Tutorial & Workshop

Tutorial 01　　　Advanced Modelling with COPASI

Date & Time：October 31, 2019 9:00-13:00　　Venue：C209

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Organizers：Sven Sahle (Heidelberg University)
Frank Bergmann (Heidelberg University)
Stefan Hoops (University of Virginia)
Ursula Kummer (Heidelberg University)
Pedro Mendes (University of Connecticut)
Jürgen Pahle (Heidelberg University)
Egils Stalidzans (University of Latvia)

Synopsis：COPASI is a widely used software tool for creating, simulating and analysing models of biochemical reaction networks. It is open source free software and available for all major operating systems. Its features include deterministic and stochastic simulation, steady state analysis, stoichiometric analysis, optimisation and parameter estimation, time scale analysis, sensitivities and metabolic control analysis, Lyapunov exponents, linear noise approximation, etc.

In the workshop we will demonstrate the use of advanced features of COPASI, focusing on parameter estimation and parameter identifiability analysis, and the use of COPASI from scripting languages. For experienced users of the software, we will present an overview of new features added in the latest releases.
A special session will demonstrate an optimisation workflow, highlighting how COPASI can be integrated in third party software projects.
The developers of COPASI will also be available for the discussion of individual questions from the participants.
More information can be found on
http://denbi-modsim.de/icsb_copasi_2019

Program：9:00 – 9:50 COPASI team: Introduction and new features
10:00 – 11:50 COPASI team: Parameter estimation and identifiability analysis, using COPASI with scripting languages
12:00 – 13:00 Egils Stalidzans: Automated metabolic network optimization workflow

Other：Participants should bring their own laptops, and ideally install the software as described on
http://denbi-modsim.de/icsb_copasi_2019

Registration ：Require registration

Capacity：30, but no hard limit.

Contact information：Name: Sven Sahle
Email address: sven.sahle@bioquant.uni-heidelberg.de
*Please provide URL if you have your own registration page.
http://denbi-modsim.de/icsb_copasi_2019

Tutorial 02　　　COMBINE & de.NBI Tutorial: Modelling and Simulation Tools in Systems Biology

Date & Time：October 31, 2019 9:00-18:00　　Venue：C210

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Organizers：Martin Golebiewski
HITS gGmbH
Schloss-Wolfsbrunnenweg 35
D-69118 Heidelberg (Germany)

David Nickerson
Auckland Bioengineering Institute
University of Auckland (New Zealand)

Synopsis：Participants will learn how to set up computer models of biological systems (e.g. metabolic or signalling networks) using experimental kinetic data and how to simulate them in different systems biology platforms. Hands-on sessions, lectures and software demonstrations will be included, providing attendees with the necessary skills to access experimental kinetics data from available resources, to assemble computer models with these data, and finally to simulate the generated models using simulation tools. Also handling and exchange of biological models based on existing community standards will be demonstrated along with the basic principles of the underlying standard formats and how they support reproducible and FAIR computational modelling.

Program：This full-day tutorial will begin with short presentations introducing COMBINE, the COMBINE standards, and the tools and repositories included in the hands-on tutorials. These will be followed by hands-on sessions and software demonstrations for practical training with participants working through prepared tutorial material on specific exemplar workflows using the introduced tools and highlighting the benefits of standards and the FAIR data principles for collaborative work and for complex workflows applying more than one tool. Participants are also encouraged to bring their own questions, models, data, simulations, and workflows that they would like to seek advice or assistance from the tutors during the afternoon session. The tutorial will conclude with a short discussion round-table.

Please see http://co.mbine.org/events/tutorial2019for complete details and the tentative agenda for the day.

Other：Attendees are expected to bring their own computer for hands-on training.
In order to profit best from the offered training they should pre-install the following software:
CellDesigner: http://www.celldesigner.org
COPASI: http://www.copasi.org/
Morpheus: http://morpheus.gitlab.io/#download
Tellurium: http://tellurium.analogmachine.org

Registration：Registration is now open, please register at http://co.mbine.org/events/tutorial2019.

