Chesapeake Community Modeling Program
the new CCMP Newsletter | October 2008
Volume 1, Issue 4
Introduction: A vision for the future Chesapeake modeling suite
The Chesapeake Bay Program (CBP) has indicated on multiple occasions that the current CBP suite of models is going to be phased out after 2010-2011. The CBP partners will continue to apply these models for management decision making beyond 2011. However they will not attempt to continue to upgrade the current versions of these models into the future.
This means that now it may be about the right time to start a community wide discussion about what the next Chesapeake Modeling and Decision Support System (CMDSS) may look like. The CCMP has proposed to organize a community effort to decide on the goals, functions, architecture and structure of the future system.
We would like to invite you to engage in an open discussion on this issue. We should include researchers that do modeling, monitoring, and data processing, as well as users that can help to identify the particular problems and goals that this system should serve. We think that Open Community Research is the ultimate level of collaborative thinking and modeling, when the project goals are decided in an open environment including researchers and users. Projects are open-ended and ongoing, while research and modeling goals can be adjusted to the changing needs of the users.
As a first step we are opening yet another blog on the CCMP web page. Click here to join the blog.
We are also organizing a workshop as part of the CRC Regional Conference on "Ecosystem Based Management (EBM): the Chesapeake Basin & Other Systems" that is to be held in Baltimore Marriott Hotel & Conference Center, March 22-25, 2009. See http://www.chesapeake.org/ for more information about the conference and please start sharing your ideas on the blog.
We hope that if we can build a joint vision of the future CMDSS during the next few years and start designing its components and overall architecture, we will be in a better position to make a smooth transition from the existing CBP suite of models to the new and expanded framework.
Contents
1. OMS - Another component integrating architecture
2. Introducing Non-native Oyster to Chesapeake Bay
3. Open Source on the March: OpenDX
4. Featured Modeler: Eileen E. Hofmann
5. Featured Model: PIHM
6. Announcement: Job opportunities @ UMCES & CCMP
7. Announcement: CSDMS Student-Modeler Award
1. OMS - Another component integrating architecture
An Object Modeling System (OMS) has been developed at the USDA Agricultural Systems Research Unit in Fort Collins, CO. The OMS is a Java-based modeling framework that facilitates simulation model development, evaluation, and deployment. It consists of a Library of "Alternate Science and Database Modules", which facilitates the assembly of a modeling package, tailored to the problem, data constraints, and scale of application. Point of Contact: Olaf David at Olaf_dot_David_at_ars_dot_usda_dot_gov.
The OMS framework can be used to develop customized, modular field to watershed system models with interchangeable components for assessing the effects of conservation practices. OMS represents an ARS-led effort in partnership with the NRCS, USGS, and university collaborators (e.g., CO State University). The system has a nice interface that allows one to plug various components together. The only catch is that pretty much everything has to be rewritten in Java. If you model is already in Java you might consider exploring the OMS to make your model and its components compliant.
At this time there are active interactions with the CSDMS group in an attempt to synchronize OMS with the CCA architecture that CSDMS has adopted, and which CCMP is also looking at as a standard.
2. Report Assesses Introducing Non-native Oyster to Chesapeake Bay
The U.S. Army Corps of Engineers and the state governments of Maryland and Virginia released an Environmental Impact Statement today that evaluates a proposal to introduce oysters from Asia into Chesapeake Bay. The EIS assesses the potential impact of this non-native species on the United States' largest estuary. The report is the result of a 5-year, $17 million research study that aims to evaluate the possible effects of introducing the Suminoe oyster, a native of the China Sea, which has the potential to thrive in the Chesapeake because it is resistant to diseases that have adversely affected native Eastern oysters. The downside is that this species has a lower hypoxia tolerance, thinner shell, and potentially supports new parasites.
A public comment period on the report will be open for 60 days, beginning Friday, Oct. 17. Scientists and the public are urged to review the report and submit comments at http://www.nao.usace.army.mil/OysterEIS/.
There are a number of models involved in the study, among them the E.North et al. Larval Transport model, which is also part of the CCMP distribution.
A version of Carl Cerco's model is also available from CCMP, however without the extensions that were added for the oyster analysis. This is a good example of how the CCMP models in general could benefit from more modular architecture that would allow components to be plugged in as needed.
