nd febs advanced lecture course on systems …...febssysbio2007: advanced lecture course on systems...

FEBSSysBio2007: Advanced Lecture Course on Systems Biology, Gosau

Introduction

2nd FEBS Advanced Lecture Course on

Systems Biology:

From Molecules to Life Gosau, Austria, EU, March 10-16, 2007

Organizers

Karl Kuchler Medical University Vienna Max F. Perutz Laboratories Campus Vienna Biocenter Edda Klipp Computational Systems Biology Max-Planck Institute for Molecular Genetics Berlin Uwe Sauer Institute for Molecular Systems Biology ETH Zürich Hans V. Westerhoff (program chair) AstraZeneca Chair for Systems Biology, Manchester Centre of Integrative Systems Biology, The University of Manchester and

Department of Molecular Cell Physiology, Netherlands Institute for Systems Biology,

Free University Amsterdam Anneke (J.G.) Koster (course secretary) Institute for Systems Biology Amsterdam Walter Glaser (IT) Medical University Vienna Max F. Perutz Laboratories Campus Vienna Biocenter


The Course contents: 2

Teachers

Alan Aderem Lilia Alberghina Judy Armitage Barbara Bakker Frank Bruggeman Marta Cascante Marileen Dogterom Måns Ehrenberg Igor Goryanin Adriano Henney Jannie Hofmeyr Leroy Hood

Jeroen Jeneson Tom Kirkwood Hiroaki Kitano Ursula Klingmüller Edda Klipp Karl Kuchler Ursula Kummer Doug Lauffenburger Hans Meinhardt Erik Mosekilde Bela Novak Jens Nielsen

Steve Oliver Johan Paulsson Uwe Sauer Johannes Schlöder Guy Shinar Jacky Snoep Jaroslav Stark Jens Timmer Hans van Leeuwen Nathal van Riel Hans V. Westerhoff

Other Members of the Scientific Advisory Board

Ruedi Aebersold Uri Alon Roland Eils Stefan Hohmann Mariko Hatakeyama

Douglas Kell Boris Kholodenko Sang Yup Lee Bernard Palsson Masaru Tomita

Roel van Driel Barry Wanner Shoshana Wodak

Technical Support & Registration & Course Office

FEBS- Sysbio Course Office: Anneke (J.G.) Koster Amsterdam Systems Biology Institute Charlie Parkerstraat 25 NL-1066 GV Amsterdam, EU Phone: +31-20-6143163 FAX: +31-20-6143163 e-mail: systems.biology [at] inter.nl.net wwweb: http://www.febssysbio.net and http://www.univie.ac.at/sysbio2007/ At the Venue in Gosau: Anneke (J.G.) Koster Sport und Erlebnis Hotel**** Gosau A-4824 Gosau am Dachstein 713, Austria, EU Phone: +43-6136-8811-390 FAX: +43-6136-8811-352 e-mail: systems.biology [at] inter.nl.net wwweb: http://www.febssysbio.net and http://www.univie.ac.at/sysbio2007/ FEBS-SysBio2007 Hotlines: +43 676 584 2185 (Regina Klaus) and +31 6 520 76 384 (Anneke Koster)


Program, abstracts and participant’s notes 3

Organizing institutions

Main Organizer:

FEBS: FEBS-SysBio2007, the 2nd Advanced Lecture Course on Systems Biology is organized on

behalf of FEBS, the Federation of European Biochemical Societies.

Co-organizing networks from the EC-FP6 programme:

YSBN: Yeast Systems Biology Network, a Coordination Action on Yeast Systems

Biology co-organized the Yeast Symposium.

BioSim: A Network of Excellence for BioSimulation co-organized the Tools and

Methods Symposium.

NucSys: A Marie Curie Training Network entitled "Systems biology of nuclear

receptors: a nutrigenomic approach to aging-related diseases" co-organized the

Mammalian Systems Biology Symposium

Other co-organizing network:

SBForum: The Scottish Bioinformatics Forum. Integrating the Bioinformatics and Life Science

research comminities, sponsors the computer/balck board workshop on the Edinburgh Pathway

Editor by Goryanin and SorokinYeast Systems Biology Network, a Coordination Action on Yeast

Systems Biology co-organized the Yeast Symposium.


4

FEBS-SysBio2007 was supported by

FEBS [The Federation of the European Biochemical Societies]

YSBN: Yeast Systems Biology Network

BMBF [German Bundesministerium für Bildung und

Forschung]

BioSim Network of Excellence on BioSimulation

AstraZeneca

DKFZ [Deutsche Krebsforschungszentrum]

DSM

BioCentrum Amsterdam

The Scottish Bioinformatics Forum

European Society for Mathematical and Theoretical

Biology



Helios Biosciences: an SME for target discovery through Systems

Biology

Unilever Cosmetics

Doctoral Training Centre for Integrative Systems Biology from Molecules to Life

FEBS Journal

Amsterdam Systems Biology Institute

EML (European Media Laboratory)


6

Table of Contents

Organizers ......................................................................................................................................................... 1 Teachers ............................................................................................................................................................ 2 Other Members of the Scientific Advisory Board............................................................................................... 2 Technical Support & Registration & Course Office............................................................................................ 2 Organizing institutions ....................................................................................................................................... 3

Main Organizer: .......................................................................................................................................... 3 Co-organizing networks from the EC-FP6 programme: ............................................................................. 3 Other co-organizing network: ..................................................................................................................... 3

FEBS-SysBio2007 was supported by................................................................................................................ 4 Willkommen in Gosau, Welkom in Gosau, Welcome to Gosau! ....................................................................... 7 Scientific Program - its principles..................................................................................................................... 12 Symposia...................................................................................................................................................... 12 Symposia Morning: Lectures (L), tutorials and an issues identifiying discussion ........................................ 12 Break for Lunch, Physical Activities, Tea..................................................................................................... 12 Black-Board Teaching (BB).......................................................................................................................... 12 Computer practicals (CP)............................................................................................................................. 13 Symposia afternoon: Short Talks (S) ........................................................................................................... 13 Symposia late afternoon discussion............................................................................................................. 13 Poster Presentations (P), Poster Committees, Analyses, Discussions ....................................................... 14

Participant Task List: Contribution of each Participant and its Timing ............................................................ 15 The Course Book - its Principles ..................................................................................................................... 19 Abstracts ...................................................................................................................................................... 19 Course (‘Abstract’) Book - Paper ................................................................................................................. 19 Course (‘Abstract’) Book - Electronic ........................................................................................................... 19

Systems Biology Young Investigator Awards .................................................................................................. 19 Web Site....................................................................................................................................................... 19

Technical Local Information............................................................................................................................. 20 Connections – You and the World ............................................................................................................... 20 Internet – You and the World ....................................................................................................................... 20 Departure ..................................................................................................................................................... 20 FEBS Evaluation Form................................................................................................................................. 20 FEBS-SysBio2005 Course Office ................................................................................................................ 20 Help .............................................................................................................................................................. 21 Message Board ............................................................................................................................................ 21 Meals, Beverages & Lunch Packages ......................................................................................................... 21 Payments ..................................................................................................................................................... 21 Presentations ............................................................................................................................................... 21 Skiing and Outdoor Leasure ........................................................................................................................ 22 Social Program............................................................................................................................................. 22 Sport & Erlebnis Hotel Facilities................................................................................................................... 23

Scientific Program............................................................................................................................................ 24 Saturday March 10: Opening (co-organized with AstraZeneca) .................................................................... 24 Sunday March 11: Symposium on Principles ................................................................................................. 25 Monday March 12: Symposium on Yeast (with YSBN) ................................................................................... 30 Tuesday March 13: Symposium Mammalian (with NucSys) .......................................................................... 35 Wednesday March 14: Symposium Towards Life ........................................................................................... 36 Thursday March 15: Symposium Tools & Methods (with BioSim) .................................................................. 41 Friday March 16: The day after........................................................................................................................ 43



Willkommen in Gosau, Welkom in Gosau, Welcome to Gosau!

We heartily welcome you to the second FEBS Advanced Lecture Course on Systems Biology. It is now ten years ago that the first sequences of entire genomes were published and these ten years have revolutionized the Life Sciences. The first sequenced genomes stemmed from simple Life forms, but genomics quickly progressed to the larger human genome. Now genome sequences are available for many organisms throughout the three Kingdoms of Life. It was perhaps surprising that the human genome sequence was less than ten times larger than that of the humble intestinal bacterium E. coli. Indeed, the genomes of organisms that had always been

thought to be ‘simple’ model organisms range in the thousands of genes. The smallest genome that appears sufficient to inform Life contains more than 300 genes. Apparently these 300 genes need each other for their persistence in an organism; just having 100 organisms of three genes each, appears not to be compatible with Life as we know it.

Life as we know it appears to be of an irreducible complexity therefore. This is also understandable from biochemical first principles: The significant chemical conversions that degraded sugar molecules are most readily executed in series of steps (pathways). Each step needs to be catalyzed by a protein. All proteins need to be kept together by a membrane, which requires protein-based specific transport systems and lipid biosynthesis. The information of the amino acid sequence of all proteins needs to be stored. For many of these essential activities Gibbs free energy is needed. Proteins consist of amino acids, many of which need to be synthesized from simpler components. The essence of these first principles is not so much that many processes are needed, but that a rather significant number of processes are needed together: There is no enzyme catalyzed metabolic pathway without a membrane; no membrane without a metabolic pathway for lipid synthesis; no lipid biosynthesis without ATP to drive it; no ATP without catabolism, etc. Life itself therefore is an emergent property, as it depends critically on the interaction of its components. And, the other side of the coin is that the components of Life are non autonomous; for their functioning and maintenance they need the living organism as a whole. This whole depends on the interactions of the parts as well as on the parts themselves and the parts depend on the whole and the interactions with the other parts. This gets us very close to the definition of Systems Biology, which (in a consensus view)

1 is the Science that studies how biological function arises in the interactions between

components of living systems. One of the symposia of this course is entitled ‘ TTTowards Life’ and focuses on studies on subcellular systems that lead to Life. The emergence of new properties from interactions requires these interactions to be ‘nonlinear’, where ‘nonlinear’ may refer to a number of different aspects. These include: (i) nonlinearity of rate equations, (ii) heterogeneity (‘organization’) in time (time hierarchies), space (compartmentation) and chemistry (e.g. the mRNA-protein-metabolism hierarchy), (iii) cooperative binding, and (iv) stochasticity. When interactions are nonlinear, their strengths depend on the operating point and so does the emergence of new properties. Consequently, once needs to be precise, both in experimentation and in analysis, and one needs to study the system under physiological conditions. In addition, interactions between two components may well depend on other components; potentially one needs to consider all the components of the system. The above explains why many Systems Biologists implement quantitative experimentation, use mathematical approaches to analyze their data or model their system, or engage in genome wide analyses. The quantitative experimentation under conditions that are relevant for the in vivo situation is relatively new to Biology. Existing experimental methods are fine-tuned to these new tasks and new methods are developed. The same goes for mathematical methodologies, which used to target the simpler linear systems or to approximate nonlinear systems by linear ones, but should now be deployed in the nonlinear systems without too much linearization. This Advanced Lecture Course on Systems Biology therefore contains an entire Symposium on TTTools and Methods. This symposium was organized together with the European Network of Excellence on BioSimulation (BioSim), which is developing and applying various types of modeling with an emphasis on Systems Biology in the context of disease and drug therapy (http://biosim.fysik.dtu.dk:8080/biosim/ ).