Capacity：40-60

Contact information：Name: Martin Golebiewski, HITS gGmbH, Heidelberg (Germany)
Email address: martin.golebiewski@h-its.org

Name: David Nickerson, Auckland Bioengineering Institute (NZ)
Email address: d.nickerson@auckland.ac.nz

Workshop Website will be available here:
http://co.mbine.org/events/tutorial2019

Workshop 01　　　Precision Network Medicine in the era of big data!

Date & Time：October 31, 2019 9:00-18:00　　Venue：Auditorium

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Session Title：Precision Network Medicine in the era of big data!

Organizer：Amitabh Sharma, Jose C. Nacher, Kwang II Goh ,Vera Pancaldi

Synopsis： Network science is having a substantial impact in various aspects of health-related research. Recently, the advent of more comprehensive personalized data has fostered the emergence of "precision medicine"; an approach that considers individual genetic and physiological characteristics, lifestyle and environment in devising personalized therapies. Such an approach benefits greatly from "big data" and network approaches at multiple levels.
This symposium will bring together these two themes of precision medicine and big data analysis at multiple levels of resolution, showcasing advances in the use of molecular networks for patient data integration as well as new approaches to disease network reconstruction and modeling.

Program：9:00　Opening Remarks

9:05　Y.-H. TAGUCHI, CHUO UNIVERSITY, JAPAN
Title: Tensor decomposition based unsupervised feature extraction applied to bioinformatics

9:35　SIMONE ECKER, UNIVERSITY COLLEGE LONDON, UK
Title: Unraveling Epigenetic and Transcriptional Variability of Human Immune Cells in Health and Disease

10:05　CONTRIBUTED TALKS (SESSION I) - SATHISH PERIYASAMY, QUEENSLANDS BRAIN INSTITUTE, AUSTRALIA
Title: A novel approach for the generation of disease specific genetic interaction data using gene-based statistical epistasis

10:35　Coffee Break

10:45　TATSUYA AKUTSU, BIOINFORMATICS CENTER, KYOTO UNIVERSITY, JAPAN
Title: Boolean Network-Based Approaches towards Precisions Medicine

11:15　HYUN UK KIM, KAIST, SOUTH KOREA
Title: Systems biology approaches to characterize pharmacological effects of drugs

11:45　JOSE NACHER, TOHO UNIVERSITY, JAPAN
Title: Controllability Methods and Convolutional Neural Network Approach for Precision Network Medicine

12:15　GOKHAN ERTAYLAN, VITO, BELGIUM
Title: What do we really mean by Health? On the way towards Precision Health

12:45　Luncheon

14:00　AMITABH SHARMA, HARVARD MEDICAL SCHOOL, USA
Title: Network Medicine: A new frontier in the study of human diseases and drug development

14:30　ANDREI ZYNOVIEV, INST. CURIE, FRANCE
Title: Intratumoral heterogeneity at single cell level

15:00　BULAT ZAGIDULLIN, UNIVERSITY OF HELSINKY
DrugComb - prediction of synergistic cancer drug combinations.

15:50　Coffee Break

16:00　VERA PANCALDI, CENTER FOR CANCER RESEARCH OF TOULOUSE (CRCT) AND BARCELONA SUPERCOMPUTING CENTER
Title: An agent-based model of immune and cancer cell interactions in the tumour micro-environment

16:30　MOHAMMAD ELATI, UNIVERSITY OF LILLE, FRANCE
Title: Cell-intrinsic core-regulatory circuits driving tumor-related phenotypes with the I3-OncoNet cycle

17:00　DEOK-SUN LEE, INHA UNIVERSITY, SOUTH KOREA
Title: Cross-species study of the robustness and evolution of metabolic networks

17:30　Closing Remarks
17:35　Session Ends

Other： If there are anything you would like the participants to prepare for your session, please list those.

