Short Courses
Short Course in Computational Systems Biology
Date: May 23-24, 2012
Location: University of Sao Paulo, Brazil
Description: Neil Clark PhD (Postdoctoral Fellow in the Ma'ayan Laboratory) delivered a two-day short course on the following topics:
Mathematics: Linear Algebra, Calculus and Ordinary Differential Equations, Graph theory and Network Biology
Statistics: Fundamental principles, Descriptive statistics, Hypothesis testing
High-throughput data analysis: Principal component analysis, Gene set enrichment analysis, Network Inference
Computing and tools: The R environment, Expression2Kinases
Workshops
Network Analysis and Gene-list Enrichment Analysis in Systems Biology
Date: August 10-13, 2011
Location: This workshop will be held at the Fifth q-bio Conference on Cellular Information Processing
Description: Avi Ma'ayan PhD (SBCNY Investigator) gave a workshop divided into three separate 50 minute lectures introducing applications of graph theory and network analysis as well as gene list enrichment analysis in systems biology.
Multi-scale Modeling with MOOSEDate: July 24-30, 2010
Location: This workshop was held at the Computational Neuroscience Meeting (CNS) 2010
Description: Upinder Bhalla PhD (SBCNY Investigator) gave a tutorial on how to set up and simulate multi-scale models in MOOSE (Multi-scale Object Oriented Simulation Environment).
Construction and Analysis of the Human Kinome Network Seminar and Workshop
Date: November 9 , 2009
Location: Vanderbilt School of Medicine, Departments of Pharmacology and Oncology
Description: Avi Ma'ayan PhD (SBCNY Investigator) provided one-on-one training sessions where different labs brought in their data and worked on potential methods of analysis.
Network Analysis in Systems Biology Workshop at Vanderbilt
Date: April 22, 2009
Location: Vanderbilt School of Medicine, Departments of Pharmacology and Oncology
Description: Avi Ma'ayan PhD (SBCNY Investigator) presented "Network Analysis in Systems Biology" followed by a series of one-hour interactive workshops on "Computational Methods for Analyzing Lists of Genes/Proteins and Building Networks in Systems Biology" which highlighted the software tools and databases developed within the Center.
Specification of Rate Constants for Kinetic Models Workshop (Sponsored by SBCNY)
Date: November 19, 2008
Location: Mount Sinai School of Medicine
Description: This workshop was a follow-up on our Spring 2008 workshop where we discussed the feasibility of experimentally obtaining kinetic constants for cellular interactions between all of the proteins encoded by the human genome. This workshop assessed the currently available kinetic data for the development of quantitative models of signaling pathways.
The Quantitative Human Interactome Workshop (Sponsored by SBCNY)
Genome-wide Approaches to Gather Quantitative Parameters for Mechanistic Models: Relevance for Systems Pharmacology
Date: March 26, 2008
Location: Mount Sinai School Medicine
Description: This workshop was held as part of the ongoing activities of the Systems Biology Center New York and coincided with the visit of Professor Bjorn Obrink from the Karolinska Institute as a Senior Visiting Scholar to the Center. The purpose of the workshop was to analyze the current state and develop a plan to obtain kinetic constants for interactions on a genome wide basis to permit the development of large scale quantitative models.
Seminars and Symposia
Systems Biology Center New York Seminars/Symposia
Description: The Center sponsors seminars by outside speakers on topics in computational and systems biology. The outreach activities of the Center also include the Annual SBCNY Symposium held at the Mount Sinai School of Medicine. The symposium is free of charge and open to the public. Information on upcoming seminars and symposia is located in the Events section of this website.
Biomathematics Lunchtime Seminars
Description: Organized by Charles Peskin PhD (SBCNY Investigator) at the Courant covers a broad range of topics from molecular processes such as motors and visual signaling to organ and organismal functions such atrial fibrillation and sleep-wake cycles. Many members from SBCNY including postdoctoral fellows and graduate students from Mount Sinai attend these weekly noon-time seminars. SBCNY Investigators Lawrence Sirovich PhD and Avi Ma'ayan PhD have presented their work in this
forum in the Fall of 2009. These seminars provide a continuing opportunity to interact on a weekly basis and bring together computational systems biology researchers from the New York area.
Distinguished Visiting Faculty
John J. Tyson PhD, Virginia Polytechnic Institute & State University
Dr. Tyson is a pioneer in computational cell biology. He studies the macromolecular reaction networks that process information in living
cells and initiate appropriate responses in terms of cell growth, division and death. He represents the dynamics of these reaction networks in terms of mathematical equations (differential equations, stochastic processes, and discrete switching networks), using computer simulations to work out the precise behavior to be expected of the network. By comparing simulations with experimental data, the computer models can be tested, refined and developed, eventually, into tools for accurate predictions of the physiological responses of healthy and diseased cells.
Description: Dr. Tyson met with members of the Courant Institute of Mathematical Sciences at New York University (NYU) on Wednesday (September 23rd).
During his visit to the Courant Institute, Dr. Tyson presented a lecture titled "Reaction Motifs and Functional Modules in Protein Regulatory
Networks" at the Biomathematics Lunchtime Seminar Series. In the afternoon Dr. Tyson met individually with many students and fellows
working on systems biology problems at Mount Sinai. Dr. Tyson spent Thursday (September 24th) meeting with more students and Investigators of the Center at Mount Sinai School of Medicine. His visit concluded with a lecture titled, "Systems Biology of Eukaryotic Cell Cycle Regulation".
Walter Kolch MD, FRSE, University of Glasgow
Bjorn Obrink MD, PhD, Karolinska Institutet