1 Albergina L. & Westerhoff H.V. (Editors) (2005) Systems Biology: perspectives and definitions, Springer


8

By some, Biology used to be thought of as a ‘can of worms’, or a set of special cases sharing little if any, regularity. By now, we know that this is not true. All Life appears to have the DNA, mRNA, protein, metabolism hierarchy of information; a democratic hierarchy, but a hierarchy. Virtually all processes in living organisms are catalyzed by proteins. Free-energy and redox equivalents shuttle between metabolic pathways through ATP/ADP and by NADH/NAD coenzymes, with minor variations (NADP, protons). The thought that Biology is stamp collecting and that physics is … Physics, appears to be further away from the truth than anticipated. After all, Newton’s law only work in vacuo and at low speeds of matter, and the electric potential away from a point charge only follows Coulomb’s law when there is a steady homogeneously polarizable medium around that point charge, which is rarely the case. It is indeed exciting to identify what most Biologists have come to accept as truths, as empirical laws. These may often be derived from underlying principles of organization: it is a challenge to recognize principles, or even ‘laws’ of Systems Biology. Metabolic Control Analysis and network topology analyses have suggested some of these. In the former case the laws can be deduced from underlying conditions met by most realistic networks. In the latter case most laws have remained empirical until now, but who knows……; this is why we are here. At any rate, the Symposium on PPPrinciples will offer ample opportunity to learn about and discuss this aspect of Systems Biology. Function emerges from interactions at many organizational levels in Biology. If one is strict, perhaps too strict, then Biological function is only meaningful in the context of Life, hence at least in the context of unicellular organisms. In this way of defining biological function, it is something that evolution could directly select for. Molecular ‘functions’ cannot themselves be selected for. They can only be selected for if they have some control over the functioning of the intact organism. Above the level of the individual cell there are many functions that can be selected for, e.g. the fitness of a multicellular organism such as a mouse, or the fitness of an entire ecosystem. At this course we shall discuss one of these supracellular systems, i.e. mammalian systems, of course with some attention to the human and its diseases itself. The corresponding Symposium MMM was organized together with the Marie Curie Training network on Nuclear receptor Systems Biology (NucSys: http://www.uku.fi/nucsys/meetingsLeuven.htm ). It is exciting that we have most of the Ph D students of this network at the course and the discussion sessions after the lectures and around the posters will be lively. Systems Biology is still in its infancy. This is partly because it is so difficult, both in terms of experiments and in terms of theory, but also partly because until recently there has been comparatively little investment in the topic as compared to functional genomics. This is now improving in the more enlightened countries, first in Japan and the USA, but then also in Germany, the United Kingdom and Switzerland. The German Bundesministerium für Bildung und Forschung (BMBF) has catapulted Germany into Systems Biology by daring to focus on a highly ambitious project, i.e. Hepatosys; the Systems Biology of the liver cell. This is running now and it is most impressive how in many parts of this program experimental and theoretical groups are interacting. This will become clear at this course too, with many contributions coming from Hepatosys. The BMBF is an enthusiastic sponsor of this course. More recently Germany has again been active in sponsoring systems biology, both in terms of centers of excellence (ForSys) and in terms of funding Systems Biology research proposals for various areas (through a Helmholtz initiative). The United Kingdom’s Biotechnology and Biological Sciences Research Council (BBSRC) as well as its Engineering and Physical Sciences Research Council (EPSRC) have also become quite active in funding Systems Biology. In fact Systems Biology is the Leitmotiv of BBSRC’s ten year plan. BBSRC with EPSRC has been funding 6 Centers of excellence for Systems Biology, and BBSRC will soon be funding a substantial number of large systems biology projects (through its SABRE initiative). EPSRC together with BBSRC has funded three doctoral training centers for Systems Biology. Manchester is home to both such a research centre and a training centre (MCISB and its DTC-ISBML, which is involved in the organization of this course). Indeed it is a pleasure to see that the FEBS advanced course is now turning into a meeting place for the emerging human capital that populates these major new Systems Biology programs. With various Systems Biology methodologies developing, and with in principle everything being connected with everything else in Systems Biology, it should be helpful to have a system where all components can be analyzed, most functional behavior can be studied and to which most methods can be applied, all simultaneously. There are various candidate systems and world wide alliances have been formed on at least two of these, i.e. E.coli (IEcA; http://www.uni-giessen.de/~gx1052/IECA/ieca.html ) and S. cerevisiae (YSBN: http://www.gmm.gu.se/YSBN/ ). At this course we will have a symposium on the latter (YYYeast), which has been co-organized with YSBN. There was Systems Biology avant la lettre, or there have been two roots of the topic

2.

Mathematical Biology was (and is) one of these roots. It foresaw the complexity of Biology and the emergence of biological function in nonlinear processes, but it lacked the realism of molecular biology. The studies of the mechanisms of development and differentiation through partial or complete self-organization

2 Westerhoff H.V. & Palsson B.O. (2005) Nature Biotechnol. 22, 1249 – 1252. The evolution of molecular biology into Systems Biology



are important examples. Molecular biology, biophysics, genomics and functional genomics are all aspects of the second, perhaps dominant root of Systems Biology. The two roots of Systems Biology will both be presented by keynote opening lectures, i.e. one by Leroy Hood, founder of the Systems Biology Institute in Seattle and one by Hans Meinhardt, a well-known mathematical developmental biologist. These opening lectures have been organized in collaboration with one of the many pharmaceutical companies that take Systems Biology very seriously, i.e. AstraZeneca. The opening lectures aligning with the two roots of Systems Biology, they should nicely introduce the course. We shall try to make this explicit by having a discussion between students and the two lecturers following these opening lectures, where the aim is to identify what the major issues are for Systems Biology today, i.e. where the focus should be during this Course. Funding for Systems Biology is increasing rapidly in many countries. Consequently also Systems Biologists are in high demand. Unfortunately there are few true Systems Biologists around. Indeed, science education has been focusing on single disciplines like Molecular Biology without Mathematics, or on Mathematics or Physics without Biology. In addition, Systems Biology requires so much knowledge about so many disciplines that it is hard for any individual to excel in all that are needed. Therewith Systems Biologists should not only be excellent in some aspect of the field but also be able to grasp other aspects quite rapidly and to engage in fruitful collaborations with Systems Biologists who are experts on other aspects. Interdisciplinarity, which refers to being between traditional disciplines, should be paired with transdisciplinarity, i.e. the ability to combine aspects from across disciplines. This may require entirely new modes of training of beginning scientists. Various countries have begun to set up such novel training and among these the United Kingdom has been rather explicit by its EPSRC and BBSRC funding three Doctoral Training Centers of this type (of which one supports the organization of this course: http://www.mcisb.org/dtc/). New generations of Biology and Physics students are now emerging with capabilities that are different between the individuals, but also with the ability to ‘twin’ their research with others. These generations realize that the expertise in Systems Biology is not confined to the institutes or training center they are in and that the most exciting topics of research aren’t either. They wish to extend their training to other Systems Biology groups and topics, on this same planet. Part of training in Systems Biology should therefore be international and we are pleased that the Federation of European Biochemical Societies (FEBS) is highly supportive of this point of view. We appreciate the strong support from the FEBS Advanced Course Committee, which decided to continue this FEBS Advanced Lecture Course after its successful initiation in 2005 (http://www.febssysbio.net/index2005.html ) with enthusiasm of the previous chairman of the committee Karel Wirtz. The enthusiasm is now so high that indeed one of the organizers of this course is the Chair of the FEBS Advanced Course committee (Karl Kuchler). We should like to thank the members of this committee as well as Iain Mowbray for their continued support The need for training is also recognized by the national European organizations that fund modern biological and medical research. Indeed, the German Ministry for Education and Research (BMBF) has generously supported the course largely through student registration waivers. The 6

th Framework Program of the European Union has been actively supporting the development of

Systems Biology, in a number of network-like activities. Three of these have supported this course by helping in the organization and supporting their students to come here and (YSBN and BioSim) by supporting the corresponding lectures and training activities. These are the Coordination Action YSBN, which aims to organize the European Systems Biology on yeast, the network of Excellence on BioSimulation (BioSim), and the Marie-Curie Research Training Network NucSys, training Ph D students in the Systems Biology of nuclear receptors and vitamin D metabolism. At the course, YSBN is represented by Jens Nielsen, BioSim by Erik Mosekilde, and NucSys by Hans van Leeuwen. The number of new drugs that reach the market, and the number that thereafter survive, is diminishing. The cost of developing the drugs is becoming astronomical, largely because it is too difficult to choose between the large numbers of promising drug leads at an early stage. The ones that are plagued by ‘side effects’ and will not interact optimally with their target in the context of the living organism, are identified so late in the process that they absorb most of the budget. The critical issues here are again Systems Biology issues, and modern pharmaceutical companies are engaging strongly in this new field. One of these, i.e., AstraZeneca enthusiastically supports this Advanced Lecture Course, both in terms of its lectures and in terms of the USB-sticks provided to all participants. The course is also supported by a small company specializing in drug target finding using Systems Biology (Helios-Biosciences). It is unbelievable how ill-defined some of the food is that we enjoy on a daily basis. Both in terms of food safety, and in terms of improvements in the contribution of food to health, food production methodology is a field that may also be inspired by Systems Biology developments. The same goes for the production of fine


10

chemicals by living organisms. DSM is supporting this Course. The cosmetics industry has always been on the brink of suspicion that their products might not deliver what the glossy journals claim, i.e. eternal youth. Actually it is a bit surprising that there is little we can do about ageing and about skin ageing in particular, but see perhaps the closing lecture of this Course. Unilever is now gearing up System Biology to modernize the approaches to cosmetics, in terms of studying the interaction of skin with its microbial guests. Unilever also supports this course. The FEBS Journal has been a pillar under Biochemistry and Molecular Biology in more than one way. First, it has always published scientific articles of high quality and significance. Second, it has always earned much of the money that is used to subsidize FEBS courses. At present, the journal is even more relevant to the emerging field of Systems Biology: (i) it is one of the earliest journals that highlighted the topic, such as through the direct link to the JWS (silicon cell) model-base (e.g. www.siliconcell.net ), and (ii) it has just undergone a facelift, orienting itself more towards quantitative cell biology and systems biology. To celebrate this, the journal offers us drinks at the Welcome Reception. It also invites the participants to the course to submit expressions of interest for writing minireview articles for the journal (you may wish to contact their System Biology editor Hans V. Westerhoff). Molecular Systems Biology is a comparatively new journal addressing much of the field covered by this course. Each original research article published in this journal is accompanied by a synopsis, produced with the support of the EMBO editorial team, to ensure maximum readability. This journal also supports this lecture course. Europe already has a number of Centers for Systems Biology. Of these, the BioCentrum Amsterdam (or Netherlands Institute for Systems Biology), the Deutsche KrebsForschungsZentrum, Systems X, and the European Media Laboratory are among those that support this course financially. We expect that many Systems Biologist of the future will have been nurtured at these institutions.

Of course, the home institutions of the organizers have contributed rather importantly to the organization, i.e. the BioCentrum Amsterdam and the Free University in Amsterdam, the Max F. Perutz Laboratories of the Vienna Biocentre, the Institute for Molecular Systems Biology of the ETH Zürich and the Max-Planck Institute for Molecular Genetics in Berlin. We also thank the Institute of Molecular Pathology (IMP) and the Vienna Veterinary University for providing us with the poster walls, and the Institute for Molecular Cell Biology, Amsterdam for lending some of the additional equipment. Likewise the Teachers of the course (i.e. the Lecturers and the members of the Scientific Advisory Board, see above) have spent quite some time in order to optimize their teaching at this course; their institutes have thereby also contributed. A course is a matter of human beings, much more than of institutions. This course is possible thanks to the enthusiasm of the many people involved in the actual organization. Jacky L. Snoep has provided us with artwork for the abstract book. We thank Regina Klaus for secretarial assistance during the course, and Walter Glaser for getting the IT and webpages right. Of course the local organizing committee is quite important: we thank the team with colleagues from Amsterdam, Berlin, Manchester, Vienna and Zürich for their enthusiasm and efforts: Nils Blüthgen, Jildau Bouwman, Frank Bruggeman, Jurgen Haanstra, Helmut Jungwirth, Regina Klaus, Alexey Kolodkin, Nathalie Landstetter, Maria Nardelli, Katja Rybakova, Martin Rühl, Jannis Uhlendorf, and others. In addition we thank Barbara Bakker, Nils Blüthgen, Jildau Bouwman, Frank Bruggeman, Jurgen Haanstra, Alexey Kolodkin, and Katja Rybakova, for much help in getting the abstract booking in shape. The director and staff of the Sport und Erlebnis Hotel Gosau are thanked for the professional way they arrange for infrastructure and food. And we thank Emilia, once again our youngest course participant, for her help in many ways. But of course, we should not forget the all-but-silent majority, i.e. the participants and their supporters (institutions and mentors), who contributed much effort and inspiration. Reading the abstracts we found that a great many innovative ideas were going to be contributed by the participants in spe. This course is perhaps the second of its kind in Systems Biology. Because of the novelty of the field we had applied to FEBS for a course of 120 students. When the number of registrants exceeded 200, we were pleased because it demonstrated great interest and enthusiasm, but saddened because we had to deny many high quality applicants participation. Because quality and potential of most abstracts was high, we also had to select on the basis of