Registration： Free

Capacity： 50～100

Contact information： Name: Amitabh Sharma or Jose C. Nacher
Email address:
reash@channing.harvard.edu
nacher@is.sci.toho-u.ac.jp
*Please provide URL if you have your own registration page.
http://sharmalab.bwh.harvard.edu/premed19/

Workshop 02　　　BioNetVisA: from biological network reconstruction to data visualization and analysis in molecular biology and medicine

Date & Time：October 31, 2019 9:00-18:00　　Venue：B250

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Session Title：BioNetVisA: from biological network reconstruction to data visualization and analysis in molecular biology and medicine
Website: https://bionetvisa.github.io

Organizer：Emmanuel Barillot (Institut Curie, France)
Hioraki Kitano (RIKEN Center for Integrative Medical Sciences, Japan)
Alfonso Valencia (Spanish National Bioinformatics Institute, Madrid, Spain)
Samik Ghosh (Systems Biology Institute, Tokyo, Japan)
Inna Kuperstein (Institut Curie, France)
Luis Cristobal Monraz Gomez (Institut Curie, France)
Robin Haw (Ontario Institute for Cancer Research, Canada)
Andrei Zinovyev (Institut Curie, France)
Patrick Kemmeren (Princess Maxima Center for Pediatric Oncology, Utrecht, Netherlands)

Synopsis： The goal of BioNetVisA workshop is to bring together the different actors of network biology, whether database providers, experimental biologists and clinicians involved in systems biology approaches, as well as computational biologists involved in data analysis and modeling. The participants will be exposed to the different paradigms of network biology and the latest achievements in the field. The BioNetVisA workshop also aims at identifying bottlenecks and proposing short- and long-term objectives for the community as discussing questions about accessibility of available tools for wide range of user in every-day standalone application in biological and clinical labs. In addition, the possibilities for collective efforts and future development directions will be discussed during the round table panel.

Program (speakers and allotted time) ：
Session 1: Pathway resources and maps construction in the AI era

8:50-9:00　Opening

9:00-9:25　Deriving structured representations from natural language to aid scientific discovery: Case studies from reconstructing large pathway maps
Abstract
Sucheendra Kumar Palaniappan
The Systems Biology Institute, Tokyo, Japan

9:25-9:50　Talks selected from abstracts

Session 2: AI for network-based drug discovery and repositioning

9:50-10:15　Pharma Databases Integration coupled with human curation for Drug Development/Repurposing
Abstract
Junhyung Park
3BIGS CO., LTD. Suwon, Republic of Korea

10:15-10:40　Network-based and data-driven drug discovery by machine learning
Abstract
Yoshihiro Yamanishi
Kyushu Institute of Technology, Fukuoka, Japan

10:40-11:05　Network-based knowledge for drug discovery: Application in pharmaceutical industry
Abstract
Tatsuya Ando
Takeda Pharmaceuticals, Tokyo, Japan

11:05-11:15　Break

Session 3: Cancer evolution and medical applications of systems biology

11:15-11:40　The Reconstruction of Cancer Phylogenies
Abstract
David Wedge
Big Data Institute, University of Oxford, UK

11:40-12:05　Challenges to integrating systems biology and artificial intelligence in medical applications
Abstract
Yoshiyuki Asai
Yamaguchi University, Yamaguchi, Japan

12:05-12:30　Towards Data-Integrated Medicine
Abstract
Natasa Przulj
Barcelona Supercomputing Center, Barcelona, Spain

12:30-13:00　Talks selected from abstracts

13:00-14:00　Lunch

Session 4: Big data: integration, visualization interpretation

14:00-14:25　Multi-omics and medical data integration and visualization
Abstract
Reinhard Schneider
Luxembourg Centre for Systems Biomedicine, Luxembourg

14:25-15:10　Keynote
Joint analysis of large single-cell dataset collections
Abstract
Peter Kharchenko
Harvard medical school, Boston, USA

15:10-15:35　Multiscale molecular exploration of medulloblastoma tumors
Abstract
Emmanuel Barillot
Institut Curie, Paris, France

15:35-16:00　Talks selected from abstracts

16:00-16:10　Break

Session 5: Modelling of biological and disease networks

16:10-16:35　Towards Predictive Biology: Applications and challenges of mechanistic modeling and machine learning
Abstract
Ayako Yachie
The Systems Biology Institute, Tokyo, Japan

16:35-17:00　A universal network mechanism governing heterogenous ErbB signaling dynamics
Abstract
Hiroaki Imoto
Institute for Protein Research, Osaka University, Osaka, Japan

17:00-17:15　Mapping Interactions at Genome Scale for a Specific Biological Context: A Case Study in Epithelial-Mesenchymal Transition
Abstract
Ian Overton
Queen's University Belfast, Belfast, UK

17:15-17:30　Talks selected from abstracts

17:30-18:00　Round table discussion and closing remarks

Other： If there are anything you would like the participants to prepare for your session, please list those.

