Chesapeake Community Modeling Program

the CCMP Newsletter | June 2009

Volume 2, Issue 3

Introduction

The CCMP Steering Committee met on May 4th with several important items on the agenda. Two new members have joined the SC: Kevin McIlhaney from the Naval Academy will bring in new ideas and resources from the engineering and physics side, while Barry Stamey from Noblis will bring the business and consultancy perspective in addition to his knowledge of sensors and experience running large scale integrated projects. Welcome Kevin and Barry!

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Contents

1. CCMP News in brief
2. News from other communities
3. Open Source on the March
4. Featured Modeler: Raleigh Hood
5. Featured Model: CBEO

6. Job Announcements

1. CCMP News in Brief

Steering Committee rotation

The new by-laws have been approved and provide formal regulations that govern the functioning of the CCMP and the steering committee. This includes specification of SC membership and rotations. It is now time to implement these by-laws. We are open for nominations for the SC. If you wish to nominate a colleague, please contact Dave Jasinski or Raleigh Hood.

Chesapeake Modeling Symposium 2010

The CCMP sponsored a major Chesapeake Bay-focused modeling meeting in the spring of 2008 (CheMS08, May 12-14, 2008). Participation in this meeting was high and has helped raise the profile of the CCMP in the Chesapeake Bay modeling research and management communities. According to our by-laws, this meeting is to be convened every two years, or approximately 1 year from now. Preparations for CheMS ’10 have begun and an organizing committee has been formed. The meeting format will be the same, so start thinking about session themes and workshops that you wish to propose. An official invitation will be distributed shortly.

Resignation of Alexey Voinov as CCMP Program Manager in August.

ITCAlexey has decided to accept a faculty position with the International Institute for Geo-Information Science and Earth Observation (ITC) in the Netherlands. He will be stepping down as the CCMP Program Manager in mid-August. The Steering Committee has discussed the possibility of setting up the Program Manager position a little differently after Alexey departs. It was suggested to split the responsibilities of Program Manager between David Jasinski and Raleigh Hood. Dave will be responsible for daily activities and technical support, while Raleigh will have some time committed to focus on strategic decisions and scientific representation of CCMP externally. Both Dave and Raleigh have agreed to try this new arrangement for a few months.


2. News From Other Communities

Open Geospatial Consortium (OGC)

OGCThe Open Geospatial Consortium, Inc.® (OGC) is a non-profit, international, voluntary consensus standards organization that is leading the development of standards for geospatial and location based services (). Alexey Voinov from CCMP was invited to give a talk on “Integrated Environmental and Earth Systems Modeling: a Community Approach” at its recent June '09 Technical Committee Meeting in Boston. There is much to learn for us from OGC about developing standards and making programs interoperable. They also have been in the lead at exploring the rights management and intellectual property issues. OGC is interested in developing standards for models that would allow models to interact and seamlessly access data and other model output, seeking collaborators to work on these issues. It will be certainly to the benefit of CCMP of partner with OGC and other communities.

ADCIRC

OGCThe (parallel) ADvanced CIRCulation model for oceanic, coastal, and estuarine waters (ADCIRC) community had its 13th Workshop on April 20 – 21, 2009 at NOAA, Silver Spring, MD. Two days were filled with presentations on various aspects of development and application of the ADCIRC model. Applications include storm surge simulations in Southern Louisiana, Lake Pontchartrain Forecast System, flood hazards for Northwest Florida, storm surge for Puerto Rico, baroclinic modeling for the Turkish Straits system, Delaware Bay water levels and currents, etc. Nothing was presented for the Chesapeake Bay. The model development discussions were dominated by research on unstructured grids, standards, and catalogs, as well as coupling of ADCIRC with other models.

STAC Workshop on Nearshore Suspended Sediment Transport, Turbidity, and Impacts to SAV

A group of scientists gathered on May 28th to examine the CBP WQSTM predictions in the nearshore, for both turbidity and SAV. The goal was to ascertain next steps in using the model for regulatory purposes within the next year. The overall consensus was that it is unlikely that the model can be used reliably for forecast purposes. It will still be a good research tool for understanding how various processes play into overall dynamics. However, it would be more prudent to rely on empirical evaluations in the meantime.

U.Va.'s New 'Bay Game' was launched on Earth Day

Bay GameBay Game is a unique sustainability simulation based in the Chesapeake Bay watershed. An interdisciplinary team has pulled together many complex pieces of a simulation, incorporating 43,000 mathematical equations. The Stella modeling package was used for the game's interface. Faculty members and students from 10 departments in seven schools contributed the expertise and data for the back end of the simulation, including real statistics on variables such as crab population and pollution. The effort promises to inform future public policies, private investment trends, and societal behaviors in ways that enhance human health, economic prosperity, and environmental sustainability.