3. Open Source on the March
A powerful visiualization package is available as open source
As its name implies, OpenDX is Open Source. The license allows you to freely create, distribute, and develop visualization solutions as you see fit. The software was mostly developed by IBM, but is released as open source. It allows one to create all sorts of animations, graphics and other display in several dimensions.
VIS, Inc. does much of the building of binaries and offers paid support to help troubleshoot any problems you may have. The binaries for Linux and Unix are free; however the binaries for MacOSX cost $25.
There is an interesting discussion on the VIS about the fact that they charge for open source software. One client asks: "How dare you charge for free software!"
The answer is: "Why are we selling our version of OpenDX when you could download it free or compile it yourself? The main reason, cost!! We have worked very hard to add the code needed in order to compile OpenDX on MacOS X. That doesn't include the time and effort involved compiling all the support libraries, etc. So we are trying to recoup some of our costs and generate revenue to help us improve OpenDX. We have also added special features to make OpenDX more Mac-like even though it is UN*X based software." This is a good example of how the two software development modes can coexist. The kernel can be open source, but this does not preclude that interfaces, or extensions will be developed and sold for a cost. However, in most cases there will still be a free version that with some additional effort a user could use.
The USGS open source model MODFLOW followed a similarstory. The model itself is available as a free download. However, most of the consultancies prefer to use the proprietary version that comes with a very useful GUI called Visual MODFLOW and has become a "proven standard for professional 3D groundwater flow and contaminant transport modeling using MODFLOW-2000, MODPATH, MT3DMS, RT3D, PHT3D and SEAWAT." At the same time the open source version is also available for free from USGS.
4. Featured Modeler: Eileen E. Hofmann
Eileen E. Hofmann, ODU [homepage]
Eileen is Professor of Oceanography at the Center for Coastal Physical Oceanography, Old Dominion University, Norfolk, VA. Her work is focused on coupled physical-biological models. Her research interests cover a variety of topics, which range from mathematical modeling of marine ecosystems to descriptive physical oceanography. Currently she is working in two areas. The first is the development of coupled circulation-population models that can be used to investigate the factors controlling the larvae and adults of the Eastern oyster, Crassostrea virginica. These models have been applied to a variety of estuarine systems to study the role of environmental conditions on structuring oyster populations.
The second area of research involves the development of data assimilative models for investigating circulation and biological processes in coastal marine systems. The overall goal of this research is to develop a predictive capability for biological distributions in marine environments.
Eileen also plays an important role in the Southern Ocean Global Ocean Ecosystems Dynamics (GLOBEC) project , where she is member of the Science Steering Committee, the GLOBEC International Science Steering Committee, and the Ocean Studies Board of the National Research Council.
Some of her recent projects are:
- Seasonal Biogeochemical Processes in the Ross Sea: A Modeling Approach;
- Comparative Modeling and Data Analysis Studies for the Ross Sea and West Antarctic Peninsula Regions: A JGOFS synthesis and Modeling Project;
- U.S. SO GLOBEC Synthesis and Modeling: Circulation and Hydrographic Data Analyses and Modeling Studies.
She is a leader on the project on U.S. Eastern Continental Shelf Carbon Cycling (USECoS): Modeling, Data Assimilation, and Analysis
The CCMP suite of models features one of the models that was developed by Eileen to describe the development of larvae of Crassostrea virginica.
Eileen was part of the Linden Group that triggered the CCMP initiative, and has been an active member of the CCMP steering committee since its inception.
5. Featured Model: PIHM
Our featured model in this issue of the newsletter is: PIHM
PIHM The Penn State Integrated Hydrologic Model (PIHM) is a multi-process, multi-scale hydrologic model where the major hydrological processes are fully coupled using the semi-discrete finite volume method. PIHM runs on unstructured triangulated grids, which makes it useful in resolving spatial features such as riparian zones, boundary conditions, and particular areas that need more spatial detail for the processes involved. Given a set of constraints (e.g., river network support, watershed boundary, altitude zones, ecological regions, hydraulic properties, climate zones, etc.), an "optimal" mesh is generated. River volume elements are also prismatic, with trapezoidal or rectangular cross-section, and are generated along edges of river triangles. The global ODE system is assembled by combining all local ODE systems throughout the domain and then solved by a state-of-the-art parallel ODE solver known as CVODE developed at the Lawrence-Livermore National Laboratory.