Important dates
October 24　　　Abstract submission deadline Submit now!
October 25　　　Abstract acceptante notification
October 30　　　Workshop's registration deadline (no fee) Register here
October 31　　　BioNetVisA 2019

Abstract submission and registration
We invite to submit your abstract for a talk
The submission deadline is October 24, 2019
For further details, abstract submission and registration link please access https://bionetvisa.github.io

Key themes
Graphical representation of biological knowledge
Molecular interaction and pathway databases
Comprehensive signalling networks
Networks annotation and curation
High-throughput data visualization, analysis and interpretation
Multi-scale networks
Network modelling
Machine learning/Artificial Intelligence approaches in network biology
Basic research and clinical application of networks
Microbiome and networks
Single-cell data and network inference
Metabolomics and networks
Networks for drug repositioning

Description of the target audience and expected audience numbers
The workshop targets computational systems biologists, molecular and cell biologists, clinicians and a wide audience interested in update and discussion around current status of network biology, pathway databases, and related analysis tools, including visualization, statistical analysis and dynamic modelling. No computational background is required to attend the workshop.

Contact
bionetvisa@curie.fr

Registration：Require registration (no fee)
*Please delete the unnecessary choice

【Please answer followings if you choose “Require registration 】

Capacity：120

Contact information：Name: Inna Kuperstein
Email address: inna.kuperstein@curie.fr
https://bionetvisa.github.io
*Please provide URL if you have your own registration page.

Workshop 03　　　Singularity Biology: small elements change the function of the whole systems

Date & Time：October 31, 2019 9:00-14:00　　Venue：Meeting room 1

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Workshop 04　　　Trans-Omics workshop – The 3rd International Symposium for Trans-Omics –

Date & Time：October 31, 2019 14:00-18:00　　Venue：Meeting room 1

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Session Title：Trans-Omics workshop
– The 3rd International Symposium for Trans-Omics –

Organizers：Shinya Kuroda (University of Tokyo, Japan) Mariko Okada (Osaka University, Japan)
Mariko Okada (Osaka University, Japan)

Synopsis：The life system is a "trans-omic" network, consisting of interactions between numerous molecules across multi-omic layers, such as genome, transcriptome, proteome, and metabolome. Lifestyle diseases can be regarded as complex multifactorial diseases caused by breakdowns in a trans-omic network rather than breakdown of a single molecule. Due to recent advances in methods of measurements and analyses for single-omic layers, trans-omic analyses integrating multi-omic data are in state-of-the-art development. We hold this workshop to discuss new trans-omic technologies and advanced interpretation of multi-omics data.

Program（speakers and allotted time)：
14:00 ~ 14:05　Opening Remarks (5 min)
14:05 ~ 15:05　Session I (2 talks)
14:05 ~ 14:40　Matthias Heinemann (Univ. Groningen, Netherlands)
Title: Unraveling the traffic through the highways of metabolism

The metabolic fluxes in cells emerge from environmental factors and various regulatory mechanisms. Knowing these fluxes, i.e. traffic through the highways of metabolism, is key for fundamental and applied research. However, our current methods to experimentally resolve metabolic fluxes, based on 13C labeling experiments, still have a number of severe limitations. Here, I will introduce a new method to map the metabolic fluxes with unprecedented precision. In this method, we integrate metabolome, physiological and 13C labeling data with reaction stoichiometry, thermodynamic laws and constraints, using highly complex regression and sampling approaches. At this point, where we then know the metabolic fluxes, I will show results of our recent effort towards understanding the logic of the ‘traffic control system’ that governs metabolism. Specifically, I will present evidence that cellular metabolism might be constrained by the rate at which cells can dissipate Gibbs energy to the environment. This newly identified constraint has to potential to lead us to a radically new understanding of how cells function.

