DOCSLIB.ORG

Enhancing Systems Biology Models Through Semantic Data Integration

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read 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. This method of ontology-based integration is generic and can be used in any context, but has been implemented specifically to integrate systems biology data and to enrich systems biology models through the creation of new biological annotations. The work described in this thesis is one step towards the formalisation of biological knowledge useful to systems biology. Experimental metadata has been transformed into common structures, a Web application has been created for the retrieval of data appropriate to the annotation of systems biology models and multiple data models have been formalised and made accessible to semantic integration techniques. i This thesis is dedicated to my parents, who encouraged me in all things, and is particularly dedi- cated to my husband and my son, without whose patience and support I could not have finished this research. “Among those who have endeavoured to promote learning and rectify judgement, it has long been customary to complain of the abuse of words, which are often admitted to signify things so different, that, instead of assisting the understanding as vehicles of knowledge, they produce error, dissension, and perplexity....” Dr. Samuel Johnson, 1752, via Nature Structural & Molecular Biology 14, 681 (2007). “Metadata is a love note to the future.” (NYPL Labs, http://twitpic.com/ 6ry6ar, via @CameronNeylon @kissane) Acknowledgements Many thanks go to my supervisors Dr. Anil Wipat, Dr. Phillip Lord and Dr. Matthew Pocock. A special thanks goes to those people who found extra commas and other errors: Phoebe Boatright, Dr. Dagmar Waltemath, Lucy Slattery, Mélanie Courtot and Dr. Paul Williams, Jr. Past and present colleagues at Newcastle University have provided much support and inspiration, including Dr. Frank Gibson and Dr. Katherine James. I gratefully acknowledge the support of the BBSRC and the EPSRC for funding CISBAN at New- castle University. I also acknowledge the support of the Newcastle University Systems Biology Resource Centre, the Newcastle University Bioinformatics Support Unit and the North East regional e-Science centre. iii Declaration I declare that the following work embodies the result of my own work, that it has been composed by myself and does not include work forming part of a thesis presented successfully for a degree in this or another University. Allyson Lister iv During the course of this work, I have been involved both in the development of a number of standards efforts and in the publishing of a number of papers. The list below describes the standards efforts to which I have contributed and the roles I have had within those efforts: • a developer of UniProt/TrEMBL [1]; • a program developer and contributor to the Functional Genomics Experiment (FuGE)[2,3,4], a standard XML syntax for describing experiments; • a core developer and coordinator of the Ontology of Biomedical Investigations (OBI)[5,6,7], a standard semantics for describing experiments; • an early developer of the ISA-TAB [8] tab-delimited syntax for describing experiments; • a developer of the minimal information checklist MIGS/MIMS for genomics and metage- nomics information [9]; • an advisor for the Systems Biology Ontology (SBO), the Kinetic Simulation Algorithm Ontology (KiSAO) and the TErminology for the Description of DYnamics (TEDDY); • a co-author of the Systems Biology Markup Language (SBML) Level 3 Annotation pack- age [10]; • an advisor for the Cell Behavior Ontology1; and • an advisor in the nascent synthetic biology standards2. I have co-authored 20 papers, specification documents, articles and technical reports during the course of this work: 1. Mélanie Courtot, Nick Juty, Christian Knupfer, Dagmar Waltemath, Anna Zhukova, Andreas Drager, Michel Dumontier, Andrew Finney, Martin Golebiewski, Janna Hastings, Stefan Hoops, Sarah Keating, Douglas B. Kell, Samuel Kerrien, James Lawson, Allyson Lister, James Lu, Rainer Machne, Pedro Mendes, Matthew Pocock, Nicolas Rodriguez, Alice Villeger, Darren J. Wilkinson, Sarala Wimalaratne, Camille Laibe, Michael Hucka, and Nicolas Le Novère. Controlled vocabularies and semantics in systems biology. Molecular Systems Biology, 7(1), October 2011. 