The model itself is "tightly-coupled" with PIHMgis, an open-source Geographical Information System designed for PIHM. The PIHMgis provides the interface to PIHM, access to the digital data sets (terrain, forcing, and parameters) and tools necessary to drive the model, as well as a collection of GIS-based pre- and post-processing tools. Collectively the system is referred to as the Penn State Integrated Hydrologic Modeling System. The modeling system has been written in C/C++, while the GIS interface is supported by Qt. The Penn State Hydrologic Modeling System is open source software, freely available for download at this site along with installation and user guides.
The major players on the project are Christopher J. Duffy, Yizhong YizhongQu, Mukesh Kumar, Gopal Bhatt and Shuangcai Li. PIHM is also on SourceForge (https://sourceforge.net/projects/pihmmodel/) and welcomes collaborators.
6. Announcement: Job opportunity @ UMCES and CCMP
PhD Research Opportunity at UMCES
PhD Research Opportunity at University of Maryland Center for Environmental Science (UMCES). We invite applications from talented and motivated students interested in pursuing a PhD in fisheries oceanography, larval transport, and/or zooplankton ecology. Applicants with a M.S. degree or three years of relevant post-undergraduate experience as well as strong computer and field research skills are encouraged. The prospective student must be admitted to the University of Maryland Marine-Estuarine-Environmental Sciences (MEES) graduate program and is expected to participate in a research program at the UMCES Horn Point Laboratory (http://hpl.umces.edu/) under the tutelage of Dr. Elizabeth North (http://hpl.umces.edu/faculty/enorth.html). The student will take a leadership role in field component of the NSF-sponsored TRANSPORT program.
The PhD position starts in late spring 2009 and includes stipend, tuition, research support, and travel to domestic and international conferences. If you are interested in this position, please send Elizabeth North at enorth_at_hpl_dot_umces_dot_edu) an e-mail with "PhD position" in the subject line. Review of applications will begin on December 1. The deadline for applications to the MEES graduate program is February 1, 2009.
Tech Assistant at CCMP
Applications are being sought for a technical assistant with strong IT skills to work with the Chesapeake Community Modeling Program (CCMP). The assistant should have interest in environmental protection, management, and modeling and have some vested interest in the future of the Chesapeake Bay system. The ideal candidate for the position will have:
- good web development skills, including knowledge of PHP and MySQL;
- experience working with and supporting web application and web based collaborative tools: wikis, CVP, SourceForge, etc.;
- some programming capabilities with C++ and/or Java.
Other duties include facilitating communications and assisting with logistical planning of workshops and presentations.
The position offers great opportunity for networking with teams of outstanding scientists in the Bay area, participation in research projects, and could be a great bridge position to prepare for graduate school. Professional development funding is available for this position, which can be used for training and education that is relevant to the position.
Qualified applicants will have strong technology, organization, and communication skills, ability to travel within the watershed, and interest/background in science and policy of the Chesapeake Bay. Send a detailed cover letter and CV/resumé to A. Voinov, at avoinov_at_uvm_dot_edu.
7. CSDMS Student Modeler Award
The Community Surface Dynamics Modeling System (CSDMS) has announced its first 'CSDMS Student Modeler Award'!
CSMDS will invite graduate students from Earth and computer sciences to an annual competition for this award.
If you know of a graduate student who has completed an outstanding research project in 2008, which involved developing an Earth science model (terrestrial, coastal, marine or biogeochemistry), a modeling tool, or model linking technology, they can qualify for this award! Entries will be judged by a panel of experts in the field on the basis of ingenuity, applicability, and contribution towards the advancement of geoscience modeling. The winner will receive a prize and a funded visit to the CSDMS Integration Facility in Boulder, Colorado, to learn and work with CSDMS scientists to develop their model into a CSDMS component. Entries may be sent to: csdms@colorado.edu. Deadline for submission is December 1, 2008. The recipient of this year's award will be announced at the CSDMS Town Hall meeting, AGU, in San Francisco, CA. Please read the attached announcement for full information.
Since CCMP is now participating in CSDMS and is running a Geographically Focused Research group there we encourage our members to apply, and to bring this award to the attention of your students.
Chesapeake Community Model Program
http://ches.communitymodeling.org/
Chesapeake Research Consortium
Edgewater, MD
410-798-1283