14:40 ~ 15:05　Mariko Okada (Osaka Univ., Japan)
Title: Analyze immune response using Omics and imaging

Gene expression is controlled by multi-omics layers. To understand gene regulatory mechanism, we analyze omics data using a mathematical model by focusing on transcription factor dynamics in B cell. Our study combined with bioinformatics and modeling and validation analysis using live cell imaging indicated that the cooperativity in enhancer regulation is important for quantitative control of target gene expression in B cell differentiation.

15:05 ~ 15:20　Coffee Break (15 min)
15:20 ~ 16:45　Session II (3 talks)
15:20 ~ 15:45　Shinpei Kawaoka (Kyoto Univ., Japan)
Title: Dissecting significance of single gene expression rhythm via enhancer genetics and multi-omics analyses

Circadian gene expression rhythm is disrupted in various diseases. We recently found that breast cancers distantly rewire hepatic circadian transcriptiome and cause a series of physiological alterations such as hepatomegaly (enlarged liver). Yet, whether the rewired circadian rhythm is a cause for physiological alterations remains unknown. To address this issue, we aimed to disrupt expression rhythm of single gene via deletion of genomic enhancers. Enhancers are non-coding genomic elements that determine spatio-temporal gene expression patterns. Enhancer deletion when properly done enables us to ablate specific gene regulation for example rhythmic expression in vivo. We successfully obtained single rhythm-deficient mice and performed multi-omics analyses on the mutant. In the talk, I would like to discuss how the deficiency of single gene expression rhythm impacts liver physiology (multi-layered network) at the gene, protein, metabolite, and phenotypic levels.

References
1) Hojo, H., Enya, S., Arai, M., Suzuki, Y., Nojiri, T., Kangawa, K., Koyama, S., and Kawaoka, S.: Oncotarget. 8(21), 34128-34140, 2017
2) Enya, S., Kawakami, K., Suzuki, Y., and Kawaoka, S.: Dis. Model Mech., 11, dmm032383, 2018
3) Hojo, M.A., Masuda, K., Hojo, H., Nagahata, K., Yasuda, K., Ohara, D., Takeuchi, Y., Hirota, K., Suzuki, Y., Kawamoto, H., Kawaoka, S.: Nat. Commun., 10, 2603, 2019

15:45 ~ 16:10　Fumio Matsuda (Osaka Univ., Japan)
Title: Trans-omic analysis of the central metabolism of Saccharomyces cerevisiae by integration of metabolome, metabolic flux, and proteome data

Introduction: In the living organisms, homeostasis of the central metabolism is maintained by coordinated regulation of the metabolic system. A failure of the metabolic homeostasis would cause severe cellular phenotypes. However, a relationship among the gene deletion, the metabolic adaptations to maintain the homeostasis, and resultant phenotypes such as slow rates of cell growth remains unclear. To address the relationship, we investigated metabolic adaptation mechanisms in the knockout strains of S. cerevisiae lacking the central metabolism-related genes.
Results and discussions: A transomics dataset including fermentation profile, intracellular metabolic flux distribution, enzyme abundance, and metabolite concentration was obtained from a wild type S. cerevisiae and 11 single-gene deletion strains. The transomics data confirmed that the ATP homeostasis was one of the core homeostasis since the ATP concentration was the least fluctuating metabolic features. The data also showed that the single gene deletion strains commonly employed two metabolic adaptation mechanisms. In pfk1Δ and gcr1Δ, ATP shortage by the malfunction of the EMP pathway was complemented by activation of the oxidative phosphorylation. In other mutant strains, their growth was voluntarily reduced to avoid metabolic imbalance such as by the Gcn4p dependent control of the cell component biosynthesis.

16:10 ~ 16:45　Jason Locasale (Duke Univ., USA)
Title: Using metabolomics and computational biology to study metabolism in health and cancer

This presentation will discuss efforts to understand glucose and amino acid metabolism in cancer biology using metabolomics approaches and mathematical modeling. First I will discuss new work on mechanisms of de novo acetate production in mammals. I will discuss work on dietary influences on the activity of metabolic pathway and relations to metabolic health and cancer. As an example, I will discuss how methionine restricted diets may allow for interventions in cancer treatment will also be discussed. This concept also provides a link between nutrient status and chromatin biology which I will briefly touch upon.

