Tutorials

From BioNetWiki

The developers of BioNetGen are dedicated to making dependable software tools for rule-based modeling available to the scientific community and helping researchers learn how to use these tools. We often present tutorials about rule-based modeling and BioNetGen at conferences and lecture at summer schools. In addition, courses are available in which rule-based modeling is emphasized. Information about upcoming and past learning opportunities is provided below.

Upcoming learning opportunities

1. Modeling Cell Signaling Systems, Fifth Annual q-bio Summer School, Los Alamos, NM, July 25-August 9, 2011
2. Tutorial, "Rule-based Modeling with BioNetGen," The Fifth Annual q-bio Conference on Cellular Information Processing, Santa Fe, NM, August 10, 2011 (Faeder).

Available courses

1. Summer and Fall 2011, Undergraduate Problems (BIOL 499), Department of Biology, University of New Mexico (contact Dr. Hlavacek)
2. Summer and Fall 2011, Research Problems (BIOL 551), Department of Biology, University of New Mexico (contact Dr. Hlavacek)

Past tutorials, summer school/educational workshop lectures, and courses (since 2007)

1. Tutorial, "Rule-based Kinetic Modeling using BioNetGen", The 11th International Conference on Systems Biology, Edinburgh, UK, October 10, 2010 (Blinov, Chylek and Faeder).
2. Tutorial, “Rule-based Modeling of Biochemical Systems with BioNetGen,” Fourth Annual q-bio Conference on Cellular Information Processing, Santa Fe, NM, August 11, 2010 (Faeder).
3. Summer School Lecture, “A Tutorial on Rule-based Modeling with BioNetGen”, The Fourth Annual q-bio Summer School on Cellular Information Processing, Los Alamos, NM, August, 9, 2010 (Faeder).
4. Summer School Lecture, "Rule-based Modeling," Fourth Annual q-bio Summer School on Cellular Information Processing, Los Alamos, NM, July 27, 2010 (Hlavacek).
5. Lectures as part of a public outreach event, "Agent-based Modeling," The Art and Science of Systems Biology, Santa Fe Complex, Santa Fe, NM, March 27, 2010 (Gutenkunst, Hlavacek and Hu).
6. Lecture as part of an undergraduate research experience program, Computational Modeling and Analysis for Complex Systems (CMACS) Workshop, Lehman College, New York, NY, January 6-26, 2010 (Faeder).
7. Lecture and Lab Session, 2010 Training and Experimentation in Computational Biology (TECBio), Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA (Faeder).
8. Tutorial, "Rule-based Kinetic Modeling of Signal Transduction Networks", The 10th International Conference on Systems Biology, Stanford, CA, August 30, 2009 (Blinov).
9. Tutorial, “Rule-based Modeling of Biochemical Systems with BioNetGen,” Third Annual q-bio Conference on Cellular Information Processing, Santa Fe, NM, August 5, 2009 (Faeder).
10. Tutorial, "Rule-based Modeling," Workshop on Rule-Based Modeling, Farmington, CT, July 24, 2009 (Blinov).
11. Summer School Lecture, "Rule-based Modeling," Third Annual q-bio Summer School on Cellular Information Processing, Los Alamos, NM, July 22, 2009 (Hlavacek).
12. Tutorial, “Unleashing the Power of Rule-based Modeling BioNetGen/NFsim,” 2009 CSHL Meeting on Computational Cell Biology, Cold Spring Harbor, NY, March 24-27, 2009 (Faeder and Sneddon).
13. Lecture and Lab Sessions, Cellular and Systems Modeling (CMPBIO2040), a core course in the joint Carnegie Mellon--University of Pittsburgh PhD Program in Computational Biology, annually since 2009 (Faeder).
14. Lecture and Lab Session as part of an undergraduate research experience program, 2009 Bioengineering and Bioinformatics Summer Institute, University of Pittsburgh, Pittsburgh, PA (Faeder).
15. Summer School Lecture, "Rule-based Modeling," and Lab Session, Third Annual Summer School in Computational Immunology, Yale University School of Medicine, New Haven, CT, August 2008 (Hlavacek).
16. Tutorial, “Rule-based Modeling of Biochemical Systems,” Second Annual q-bio Conference on Cellular Information Processing, Santa Fe, NM, August 6, 2008 (Faeder).
17. Summer School Lecture, "Rule-based Modeling," Second Annual q-bio Summer School on Cellular Information Processing, Los Alamos, NM, July 22, 2008 (Hlavacek).
18. Lecture and Lab Session as part of an undergraduate research experience program, 2008 Bioengineering and Bioinformatics Summer Institute, University of Pittsburgh, Pittsburgh, PA (Faeder).
19. Lecture and Lab Session, Systems Modeling of Inflammation course, University of Pittsburgh School of Medicine, Fall semester 2008-2010 (Faeder).
20. Tutorial, "Rule-based Kinetic Modeling of Signal Transduction Networks," The 8th International Conference on Systems Biology, San Diego, CA, October 1, 2007 (Blinov).
21. Tutorial, "Rule-based Modeling using BioNetGen and the Virtual Cell," The First Annual q-bio Conference on Cellular Information Processing, Santa Fe, NM, August 8, 2007 (Blinov).