more technical parameters, e.g. we limited the number of students coming from any same institution. We hope that the students we could not be admit will come to a next course. Likewise, we have to admit that although our speakers/teachers are excellent Systems Biologists, we have not been able to get all excellent Systems Biologist to the course: we had too few speaker slots. What is next? An exciting course here in Gosau with lots of excellent teaching. The teaching program is special in that it hosts a number of unconventional teaching elements. The latter include the systematic discussion of each poster contribution by a number of senior scientists, black-board teaching, power-poster presentations, discussion sessions formulating key questions and subsequent sessions trying to address these. The lectures are also special in that some of them are explicitly didactic. All of them have an add-on of informal discussion of methodology with a smaller group of students. Most of them are also split into a methodological part and a part with the most recent results. Equally importantly, new and more established Systems Biologists from various science directions will meet and discuss science intensively. What has been? There is one very sad note. As we were preparing for this course, one of the scientific pillars under Systems Biology left us. Reinhart Heinrich died October 23, 2006, at much too young an age. Reinhart has been a continuous motor driving biophysics and mathematical biology. He was one of the two main originators of Metabolic Control Theory/Analysis, which is now widely recognized as the clearest forerunner to Systems Biology. After continuing the discipline in the dark years of the sixties-eighties of the last century, Reinhart brought it to great expansion in the last ten years. In the 2005 Gosau course Reinhart taught the Dynamics and Design of cellular reaction networks, as well as stability and flux-mode analysis, and he contributed through a great many presentations of his colleagues and students. It will not be the same without him, neither in Systems Biology in general, nor at the Gosau course. We will miss his very subtle sense of humor, and his scientific justness and precision. The best we can do perhaps, is live the tradition that he started. In many ways, the Gosau course does what he initiated with the many workshops he organized, e.g. in Magdeburg. We are pleased that Hans Meinhardt is willing to give the first Reinhart Heinrich Memorial Lecture. Realizing that Science must go on, even after the very sad turns it often takes, we expect that Gosau will continue to be a cradle of a network of excellent Systems Biologists who will know to find each other in the future for advice and collaboration. We hope that the interdisciplinary activities that are so important for Systems Biology, will take off and make excellent new Science. The organizers,

andndndnd her her her her teamteamteamteam

((((i.e.i.e.i.e.i.e..,.,.,., Walter GlaserWalter GlaserWalter GlaserWalter Glaser, Edda Klipp, Edda Klipp, Edda Klipp, Edda Klipp, Karl Kuchler, Karl Kuchler, Karl Kuchler, Karl Kuchler, , , , Uwe SauerUwe SauerUwe SauerUwe Sauer, , , , and Hans V. Westerhoffand Hans V. Westerhoffand Hans V. Westerhoffand Hans V. Westerhoff) ) ) )


12

Scientific Program - its principles

Symposia

The course has been organized in terms of 5 Symposia, dedicated to areas within Systems Biology, i.e. ‘PPPrinciples’, TTTools and Methodology’, Towards LLLife, YYYeast, and

MMMammalian Systems Biology. Each symposium has its dedicated day, consisting of a morning, the later part of the afternoon and parts of three evening sessions dedicated to teaching around the posters. In the afternoon, there will be black board and computer sessions. Discussions and short talks by invited principal Investigators and students follow. The posters corresponding to the symposium have been grouped together physically but will be presented in sequel on the three poster evenings (Sunday, Monday and Wednesday).

Symposia Morning: Lectures (L), tutorials and an issues identifiying discussion

Mornings have didactic lectures, topical elctures (all with an additional tutaotial) and the Resulst lectures. Tuesday morning has an extra lecture that bridges symposia Y and M, i.e. the lecture by Bela Novak. At the end of the morning session the Chair of the symposium will summarize the morning session and elicit a general discussion between students and speakers where they will identify issues that are most exciting in the particular area of Systems Biology addressed by the Symposium.

Break for Lunch, Physical Activities, Tea

Lunch will be in the hotel restaurant. Course teachers are requested not to seat together. They should rather sit at their own table and be joined by students. Similarly, students are kindly requested not to sit together with other students from their own institute, but with Teachers, or with students and principal investigators from other institutes. After lunch there is a break for physical activities, such as ski-ing, rock climbing, chess, or hang gliding. You may also take a lunch bag rather than engage in a seated lunch and engage in scientific discussion in the ski-lift or when gliding down the slopes. We are sure that you may be spotting some of the teachers up there and you may be able to reciprocate in teaching them how to ski! Be back for tea (coffee if you wish) shortly after 16h00 though, to engage in the afternoon session, which begins at 16h30.

Black-Board Teaching (BB)

On Sunday, Monday and Wednesday afternoons, two Blackboard Teaching courses (three sessions each) will be held after the physical activity break and tea, one from 16h30 until 17h15 and one from 17h20 until 18h05. These are optimized for interactive teaching. Key concepts for Systems Biology will be explained, in interactive mode, using blackboard and chalk, or equivalent. 4 Blackboard courses will be held in parallel, such that each should be expected to host some 20 students.



A Black Board course is typically taught by a teacher for three days on end, the total teaching taking 140 minutes, extending over three 45 minutes sessions. The student should therefore choose beforehand which two Black Board (or computer) courses (s)he will wish to follow. Switching between topics will mean that the student will have missed the important introductory parts of the course. The following topics will be taught in this mode: 16h30 - 17h15:

• Hierarchical regulation analysis of cellular adaptive responses (Frank Bruggeman and Hans Westerhoff)

• Dynamic modeling of biochemical networks (Edda Klipp) • Biological pattern formation (Hans Meinhardt) • Network motifs (Guy Shinar) 17h20 - 18h05: • Physiological modeling (Jeroen Jeneson and Natal van Riel) • Differential equation models (Johannes Schlöder) • Flux analysis (Uwe Sauer)

Computer practicals (CP)

On Sunday, Monday and Wednesday afternoons, three Computer practical courses will be run in parallel. Like Blackboard Teaching courses these are optimized for interactive teaching, with the difference that the students will be taught to use systems Biology computing facilities, such as CCCoooPPPaaaSSSiii, EEEdinburgh PPPathway EEEditor, and JJJWWWSSS/SSSiiilicon CCCell. Key concepts for Systems Biology will be explained, in interactive mode, using the computers that will be made available, or laptops brought by the students. The students should therefore choose beforehand which two computer (or Black Board) courses (s)he will wish to follow. Switching between topics will mean that the student will have missed the important introductory parts. The following topics will be taught in this mode:

16h30 - 17h15: • CoPaSi (Ursula Kummer) • Dynamic modeling of biochemical networks (Edda Klipp) 17h20 - 18h05: • JWS & Silicon cell (Jacky Snoep and Hans Westerhoff) • Edinburgh Pathway Editor (Igor Goryanin & Anatoly Sorokin)

Symposia afternoon: Short Talks (S)

A number of students and Principal Investigators have been invited to give a brief oral presentation about recent discoveries and developments (10 + 5 minutes)

Symposia late afternoon discussion

During the late-afternoon discussion, the issues raised at the end of the morning discussion session will be addressed by the Lecturers and other Teachers of that symposium. This will be followed by a general discussion.


14

Poster Presentations (P), Poster Committees, Analyses, Discussions

The posters are up throughout the meeting in the large hall, just outside the hotel proper (after entering the hotel, turn right and continue in that direction for 100 m); they should be mounted before Sunday evening and removed Thursday evening. Each poster will be presented for at least an hour by its prime author, as indicated in the program: Poster numbers n-2 will be presented/analyzed/discussed Sunday evening from 21h00 for at least an hour. Numbers 3n-1 will be similarly presented/analyzed/discussed Monday evening. Numbers 3n-3 will be presented/analyzed/discussed Wednesday evening. The presenters of short talks are requested to present their poster (also) on the day of their short talk. Authors presenting posters are asked to indicate on their poster additional times when they will be available at their poster for discussion. At other times during poster sessions the poster authors are supposed to discuss the posters of their colleagues. Every student will get to speak with the teachers in her/his symposium: each symposium has a corresponding Poster Committee, which consists of all lecturers at that symposium plus: Symposium PPPrinciples: Klipp (chair) plus P lecturers Symposium YYYeast: Alberghina & Nielsen (chairs) plus Y lecturers Symposium on MMMammalian Systems Biology: Van Leeuwen (chair) plus M lecturers Symposium Towards LLLife: Cascante (chair) plus L lecturers Symposium TTTools and Methods: Sauer & Mosekilde (chairs) plus T lecturers During the first 45 minutes of each of the three poster sessions, this committee will inspect the one third of the posters belonging to their symposium that is being presented by their author that evening (i.e. up to ten posters). At the end of the poster session, i.e. from 22h30 – 23h00), i.e. in the ‘poster round table discussion’, the poster committee will discuss in a session with all poster presenters of their symposium all the posters they have seen that evening (i.e. this will be a self-organizing (drinks provided by the Course committee) non-plenary session with approximately 4 committee members and 10 poster presenters). Please note that for each symposium posters will be discussed Sunday, Monday and Wednesday evening. Each poster presenter will only present during the early half of one of these evenings and then be in a discussion groups later that evening.