16:45 ~ 16:55　Coffee Break (10 min)
16:55 ~ 17:55　Session III (2 talks)
16:55 ~ 17:20　Katsuyuki Yugi (RIKEN, Japan)
Title: Dose-selective metabolic regulation by insulin across multiple omic layers

Insulin selectively regulates multiple cellular functions via its concentrations and temporal patterns. However, the cellular network that realizes selective responses to the insulin concentrations remains poorly understood. Here we reconstructed dose-selective networks of insulin action over multiple omic layers based on time-series measurements of phosphoproteome, transcriptome, and metabolome in rat hepatoma Fao cells stimulated by multiple insulin doses. In the reconstructed network, we identified two ‘trans-omic’ regulatory axes that respond to high and low doses of insulin in a mutually exclusive manner: a high-dose responsive ERK regulatory axis and a low-dose responsive AKT regulatory axis. High dose insulin signals were transmitted by ERK via the immediate early genes (IEG) to the upregulated genes. On the other hand, the low-dose insulin signal was transmitted by AKT to its target genes. Furthermore, we found that the ERK regulatory axis mainly regulates gene expression at the transcription level, whereas the AKT regulatory axis regulates gene expression at the translation level. This study reveals the system by which the liver cells interpret physiological insulin signals and regulate various cellular functions.

17:20 ~ 17:55　Uwe Sauer (ETH Zurich, Switzerland)
Title: Metabolic Coordination Through Metabolite-Protein Interactions

How do bacteria know what goes on in their environment and how do they make appropriate decisions? While some bona fide extracellular sensors are known, there are far more environmental conditions and cellular responses than could possibly be dealt with through dedicated sensors. Instead, most microbial responses are based on direct intracellular consequences of environmental changes. One of the first affected networks to just about any extracellular change is metabolism that passively responds to nutritional or chemical/physical challenges. Since fluxes and intracellular metabolite levels respond within seconds, allosteric binding of metabolites to regulatory proteins and enzymes is a highly effective and rapid sensing mechanism. Different from well-establish methods to assess physical interaction between proteins and between proteins and nucleic acids, however, methods to assess metabolite-protein interactions are still in their infancy. At present we know on the order of 1500 unique regulatory metabolite-protein interactions (1). Using limited proteolysis mass spectrometry (2) and NMR (3), we have recently begun to systematically map out the physical interactions space in E. coli. Even for the well-investigated central metabolism we more than doubled the known metabolite-protein interactions (3). Beyond mapping the regulation network, I will focus on the even more challenging and conceptual problem: understanding which of the many regulation mechanisms actually matter for a given adaptation to elicit an appropriate physiological response.

1. Reznik, Christodoulou, Goldford, Briars, Sauer, Segre & Noor. Cell Reports 20: 2666-2677 (2017).
2. Piazza, Kochanowski, Cappelletti, Fuhrer, Noor, Sauer & Picotti. Cell 72:358-372 (2018).
3. Diether, Nikolaev, Allain & Sauer. Molecular Systems Biology 15:e9008 (2019).

17:55 ~ 18:00　Closing Remarks (5 min)
Registration ：No registration is needed

Registration ：No registration is needed

Workshop 05　　　Qualitative computational modeling for biological networks

Date & Time：October 31, 2019 9:00-18:00　　Venue：Meeting room 3

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Session Title：Qualitative computational modeling for biological networks

Organizers：Adrien Fauré (Yamaguchi University, Japan)
Denis Thieffry (Ecole Normale Supérieure, Paris, France)

Synopsis：Interactions networks have been used to represent and study biological systems small and large, ranging from genes and metabolites all the way to ecosystems, and from a handful of components to several hundreds and more. Recent technical developments have brought new challenges to the field: more data to exploit, integrate and interpret, multi-scale modeling, larger networks and models to annotate and parametrize, analyze and simulate. Meanwhile, questions regarding fundamental properties of these systems, such as the role of motifs and circuits in the emergence of dynamical properties, are still being actively pursued. Furthermore, although qualitative approaches such as logical models and Petri nets have been used for several decades, new methods and formats and tools keep appearing, calling for the development of common standards to ensure interoperability. In this context, this workshop aims at gathering the network modeling community, sharing progress among its members, and strengthening the links within the community as a whole.