2. Stephen G. Addinall, Eva-Maria Holstein, Conor Lawless, Min Yu, Kaye Chapman, A. Peter Banks, Hien-Ping Ngo, Laura Maringele, Morgan Taschuk, Alexander Young, Adam Ciesi- olka, Allyson L. Lister, Anil Wipat, Darren J. Wilkinson, and David Lydall. Quantitative fit- ness analysis shows that NMD proteins and many other protein complexes suppress or enhance distinct telomere cap defects. PLoS Genet, 7(4):e1001362+, April 2011. 1http://cbo.biocomplexity.indiana.edu 2http://www.sbolstandard.org/ v 3. Mélanie Courtot, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan R. Brinkman, and Alan Ruttenberg. MIREOT: The minimum information to reference an external ontology term. Applied Ontology, 6(1):23–33, January 2011. 4. Allyson L. Lister, Phillip Lord, Matthew Pocock, and Anil Wipat. Annotation of SBML mod- els through rule-based semantic integration. Journal of biomedical semantics, 1 Suppl 1(Suppl 1):S3+, 2010. 5. Andrew R. Jones and Allyson L. Lister. Managing experimental data using FuGE. Methods in molecular biology (Clifton, N.J.), 604:333–343, 2010. 6. Allyson L. Lister. Semantic integration in the life sciences. Ontogenesis, http://ontogenesis.knowledgeblog.org/126. January 2010. 7. Allyson L. Lister, Ruchira S. Datta, Oliver Hofmann, Roland Krause, Michael Kuhn, Bet- tina Roth, and Reinhard Schneider. Live coverage of intelligent systems for molecular Biol- ogy/European conference on computational biology (ISMB/ECCB) 2009. PLoS Comput Biol, 6(1):e1000640+, January 2010. 8. Allyson L. Lister, Ruchira S. Datta, Oliver Hofmann, Roland Krause, Michael Kuhn, Bettina Roth, and Reinhard Schneider. Live coverage of scientific conferences using Web technolo- gies. PLoS Comput Biol, 6(1):e1000563+, January 2010. 9. Allyson Lister, Varodom Charoensawan, Subhajyoti De, Katherine James, Sarath Chandra C. Janga, and Julian Huppert. Interfacing systems biology and synthetic biology. Genome biology, 10(6):309+, 2009. 10. Allyson L. Lister, Matthew Pocock, Morgan Taschuk, and Anil Wipat. Saint: a lightweight integration environment for model annotation. Bioinformatics, 25(22):3026–3027, November 2009. 11. Mélanie Courtot, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan R. Brinkman, and Alan Ruttenberg. MIREOT: the minimum information to reference an exter- nal ontology term. In Barry Smith, editor, International Conference on Biomedical Ontology, pages 87–90. University at Buffalo College of Arts and Sciences, National Center for Onto- logical Research, National Center for Biomedical Ontology, July 2009. 12. Allyson L. Lister, Phillip Lord, Matthew Pocock, and Anil Wipat. Annotation of SBML models through Rule-Based semantic integration. In Phillip Lord, Susanna-Assunta Sansone, Nigam Shah, Susie Stephens, and Larisa Soldatova, editors, The 12th Annual Bio-Ontologies Meeting, ISMB 2009, pages 49+, June 2009. 13. The OBI Consortium. Modeling biomedical experimental processes with OBI. In Phillip Lord, Susanna-Assunta Sansone, Nigam Shah, Susie Stephens, and Larisa Soldatova, editors, The 12th Annual Bio-Ontologies Meeting, ISMB 2009, pages 41+, June 2009. 14. Andrew R. Jones, Allyson L. Lister, Leandro Hermida, Peter Wilkinson, Martin Eisenacher, Khalid Belhajjame, Frank Gibson, Phil Lord, Matthew Pocock, Heiko Rosenfelder, Javier Santoyo-Lopez, Anil Wipat, and Norman W. W. Paton. Modeling and managing experimental data using FuGE. OMICS: A Journal of Integrative Biology, 13(3):239–251, June 2009. 15. Mélanie Courtot, William Bug, Frank Gibson, Allyson L. Lister, James Malone, Daniel Schober, Ryan
Load more

Recommended publications
  • Metabolic Footprinting and Systems Biology: the Medium Is the Message
    Nature Reviews Microbiology | AOP, published online 10 June 2005; doi:10.1038/nrmicro1177 REVIEWS METABOLIC FOOTPRINTING AND SYSTEMS BIOLOGY: THE MEDIUM IS THE MESSAGE Douglas B. Kell*, Marie Brown*, Hazel M. Davey‡, Warwick B. Dunn*, Irena Spasic* and Stephen G. Oliver§ Abstract | One element of classical systems analysis treats a system as a black or grey box, the inner structure and behaviour of which can be analysed and modelled by varying an internal or external condition, probing it from outside and studying the effect of the variation on the external observables. The result is an understanding of the inner make-up and workings of the system. The equivalent of this in biology is to observe what a cell or system excretes under controlled conditions — the ‘metabolic footprint’ or exometabolome — as this is readily and accurately measurable. Here, we review the principles, experimental approaches and scientific outcomes that have been obtained with this useful and convenient strategy. The METABOLOME is defined as the quantitative comple- either the transcriptome or proteome. This