también "conocíamos nuestro lugar". Se me ocurrió que la única manera de mejorar era a través de la educación, es decir, trabajando duro en la escuela y, sin embargo, más tarde, cuando tenía 15 años, tuve que decidir entre dejar la escuela para conseguir un trabajo o bien quedarme para hacer el nivel A (y, de hecho, de ello surgiría la posibilidad de asistir a la universidad); ello no era una conclusión inevitable para que se me permitiría continuar mi educación.
    [Show full text]
  • SIGEVO Newsletter
    Spring 2007 SIGEVOlution Volume 2 Issue 1 newsletter of the ACM Special Interest Group on Genetic and Evolutionary Computation in this issue EC Practitioners Gregory S. Hornby & Tina Yu Interactive Music Composition Ying-ping Chen The Columns GECCO-2007 Highlights announcements dissertation corner forthcoming papers calls & calendar EDITORIAL SIGEVOlution Spring 2007, Volume 2, Issue 1 Newsletter of the ACM Special Interest Group Editorial on Genetic and Evolutionary Computation. appy Birthday SIGEVOlution! One year ago the first issue of the first volume was distributed SIGEVO Officers to the ACM SIGEVO mailing list. The newsletter has its own website since June 2006 and, Erik Goodman, Chair since then, Google Analytics has been used to keep track of several statistics. So far, the John Koza, Vice Chair H website had 1655 unique visitors (30% of them returned more than once) and around 3200 Erick Cantu-Paz, Secretary downloads. 52% of the visitors reached the newsletter directly, through www.sigevolution.org, 41% came Wolfgang Banzhaf, Treasurer from a referring site, while 7% came from search engines. Among the referring web sites www.sigevo.org is responsible for 20% of the visits while www.kdnuggets.com, the major data mining web site, contributes SIGEVOlution Board to 4% of the visits. The newsletter is also available on www.slideshare.net where I uploaded the first four Pier Luca Lanzi (EIC) issues (spring 2006, summer 2006, autumn 2006, and winter 2006). The plan for the forthcoming year Lawrence "David" Davis is to host the online versions of the published articles on the SIGEVOlution web site so that they can be Martin Pelikan indexed by search engines and comfortably browsed online.
    [Show full text]
  • Dr Miguel Angel Beltrán
    Open Letter to President Juan Manuel Santos Dear Mr. President, We, the undersigned, are writing to demand the immediate release from prison of Colombian academic Dr Miguel Angel Beltran. Dr Beltran has been imprisoned since May 2009 without being convicted of any crime whatsoever. He has been accused of 'rebellion' and branded a terrorist by the Colombian State, yet no evidence has been provided to back up the allegations. We are deeply concerned that Dr Beltran, like so many others in Colombia, has been jailed for his political beliefs rather than for any crime; that he is being deprived of his liberty in order to silence him and discourage others like him from speaking out. We believe that academic freedom and freedom of expression are fundamental rights, and a pillar of democratic society, but Dr Beltran’s ongoing detention shows that Colombia currently respects neither. We therefore urge you to order his immediate release. The large number of political prisoners in Colombia's jails – be they academics, trade unionists, community leaders or other civil society activists – belies claims that human rights are being respected by the Colombian State. We urge you to put an end to this shameful situation without delay. Yours sincerely, Professor Sir Richard Roberts, Nobel Prize Winner Professor Sir John Ball, Sedleian Professor of Natural Philosophy, University of Oxford Professor Dame Janet Nelson, Emeritus Professor of History, King's College London Alan Whitaker, President, University and College Union Terry Hoad, Vice President, University
    [Show full text]
  • Statement on the Research Excellence Framework Proposals
    Statement on the Research Excellence Framework proposals The latest proposal by the higher education funding councils is If implemented, these proposals risk undermining support for for 25% of the new Research Excellence Framework (REF) to basic research across all disciplines and may well lead to an be assessed according to 'economic and social impact'. As academic brain drain to countries such as the United States academics, researchers and higher education professionals we that continue to value fundamental research. believe that it is counterproductive to make funding for the best research conditional on its perceived economic and social Universities must continue to be spaces in which the spirit of benefits. adventure thrives and where researchers enjoy academic freedom to push back the boundaries of knowledge in their The REF proposals are founded on a lack of understanding of disciplines. how knowledge advances. It is often difficult to predict which research will create the greatest practical impact. History We, therefore, call on the UK funding councils to shows us that in many instances it is curiosity-driven research withdraw the current REF proposals and to work with that has led to major scientific and cultural advances. academics and researchers on creating a funding regime which supports and fosters basic research in our universities and colleges rather than discourages it. Signed: Name Institution Relevant titles/positions Sir Tim Hunt Cancer Research UK FRS, Nobel Laureate 2001 Professor John Dainton University of Liverpool Fellow of the Royal Society Fellow of the Institute of Physics Fellow of the Royal Society for the encouragement of Arts, Manufactures and Commerce (RSA) Name Institution Relevant titles/positions Professor Venki Ramakrishnan University of Cambridge FRS, Nobel Prize in Chemistry Professor Brian Josephson University of Cambridge Nobel Laureate in Physics Professor Harry Kroto The Florida State University FRS Professor Donald W Braben UCL Sir John Walker Medical Research Council and University of FRS, F.
    [Show full text]
  • Enhancing Systems Biology Models Through Semantic Data Integration
    School of Computing Science Enhancing Systems Biology Models Through Semantic Data Integration Allyson L. Lister Submitted for the degree of Doctor of Philosophy in the School of Computing Science, Newcastle University December 2011 c 2011, Allyson L. Lister Abstract Studying and modelling biology at a systems level requires a large amount of data of different ex- perimental types. Historically, each of these types is stored in its own distinct format, with its own internal structure for holding the data produced by those experiments. While the use of community data standards can reduce the need for specialised, independent formats by providing a common syn- tax, standards uptake is not universal and a single standard cannot yet describe all biological data. In the work described in this thesis, a variety of integrative methods have been developed to reuse and restructure already extant systems biology data. SyMBA is a simple Web interface which stores experimental metadata in a published, common format. The creation of accurate quantitative SBML models is a time-intensive manual process. Modellers need to understand both the systems they are modelling and the intricacies of the SBML format. However, the amount of relevant data for even a relatively small and well-scoped model can be overwhelming. Saint is a Web application which accesses a number of external Web services and which provides suggested annotation for SBML and CellML models. MFO was developed to for- malise all of the knowledge within the multiple SBML specification documents in a manner which is both human and computationally accessible. Rule-based mediation, a form of semantic data inte- gration, is a useful way of reusing and re-purposing heterogeneous datasets which cannot, or are not, structured according to a common standard.
    [Show full text]