Program：

9:00-9:15　Introduction
Adrien FAURÉ (Yamaguchi)

Session 1 Regulatory circuits Chair: Takeyuki TAMURA 9h

9:15-10:00　Link between logical structure and dynamics in genetic and (bio)chemical reaction networks
Marcelline KAUFMAN (Brussels)

10:00-10:30　Circuit functionality: towards a new definition
Adrien FAURÉ (Yamaguchi)

Session 2 Signalling/regulatory networks Chair: Marcelle KAUFMAN

11:00-11:45　Petri net modelling in the context of big data omics
Ina KOCH (Frankfurt)

11:45-12:15　Computational verification of large logical models - application to the prediction of T cell response to checkpoint inhibitors
Denis THIEFFRY (Paris)

12:15-12:30　Discussion

Session 3 Hybrid and multiscale models Chair: Adrien FAURÉ

14:00-14:45　Integer linear programming-based methods for controlling Boolean metabolic networks
Takeyuki TAMURA (Kyoto)

14:45-15:15　Deciphering Yeast Physiology by a Multi‐scale Framework Integrating Cell Cycle and Metabolism
Matteo BARBERIS (Surrey)

Session 4 Tools Chair: Ina KOCH

16:15-16:45　Stochastic simulations with MaBoSS ecosystem
Vincent NOËL (Paris)

16:45-17:15　The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks
Aurélien NALDI (Paris)

17:15-17:30　Wrap-up
Denis THIEFFRY (Paris)

Workshop 06　　　KBase: free, open platform for genomics analysis of microbes, plants, and their communities.

Date & Time：October 31, 2019 9:00-12:00　　Venue：Meeting room 4

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Session Title：KBase: free, open platform for genomics analysis of microbes, plants, and their communities.

Organizers：Adam Arkin, Lawrence Berkeley National Laboratory
Bob Cottingham, Oak Ridge National Laboratory
Christopher Henry, Argonne National Laboratory

^*José P. Faria, Argonne National Laboratory
^*Janaka N. Edirisinghe, Argonne National Laboratory
^*Paramvir S. Dehal, Lawrence Berkeley National Laboratory
^*presenters

Synopsis： Please register here (free workshop)
The Department of Energy Systems Biology Knowledgebase (KBase; http://kbase.us) is a free, open-source knowledge creation and discovery environment designed for biologists and bioinformaticians. KBase integrates a variety of data and analysis tools that run on DOE compute resources, enabling scientists to perform sophisticated systems biology analyses on their own data, within the context of public data, and to share findings with other users.
KBase serves the ISSB community by providing a range of integrated biological data types and over 200 analytical tools (https://kbase.us/applist/) for microbes, plants, and their communities. This includes tools for gene expression and transcriptomics, comparative genomics, genome annotation, metabolic simulation, and visualization.

Description：

The KBase team is providing a free 3-hour workshop for a maximum of 30 participants.

The hands-on KBase workshop will cover：

Introduction to KBase Narrative Interface
Search and access to public reference data
Upload of sequencing reads in KBase (metagenome and isolates)
Quality assessment of reads
De-novo assembly of reads into contigs
Contig binning, extraction and genome annotation
Constraint-based genome-scale metabolic models for isolates and microbiomes
KBase Knowledge Engine: Exploration of relevant public data for organism of interest

Participants will be guided through a hands-on exploration of KBase’s features, tools for collaboration and data management, and how to use KBase to drive discovery in microbiome data science.

Program(speakers and allotted time)：
Presenter：José P: Faria, Argonne National Laboratory
9:00 – 9:30
Introduction to KBase and the Narrative Interface
Short break/ 5mins
Presenter： Janaka N. Edirisinghe, Argonne National Laboratory
9:35 - 10:25
Overview of KBase functionality for Isolate Genomes Analysis:

Attendees will learn how to find data and use tools for quality control and assessment of NGS reads, de novo assembly, genome annotation, and how to analyze features of genomes within KBase. Metabolic Modeling will also be introduced in this section.

