ICSB 2017: INTERNATIONAL CONFERENCE ON SYSTEMS BIOLOGY 2017
PROGRAM FOR SUNDAY, AUGUST 6TH
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08:00-17:00 Session : Registration
Location: Williamsburg Room
09:00-18:00 Session 1A: Tutorial: COMBINE Tutorial - Modelling and Simulation Tools in Systems Biology

For more details, please see

http://co.mbine.org/events/tutorial2017 

Location: Brush Mountain A & B
09:00
COMBINE Tutorial - Modelling and Simulation Tools in Systems Biology

ABSTRACT. 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.

Topics: 

  • Model setup using different software tools and systems biology platforms 
  • Using experimental data for setting up quantitative models 
  • Parameter estimation, optimization and model fitting 
  • Simulation, analysis and visualization of biochemical models 
  • Database supported modelling: integrated data management and model databases 
  • Community standards and formats for systems biology models

Target audience: 

Experimentalists and modellers with some very basic experience in modelling and simulation of biological networks and everybody who would like to learn more about the tools and standards. Attendees are expected to bring their own computer for hands-on training.

Covered tools, platforms and databases: 

Introduced standard formats: 

Some commonly used community standards for model and modelling data exchange, as well as for model visualization will be introduced (SBGN, SBML and SED-ML) in practical examples using the covered tools. More information about the standards can be found on the COMBINE (Computational Modeling in Biology Network) website: http://co.mbine.org

 

Tutors: 

09:00-18:00 Session 1B: Tutorial: Metabolic flux modeling and computer aided strain design with cobrapy, cameo and DD-DeCaF
Location: Colonial Hall
09:00
Tutorial: Metabolic flux modeling and computer aided strain design with cobrapy, cameo and DD-DeCaF

ABSTRACT. Good software is essential for most modern systems biology applications. Part of the growing cobrapy community, the freely available Python packages cobrapy, cameo and escher together implement numerous popular visualization, analysis and simulation methods for metabolic flux models, as well as search and optimization algorithms for designing novel pathways.

The cobrapy software collection lays a stable foundation for constraints-based modeling and strain design using a popular language that additionally boasts a wide array of packages for data handling, visualization and application development. In this full-day tutorial, we first give an introduction to the web-based graphical interface that is based on these packages, the data-driven design of cell factories and communities platform (DD-DeCaF), and then proceed to provide programming examples using the Jupyter notebook. Participants of all backgrounds are welcome, prior programming experience is not required.

09:00-18:00 Session 1C: Workshop: The PATRIC bioinformatics resource center for omic data analysis
Location: Old Dominion Ballroom
09:00
The PATRIC bioinformatics resource center for omic data analysis

ABSTRACT. Resource Center (BRC) (https://www.patricbrc.org). PATRIC provides a necessary “first-step” for any Systems Biology or Omics data exploration. Established by the National Institute of Allergy and Infectious Diseases (NIAID) in 2004, PATRIC provides researchers with an online resource that stores and integrates a variety of data types—e.g. genomics, transcriptomics, protein–protein interactions, 3D protein structures and sequence typing data, and associated metadata. Currently, PATRIC has more than 93,000 bacterial genomes, more than 1000 archaeal genomes, and genomic data for 10 eukaryotic organisms that include humans, mice and rats. PATRIC has expanded and improved its research capabilities for users by building and incorporating a set of services that are designed to streamline and simplify common bioinformatic workflows. These services include genome assembly, genome annotation, RNA-Seq analysis, expression import, proteome comparison, metabolic model reconstruction and variation analysis. All of these services are available through a private workspace that allows users to compare their private data to any of the public data in the PATRIC database. Researchers can upload their data files (e.g. sequence reads, assembled genomes, transcriptomic data), run the desired analysis services, integrate their private data with the data in PATRIC for comparative analysis, store the resulting output files and download the results.

09:00-18:00 Session 1D: Workshop: Multi-scale metabolic modeling and engineering
Location: Goodwin Hall, Room 190 
09:00
Workshop: Multi-scale metabolic modeling and engineering
SPEAKER: Justin Barone

ABSTRACT. A need for the ability to apply fundamental mathematical models to current industrial fermentation processes was identified. These models would not be empirical and would help industrial researchers increase processing efficiencies. Since the models would be fundamental, they would better connect the molecular to the macroscopic scales, which is currently lacking in the industry. In other words, it is anticipated that the workshop will be the first meeting of academic and industrial researchers on this advanced metabolic engineering topic and that eventually, metabolic models applied to industrial fermentation processes will connect molecules to titer to increase efficiency. Industrial researchers are really good at empirical models derived from experiments. However, what does not exist in the bioprocessing industry is the use of fundamental models where metabolic processes are described from the ground up using the latest technology in metabolic engineering. These techniques are only now being taught at universities at the advanced undergraduate and graduate levels so most current industrial researchers have not been exposed to these metabolic engineering techniques. Metabolic modeling techniques could help the pharmaceutical, chemical, and fuel industries.

12:30-18:30 Session 2: Tutorial: 4th International Hands-on Tutorial on Logical Modeling
Location: Torgersen Hall - Room 1010
12:30
Workshop: 4th International Hands-on Tutorial on Logical Modeling​​​​​​​
SPEAKER: Tomas Helikar

ABSTRACT. The motivation of this tutorial is to provide hands≠on experience with several logical modeling software tools. This tutorial will be made accessible to participants with no modeling experience as well as to those who are seasoned modelers. 

Logical modeling provides a computational approach to the visualization and analysis of the dynamics of biochemical and biological systems complementary to others such as reaction≠based or rule≠based modeling. One of the main advantages of logical models is their scalability and the relatively easy method of construction. In part due to these attributes,  logical models have become increasingly more popular  among the computational biology community. This has,  in turn,  led to the development of different techniques and software tools that enable the construction,  simulation,  and analysis of logical models and their variants (Boolean, multilevel, deterministic, stochastic, etc.) to address various biological questions.

This workshop aims at extending the outreach of the logical modeling community (namely,  the Consortium for Logical Modelling and Tools,  CoLoMoTo,  colomoto.org),  and providing an overview of recent achievements in tool development that render possible the modeling and the analysis of large cellular networks,  covering intricate signaling pathways,  sophisticated transcriptional networks,  as well as novel regulatory mechanisms.

Specifically,  two hands≠on tutorials will cover the Cell Collective ( www.cellcollective.org ) and CellNOpt ( www.cellnopt.org ) software tools.

13:00-18:00 Session 3: Tutorial: Network Dynamics and Cell Physiology (first session)
Location: Torgersen Hall - Room 3100
13:00
Network Dynamics and Cell Physiology
SPEAKER: John Tyson

ABSTRACT. A major theme of the International Conference on Systems Biology will be mathematical models of the molecular regulatory networks that underlie cell signaling, cell differentiation, cell growth and division, cell stress responses, cancer cell development, and other aspects of cell physiology. Because we expect many ‘newcomers’ to be attending the conference, it seems appropriate to hold an introductory tutorial on mathematical modeling on Sunday afternoon and Monday morning before the conference begins. The tutorial will be taught by two pioneers of the field, Professors John Tyson and Bela Novak, who have worked together for 25 years on mathematical models of cell growth and division, who have published some of the foundational papers in the field, and who have written several highly cited tutorial papers on “network dynamics and cell physiology”. The tutorial will combine lecture-style instruction with hands-on problem solving and computer exercises.