Participant Task List: Contribution of each Participant and its Timing

Full Name Day Type of Contribution Contribution

Number

Jure Acimovic Sunday poster M-P01

Alan Aderem Tuesday lecture M-L04

Doryaneh Ahmadpour Sunday poster Y-P01

Timothy J Akhurst Sunday poster T-P01

Ross Alexander Monday poster Y-P02

Lilia Alberghina Monday chair Ch-Y

Roberta Alfieri Monday poster M-P02

Richard John Allen Wednesday poster M-P03

August Andersson Sunday poster P-P01

Joaquin Arino Monday poster Y-P28

Judith Armitage Wednesday lecture L-L02

Ilka Maria Axmann Su, Th short talk/poster L-S02/L-P01

Anastasia Bachmann Monday poster L-P02

Juerg Baehler Monday short talk Y-S02

Barbara Bakker Monday didactic lecture Y-L01

Eva Balsa-Canto Monday poster T-P02

Matteo Barberis Wednesday poster/short talk Y-P03/Y-S01

David Barrass Sunday poster Y-P04

Sebastiano Battaglia Sunday poster M-P04

Kristin Baumann Monday poster Y-P05

Rod S.P. Benson Wednesday poster T-P03

Basti Bergdahl Wednesday poster Y-P06

Nils Blüthgen Monday poster M-P05

Sebastian Bohl Wednesday poster M-P06

Jildau Bouwman Sunday poster Y-P07

Gordon Breen Sunday poster T-P04

József Bruck Monday poster T-P05

Claudia Bruedigam Sunday poster M-P07

Frank Bruggeman Su, Mo, We short talk/blackboard P-S03/BB-01

Stanley Brul Wednesday poster L-P27

Marcin Buler Wednesday poster L-P03

Ayça Cankorur Monday poster Y-P08

Fabrizio Capuani Wednesday poster T-P06

Marta Cascante Wednesday chair Ch-L

Xiao Chen Monday poster P-P02

Ksenia Cheremisina Monday poster M-P08

Luna De Ferrari Sunday poster T-P07

Tatjana Degenhardt Wednesday poster M-P09

Marileen Dogterom Wednesday lecture L-L03

Ksenija Drabek Wednesday short talk M-S03

Birgitta Ebert Wednesday poster P-P03

Mans Ehrenberg Wednesday lecture L-L01

Marco Eijken Sunday poster P-P04

Abraham Ericsson Wednesday poster Y-P09

Dirk Fey Sunday poster L-P04

Sarah Frank Monday poster L-P05

Paul Fransz Wednesday poster M-P28

Felix E Frenkel Monday poster T-P08


16

Sabrina Froels Wednesday poster L-P06

Matthias E. Futschik Sunday poster M-P10

Anastasia Georgiadi Monday poster P-P05

Walter Glaser all days organization O

Miguel Godinho Sunday poster L-P07

Martin Golebiewski Wednesday poster P-P06

Igor Goryanin Su, Mo, We computer practical CP-03

Bettina Greese Sunday poster P-P07

Sergio Grimbs Wednesday poster T-P09

Willemijn Groenendaal Sunday poster T-P10

Mika Gustafsson Monday poster P-P08

Jurgen R. Haanstra Monday poster L-P08

Niclas T. Hansen Monday poster T-P11

Feng He Wednesday poster P-P09

Stefan Hengl Wednesday poster T-P12

Adriano Henney Sunday lecturer P-L02

José Oscar Hernández Sendín

Sunday poster T-P13

Jannie Hofmeyr Sunday didactic lecture P-L01

Stephan Hohmann Monday short talk Y-S03

Leory Hood Saturday Opening lecture OL-01

Papapit Ingkasuwan Sunday poster P-P10

Sergii Ivakhno Monday poster M-P11

Jeroen A.L. Jeneson Su, Mo, We blackboard BB-05

Paula Jouhten Sunday poster Y-P10

Helmut Jungwirth all days organization O

Peter Juvan Monday poster T-P14

Daniel Kahn Thursday short talk L-S03

Saowalak Kalapanulak Wednesday poster T-P15

Shichina Kannambath Wednesday poster L-P09

Orsolya Kapuy Monday poster Y-P11

Sabrina S Khaliq Sunday poster L-P10

Tom Kirkwood Thursday closing lecture CL-01

Hiraoki Kitano Thursday lecture T-L03

Regina Klaus all days organization O

Roelco Kleijn Wednesday poster Y-P12

Ursula Klingmüller Tuesday didactic lecture M-L01

Edda Klipp Su, Mo, We chair/blackboard Ch-P/BB-02

Beate Knoke Monday poster P-P11

Heinz Koeppl Wednesday poster P-P12

Bente Kofahl Wednesday poster M-P12

Jukka Kohonen Sunday poster T-P16

Alexey Kolodkin Sunday poster P-P13

Oliver Kotte Monday poster P-P14

Carsten Kriebitzsch Sunday poster M-P13

Karl Kuchler Thursday chair Ch-Closing

Ursula Kummer Su, Mo, We computer practical CP-01

Nathalie Landstetter Monday poster L-P11

Ho-Joon F. Lee Sunday poster Y-P13

Wolfram Liebermeister Monday poster T-P17

Willem P. A. Ligtenberg Wednesday poster T-P18

Linda Lövdok Wednesday poster P-P18

Alan Lauffenburger Tuesday lecture M-L03

Paul K. Maciejewski Thursday short talk T-S01

Mads F. Madsen Wednesday poster L-P12

Thomas Maiwald Sunday poster T-P19



Christiaan J. Malherbe Monday poster Y-P14

Eduard M. Mateescu Sunday poster L-P13

Hans Meinhardt Sa, Su, Mo,

We lecture/blackboard OL-01, BB-03

Julien Modolo Monday poster T-P20

Francis Molino Monday poster M-P14

Patrice Mollard Wednesday poster M-P29

Erik Mosekilde Thursday didactic lecture/chair T-L01/Ch-T

Ettore Murabito Monday poster L-P14

Maria Nardelli all days organization O

Nuno Nene Wednesday poster T-P21

Peter J. Nickel Sunday poster M-P16

Jens Nielsen Monday lecture/chair Y-L03/Ch-Y

Thomas Nittke Monday poster M-P17

Bela Novak Tuesday lecture M-L02

Jun Ohta Sunday poster T-P28

Roberto Olivares Wednesday poster Y-P15

Steve Oliver Monday lecture Y-L02

Ivan Orlandi Sunday poster Y-P16

Kiran Raosaheb Patil Sunday poster P-P16

Johannes H.G.M. Paulsson Sunday lecture P-L03

Elzbieta Petelenz Monday poster Y-P17

Ion Petre Sunday poster P-P25

Benjamin Pfeuty Wednesday poster L-P15

Esa Pitkänen Wednesday poster Y-P18

Peter Pivonka Wednesday poster M-P18

Robert Platt Monday poster P-P16

Samrina Rehman Monday poster L-P17

Benjamin Ribba Wednesday poster L-P18

Orlando Rocha Sunday poster T-P22

Pedro Rocha Sunday poster M-P19

Martin Rühl all days organization O

Katja N. Rybakova Monday poster M-P20

Julio Saez-Rodriguez Wednesday poster M-P21

Sven Sahle Monday poster T-P23

Treenut Saithong Sunday poster L-P19

Uwe Sauer Su, Mo, We,

Th chair/blackboard BB-06/Ch-T

Reinhold Schäfer Wednesday poster M-P30

Marcel Schilling Sunday poster M-P22

Johannes Schlöder Su, Mo, We blackboard BB-07

Bernhard Schmierer Monday poster M-P23

Falk Schubert Sunday poster Y-P19

Robert Schuetz Mo, Th short talk/poster L-S01/L-P20

Matthias Seeger Wednesday poster T-P24

Alex Shaw Wednesday poster L-P21

Guy Shinar Su, Mo, We blackboard BB-04

Bettina Siebers Sunday poster P-P26

Naomi Siew Sunday poster/short talk P-P19/P-S01

Oliver Slaby Sunday poster L-P22

Jacky Snoep Su, Mo, We computer practical CP-02

Anna Slavokhotova Monday poster L-P23

Anatoly Sorokin Su, Mo, We poster/comp practical L-P24/CP-03

Egils Stalidzans Sunday poster T-P25

Maike Stam Wednesday poster L-P28

Jaroslav Stark Thursday lecture T-L02

Florian Steinke Monday poster P-P20


18

Ralf Steuer Sunday poster P-P28

Tom Sumner Wednesday poster M-P24

Neil Swainston Monday poster Y-P20

Jens Timmer Tuesday didactic lecture M-L01

Julia Tischler Wednesday poster P-P21

Alexander Tournier Sunday poster M-P25

Jannis Uhlendorf Wednesday poster Y-P21

Najl Valeyev Sunday poster P-P22

Johannes H.G.M. van Beek Wednesday short talk M-S02

Jeroen Bastiaan van der Steen

Sunday poster L-P25

Hans van Leeuwen Tuesday chair Ch-M

Natal A.W. van Riel Su, Mo, We blackboard BB-05

Pedro Veliça Monday poster M-P26

Ilya Venger Sunday poster Y-P22

Todor Vujasinovic Wednesday short talk M-S01

Steffen Waldherr Monday poster T-P26

Christian Waltermann Monday poster Y-P23

Andreas Weidemann Monday poster P-P23

Hans V. Westerhoff Sa, Su, Mo,

We chair/blackboard Ch-Opening/BB-01

Jennifer Withers Monday poster L-P26

Jana Wolf Wednesday poster P-P24

Shu Ye Sunday poster P-T29

Tetsuya Yomo Sunday short talk/poster P-S02/P-P27

Esra Yucel Wednesday poster Y-P24

Theresa Yuraszeck Sunday poster Y-P25

Jie Zhang Monday poster Y-P26

Zhike Zi Wednesday poster M-P27

Sandra Zinke Wednesday poster Y-P27

Guy E. Zinman Wednesday poster T-P27

P - poster, S - short talk, Ch - chair, BB - blackboard, O - organization, L - lecture, CP-computer practical; sessions: P-principles, L-life, T-tools, Y-yeast, M- mammalian



The Course Book - its Principles

Abstracts

All scientists present at the Course have been asked to formulate an abstract concenring their work or their interests in Systems Biology, even those that are too new to the field to have much to report on Systems Biology itself. Most have complied. Accordingly the abstracts vary widely in content and quality. Constructive criticism will be formulated for all student abstracts, and it is in this constructive mode that all discussions should proceed; after all this is a Course, not just a conference. Please note that all abstracts, posters as well as oral presentations, must be considered “privileged personal communications”. No data may be cited or used in any kind of verbal or written scientific correspondence with third parties without explicit permission of the presenting author.

Course (‘Abstract’) Book - Paper

The Course book on paper is meant to serve as an in-hand tool at the course. It contains: - Most Course information - A list of when each participant has to present her/his work, or fulfill some other function - The program, described linearly in time, with all presentations represented by their

authors and titles - Abstracts:

o first the abstracts of the oral presentations in the sequence of the (day-time) program

o Then the abstracts of the poster presentations (including the ones also presented as short talks), ordered per Symposium, then per type and then alphabetically.

Abstracts have been giving codes. The first letter refers to the symposium (P, Y, M, L, T; for

PPPrinciples, YYYeast, MMMammalian System Biology, Towards LLLife, and TTTools and Methods, respectively). The second letter denotes the type of presentation (OL for opening lectuire, L for lecture, CL for closing lecture, S for short talk, P for poster, BB for Black Board, and CP for computer practical). Then a sequence number follows. For instance P-P22 refers to poster number 22 in the Symposium on Principles. - a list of addresses

Course (‘Abstract’) Book - Electronic

The Course book can also be found as a pdf file on the USB stick provided. The file should be considered non-citable ‘preprints’. The program will also be published on the world wide web (www.FEBSsysbio.net and http://www.univie.ac.at/sysbio2007/ ).

Systems Biology Young Investigator Awards

The scientific merit of all abstracts (posters and oral presentations) submitted by graduate students and postdoctoral researchers as presenting authors will be evaluated by the teachers in the corresponding symposium. The best abstracts will be awarded a surprise prize, the "Gosau Young Investigator Award" during the Farewell Party.

Web Site

The course and a set of related activities share a website (www.FEBSsysbio.net ), which will remain live before, during and long after the meeting. The meeting itself has a more dedicated website http://www.univie.ac.at/sysbio2007/ as well. Either website can be checked using the wireless network in many areas of the hotel, and using any of the host


20

computers in the computer rooms. The abstract book can also be found as a pdf file on the USB stick provided. The poster file should be considered a non-citable ‘preprint’. The program will also be published on the web sites.

Technical Local Information

We wish you a very pleasant stay at the venue of the 1st FEBS Advanced Lecture Course on Systems Biology in Gosau. We need to draw your attention to the following points:

Connections – You and the World

The meeting office has a laser printer, a copy machine, as well as phone (+43-6136-8811-390) and FAX (+43-6136-8811-352). Its mobile phone numbers are: +43 676 584 2185 (Regina Klaus) and +31 6 520 76 384 (Anneke Koster). Any incoming FAX and phone call should clearly identify the addressee. You may not want to use the expensive phone in your hotel room, unless you have a calling card. When available, you can use our phone/FAX machine at regular post office-rates. At the venue, you can be reached, for urgent matters only, at the following e-mail address: [email protected] , identifying the addressee by having: ‘Urgent e-mail for xxx’ on the subject line. For non-urgent matters use www.mail2web.com to inspect your own e-mail account, or use www.hotmail.com. At many locations in the hotel there is wireless internet. Please refrain from downloading gigabytes; as the width of the broadband to the outside worlds is limited; there is too many Alps in the way… Computers, some of which are linked to the internet, are available close to/in the computer rooms.

Internet – You and the World

A local network will be set up for the course. Because of limited connectivity with the outside world, we cannot guarantee its performance when used for that, unless our course attendees refrain from downloading large files.

Departure

Regular departure from the course is Friday morning after breakfast. At the message board near the Meeting Office there is a ‘Departure sheet’ which contains your name. Please be so kind to write the date and time of departure you request next to your name. The organizers will ‘OK’ your name, when they ensured transportation for you to Salzburg airport/train station. Please allow 90 minutes for the transportation from the hotel to the airport (and then of course more than 60 minutes for boarding the flight).

FEBS Evaluation Form

Most importantly, the FEBS EVALUATION FORM! Please complete and return the lilac FEBS Evaluation Form you will find in your Meeting Pack to the meeting office no later than Thursday, March 17. Any and all criticisms (both positive and negative) are highly appreciated, because we are aware that nothing in this world can be perfect, but many things can be improved. It is imperative that we receive feedback from as many participants as possible (the best of course would be from all of you). Think about it, no return of evaluation forms - no more FEBS Courses on Systems Biology in the future, and, lack of gratitude to FEBS for sponsoring so much of the present course.