3. Open Source on the March

Universities Join Yahoo Internet-Scale Research Project

Yahoo!Yahoo is running an "Internet-scale computing research" project which gives Universities "access to a cluster of Yahoo computers called M45 that runs open-source software called Hadoop that can be used to process data rapidly."

Recently the University of California-Berkeley, Cornell University, and the University of Massachusetts-Amherst have joined the project. The software "can be used for tasks such as finding, relatively rapidly, all Web sites that link to a particular Web site." It can be used by the different schools to research a variety of topics.

Open Source vs. Open Models

SimileCCMP has been advocating making models open by sharing source code. However, there is another approach that deserves consideration. The software implementation of a given model could potentially be in a variety of languages and platforms and, therefore, may not necessarily be open source. However, the model can be shared if it is described in some standard language, such as XML. This is the approach advocated, for example, by Robert Muetzelfeldt, the founder of the Simulistics company that develops Simile.

Simile, which is proprietary, has the functionality to save models in XML. It uses XSugar, a technology which allows for bi-directional transformation between a non-XML format and an XML format, using a single set of transformation rules. The idea is then to share models and tools in MultiGuise, a web-based tool for allowing any of several stylesheets to be applied to any of several XML documents (see Muetzelfeldt's presentation).

So, it appears that open source code is not the only way for a model to be open to the community at large. On the other hand, XML or the like is also code, so this approach is simply considering a different language to describe models. However, using this approach might make it easier to share an XML version of a model than to require publishing all the interfaces, input/output, and analysis tools that come when we share a software implementation of a model.

Mendeley

mendeleyPdf files fly back and forth over the internet and accumulate on hard discs, sometimes making it difficult to remember what has already been downloaded and where the file is stored. A possible remedy might be available. Mendeley Desktop is free academic software for managing and sharing research papers. It permits tracking of all the papers downloaded to your hard disk and works like iTunes does for music.

Mendeley Web lets you manage your papers online, discover research trends, and connect to like-minded researchers. The more of us join, the larger the WWW library that is accessible. Please consider joining. There are 2,468 research groups collaborating now and 29,757,123 references in participants’ libraries.

Check out an article that describes what Mendeley can do for you. It also gives some background about the company. If we could all subscribe and upload our publications to Mendeley, we could solve issues with access to personal publications.


4. Featured Modeler: Raleigh Hood

Raleigh HoodHorn Point Laboratory
University of Maryland Center for Environmental Science
P.O. Box 775
Cambridge, Maryland 21613
University Park, PA 16802

- 1983 B.Sc. University of Washington, Oceanography.
- 1990 Ph.D. University of California, San Diego, Scripps Institution of Oceanography.

Raleigh is Professor of oceanography at University of Maryland, Center for Environmental Science, Horn Point Laboratory, Cambridge Maryland. He conducts research in phytoplankton production and light response; analytical and numerical modeling of primary production and pelagic ecosystems; bio-optical oceanography; phytoplankton physiology; and carbon dioxide flux at the air/sea interface. He also teaches courses in Biological Oceanography

Raleigh has been an initial advocate and leader for CCMP and has been Chair of the CCMP Steering Committee since August 2002.

mendeleyHis areas of Interest include coupled biological - physical modeling in Chesapeake Bay, the Atlantic Ocean and the Indian Ocean. He was instrumental in developing one of the first open source models in the CCMP model suite - the ChesROMS package (ChesROMS), a community ocean modeling system for the Chesapeake Bay region being developed by scientists in NOAA, University of Maryland, CRC (Chesapeake Research Consortium), and MD DNR (Maryland Department of Natural Resources). It has been supported by the NOAA MERHAB program. The model is built based on the Rutgers Regional Ocean Modeling System (ROMS) with significant adaptations for the Chesapeake Bay. The model was featured in our #1.2 Newsletter.

Some of his major current research efforts include a NOAA funded project on “Development and Implementation of an Operational Harmful Algal Bloom Prediction System for Chesapeake Bay”, and an NSF funded project on “Dynamic stability and particle transformations: Tracing pathways of production in estuarine turbidity maxima”.

CCMP would not have been formed without Raleigh’s leadership, close attention, and TLC. His role is likely to increase in the years to come.


5. Featured Model: CBEO

CBEO The Chesapeake Bay Environmental Observatory (CBEO) is not really a model. It is more than that. The project is organized into four concurrent interacting elements:

CBEO:T -- Test Bed & Prototype

CBEO:T integrates a subset of currently available large data sets characterized by multiple variables and widely disparate time and space scales - grab and continuous sampling at fixed stations, undulating towed sensors, and satellite and aircraft remote sensing. A novel and exciting feature of the CBEO is the inclusion of the fifteen year (1986- 2000) simulated data from the Bay-wide fine spatial (1-10 km) and temporal (0.02-1 h) scale hydrodynamic and water quality model. This test bed serves as the platform for the development of data integration, interpolation, and visualization functionalities.

