Tuesday, December 15, 2015

Google Presents River Stories Live

Last week I was at Google in Cambridge, where we had an event celebrating the recently published River Stories book and the new Google Trekker image library of the river. I participated in a panel discussion with other River Stories authors where we shared some of our thoughts about the river.





Wednesday, December 9, 2015

Dr. Indrani Ghosh named in Top 10 Young Professionals by ENR

ENR editors select young professionals who have “advanced into leadership roles at design and construction firms, and are making an impact in [New England].” Congratulations to my former PhD student Indrani Ghosh, Team Leader of the Sustainability Group at Kleinfelder, who was named as one of the Engineering News-Record’s (ENR) Top 10 Young Professionals. Indrani has established herself as a leader in reframing the engineering design process to include climate change impacts. Congratulations Indrani!

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, ferdi@coe.neu.edu
Ramunas Stepanauskas, Bigelow Laboratory for Ocean Sciences, rstepanauskas@bigelow.org
John Berges, University of Wisconsin-Milwaukee, berges@uwm.edu
Ben Twining, Bigelow Laboratory for Ocean Sciences, btwining@bigelow.org

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:




Monday, July 27, 2015

The tradition continues: Swimming in the Charles

This is turning into a tradition (see my blog posts from  July 28, 2014 and July 16, 2013). Last weekend, I participated in the annual swim in the Charles River. See picture below (if you have good eyesight, I am the guy waving near the edge of the swimming area). Every year I am reminded how nice of a river we have in our backyard. And its swimmable! I hope someday we can jump in whenever we want.

All you ever wanted to know about swimming in the Charles:

Wednesday, July 15, 2015

Boston’s Snow Mountain

Last week, Northeastern’s media people interviewed me about the slowly melting snow pile left over from this year’s snowy winter. If it takes something like this to raise awareness about nonpoint source pollution, then so be it. You can check out the post here:

Monday, June 8, 2015

“Modeling in lakes”

Northeastern’s media people worked with Len Rubenstein, a very talented photographer/artist (http://www.lenrubenstein.com/), to make a picture of me for Northeastern’s “Making Tomorrow Happen” campaign (see link below). The idea of the picture (shown below) is to encapsulate my research, here modeling of urban water water quality to support swimming. It reminds me of when I was in graduate school working on a paper. I came up with a title that was something like “Modeling Arsenic Speciation in Lakes”. One of my collaborators told me that sounds like you are sitting in the lake with the laptop...

Wednesday, May 27, 2015

IAGLR Conference Report

I am at the IAGLR meeting in Burlington, Vermont. Yesterday, Neil made a presentation about his Lake Taihu model and on Friday I will talk about my Anabaena - nitrogen interaction model. Sahar is also here, learning about cyanobacteria in the Great Lakes for her neutral evolution model. As expected, there is a lot of talk about Lake Erie at this meeting. The lake is experiencing severe cyanobacteria blooms, which led to the shutdown of Toledo’s drinking water supply last summer. As a civil engineer, I think of this as an engineered system failing (of course the lake is natural, but we have “engineered” what we put into it). This happens in our field, a prominent example is the Tacoma Narrows Bridge, which dramatically collapsed the same year it opened. Following that failure, the structural engineering community figured out what they did wrong and changed how they design bridges. The environmental engineering community needs to engage in a similar effort now. Meeting web site: http://iaglr.org/iaglr2015/

Wednesday, May 20, 2015

Happy Birthday, Streeter and Phelps Equation

This year marks the 100th anniversary of the famous Streeter and Phelps water quality model. Unfortunately, despite incredible progress in the biological sciences, the biology in our operational water quality models has not changed much since then. In a vision paper, which just came out in ES&T (see link below), I critique the state of biology in our water quality models, and argue for updating it. I am happy that ES&T agreed to publish this paper and hope it will lead to some discussion about this important topic.
Link to paper: http://pubs.acs.org/doi/full/10.1021/acs.est.5b02130

Thursday, April 30, 2015

Lake Taihu Collaborators Visit

Last week we hosted Prof. Jackie Qin, Prof. Guangwei Zhu and Dr. Wei Li of the Chinese Academy of Sciences at Nanjing. We are working together on the Lake Taihu eutrophication project, which is now in its 3rd year. We had some very productive meetings talking about Taihu, and also some fun at the Beehive restaurant (see below).

Wednesday, April 22, 2015

UWM seminar visit

Last week I was at the University of Wisconsin at Milwaukee. This is a really nice place to visit, a beautiful town with a great waterfront to go for a run on. I had some very interesting discussions with researchers there. Specifically, I got to talk about the Anabaena - nitrogen interaction model we are developing. The model simulates individual cells with genes, transcripts, proteins and metabolites (see figure below). It exhibits some cool emergent behavior, like differentiating specialized N-fixing cells (heterocysts) as fixed N gets depleted. The model predicts several parameters, like nitrogenase (nifH) transcript levels and we are presently comparing the model to observations from laboratory experiments (see figure for an example, data are from Martı́n-Figueroa et al., FEBS Letters, 2000). The next step is to apply the model at the field scale. As I talk to people I always ask them if they have or know of any field data that we can use to compare the model to. The technology certainly exists, but there are only few published studies that show metatranscriptomics over time in surface waters, and none of them are really applicable to our model. So the data don’t seem to exist yet. This is an important milestone for me, because I have been working for the past 10 years to make our models catch up with observations. And now it seems we are actually ahead of them :)

Thursday, March 12, 2015

Aging in bacteria

I am please to announce the publication of our paper on aging in bacteria “From protein damage to cell aging to population fitness in E. coli: Insights from a multi-level agent-based model” in Ecological Modelling. This paper explores the fitness benefit of asymmetric damage partitioning (aging) in E. coli using an ABM. Specifically, we find that aging is beneficial, but the magnitude of the benefit is very small, so its probably a side-effect of some other process (see discussion in paper for more)We think this paper is an important contribution to understanding the role of aging in bacteria. In this post I want to do some mixing of art and science. In 2013 I attended the Congress of European Microbiologists (FEMS) in Leipzig, Germany. In his keynote address, Johan Leveau related the artwork of Ursus Wehrli (“The Art of Tidying Up”, http://www.kunstaufraeumen.ch) to microbiology. I was really impressed by this and decided to apply that concept to our model to point to the role of spatial organization in aging of bacteria. 

Link to paper:

Thursday, January 1, 2015

New graduate student in my group

On Monday morning, Gunes and I welcomed a new member of our family: Mario Emre Ferdinand Hellweger. We are still a bit tired and overwhelmed, but very happy that everyone is healthy and to begin this new chapter in our lives. (This blog is for official research business only, so this guy has to be named a research assistant solely to indicate this fact.)