Workshop
To participate in one of the workshops below, please register by selecting your preferred session.
Workshop 1. Metabolic Modeling and Analysis in the DOE Systems Biology Knowledgebase (KBase)
Presenters: Adam Arkin (UC Berkeley), Janaka N. Edirisinghe (Argonne National Labs), and Filipe Liu (Argonne National Labs)
Join us for a workshop on Metabolic Modeling and Analysis in KBase on July 27th, from 9:00 – 10:20 AM, 600th Anniversary Hall, 6th floor, Multimedia room
The workshop will cover:
Short talk: Advancing science in KBase (by Adam Arkin)
Introduction to KBase narrative interface
Search and access to public reference data for analysis
Assembly and genome annotation
Draft metabolic model reconstruction and analysis
Overview science workflows demonstrating cheminformatics integration onto models, omics visualization, and reconciliation
KBase provides a user-friendly platform that empowers users to seamlessly upload their data or easily access publicly available data (e.g., Refseq) then analyze it alongside user, collaborator, and public data, develop realistic models, and share their workflows and findings. With KBase, users can perform complex systems biology analyses without the need to navigate through multiple sources or learn various systems.
To attend KBase workshops:
(1) Sign up for a KBase account at
http://kbase.us/sign-up-for-a-kbase-account/
(2) Fill the form of the link below to register the workshop
https://forms.gle/nC3STLisp4TBR3Qv9
Workshop 2. Developing Reproducible Mechanistic Models of Metabolism and Linting Tool for Modelers
Presenters: Herbert Sauro (University of Washington), Janis Shin (University of Washington), and Woosub Shin (NZ, Auckland, and UW Seattle)
Join us for a workshop on Developing Reproducible Mechanistic Models of Metabolism and Linting Tool for Modelers on July 27th, from 9:00 – 10:20 AM, 600th Anniversary Hall, 5th floor, Seminar room 10504
Short talk: What is reproducibility?
A brief discussion on potential solutions to publishing reproducible models
Examples of metabolic modeling software that support reproducibly standards
Introduction to our software platform Tellurium
Running Tellurium on the desktop or web
Writing simple metabolic models using Tellurium
A simple introduction to metabolic control analysis
Exporting models as SBML
Checking models for errors
Automatically annotating models using AMAS
Tellurium is a powerful python based platform for building, simulating and analyzing models of metabolic, signaling and gene regulatory networks.
Tellurium can be installed on Windows OS X or Linux. Instructions can be found at:
https://github.com/sys-bio/tellurium
For Windows the easiest thing to do is use our Windows installer at:
https://github.com/sys-bio/tellurium#front-end-1-spyder-for-tellurium-ide
For Mac we recommend installing python and then installing tellurium by running pip install tellurium from the Mac terminal.
Tellurium can also be run from free online services such as Google’s colaboaratory within Jupyter notebooks.
To attend Workshop 2:
Fill the form of the link below to register the workshop:
https://forms.gle/dHkKA9U2o28hUpqs7