FEBS-SysBio2005 Course Office

The meeting office is located in the basement of the Sport & Erlebnis Hotel**** (please follow the signs). If you need help in any way, please contact the meeting office ((+43-6136-8811-390; do not contact the hotel



reception desk, please) or call the 24-hour FEBS-SysBio2005 hotline (+43 676 584 2185 (Regina Klaus) or +31 6 520 76 384 (Anneke Koster)). Daily office hours are in the morning from 7.30 – 8.30 am, at noon from 12.00 – 13.00 hours and in the evening from 7.30 – 9.00 pm.

Help

Any member of the local organizing staff, who wears FEBSSYSBIO2007 neck cords, will try to help you anytime with any problem you may encounter. Alternatively, turn to the Meeting Office, or call the hotline phones +43 676 584 2185 (Regina Klaus) and +31 6 520 76 384 (Anneke Koster)

Message Board

Next to the Meeting Office there is a board for messages.

Meals, Beverages & Lunch Packages

Your registration fee includes all meals (breakfast, coffee and tea during the program’s tea and coffee breaks, lunch, and dinner) and some non-alcoholic beverages at lunch, dinner and in the poster halls during the poster sessions. Other beverages consumed during lunch and dinner, are not included. For technical reasons, you cannot charge your beverages to your room: You must pay for your beverages at the table in cash in €uros. All beverages and drinks at the Welcome Party (thanks to FEBS Journal; please promise to submit at least one paper to this journal this year) and the Farewell Banquet, and many at the Poster sessions are free of charge. If you intend to hit the slopes or otherwise go out early for the afternoon break, you may wish to take a lunch package with you, rather than to eat lunch in the restaurant. You must then pick up a “Lunch Ticket” at the meeting office. Each day has a different color-coded Lunch Ticket with your name on it. You can pick up your Lunch Ticket at the meeting office for any day of the week during regular office hours, at the latest the day before consumption. IMPORTANT, should you for whatever reason not consume your lunch package, you cannot have regular lunch instead on the same day, because the kitchen prepares a limited number of meals, based on the number of meeting participants. Lunch packages themselves can be picked up in the HOTEL BAR around noon time in exchange for YOUR LUNCH TICKET for that day.

Payments

Any substantial payment to the course organization must have been made by giro/bank transfer before the course (cf. www.febssysbio.net ff.). Reimbursements will follow the same route. The course currency is euros. We accept cash (€UR/US$/UK£,JP¥) at current exchange rates (plus exchange cost) we obtain through the www (no credit cards). A bank and a cash machine are located on the main road in the nearby village. Banks are open from 8 AM-12 AM and 2 AM to 5 AM in the afternoon (Mon-Fri).

Presentations

Oral presentations: All participants giving oral presentations are requested to be present in the lecture hall half an hour before their session starts (i.e. at 8.00 a.m. for talks in the morning and at 16h00 for talks in the afternoon; a member of the organizing committee will assist you). We prefer your files (i.e. Powerpoint) as a directory called ‘’yournameSBcourse’ [e.g. WesterhoffSBcourse] on a USB stick or CD-ROM. If your presentation links to any other files (e.g. movies), these should be in a single directory as the presentation with appropriate links. After copying the directory with your name to the hard disk of either of the two presentation computers in the lecture Hall (i.e. a MacIntosh Powerbook or a PC Laptop), you should check whether your presentation and its links actually function. Alternatively, you may connect your own computer to the LCD projector for your talk, but only if you have checked this with the assistant, half an hour in advance.


22

You can use the computers in the computer rooms and near the Meeting Office to check your presentation beforehand. In case of a presentation that uses media other than LCD projection from computer, please inform the organizers well in advance: [email protected] . Posters: Course participants presenting Posters (including presenters of Short Talks) are requested to mount their posters in the dedicated poster areas on the poster board with their poster number (follow the signs) on Saturday evening. Your poster number is identical to the number you will find in the Course book next to the title of your abstract, in the Course book in the address list next to your name, and in the task list in the Course book (e.g. P-P04) (a Poster number always has a ‘P’ for ‘Poster’, or an ‘S’ for ‘Short Talk’ subsequent to the hyphen). Tape and/or pins must NOT be used to mount posters placed behind acrylic glass. If necessary, members of the organizing committee will help you mounting your poster on paper sheets first. For all other poster walls, pins are provided and local organizers will be pleased to assist you if necessary. Posters will stay on display until the evening of Thursday, March 15. The presenting authors needs to be present for at least one hour at the beginning of their poster session. Poster numbers n-2 will be presented / analyzed / discussed Sunday evening from 21h00 for at least an hour. Numbers 3n-1 will be presented / analyzed / discussed Monday evening. Numbers 3n-3 will be presented/analyzed/discussed Wednesday evening. Presenters of short talks are requested to present their poster on the day of their short talk. The dates of presentation can also be gleaned from the Participant task list in this course book (cf. above). Blackboard presentations: A data projector (beamer) will be available if necessary but please enquire with the conference office when you need them. Presenters are expected to connect their own personal computer. Flipovers will be available as well. Computer presentations: A local wireless intranet and 20 password protected portable computers wil be available, distributed over 1 or 2 parallel sessions. Anyone wishing to demonstrate a computer program, or to access e-mail or internet through these computers should first ask at the course office. Presenters of Computer Practicals should consult with the organizing committee (e.g. [email protected] ) beforehand about the software to be used, as it will need to be preinstalled.

Skiing and Outdoor Leasure

A daily bus shuttle to the “Hornspitzbahn” organized by FEBSSysBio2007 will leave the hotel 20 minutes after the last morning lecture. The return shuttle from the "Hornspitzbahn" to the Hotel will leave the "Hornspitzbahn" at 4.00 PM sharp. A schedule for the daily public ski bus, as well as a ski route map is included in your registration package. On Saturday and Sunday, you can go to the local ski school, located at the chair lift of the "Hornspitzbahn" for rental equipment such as alpine ski sets, snowboards and cross-country skis. If you show your FEBSSysBio2007 name badge, you will receive a discount on your rental gear. Moreover, you can sign up for skiing lessons, which usually last three to five days. We urge you to finish boot fitting and check-in as soon as possible after your registration, in order to avoid delays during the big rush on Monday.

Social Program

Salzburg. On Tuesday, we have scheduled for all course participants to visit Salzburg, the city of Mozart, with lots of surprises. Buses will leave the hotel around 13h30 (precise times to be announced) and return to the Hotel around 23h30. There will be time for walks or shopping in romantic downtown Salzburg, but there will also be a common program. As you might expect, you should not forget to bring your ears, eyes, and taste buds …… Also, be ready to discuss Systems Biology, on the bus, or in the ……….. This excursion is mandatory for all students as this is meant for networking! For before and after the meeting we recommend the following places to visit:



Bad Ischl: A trip to Bad Ischl, the favorite retreat of the one-time Austrian Emperor Franz Josef. Surrounded by spectacular scenery you can enjoy the rich leisure offered of the magnificent little town Bad Ischl, just like Franz Josef did for more than forty years.

Hallstadt: A visit to this restored centre of a Salt and Copper mining town is a thrill. Ice Cave: A visit to the “Koppenbrüller Ice Cave” leading you into the mighty Dachstein

mountain range. Due to expected snowfall, this excursion may not be available.

Sport & Erlebnis Hotel Facilities

The hotel offers an indoor pool, two saunas, steam bath, gym, whirl pool, and solarium at no extra charge to the Course participants. Solarium and whirl pool take tokens that are available free of charge at the hotel reception desk, where further information is also available. Indoor tennis courts are available for a surcharge; please enquire at the hotel reception desk.


24

Scientific Program

Saturday March 10: Opening (co-organized with AstraZeneca)

Course Registration & Hotel Check-In 11:00 am - 6:00 pm

Welcome Reception 5:30 pm - 6:15 pm

Official Course Opening 6:15 pm - 6:25 pm

Hans Westerhoff and Karl Kuchler

AAssttrraaZZeenneeccaa OOppeenniinngg LLeeccttuurree

CChhaaiirr:: HHaannss VV.. WWeesstteerrhhooffff

OOLL--0011 LLeerrooyy HHoooodd 66::3300 ppmm –– 77::3300 ppmm

MMaakkiinngg SSyysstteemmss BBiioollooggyy wwoorrkk

Welcome Dinner & Music 7:30 pm – 8:30 pm

RReeiinnhhaarrtt HHeeiinnrriicchh MMeemmoorriiaall LLeeccttuurree

CChhaaiirr:: HHaannss VV.. WWeesstteerrhhooffff

OOLL--0011 HHaannss MMeeiinnhhaarrddtt 88::3300ppmm--99::3300ppmm

MMaakkiinngg SSyysstteemmss BBiioollooggyy wwoorrkk --MMooddeellss ooff bbiioollooggiiccaall ppaatttteerrnn ffoorrmmaattiioonn:: ffrroomm eelleemmeennttaarryy sstteeppss ttoo tthhee oorrggaanniizzaattiioonn ooff eemmbbrryyoonniicc aaxxeess

Opening discussion 9:30 – 10:00 pm

Bar 10:00– :00 am



Sunday March 11: Symposium on Principles

Breakfast 7:00 - 8:30 am

rinciples of Systems Biology Lectures 8:30 am - 12:30 pm

Chair: Edda Klipp

Chairs introduction 8:30 am -8:35 am

P-L01 Jan-Hendrik S. Hofmeyr (plenary) 8:35 am - 9:20 am

The Regulatory Design of Cellular Processes:

Principles of Supply and Demand (didactic lecture)

P-L02 Adriano Henney (plenary) 9:20 am - 9:40 am

How does systems biology work in and for industry? (methodology)

P-L02 Johan Paulsson (plenary) 9:40 am - 10:00 am

Towards a coherent stochastic theory for cellular kinetics (methodology)

Coffee & Refreshment Break 10:00 am - 10:20 am

Tutorials corresponding to lectures (3 in parallel) 10:20 am – 11:05 am

Jan-Hendrik S. Hofmeyr, Adriano Henney and Johan Paulsson

Coffee & Refreshment Break 11:05 am-11:20 am

P-L02 Adriano Henney (plenary) 11:20 am - 11:40 am

How does systems biology work in and for industry? (Results)

P-L03 Johan Paulsson (plenary) 11:40am-12:00 noon

Towards a coherent stochastic theory for cellular kinetics (Results)

Chair’s Resumé and students posing issues; General discussion 12:00 noon–12:30 am

Lunch & Afternoon Break 12:30 am - 4:30 pm

Coffee & Tea 4:00 pm - 4:30 pm


26

lack Board Teaching / Computer practicals (parallel) 4:30 pm – 6:05 pm

Session 1-Sunday (parallel) 4:30 pm – 5:15 pm

BB-01- Frank J. Bruggeman and Hans V. Westerhoff 4:30 pm – 5:15 pm

Hierarchical regulation analysis of cellular adaptive responses (black board teaching)

BB-02- Edda Klipp 4:30 pm – 5:15 pm

Introduction to dynamic modeling of biochemical networks (black board teaching)

BB-03- Hans Meinhardt 4:30 pm – 5:15 pm

Model of biological pattern formation (black board teaching)

BB-04-Guy Shinar 4:30 pm – 5:15 pm

Motifs (black board teaching)

CP-01- Ursula Kummer 4:30 pm – 5:15 pm

CoPaSi (computer practical )

Coffee & Refreshment Break 5:15 pm – 5:20 pm

Session 2 - Sunday (parallel) 5:20 pm – 6:05 pm

BB-05 Jeroen Jeneson 5:20 pm – 6:05 pm

Physiological modeling (black board teaching)

BB-06-Uwe Sauer 5:20 pm – 6:05 pm

Metabolomics and Flux analysis (black board teaching)

BB-07 Johannes P. Schlöder 5:20 pm – 6:05 pm

Differential Equation Models: Parameter Estimation and Optimum Experimental Design (Black Board Teaching)

CP-02 Jacky L. Snoep 5:20 pm – 6:05 pm

Tools for Systems Biologists: using JWS Online for integration and storage of data and models (Computer Practicals)

CP-03-Igor Goryanin and Anatoly Sorokin 5:20 pm – 6:05 pm

Edinburgh Pathway Editor (Computer Practicals)




rinciples of Systems Biology Short Talks and discussion (plenary) 6:20 pm – 7:05 pm

P-S01 Naomi Siew (plenary) 06:20 pm -06:35 pm

Shedding Light on the ORFan Puzzle (Short Talk)

P-S02 Tetsuya Yomo (plenary) 06:35 pm- 06:50 pm

Adaptive response of a gene network to environmental changes by fitness-induced attractor selection (Short Talk)

P-S03 Frank J Bruggeman (plenary) 06:50pm–07:05 pm

Analysis of noise in a detailed kinetic model of an operon (glnALG) activated by two-component signal transduction (NRI/NRII) (Short Talk)

Speaker’s Panel addressing issues raised in the morning 07:05 pm – 07:25 pm

Dinner 7:30 - 9:00 pm

Poster Session 1 9:00 - 11:00 pm

Viewing posters 9:00 - 9:45pm

Free poster wandering 9:45 – 10:30pm

Round table poster discussion (presenters and teachers only) 10:30 – 11:00pm

Today’s (Sunday’s) Poster Presentations:

Principles of Systems Biology P-P01 A kinetic model for peptide-induced leakage from cells August Andersson, Jens Danielsson, Lena Mäler & Astrid Gräslund

P-P04 Autoregulation of cortisol action and differentiation in human bone cells Marco Eijken, Ksenija Drabek, Katja Rybakova, Alexey Kolodkin, Frank Bruggeman, Hans V.

