Friday, November 20, 2015

Agent-Based Modeling Class

Please consider taking my ABM class in the Spring 2016 Semester

What is ABM? Agent-based modeling (ABM) is a growing technology that is finding application in many areas from environmental chemistry to microbial ecology to transportation engineering to social sciences and business. It is a "systems" or "bottom-up" approach for understanding how complex systems behave. Individual low-level elements of the system (e.g. bacteria, cars) are simulated and the system-level behavior (e.g. population density, traffic congestion) emerges as a result of the cumulative action and interaction of these low-level entities. This is different from the traditional "top-down" approach where system-level state variables are modified directly using differential equations.

Course overview. The course is geared towards a multi-disciplinary audience, and open to students from engineering, environmental science, biology and chemistry, sociology, business and others. Topics include introduction and motivation of ABM, basic principles, comparison to other methods (e.g. cellular automata, individual-based modeling), available software, computational strategies (e.g. up-scaling, agent accounting), model development, model calibration and testing, and model application.  A number of case studies from the literature in various disciplines will be reviewed and discussed. A major part of the course will be a hands-on term project. Students are encouraged to explore the use of ABM for their own research interests for the term project. The project will be implemented using the NetLogo ABM framework. NetLogo models can be served as Java Applets on the Internet and the students will be required to submit their final papers as web pages, which will be published on the course web page. The text will be "Agent-based and Individual-based Modeling: A Practical Introduction" by Grimm and Railsback (2011).

Friday, October 9, 2015

My Charles on the computer

I am excited to share with you that the Charles River Conservancy's “River Stories III” book is now out. The book is a collection of memoirs, poems, reflections, and artwork about the Charles River by local writers and artists. It celebrates the Charles River Parklands, and the experiences and memories of those who cherish them. I contributed a chapter “My Computerized Charles River“, where I share some of my personal feelings about the river and our work to help make it swimmable. It was a real pleasure to work on this piece, because it was so different from the other type of writing I typically do (i.e. technical journal articles). Here is a link to the book.

Friday, October 2, 2015

ASM Conference

In the Spring of 2016 we are organizing an ASM conference focusing on individual-based modeling and observations in microbiology. See the link below. This should be an exciting meeting and we hope to see you there. Application deadline is November 10.

Wednesday, September 16, 2015

IWA DIPCON Conference Report

I am in Berlin for the IWA Conference on Diffuse Pollution and Eutrophication. Yesterday I gave a  presentation on our Anabaena-nitrogen interaction model. At this conference I am learning a lot about water quality problems around the world. Most notably: Cyanobacteria are a growing problem everywhere. Today I had a chance to visit the Stechlin LakeLab, which is a very nice facility with a really impressive set of large-scale mesocosms (see picture). And of course they now also have Anabaena...

Friday, September 4, 2015

UT Knoxville Seminar Visit

Earlier this week I was in Knoxville visiting the Department of Microbiology at the U. of Tennessee. I gave a seminar talking about our research on bet hedging in yeast, neutral evolution of ocean bacteria and cyanobacteria-nitrogen interaction. I also had the opportunity to meet a lot of their faculty and students and learned a lot. And we had a Lake Taihu project meeting with Steve Wilhelm and students. A busy time...

Friday, August 28, 2015

The Individuality of the Plankton

Dear Colleague:

You or someone you know may be interested in presenting at this session at the AGU/ASLO/TOS Ocean Sciences Meeting 21-26 February 2016 in New Orleans.

The Individuality of the Plankton: Single-cell analysis and agent-based modeling

Fascinating advances in individual and single cell analytical techniques (e.g., flow cytometry, chemical analyses, genomics) are providing an unprecedented view into the individuality of planktonic organisms (viro-, bacterio-, phyto- and zoo-plankton). Plankton populations, which have traditionally been viewed as homogeneous collections of individuals with identical properties and behavior, are now recognized to be heterogeneous, even in environments commonly considered to be well mixed, like the open ocean. At the same time, agent-based modeling (ABM, aka individual-based modeling, IBM) technology is evolving as a powerful approach to analyze and interpret these observations. These models provide insights into the mechanisms underlying the heterogeneity (e.g., mutations, stochastic gene expression, deterministic aging, microscale patchiness) and put them into ecological context (e.g., fitness benefits of bet hedging strategies). The combination of individual and single cell analyses and ABM has the potential to transform plankton and microbial ecology across the freshwater-marine continuum and in other environments. In this session, we aim to bring together scientists to share individual and single-cell research, to take a snapshot of the state-of-the-science in this field, and to connect researchers with synergistic skills and interests.

Ferdi Hellweger, Northeastern University,
Ramunas Stepanauskas, Bigelow Laboratory for Ocean Sciences,
John Berges, University of Wisconsin-Milwaukee,
Ben Twining, Bigelow Laboratory for Ocean Sciences,

Here is a link to the session and abstract submission site.
Abstract Submittal Deadline = 23 September 2015.

Please feel free to forward this announcement on to other people that may be interested.



Wednesday, August 19, 2015

Cyanobacteria bloom season is here

The Charles River and Lake Erie are in the midst of massive cyanobacteria blooms. Northeastern’s media people interviewed me on the topic. See the link below for the interview and other links for the Charles: