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Chesapeake Community Modeling Program the new CCMP Newsletter | August 2008 Volume 1, Issue 3 |
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Introduction We all hate spam, and the CCMP does not want to contribute to the flood of unwanted emails. You have received this newsletter because of your presence on the CCMP mailing list, meaning you have participated in a past community event or otherwise expressed interest in CCMP (if not, you can opt out here). |
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Contents 1. CCMP
News in brief |
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1. CCMP News in brief CCMP By-Laws The Draft of CCMP Governance Rules has been pre-approved by the CCMP Steering Committee and is now available for the CCMP Members to explore. You can view the draft by logging in at the MyCCMP webpage. We are very interested in your comments and suggestions. In two months the draft will be submitted to the Membership for approval. Dave Potsiadlo
takes off on new career With much chagrin, we announce the departure of the CCMP administrative assistant, David Potsiadlo. Dave was instrumental in delivering CCMP to the web. With his arrival, the CCMP acquired the look and feel that we enjoy today. More recently, he has made a huge jump mastering more advanced web programming skills that brought new functionality to our web pages. We enjoyed working with you, Dave. Best wishes in your future work. LTRANS Yet another addition to the CCMP family of open source models - LTRANS, the Larval TRANSport Lagrangian model - is an off-line particle-tracking model that runs with the stored predictions of a 3D hydrodynamic model, specifically the Regional Ocean Modeling System (ROMS). LTRANS has also been implemented for a finite element hydrodynamic model (QUODDY) but the code is not quite ready for release. Although LTRANS was built to simulate oyster larvae, it can easily be adapted to simulate transport of passive particles and other plankton. LTRANS is written in Fortran 90. It includes a 4th order Runge-Kutta scheme for particle advection and a random displacement model for vertical turbulent particle motion. Reflective boundary conditions, larval behavior, and settlement routines are also included. LTRANS was built by Elizabeth North and Zachary Schlag of the University of Maryland Center for Environmental Science Horn Point Laboratory. Check out the project web site here or download a flyer. iEMSs'08 International Congress The Biannual conference of the International Environmental Modeling and Software Society (iEMSs) featured a session and workshop on "Community modeling, data and model interoperability", organized among others by two CCMP Board members - Chris Duffy and Alexey Voinov. The session focused on
several issues relevant to CCMP, such as:
Other sessions at the conference included such topics as Data and Sensor Networks and Environmental Modeling, Intelligent Environmental Decision Support Systems, Integrated Catchment Management: How can modeling tools and techniques help?, Participatory and Conceptual Modelling – Making Models Amenable to Stakeholders’ Concerns, OpenMI Applications and Innovations, Environmental Modeling and Decision Support Systems, and others. The proceedings are available from the conference web site. 2. News from other communities At its Executive Meeting, the Community Surface Dynamics Modeling System (CSDMS) has discussed how CCMP and CSDMS might support overlapping community modeling efforts. There was excitement in having a Geographically-Focused Research Group (GFRG) associated with CSDMS and CCMP will set up a CCMP-GFRG within CSDMS, co-sponsored by CCMP and CSDMS. CCMP-GFRG would, therefore, have joint representation on the CCMP and CSDMS web sites, share models and data, have mutual access to the CSDMS High Performance Computer(s), receive updates and advice from the CSDMS Computational Team and their products, and receive CSDMS IF support of meetings/workshops. The activity might involve a subset of members of the CCMP, and once advertised, CSDMS community members that wished to support both the CSDMS and the CCMP visions through the GFRG. The CCMP-GFRG chair would report directly to the CSDMS and the CCMP Chair/Coordinator, and work with other CSDMS working group chairs and CCMP Steering Committee. For more information, visit the CFRG website. Alexey Voinov will serve as an interim chair of the CCMP-CFRG. At the same time, we will be looking for permanent chair and the CCMP SC is considering candidates. It can be a perfect opportunity for an early career scientist to get well connected to both communities. Please contact Alexey Voinov if interested. 3. Open Source News Ruling is a Victory
for Supporters of Free Software (The following is paraphrased from the NY
Times link below) The decision legitimizes the use of commercial contracts for the distribution of computer software and digital artistic works for the public good. The court ruling also bolsters the open-source movement by easing the concerns of large organizations about relying on free software from hobbyists and hackers who have freely contributed time and energy without pay. It also has implications for the Creative Commons license, a framework for modifying and sharing creative works that was developed in 2002 by Larry Lessig, a law professor at Stanford. Click here
to read the full text of the NY Times article by John Markoff Doxygen - an ultimate model and code
documentation tool Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. It can help you in
three ways: 1.It can generate an on-line documentation browser (in HTML) and/or an off-line reference manual (in $\mbox{\LaTeX}$) from a set of documented source files. There is also support for generating output in RTF (MS-Word), PostScript, hyperlinked PDF, compressed HTML, and Unix man pages. Documentation is extracted directly from the sources, which makes it much easier to keep the documentation consistent with the source code. 2.You can configure doxygen to extract the code structure from undocumented source files. This is very useful to quickly find your way in large source distributions. You can also visualize the relations between the various elements by dependency graphs, inheritance diagrams, and collaboration diagrams, all generated automatically. 3. You can even ‘abuse’ doxygen for creating normal documentation. Doxygen is developed under Linux and Mac OS X, but is set-up to be highly portable. As a result, it runs on most other Unix flavors as well. Furthermore, executables for Windows are available. An example is at http://ecolandmod.ifas.ufl.edu/models/doxy_ELM/index.html
4. Featured Blog Question: None We are not asking any questions this time as we have not received a single suggestion in response to our last question: "How can we improve the CCMP Newsletter?". This makes us think that either the Newsletter is perfect and there is no improvement needed. Or, perhaps, nobody cares and the newsletter is not read. If that is the case, then perhaps the Newsletter is not an asset for the community and not needed. To identify which option is correct, I will mail a $10 check to the first person who sends me an e-mail indicating that s/he actually read this paragraph in the Newsletter. 5. Featured Modeler: Don Weller Don Weller, SERC [homepage] Don Weller is a Senior Scientist and Principle Investigator at the Smithsonian Environmental Research Center (SERC). His research interests include: landscape ecology, nutrient transport and transformation in watersheds, the role of wetlands in moderating nutrient transport, relationships between watershed geography, and ecological condition of wetlands and streams.
Don was part of the Linden Group that brought the CCMP into a reality. He is still one the primary participants in CCMP, serving on the Steering Committee since the beginning of the program. 6. Featured Model: Our featured model in
this issue of the newsletter is:
The CBP Watershed model was one of the first to endorse the "community" approach and the model was designated the Chesapeake Bay Community Watershed Model several years ago. At its core, the model is an implementation of a well known model HSPF (Hydrological Simulation Program--Fortran) applied to and calibrated for the Chesapeake Bay watershed. The model has gone through many development cycles and is currently available as "Phase 5". The Phase 5 Chesapeake Bay Watershed Model has been intentionally designed to be made available through the web and has the following community model features:
With Phase 5 implementation, the model went far beyond the HSPF application, focusing on pre- and post-processing, calibration, more detailed spatial implementation, and computational efficiency. Through the watershed model, the CBP has become a strong supporter of the CCMP efforts: Lewis Linker and Gary Shenk (the latter on the CCMP Advisory Committee) are active participants in CCMP and promote ideals of open research and modeling. 7. Position announcement 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:
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. |
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Chesapeake Community Model Program |
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