Presenter： Paramvir S. Dehal, Lawrence Berkeley National Laboratory
10:30 – 11:20

Overview of KBase functionality for Microbiome and Community Analysis:

Discussion and practical sessions to educate users on the capabilities of the KBase platform for the analysis of population structure of Microbiomes, assembly of metagenomes with the recovery of genomes from environmental sequences, and comparative analysis of functional complements. It also includes model-driven prediction of species interactions within a microbiome.

Presenter： José P: Faria, Argonne National Laboratory
11:30 – 12:00
Future directions - Introduction to the Knowledge Engine:

The Knowledge Engine builds relationships between all data in the system using both biological information, such as taxonomy, and non-biological such as data provenance to find and return reference data along with public and shared user data and Narratives on system related to your organism or other areas of interest.

Additional time： Depending on demand, the KBase Team members will be available to provide additional in-person, one-on-one help for participants that show interest in getting an analysis started with their own data.

Other：Attendees can sign-up for an account ahead of the workshop here:
http://kbase.us/sign-up-for-a-kbase-account/

Registration：Free registration here

Capacity：30

Contact information：Please feel free to contact José P. Faria directly at jplfaria@anl.gov for any questions related to the workshop and email engage@kbase.us for any inquiry regarding KBase.
Sign-up for the workshop by clicking here or by copying and pasting the following URL:
https://forms.gle/zpeL27vRYqo2SBQ49

Workshop 07　　　Withdrawn

Call for Workshop & Tutorial Proposals

International Conference on Systems Biology (ICSB) is a premier conference in systems biology, organized by the International Society for Systems Biology (ISSB) and hosted by leading research institutions around the world. In previous years, ICSB was held in France (2018), USA (2017), Spain (2016) and Singapore (2015); for details, please check http://www.issb.org/conferences.html for previous meetings.
ICSB 2019 will be held in Okinawa, Japan, on Oct 31- Nov 5, 2019. We invite submissions of workshop/tutorial proposals on a broad range of topics of interest to the ISSB community. Examples of relevant topics include, but are not limited to, the following:

Methodological Developments for Systems Biology
Modeling Networks and Circuits
Multi-omics
Single-cell Systems Biology
Quantitative Systems Biology
Developmental Systems Biology
Systems Biology for Neurosciences and Neural Circuits
Systems Medicine and Healthcare
Synthetic Biology
Multiscale Systems Biology
EcoSystems Biology
Systems Biophysics
BigData, AI & Laboratory Automation
Systems Biology Consortia

Important Dates:

Proposal Submission Deadline for Workshop & Tutorial: Mar 21, 2019
Acceptance Decision: Apr 4, 2019
Workshop & Tutorial Date: Oct 31, 2019

Submission Process:

Each workshop/tutorial proposal should include the following information:
- The title of the workshop/tutorial
- Names and affiliations of main organizers
- Motivation and rationale for the workshop/tutorial
- Proposed workshop/tutorial length
- A description of the workshop/tutorial format
- A detailed timeline for inviting and accepting papers and presenters for the workshop/tutorial should be presented
- A detailed list of the equipment required for the workshop/tutorial
- Any other relevant information to your proposal workshop/tutorial
Each workshop/tutorial proposal can be up to 2 pages (11pt Times New Roman, single line spacing, 1” page margins on all sides, PDF format).
The proposal should be submitted to the secretariat (icsb2019@aeplan.co.jp) of the conference on or before Mar 21, 2019.
Notification of workshop/tutorial acceptance will be sent out by Apr 4, 2019.
For further questions, please contact the secretariat (icsb2019@aeplan.co.jp).

General information for ICSB 2019:

Date: Oct 31- Nov 5, 2019
Venue: Okinawa Institute of Science and Technology Graduate University (OIST)
https://www.oist.jp/access-map
Tentative Program

Tutorial & Workshop

Call for Workshop & Tutorial Proposals

Important Dates:

Submission Process:

General information for ICSB 2019:

Secretariat