Westerhoff, Huib Pols & Hans van Leeuwen

P-P07 Pattern formation in plant development Bettina Greese, Jens Timmer, Martin Hülskamp & Christian Fleck

P-P10 Inferring the starch-regulating gene network in Arabidopsis thaliana Papapit Ingkasuwan, Stijn Meganck, Supapon Cheevadhanarak, Supatcharee Netrphan, Asawin Meechai, Sukon Prasitwattanaseree, Jeerayut Chaijaruwanich, Morakot Tanticharoen & Sakarindr Bhumiratana

P-P13 A systems-biological approach to nuclear receptor signalling by PPARs: from model to experiment Alexey Kolodkin, Katja Rybakova, Claudia Bruedigam, Marco Eijken, Frank Bruggeman, Hans van Leeuwen, Barbara Bakker & Hans V. Westerhoff

P-P16 Transcriptional regulation evolves around conserved and metabolically related genes Kiran Raosaheb Patil, Prashant M Bapat, Ana Paula Oliveira & Jens Nielsen

P-P19 Underground metabolic routes in E. coli Naomi Siew, Yizhak Pilpel & Dan S. Tawfik

P-P22 Modeling Ca2+-calmodulin-dependent selective target activation Najl Valeyev, Nikolai Kotov, Ian Postlethwaite & Declan Bates

P-P25 no abstract Ion Petre

P-P26 Central carbohydrate metabolism of the archaeon Sulfolobus solfataricus


28

Bettina Siebers1& Christa Schleper

2

P-P27 Adaptive response of a gene network to environmental changes by fitness-induced attractor selection Tetsuya Yomo

1, Akiko Kashiwagi

1, Kunihiko Kaneko

2& Itaru Urabe

1

P-P28 Mathematical modeling of metabolic networks: From topology to dynamics of metabolic pathways

Ralf Steuer

Yeast Systems Biology Y-P01 Robustness analysis of HOG pathway related genes in Saccharomyces cerevisiae

Doryaneh Ahmadpour, Lars-Göran Ottosson, Markus Krantz, Jonas Warringer, Anders Blomberg & Stefan Hohmann

Y-P04 Microarray investigation of pre-mRNA processing David Barrass & Jean Beggs

Y-P07 Regulation of the glycerol pathway during osmotic stress Jildau Bouwman, Stanley Agbo, Alexander Lindenbergh, Karen van Eunen, Hans V. Westerhoff & Barbara M. Bakker

Y-P10 The effect of external oxygen conditions on the metabolic flux distribution of Saccharomyces cerevisiae Paula Jouhten, Eija Rintala, Anne Huuskonen, Anu Tamminen, Mervi Toivari, Marilyn Wiebe, Ari Rantanen, Laura Ruohonen, Merja Penttilä & Hannu Maaheimo

Y-P13 Systems analysis of transcriptional co-regulation of protein complexes Ho-Joon F. Lee, Tomasz Zemojtel & Martin Vingron

Y-P16 A network identification of the mitotic exit in budding yeast Saccharomyces cerevisiae Ivan Orlandi & Lilia Alberghina

Y-P19 Modeling of translational efficiency in fission yeast based on genome sequence and microarray data

Falk Schubert, Daniel H Lackner, Samuel Marguerat & Jurg Bahler

Y-P22 Robustness of Saccharomyces cerevisiae to deletion mutations and response to environmental stimuli as seen through the lens of high-throughput metabolic profiling

Ilya Venger, Ilana Rogachev, Yitzhak Pilpel & Asaph Aharoni

Y-P25 Dynamic analysis of the UPR suggests a pathway conferring down-regulation in Saccharomyces cerevisiae

Theresa Yuraszeck, David Raden, Anne Robinson & Francis J. Doyle III

Mammalian Systems Biology

M-P01 The role of Crem on circadian rhythm in the mouse model: a systems biology approach combining transcriptomics with metabolomics

Jure Acimovic, Martina Fink, Ingemar Bjorkhem, Marko Golicnik & Damjana Rozman

M-P04 Activity of the vitamin d receptor during the cell cycle Sebastiano Battaglia, James Thorne & Moray J. Campbell

M-P07 Human osteoblasts as a model to study Peroxisome Proliferator-Activated Receptor Gamma (PPARG) signaling during differentiation and proliferation using integrative systems-biology approaches Claudia Bruedigam, Marco Eijken, Alexey Kolodkin, Katja Rybakova, Marijke Koedam, Frank Bruggeman, Hans Westerhoff, Huib Pols & Hans van Leeuwen

M-P10 Setting the framework for large scale system biology: The integration of human protein interactome

Matthias E. Futschik, Gautam Chaurasia, Erich Wanker & Hanspeter Herzel

M-P13 Gene expression profiling in Vitamin D3 treated MC3T3-E1 mouse osteoblasts. Carsten Kriebitzsch, Lieve Verlinden, Guy Eelen, Roger Bouillon & Mieke Verstuyf

M-P16 Dynamic modeling of dual negative feedback regulation of TGFbeta-SMAD signaling in primary hepatocytes Peter J. Nickel, Thomas Maiwald, Stefan Legewie, Patricio Godoy, Sebastian Bohl, Thomas Frahm, Steven Dooley, Hanspeter Herzel, Jens Timmer

& Ursula Klingmüller

M-P19 Analysis of murine models with tissue-specific nuclear receptor deficiency using systems biology approaches

Pedro Rocha, Heiner Schrewe & Chris Bunce



M-P22 Erythroid progenitor cell development elucidated by a dynamic pathway model of MAP-kinase signaling

Marcel Schilling, Thomas Maiwald, Jens Timmer & Ursula Klingmüller

M-P25 A mathematical model of Smad nucleocytoplasmic shuttling Alexander Tournier, Bernhard Schmierer, Paul A. Bates & Caroline S. Hill

Towards Life:

Principles and studies of simpler systems L-P01 Regulation at the RNA level Ilka Maria Axmann, Dennis Diens & Annegret Wilde

L-P04 Integration of signal transduction and firing behavior in neurons by means of multiscale modeling

Dirk Fey, Rajanikanth Vadigepalli, Thomas Sauter & James Schwaber

L-P07 Tobin - a toolbox for biochemical networks Miguel Godinho & Vitor Martins dos Santos

L-P10 Robustness of metabolic pathways leading to drug target identification. A systems biology approach

Sabrina S Khaliq

L-P13 Bacterial control of growth, and adaptation to nutritional shifts in amino acid-limiting environments

Eduard M. Mateescu & Terence Hwa

L-P16 Control of noisy networks Robert Platt, Frank Bruggeman, Herbert Sauro & Hans V. Westerhoff

L-P19 Systematic study of the Arabidopsis circadian clock and its entrained pathway (flowering) Treenut Saithong & Andrew J. Millar

L-P22 Spatiotemporal modeling of metabolic dynamics in human immune cells Oliver Slaby, Mario S. Mommer, Ursula Kummer & Dirk Lebiedz

L-P25 Photoreception in Bacillus subtilis: light activates the general stress response. Jeroen Bastiaan van der Steen, M. Avila-Perez & K.J. Hellingwerf

Tools and Methods for Systems Biology T-P01 Symbolic control analysis for cellular systems Timothy J Akhurst, Jan-Hendrik S. Hofmeyr & Johann M. Rohwer

T-P04 Predicting functional modules in Arabidopsis thaliana root hairs that drive tip growth Gordon Breen & Claire Grierson

T-P07 Database mining for systems biology with Taverna workflows and Weka Luna De Ferrari

T-P10 Mitochondrial dysfunction in type 2 diabetes: a Systems Biology approach Willemijn Groenendaal

T-P13 Multiobjective mixed-integer optimization of metabolic systems José Oscar Hernández Sendín, Oliver Exler & Julio Rodríguez Banga

T-P16 Bayesian methods for inferring protein function from diverse data Jukka Kohonen, Elja Arjas, Petri Auvinen, Jukka Corander & Sarish Talikota

T-P19 Workshop: PottersWheel – MATLAB toolbox for model creation, analysis, multi- experiment fitting and experimental design

Thomas Maiwald, Marcel Schilling, Ursula Klingmüller & Jens Timmer

T-P22 Modeling and simulation of fructo-oligosaccharides production Orlando Rocha, Ana Domingues, Clarisse Nobre, Duarte Torres, Lígia Rodrigues, José Teixeira, Isabel Rocha & Eugénio Ferreira

T-P25 Stochastic and modular approach in cellular modeling Egils Stalidzans

T-P28 Connectivity matrix method and atom mapping matrices Jun Ohta

T-P29 No abstract Shu Ye


30

Monday March 12: Symposium on Yeast (with YSBN)


east Lectures 8:30 am - 12:30 pm

Chair: Lilia Albergina

Co-chair: Jens Nielsen

Chairs introduction (plenary) 8:30 am - 8:35 am

Y-L01-Barbara Bakker (plenary) 8:35 am - 9:20 am

Vertical Genomics (didactic lecture)

Y-L02-Steve Oliver (plenary) 9:20 am - 9:40 am

How to deal with the complexity of a ‘simple’ eukaryotic cell. (Methodology)

Y-L03-Jens Nielsen (plenary) 9:40 am - 10:00 am

Metabolic networks and fluxes. (Methodology)


Tutorials corresponding to lectures (3 in parallel) 10:20 am–11:05 am

Barbara Bakker, Steve Oliver and Jeans Nielsen


Y -L02- Steve Oliver (plenary) 11:20 am – 11:40 am

How to deal with the complexity of a ‘simple’ eukaryotic cell. (results)

Y-L03- Jens Nielsen (plenary) 11:40 am – 12:00 am

Metabolic networks and fluxes. (Results)

Chair’s Resumé and students posing issues. General discussion. 12:00 noon – 12:30 am





lack Board Teaching / Computer practical

Session 1-Monday (parallel) 4:30 pm – 6:05 pm

BB-01- Frank J Bruggeman and Hans V. Westerhoff 4:30 pm – 5:15 pm

Hierarchical Regulation Analysis of Cellular Adaptive Responses (black board teaching)


Introduction to Dynamic Modeling of Biochemical Networks (black board teaching)


Models of biological pattern formation (black board teaching)


Motifs (black board teaching)


CoPaSi (computer practical)


Session 2 – Monday (parallel) 5:20 pm – 6:05 pm

BB-05 Jeroen A.L. Jeneson 5:20 pm – 6:05 pm

Physiological modeling (Black Board Teaching)


Flux analysis (Black Board Teaching)





CP-03- Igor Goryanin and Anatoly Sorokin 5:20 pm – 6:05 pm

Edinburgh Pathway editor (Computer Practicals)