is because ment of low-molecular-weight metabolites present in the activities of metabolic pathways are reflected a cell under a given set of physiological conditions1–9. more accurately in the concentrations of pools of It lends itself readily to functional genomic and other metabolites than in the concentrations of the relevant analyses, as changes in a cell’s physiology as a result of enzymes (or indeed the concentrations of the mRNAs gene deletion or overexpression are amplified through encoding them). the hierarchy of the TRANSCRIPTOME and the PROTEOME, Metabolomics is therefore considered to be, in *School of Chemistry, and are therefore more easily measurable through the many senses, more ‘useful’ (that is, ‘discriminatory’) University of Manchester, metabolome, even when changes in metabolic fluxes than transcriptomics and proteomics, for the following Faraday Building, are negligible1,10–12.
    [Show full text]
  • We Wish to Share That with You By
    T HE DEPARTMENT OF BIOENGINEERING The UCSD Bioengineering Program was initiated in 1966 by Drs. Y.C. Fung, Marcos Intaglietta, and Benjamin Zweifach within the Department of Aeronautical Mechanics and Engineering Science. In August 1994 the UC Office of the President approved our request to form a Department of Bioengineering, the first in the UC System. It is wonderful that our Department is celebrating the tenth anniversary of its establishment. While an age of 10 years is young, we had a gestation period of 28 years, which are covered in this book together with the last 10 years. At this momentous occasion, I wish to express my sincere thanks to all my colleagues: faculty, research scientists, staff and students, for their wonderful work as a team in making the Department such a marvelous place to be, both scientifically and interpersonally. On behalf of the Department, I also wish to take this opportunity to thank the generous support and strong encouragement by our friends everywhere in the country and our administration at UCSD and the UC system. Our friends and colleagues are extremely precious, much more than the diamond on the cover of this book*, which is a symbol that represents the tenth anniversary. Sincerely, Shu Chien Chair, Department of Bioengineering NNIVERSARY A * The preparations for this book and the celebration on August 14, 2004, have been made TH possible by the outstanding work by the following members of UCSD central administration, Jacobs School External Relations Office, and Department of Bioengineering (listed alphabetically): 10 Kelly Briggs, Suzie Dandos, Chandra Ewell. Jennifer Griffin, Denine Hagen, Irene Jacobo, Paul Laperruque, Beth Maples, Carolyn Post-Ladd, Jeff Sanchez, and Loretta Smith.
    [Show full text]
  • Models of Biological Regulation
    Models of Biological Regulation by Moritz Emanuel Beber A thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Bioinformatics Approved Dissertation Committee: Prof. Dr. Marc-Thorsten Hütt (chair), Jacobs University Bremen Prof. Dr. Georgi Muskhelishvili, Jacobs University Bremen Prof. Dr.-Ing. Katja Windt, Jacobs University Bremen Prof. Dr. Stefan Bornholdt (external), Universität Bremen Date of Defense: April 17, 2015 Department of Life Sciences & Chemistry iii Statutory Declaration I, Moritz Emanuel Beber, hereby declare, under penalty of perjury, that I am aware of the consequences of a deliberately or negligently wrongly submitted affidavit, in particular the punitive provisions of § 156 and § 161 of the Criminal Code (up to 1 year imprisonment or a fine at delivering a negligent or 3 years or a fine at a knowingly false affidavit). Furthermore I declare that I have written this PhD thesis independently, unless where clearly stated otherwise. I have used only the sources, the data and the support that I have clearly mentioned. This PhD thesis has not been submitted for the conferral of a degree elsewhere. Bremen, July 11, 2017 .................................................................................. Moritz Beber iv Preface The following people deserve my sincerest thanks, more so than I can express in words. There are others whom I do not mention here but also deserve my thanks, please know that you are appreciated nonetheless. First and foremost, I thank my family for showing me, time and again, their unconditional love. Without you I simply would not be here! In particular, I thank my mother Katinka and father Thomas for being calm and analytical when I needed them to but otherwise placing their complete trust in me to go my own way.