CBEO:N -- National Network of Environmental Observatories

The CBEO:N group incorporates the test bed cyberinfrastructure into the national network of environmental observatories via a GEON node for the CBEO and resolving complex cross-disciplinary issues of semantics, syntax, and interoperability.

CBEO:S -- Environmental Science

The CBEO:T and CBEO:N are used by the environmental science element (CBEO:S) to demonstrate its utility in addressing unresolved questions of anthropogenic and climatic factors controlling hypoxia in Chesapeake Bay, a problem shared with many other estuaries and whose consequences are severe and long lasting. The CBEO:T team is testing CBEO capabilities, suggesting modifications and additions, and providing timely user feedback.

CBEO:E -- Education

To expand the user community, the CBEO is used by the education element (CBEO:E) to translate science and technology for public consumption. Direct participation of multicultural students and a K-12 teacher is part of the project.

With help from CCMP, the CBEO is run by a research consortium from:

The project has compiled an impressive repository of data sets that are related to the Bay . The project also hosts Carl Cerco’s Simulation of Long-Term Trends in Chesapeake Bay Eutrophication, and the Three-Dimensional Eutrophication Model of Chesapeake Bay. The goal is to provide new interpolation and analysis tools, linked to available visualization software, that can take advantage of the multiple variables and types of data in the 5-D joined set.


6. Job Announcements

Database Manager

The University of Maryland Center for Environmental Science (UMCES) invites applications for database manager. The successful candidate will work in partnership with the U.S. EPA Chesapeake Bay Program staff at its Annapolis office.

The focus of the Database Manager are: (1) develop and operate the Chesapeake Bay Program agricultural and nonpoint source databases for watershed modeling; (2) coordinate with Modeling and Nutrient Teams to ensure the agricultural and nonpoint source databases are accurately populated; and (3) coordinate regularly with software developers and Nutrient and Modeling teams to ensure database solutions and analytical capabilities are meeting the Chesapeake Bay Program’s needs.

The position requires extensive knowledge of enterprise level relational database management systems (RDBMS) such as MS SQL Server and a working knowledge environmental data. Position requires the ability to develop and debug stored procedures and SSIS packages, write complicated SQL commands and quickly and accurately manipulate complicated relational database records. The ability to program in data access languages such as C#.NET or C++ and familiarity with XML is also desirable. Maintaining the highest levels of database performance and security are essential to the task.

The applicant must have 2 years experience related to the development and administration of RDBMS, preferably storing environmental, agricultural, or stormwater data, and excellent communication skills. Additionally the applicant must have a Bachelors degree or equivalent experience. The successful candidate is entitled to University benefits and salary is commensurate with experience. The funding for this position is from a federal grant to UMCES.

Please e-mail a letter of interest, resume, and contact information for 3 references prior to 6 July 2009 to Dave Nemazie . Search will remain opened until filled. The successful candidate may be required to submit to a federal background check.

Watershed Data and Modeling Specialist

The successful candidate will work directly with the Chesapeake Bay Program modeling, monitoring, and nutrient teams. The goals of the position focus on the following priorities: (1) ensure that data related to watershed modeling is properly incorporated into the agricultural and nonpoint source databases and that the resultant information is properly incorporated into the Chesapeake Bay Program Watershed Model; (2) develop modeling-related software to enhance the Chesapeake Bay Program’s analytical capabilities; (3) perform calibration of models; (4) assist partners with the development and assessment of implementation plans detailing practices necessary to meet TMDL allocations; (5) assist various tasks modeling the nutrient and sediment loads resulting from alternative management scenarios, such as developing, tracking, and, as necessary, adjusting two-year Chesapeake Bay restoration milestones; (6) assist partners to ensure that local TMDLs are coordinated with the Chesapeake Bay TMDL; and (7) conduct outreach to partners to ensure proper input and interpretation of agricultural and nonpoint source data and watershed model outputs;

Candidates should have a PhD, a Master’s degree with professional experience, or equivalent commensurate experience in environmental science or related field. The successful candidate must possess demonstrated experience and knowledge with nonpoint source data and watershed modeling in the following areas: analyze, interpret, display, and QA/QC data; develop, operate, and modify databases; and develop, operate, and interpret watershed models. Excellent communication skills are required.

The successful candidate is entitled to University benefits and salary is commensurate with experience. The funding for this position is from a federal grant to UMCES. Please e-mail a letter of interest, resume, and contact information for 3 references prior to 6 July 2009 to Dave Nemazie.

Search will remain opened until filled. The successful candidate may be required to submit to a federal background check.

Chesapeake Community Model Program
http://ches.communitymodeling.org/
Chesapeake Research Consortium
Edgewater, MD
410-798-1283

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