Coffee & Refreshment Break 06:05 pm - 06:20 pm


32

east Short Talks and discussion (plenary) 06:20pm-07:05pm

Y-S01- Matteo Barberis (plenary) 06:20 pm -06:35 pm

Cell size at S phase initiation: an emergent property of the G1/S network (Short Talk)

Y-S02 Juerg Baehler (plenary) 06:35 pm -06:50 pm

A Highly Connected Network of Multiple Regulatory Layers Shapes Gene Expression in Fission Yeast (Short Talk)

Y-S03- Stefan Hohmann (plenary) 06:50 pm -07:05 pm

Systems analysis of the yeast Snf1 pathway (Short Talk)

Speaker’s Panel addressing issues raised in the morning 07:05 pm – 07:25 pm

Dinner 7:30 - 9:00 pm


Viewing posters 9:00 - 9:45 pm

Free poster wandering 9:45 – 10:30 pm

Round table poster discussion (presenters and teachers only) 10:30 – 11:00 pm

Today’s (Monday’s) Poster Presentations

Poster session 2

Principles of Systems Biology P-P02 Analysis and function of the two PRPP synthases in Lactococcus lactis Xiao Chen, Jan Martinussen & Mogens Kilstrup

P-P05 Characterization of the role of PPARalpha in heart Anastasia Georgiadi

P-P08 Genome-wide system identification and analysis reveals stable yet flexible network dynamics in yeast

Mika Gustafsson, Michael Hörnquist, Johan Björkegren, Jesper Tegner

P-P11 Correspondence between average and steady-state levels in some nonlinear models of calcium oscillations

Beate Knoke, Marko Marhl, Matjaž Perc & Stefan Schuster

P-P14 Towards a quantitative understanding of carbon source transitions Oliver Kotte & Matthias Heinemann

P-P17 Control of noisy networks Robert Platt, Frank Bruggeman, Herbert Sauro & Hans V. Westerhoff

P-P20 Identification of gene regulatory networks by optimal experimental design in sparse linear models

Florian Steinke, Matthias Seeger & Koji Tsuda

P-P23 Database supported modelling Andreas Weidemann, Renate Kania, Ulrike Wittig, Martin Golebiewski, Olga Krebs, Saqib Mir, Sven Sahle, Ralph Gauges, Ursula Kummer & Isabel Rojas



Yeast Systems Biology Y-P02 RiboSys – systems biology of RNA metabolism in yeast Ross Alexander, David Barrass, Martin Kos, David Tollervey & Jean Beggs

Y-P05 Genome-wide comparative analysis of physiological bottlenecks in multi-subunit protein production in Pichia pastoris

Kristin Baumann, Diethard Mattanovich & Pau Ferrer

Y-P08 Expression profiling studies of the network controlling S. cerevisiae Ayça Cankorur, Duygu Dikicioğlu & Betül Kırdar

Y-P11 Mathematical model for the DNA replication checkpoint Orsolya Kapuy, Attila Csikasz-Nagy & Bela Novak

Y-P14 Systems Biology of a simple eco-system: Saccharomyces cerevisiae and Gluconobacter oxydans

Christiaan J. Malherbe, Johann M. Rohwer, Hans V. Westerhoff & Jacky L. Snoep

Y-P17 Yeast osmoregulation – quantitative approach on a single cell level Elzbieta Petelenz-Vetukuri, Emma Eriksson, Dag Hanstorp & Stefan Hohmann

Y-P20 Data Management in Yeast Systems Biology Neil Swainston, Irena Spasic, Peter Li, Giles Velarde, Steve Oliver, Douglas Kell & Norman Paton

Y-P23 Mathematical modeling of the cAMP/PKA signaling pathway in Saccharomyces cerevisiae Christian Waltermann & Edda Klipp

Y-P26 Glucose metabolism and SNF1 kinase in Saccharomyces cerevisiae Jie Zhang Y-P28 Gene interaction networks and models of cation homeostasis in Saccharomyces cerevisiae Joaquin Arino, The Translucent Consortium

Mammalian Systems Biology M-P02 Towards a nucleo/cytoplasmic model of the G1 to S transition in mammalian cells

Roberta Alfieri, Matteo Barberis, Ferdinando Chiaradonna, Daniela Gaglio, Luciano Milanesi, Marco Vanoni, Edda Klipp & Lilia Alberghina

M-P05 A Systems biological approach unveils fast, yet energy efficient, reprogramming of the MAPK signal transduction cascade Nils Blüthgen, Szymon Kielbasa, Stefan Legewie, Anja Schramme, Oleg Tschernitsa, Reinhold Schäfer, Christine Sers & Hanspeter Herzel

M-P08 Human ribosomal protein S17 inhibits splicing of its own PRE-mRNA Ksenia Cheremisina, Alexey Malygin & Galina Karpova

M-P11 Graph based clustering approach for finding communities and clusters in signaling networks

Sergii Ivakhno & Douglas Armstrong

M-P14 Stereotyped cell networks in a mammalian endocrine organ Francis Molino, Nathalie Coutry, Chrystel Lafont, Paul Le Tissier, Ian Robinson, Jacques Drouin, Philippe Thevenaz, Michael Unser & Patrice Mollard

M-P17 Potential crosstalk between VDR and PXR in regulating expression of several colonic CYP450 genes

Thomas Nittke, Enikö Kállay & Heide S. Cross

M-P20 A systems-biological approach to nuclear receptor signaling by the glucocorticoid receptor: from model to experiment. Katja N. Rybakova, Alexey N. Kholodkin, Frank J. Bruggeman, Barbara M. Bakker, Marco Eijken, Hans V. Westerhoff & Hans van Leeuwen

M-P23 A mathematical model of Smad nucleocytoplasmic shuttling Bernhard Schmierer, Alexander L. Tournier, Paul A. Bates & Caroline S. Hill

M-P26 Role of the aldoketoreductase AKR1C3 in leukaemogenesis Pedro Veliça & Christopher Bunce

Towards Life:

Principles and studies of simpler systems


34

L-P02 Dissection of the IFN-beta pathway in cervical carcinoma cell lines Anastasia Bachmann, Rainer Zawatzky & Frank Rösl

L-P05 Key determinants of abiotic stress response in Pseudomonas putida Sarah Frank, Oleg Reva, Christian Weinel & Burkhard Tümmler

L-P08 Control and regulation analysis of phoshoglycerate kinase (PGK) RNA levels in Trypanosoma brucei

Jurgen R. Haanstra, Mhairi Stewart, Hans V. Westerhoff, Christine Clayton & Barbara M. Bakker

L-P11 Global transcriptomics of genes modulated by antiviral drugs in yeast Nathalie Landstetter, Walter Glaser, Christa Gregori, Joachim Seipelt & Karl Kuchler

L-P14 An automated approach to describe biological networks in terms of functional modules Ettore Murabito

L-P17 Computability in Biology: Metabolic Networks Samrina Rehman

L-P20 Constraint-based prediction of intracellular fluxes in Escherichia coli Robert Schuetz, Lars Kuepfer & Uwe Sauer

L-P23 Plant-virus system investigation for understanding a pathogenicity mechanism and for developing new plant-virus protection methods

Anna Slavokhotova, Alexandr Shiyan & Emma Andreeva

L-P26 Research intentions for Systems Biology Jennifer Withers

Tools and Methods for Systems Biology T-P02 Optimal identification in Systems Biology: applications to cell signaling Eva Balsa-Canto, Antonio A. Alonso & Juli R. Banga

T-P05 Network of interacting reactions in metabolic networks József Bruck & Oliver Ebenhöh

T-P08 Fuzzy triplet periodicity as a footprint of coding regions evolution Felix E Frenkel & Eugene V Korotkov

T-P11 Screening the human interactome for novel disease complexes Niclas T. Hansen, Kasper Lage, Zenia M. Størling, Olof E.L. Karlberg

& Søren Brunak

T-P14 Towards ordering genes into signaling pathways on a large-scale Peter Juvan, Gad Shaulsky & Blaz Zupan

T-P17 Semantic SBML: computer-assisted construction, checking, and merging of biochemical models

Wolfram Liebermeister

T-P20 Dynamical and multiscale model of interacting populations of Izhikevich neurons: preliminary results

Julien Modolo, André Garenne, Jacques Henry & Anne Beuter

T-P23 Handling reversible reactions in stochastic simulations Sven Sahle

T-P26 Analyzing biological feedback with tools from control theory Steffen Waldherr, Thomas Eißing & Frank Allgöwer



Tuesday March 13: Symposium Mammalian (with NucSys)


ammals Lectures 8:30 am - 12:30 pm

Chair: Hans van Leeuwen


M-L01- Ursula Klingmüller and Jens Timmer (plenary) 8:35 - 9:15 am

Data based modeling and model based experimentation (didactic lecture)

M-L02- Bela Novak (plenary) 9:15 – 9:30 am

Reverse engineering of the yeast cell cycle control system (methodology)

M-L03-Douglas Lauffenburger (plenary) 9:30 – 9:45 am

Signal transduction and its constraints (methodology)

M-L04- Alan Aderem (plenary) 9:45 -10:00 am

A systems approach to dissecting immunity (methodology)

Coffee & Refreshment Break 10:00- 10:20 am

Tutorials corresponding to lectures (3 in parallel) 10:20 – 11:05 am

Coffee & Refreshment Break 11:05 - 11:20 am

M-L02-Douglas Lauffenburger (plenary) 11:20 – 11:40 am

Signal transduction and its constraints (results)

M-L03- Alan Aderem (plenary) 11:40 am – 12:00 noon

A systems approach to dissecting immunity (results)

Y-L04- Bela Novak (plenary) 12:00 noon - 12:20 pm

Reverse engineering of the yeast cell cycle control system (results)

Chair’s Resumé and students posing issues. General discussion 12:20 am – 12:45 am Excursion and lunch 1:00 pm - 11:30 pm


36

Wednesday March 14: Symposium Towards Life

Breakfast 7:00 am - 8:30 am

Towards ife Lectures 8:30 am - 12:30 pm

Chair: Marta Cascante


L-L01- Måns Ehrenberg (plenary) 8:35 am – 9:20 am

Systems biology of growing bacteria: flows, concentrations, fluctuations and control systems (didactic lecture)

L-L02- Judy Armitage (plenary) 9:20 am – 9:40 am

Nose diving into Systems Biology: Bacterial sensory networks (methodology)

L-L03- Marileen Dogterom (plenary) 9:40 am – 10:00 am

Towards macromolecular organization: assembly, forces and organization of the cytoskeleton (methodology)



Måns Ehrenberg, Judy Armitage and Marileen Dogterom

L-L02- Judy Armitage (plenary) 11:20 am–11:40 am

Nose diving into Systems Biology: Bacterial sensory networks (results)

L-L03- Marileen Dogterom (plenary) 11:40am-12:00noon

Towards macromolecular organization: assembly, forces and organization of the cytoskeleton (results)






lack Board Teaching / Computer practical (in parallel) 4:30 pm – 6:05 pm

Session 1-Wednesday (parallel) 4:30 pm – 5:15 pm

BB-01- Frank J Bruggeman and Hans V. Westerhoff 4:30 pm – 5:15 pm

Hierarchical Regulation Analysis of Cellular Adaptive Responses (Black board teaching)


Introduction to Dynamic Modeling of Biochemical Networks (Black board teaching)


Models of biological pattern formation (Black board teaching)


Motifs (Black board teaching)


CoPaSi (Computer practicals)


Session 2 –Wednesday (parallel) 5:20 pm – 6:05 pm

BB-05 Jeroen A.L. Jeneson 5:20 pm – 6:05 pm

Physiological modeling (Black Board Teaching)


Flux analysis (Black Board Teaching)





CP-03- Igor Goryanin 5:20 pm – 6:05 pm

Edinburgh Pathway Editor (Computer Practicals)

Coffee & Refreshment Break 06:05 pm-06:20 pm


38

ammals Short Talks and discussion (plenary) 06:20pm-07:05 pm

M-S01- Todor Vujasinovic (plenary) 06:20 pm -06:35 pm

Identification of new therapeutic strategies in immunology through the modeling of the Th1 lymphocyte response (Short Talk)