    [Show full text]
  • 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]
  • 8Th Conference AM.Pdf
    Measuring the interplay between uptake and loss processes of xenobiotics 13th June 2019 Maddalena Bronzato Physical Chemistry Chemical Technologies & Operations Group Chemical Research, Jealott’s Hill Understanding losses from a foliar surface Volatilisation 2 Why is pesticide volatility so important? ● Environmental fate (loss and persistence) ● Registrability ● Activity (vapour activity and volatility as a benefit) Vapour activity on Aphids Powdery mildew on Fruit Environmental fate 3 Understanding losses from a foliar surface Volatilisation Photodegradation 4 Why is pesticide photodegradation important? ● Activity (photodegradation is one of most destructive post-application pathways) ● Environmental fate (product and persistence) ● Marketability ● Registrability Pesticide sprayed on leaf surface 5 In lab test for volatility and photodegradation Photodegradation Suntest Volatilisation Wind Tunnel 6 Testing for photodegradation - Suntest ● Atlas XLS+ Suntest ● UV-filtered xenon lamp ● Mimics sunlight intensity & spectrum ● Irradiance set to 750W/m2 ● Thermostated baseplate (circulating water @ 15ºC → baseplate ≈ 20 ± 3ºC) 7 Test for volatility- The Wind Tunnel ● Very sample-efficient means of estimating vapour pressure (typically <100µg)] ● Studies are normally run at 40C with a standard wind speed of 1m/s (no control of the R.H.) 8 Photodegradation and volatility test – glass as substrate Pros: ● Good proxy for foliar surface ● Uniform, clean substrate to use for the tests ● High-throughput test ● Worst case scenario ● Indicative but imperfect Limitations: ● Different polarity and morphology between glass and leaves–> differences in redistribution mechanism and deposit shape? 9 SEM images of leaf and glass surfaces Glass 10 Surface redistribution mechanisms Volatilisation Photodegradation Vapour Phase Redistribution 11 Different deposit – effect on photodegradation and volatility Crystalline Amorphous A highly crystalline deposit The larger the deposit area, the faster the compound volatilises.
    [Show full text]
  • The Implementation of Open Access Oral and Written Evidence Contents 1994 Group – Written Evidence
    SCIENCE AND TECHNOLOGY SELECT COMMITTEE The implementation of open access Oral and Written evidence Contents 1994 Group – Written evidence ............................................................................................................. 5 Academy of Social Sciences – Written evidence ................................................................................. 8 Association for Learning Technology (ALT) – Written evidence ................................................. 13 Association of Learned and Professional Society Publishers (ALPSP) – Written evidence .... 19 Jeffrey Beall, Scholarly Initiatives Librarian, University of Colorado Denver – Written evidence ...................................................................................................................................................... 24 Dr Rick Bradford – Written evidence ................................................................................................ 25 British Academy – Written evidence .................................................................................................. 27 British Heart Foundation (BHF) – Written evidence ...................................................................... 32 British Medical Journal Group (BMJ) – Written evidence .............................................................. 34 British Psychological Society (BPS) – Written evidence ................................................................. 38 British Sociological Association (BSA) – Written evidence...........................................................
    [Show full text]
  • Download Download
    Journal of Artificial Intelligence Research 32 (2008) 825{877 Submitted 06/07; published 08/08 Qualitative System Identification from Imperfect Data George M. Coghill [email protected] School of Natural and Computing Sciences University of Aberdeen, Aberdeen, AB24 3UE. UK. Ashwin Srinivasan [email protected] IBM India Research Laboratory 4, Block C, Institutional Area Vasant Kunj Phase II, New Delhi 110070, India. and Department of CSE and Centre for Health Informatics University of New South Wales, Kensington Sydney, Australia. Ross D. King [email protected] Deptartment of Computer Science University of Wales, Aberystwyth, SY23 3DB. UK. Abstract Experience in the physical sciences suggests that the only realistic means of under- standing complex systems is through the use of mathematical models. Typically, this has come to mean the identification of quantitative models expressed as differential equations. Quantitative modelling works best when the structure of the model (i.e., the form of the equations) is known; and the primary concern is one of estimating the values of the param- eters in the model. For complex biological systems, the model-structure is rarely known and the modeler has to deal with both model-identification and parameter-estimation. In this paper we are concerned with providing automated assistance to the first of these prob- lems. Specifically, we examine the identification by machine of the structural relationships between experimentally observed variables. These relationship will be expressed in the form of qualitative abstractions of a quantitative model. Such qualitative models may not only provide clues to the precise quantitative model, but also assist in understand- ing the essence of that model.
    [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]
  • A SHORT CONFERENCE REPORT By
    < APE 2012 The Seventh International Conference “Academic Publishing in Europe” Semantic Web, Data & Publishing A SHORT CONFERENCE REPORT by Dr. Chris Armbruster and André Pleintinger 24 - 25 January 2012 Berlin-Brandenburg Academy of Sciences www.ape2012.eu APE 2012: Academic Publishing in Europe A Short Report from the International Conference: “Semantic Web, Data & Publishing” 24-25 January 2012, Berlin-Brandenburg Academy of Sciences preceded by the Education and Training Course: “Hands On! Exchange of Experiences & Updates on Technologies” on 23 January 2012 by Dr. Chris Armbruster (Research Manager, STM) and André Pleintinger (Institute for the Study of the Book, Friedrich-Alexander Universität Erlangen-Nürnberg) Day 1 Welcome and Opening Addresses Welcoming speakers and participants, Dr. Christian Sprang (German Association of Publishers and Booksellers, Frankfurt am Main), highlighted in his greetings that ‘Academic Publishing in Europe’ has built a reputation by providing a forum for all stakeholders to be heard, interact and envision solutions that benefit scholarly communication. The ongoing necessity and possibility for stakeholders to continue the discussion has been stressed by the PEER Economics report, which investigates the costs associated with the large-scale deposit of stage-two research outputs (Green OA) – for publishers and repositories.1 APE, being held in Berlin for the seventh time, constitutes a unique forum in Germany and Europe. In the opening address, Michael Mabe (CEO, International Association of STM Publishers, The Hague and Oxford), emphasized that the system of scholarly communication shows basic continuity – as demonstrated by major studies over the past years.2 Nevertheless, scholarly communication has also shifted, because its digital products are malleable, can be copied and are subject to mash-ups.
    [Show full text]
  • Dissertation / Doctoral Thesis
    DISSERTATION / DOCTORAL THESIS Titel der Dissertation /Title of the Doctoral Thesis „Proteomic studies on Chlamydomonas reinhardtii“ verfasst von / submitted by Dipl.-Biochem. Luis Recuenco-Muñoz angestrebter akademischer Grad / in partial fulfilment of the requirements for the degree of Doctor of Philosophy (PhD) Wien, 2017 / Vienna 2017 Studienkennzahl lt. Studienblatt / A 794 685 437 degree programme code as it appears on the student record sheet: Dissertationsgebiet lt. Studienblatt / Biologie field of study as it appears on the student record sheet: Betreut von / Supervisors: Univ.-Prof. Dr. Wolfram Weckwerth Ass.-Prof. Dipl.-Biol. Dr. Stefanie Wienkoop, Privatdoz. 2 Declaration of authorship I, Luis Recuenco-Muñoz, declare that this thesis, titled ‘Proteomic studies on Chlamydomonas reinhardtii’ and the work presented in it are my own. I confirm that: • This work was done wholly or mainly while in candidature for a research degree at this University. • Where I have consulted the published work of others, this is always clearly attributed. • Where I have quoted from the work of others, the source is always given. With the exception of such quotations, this thesis is entirely my own work. • I have acknowledged all main sources of help. • Where the thesis is based on work done by myself jointly with others, I have made clear exactly what was done by others and what I have contributed myself. Signed: Date: 3 4 Equal goes it loose (Ernst Goyke) 5 Aknowledgements • I wish to thank Prof. Dr. Wolfram Weckwerth and Dr. habil. Stefanie Wienkoop for giving me the chance to work in this utterly interesting field, tutoring and mentoring me throughout my PhD Thesis, and for all the teaching, support, advice and fun I have had both on a working and on a personal level during my whole stint in Vienna.
    [Show full text]