M-S02 Johannes H.G.M van Beek (plenary) 06:35 pm–06:50 pm

Dynamics of cardiac energy conversion: computational module for adaptation of oxidative phosphorilation to changing heartbeat rhythm (Short Talk)

M-S03- Ksenija Drabek (plenary) 06:50 pm–07:05 pm

A backbone to systems biology and multifactorial disease: systems biology of mineralization, bone formation and osteoporosis (Short Talk)

Speaker’s Panel addressing issues raised in the morning 07:05pm–07:25 pm

Dinner 7:30 - 9:00 pm


Viewing posters 9:00 - 9:45 pm

Free poster wandering 9:45 – 10:30 pm

Round table poster discussion (presenters and teachers only) 10:30 – 11:00 pm

Today’s (Wednesday’s) Poster Presentations

Poster session 3

Principles of Systems Biology P-P03 Using constraint-based modeling to estimate E. coli’s capacity for redox-biocatalysis Birgitta Ebert, Lars M. Blank, Bruno Bühler & Andreas Schmid

P-P06 SABIO-RK: a database for making biochemical kinetics accessible Martin Golebiewski, Renate Kania, Olga Krebs, Saqib Mir, Jasmin Saric, Andreas Weidemann, Ulrike Wittig & Isabel Rojas

P-P09 Discovery of a dynamic mechanism of quantitative gene regulation Feng He, Jan Buer, An-Ping Zeng & Rudi Balling

P-P12 Robustness analysis of the heat shock response in Escherichia coli Heinz Koeppl, Susanne Schindler & Elham Kashefi

P-P15 Gene expression noise in motility and chemotaxis of E. coli. Linda Lövdok & Victor Sourjik

P-P18 A new Bacillus thuringiensis strain isolated in Tunisia is highly toxic to Lepidopteron larvae Imen Saadaoui, Souad Rouis, Houda Boukriss K. & Samir Jaoua

P-P21 Systematic investigation of the evolutionary conservation of genetic interactions using combinatorial RNAi in C. elegans



Julia Tischler, Ben Lehner & Andrew Fraser

P-P24 Analysing the robustness of cellular rhythms: from gene-regulatory to metabolic oscillations Jana Wolf

Yeast Systems Biology Y-P03 Cell size at S phase initiation: an emergent property of the G1/S network Matteo Barberis, Edda Klipp, Marco Vanoni & Lilia Alberghina

Y-P06 Computer analysis of xylose and arabinose pathways introduced in Saccharomyces cerevisiae for optimization of the co-utilization of glucose, xylose and arabinose for ethanol production

Basti Bergdahl, Bärbel Hahn-Hägerdal & Fernando Araripe Torres

Y-P09 Modeling PDC1 and PDC5 expression as a function of thiamine availability in the yeast S. cerevisiae

Abraham Ericsson, Dominik Mojzita, Henning Schmidt & Stefan Hohmann

Y-P12 Metabolic flux analysis of a glycerol-overproducing Saccharomyces cerevisiae strain based on GC-MS, LC-MS and 2D [13C, 1H] COSY NMR derived 13C-labeling data Roelco Kleijn, Jan-Maarten Geertman, Beckley Nfor, Dick Schipper, Cor Ras, Jack Pronk, Joseph Heijnen, Ton van Maris & Wouter van Winden

Y-P15 Systems view of protein biosynthesis in Saccharomyces cerevisiae Roberto Olivares, Kiran Patil & Jens Nielsen

Y-P18 Reconstructing structurally feasible metabolic networks Esa Pitkänen, Antti Tani, Ari Rantanen, Paula Jouhten, Juho Rousu & Esko Ukkonen

Y-P21 Development of a mathematical model for the occupancy of mRNA with ribosomes in Saccharomyces cerevisiae

Jannis Uhlendorf & Edda Klipp

Y-P24 Investigation of ceramides in wild type and deletion mutants of Saccharomyces cerevisiae Esra Yucel & Kutlu Ulgen

Y-P27 Metabolic flux analysis of Pichia pastoris using stable isotopes and NMR techniques: a baseline study for metabolic engineering

Sandra Zinke & Pau Ferrer

Mammalian Systems Biology

M-P03 Spatial modeling of the endothelial cell biochemical response to shear stress Richard John Allen, Tae Yoon Kim, David Bogle, Roger Kamm & Anne Ridley

M-P06 Adaptation and regulation of the gp130-JAK1-STAT3 signaling pathway in primary hepatocytes

Sebastian Bohl, Thomas Maiwald, Thomas Frahm, Jens Timmer & Ursula Klingmüller

M-P09 The system of pyruvate dehydrogenase kinases and PPAR signaling Tatjana Degenhardt & Carsten Carlberg

M-P12 Mathematical modeling of the Wnt/beta-catenin pathway Bente Kofahl, Gebhardt Rolf, Wolf Jana & Heinrich Reinhart

†

M-P15 Poster withdrawn M-P18 Towards a mathematical description of bone remodeling

Peter Pivonka, David Smith, Bruce Gardiner, Jonathan Gooi, Natalie Sims & Colin Dunstan

M-P21 Structural Analysis of Signal Transduction Networks: T-Cell-Receptor-Induced Signaling as a Case Study Julio Saez-Rodriguez, Luca Simeoni, Jonathan Lindquist, Rebecca Hemenway, Ursula Bommhardt, Sebastian Mirschel, Martin Ginkel, Ernst Dieter Gilles, Burkhart Schraven & Steffen Klamt

M-P24 Computational modeling of liver glucose homeostasis Tom Sumner

M-P27 Mathematical modeling explains the control mechanism of the Smad dependent TGF-β-signaling pathway

Zhike Zi & Edda Klipp

M-P28 Light-induced chromatin modulation in Arabidopsis thaliana Paul Fransz

M-P29 Stereotyped cell networks within a mammalian endocrine organ


40

Patrice Mollard1, François Molino

1, Nathalie Coutry

1, Chrystel Lafont

1, Norbert Chauvet

1, Michael

Unser2, Philippe Thevenaz

2, Paul Le Tissier

3& Jacques Drouin

4

M-P30 Ras oncogene-driven MAPK pathway activation, nuclear targets and transformed phenotypes – a systematic study based on microarrays and RNA interference Reinhold Schäfer, Oleg Tchernitsa, Anja Schramme& Christine Sers

Towards Life: Principles and studies of simpler systems

L-P03 Regulation of pxr mediated gene expression by coactivator pgc-1a Marcin Buler, Olavi Pelkonen

& Jukka Hakkola

L-P06 Genome-wide transcriptional response of the hyperthermophilic archaeon Sulfolobus solfataricus and of its virus SSV1 to UV-treatment Sabrina Froels, Paul Gordon, Mayi Arcellana-Panlilio, Christoph Sensen & Christa Schleper

L-P09 Research prospects in Systems Biology Shichina Kannambath

L-P12 A framework for whole-body modeling Mads F. Madsen, Sune Danø & Bjørn Quistorff

L-P15 A minimal model of cell size control Benjamin Pfeuty & Kunihiko Kaneko

L-P18 From modeling gene networks to prediction of chemotherapy efficacy for colorectal cancer Benjamin Ribba, Nicolas Voirin, Jean Clairambault & Santiago Schnell

L-P21 Research Intentions for Systems Biology Alex Shaw

L-P24 No title submitted Anatoly Sorokin

L-P28 Molecular analysis of chromatin changes involved in b1 paramutation, an allele-dependent transfer of epigenetic information. Maike Stam, Max Haring, Marieke Louwers, Rechien Bader & Roel van Driel

L-P27 Analysis of temporal gene expression during Bacillus subtilis spore germination and outgrowth Stanley Brul

1, Bart.J.F. Keijser

2, Alex Ter Beek

3, Han Rauwerda

4, Frank Schuren

2, Roy Montijn

2&

Hans van der Spek5

Tools and Methods for Systems Biology T-P03 A data layout tool that associates the independent parameters of an experiment with the

high content data generated from plate reading machines Rod S.P. Benson

T-P06 Modeling networks of coupled enzymatic reactions using the total quasi-steady state approximation

Fabrizio Capuani & Andrea Ciliberto

T-P09 Parameterized kinetic modeling of metabolic networks Sergio Grimbs, Joachim Selbig, Hermann-Georg Holzhütter & Ralf Steuer

T-P12 Nonparametric bootstrap-based identifiability analysis of differential equations Stefan Hengl, Clemens Kreutz, Jens Timmer & Thomas Maiwald

T-P15 Genome-scale graphical model in metabolic level of Mycobacterium tuberculosis Saowalak Kalapanulak, Anatoly Sorokin, Hongwu Ma & Igor Goryanin

T-P18 ReConn: connecting Cytoscape to the Reactome database Willem P. A. Ligtenberg, Dragan Bosnacki & Peter A.J. Hilbers

T-P21 Epidermal growth factor receptor inhibition, emergent network effects and cell fate decision Nuno Nene, Taimur Shah & Sylvia Nagl

T-P24 Identification of gene regulatory networks by optimal experimental design in sparse linear models

Matthias Seeger, Florian Steinke & Koji Tsuda

T-P27 Degradome project: building models for intracellular protein degradation Guy E. Zinman, Thomas S. Jensen & Søren Brunak



Thursday March 15: Symposium Tools & Methods (with BioSim)


ools and Methods Lectures 8:30 am - 12:30 pm

Chair: Uwe Sauer

Co-chair: Erik Mosekilde

Chairs introduction 8:30 am-8:35 am

T-L01- Erik Mosekilde (plenary) 8:35 am -9:20 am

Nonlinear dynamics (didactic lecture)

T-L02-Jaroslav Stark (plenary) 9:20 am - 9:40 am

Modeling methods: hormones and cells (methodology)

T-L03- Hiroaki Kitano (plenary) 9:40 am - 10:00 am

Toward the theory of biological robustness and its application to drug design (methodology)



Erik Mosekilde, Jaroslav Stark and Hiroaki Kitano


T-L02-Jaroslav Stark (plenary) 11:20 am-11:40 am

Modeling methods: hormones and cells (results)

T-L03- Hiroaki Kitano (plenary) 11:40 am-12:00noon

Toward the theory of biological robustness and its application to drug design (results)


Lunch & Afternoon Break 12:30 pm - 4:30 pm



42

Tools and Towards ife Short Talks and discussion (plenary)4:30 pm – 5:45 pm

L-S01-Robert Schuetz (plenary) 4:30 pm -4:45 pm

Constraint-based prediction of intracellular fluxes in Escherichia coli (Short Talk)

L-S02- Ilka Maria Axmann (plenary) 4:45 pm -5:00 pm

Regulation at the RNA level (Short Talk)

L-S03- Daniel Kahn (plenary) 5:00 pm -5:15 pm

Towards an understanding of the interrelations between metabolic and gene regulation (Short Talk)

T-S01- Paul K. Maciejewski (plenary) 5:15 pm -5:30 pm

Systems biology to investigate biochemical pathways for metabolic functions in vivo (Short Talk)

L-S04-Takashi Nakakuki (plenary) 5:30 pm-5:45 pm

Integrative analyses of ErB receptor signaling and transcriptional network (Short Talk)

Coffee & Refreshment Break 5:45 pm-6:10 pm

General discussion 6:10 pm-6:45 pm

losing lecture

Chair: Karl Kuchler

CCLL--0011--TToomm KKiirrkkwwoooodd ((KKeeyynnoottee lleeccttuurree)) 77::0000 ppmm -- 88::0000 ppmm

SSyysstteemmss BBiioollooggyy aatt llaasstt:: aaggeeiinngg

Banquet and Farewell Party 8:00 pm - am

Presentation of “Gosau YOUNG SysBio INVESTIGATOR AWARDS” 8:30 - 8:45 pm

Marta Cascante, Lilia Alberghina

Official Course Closure 8:45 - 9:00 pm

Hans Westerhoff and Karl Kuchler



Friday March 16: The day after


Hotel Check-out and Departure 7:00 - 11:00 am

Shuttle buses to Salzburg (detailed schedule to be announced)

nd febs advanced lecture course on systems …...febssysbio2007: advanced lecture course on systems...

Documents