Chesapeake Community Modeling Program
the new CCMP Newsletter | August 2008
Volume 1, Issue 3
Introduction
We all hate spam. And we certainly do not want to be producing any. We don't want you to get this Newsletter unless you really want to get it. From now on the Newsletter will be no longer sent to the big spam list that we have collected over the years. It will be sent only to "members". However, we will be adding all the e-mail addresses that we have in our mail list to the membership list. We can't run the risk of loosing those of you are simply too busy to register as a memebr. This means that if you don't want to receive the letter, you will need to "unsubscribe" and remove yourself from the members list. Alternatively, just let us know and we will do it for you. Otherwise, stay with us and be informed about the latest knews of the Chesapeake Modeling Community.
Yet another development in member services is the opportunity to edit your submission of models and data into the CCMP repository. Just login as a member and you can edit the data base entries that you have created previously.
Contents
1. CCMP News in brief
2. News from other communities
3. Open Source News
4. Featured Blog Question: None
5. Featured Modeler: Don Weller
6. Featured Model: CBP Watershed Model
7. Position announcement at CCMP
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. Please login as a Member at our web site and take a look at the Draft. We are most interested in your comments and suggestions. In two months the draft will be put up for a vote by the Membership and will be enacted if approved.
Dave Potsiadlo takes off on new career
With much chagrin we announce the departure of the CCMP administrative assistant, David Potsiadlo. Dave was instrumental at making CCMP happen on 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 the more advanced web programming skills that brought a whole new level of 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 ready for release. Although LTRANS was built to simulate oyster larvae, it can easily be adapted to simulate passive particles and other plantonic organisms.
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 University of Maryland Center for Environmental Science Horn Point Laboratory.
Check out the project web site 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:
- Understanding the interoperability needs of the community in a participatory and collaborative effort;
- Developing research scenarios that would benefit from interoperability. Build consensus about interoperability architecture and standards supporting these scenarios;
- Expanding on environmental system observatory ontologies, in particular for mapping variables to concepts;
- Discussing common access protocols, enabling models to automatically search for data needed and link to data servers. Design data interoperability for model input/output to help link models.
Other sessions at the conference included such topics as Data and sensor networks and environmental modelling, Intelligent Environmental Decision Support Systems, Integrated Catchment Management: How can modelling tools and techniques help?, Participatory and Conceptual Modelling – Making Models Amenable to Stakeholders’ Concerns, OpenMI applications and innovations, Environmental Modelling 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 the overlapping community modeling efforts. There was excitement in having a Geographically-Focussed Research Group (GFRG) associated with CSDMS. CCMP will set up a CCMP-GFRG within CSDMS. CCMP-GFRG would be co-sponsored with CCMP and CSDMS. This means the CCMP-GFRG would have joint representation on the CCMP and CSDMS web sites, we will share models and data, we will have access to the CSDMS High Performance Computer(s), receive updates and advice from their Computational Team and their products, and receive CSDMS IF support of meetings/workshops. This might involve a subset of members of CCMP, and once advertised CSDMS community members that desired to support both the CSDMS vision and the CCMP vision 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.
The position of the CCMP-CFRG cahir is now vacant 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
SAN FRANCISCO, August 13, 2008 — In a ruling, the federal appeals court in Washington said that just because a software programmer gave his work away did not mean it could not be protected. This is seen as an important victory for the free software movement also known as open-source software.
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 Joh Markoff
Doxygen - an ulitmate 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:
- 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. The documentation is extracted directly from the sources, which makes it much easier to keep the documentation consistent with the source code.
- 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 means of include dependency graphs, inheritance diagrams, and collaboration diagrams, which are all generated automatically.
- You can even `abuse' doxygen for creating normal documentation (as I did for this manual).
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. We have not recieved 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 improvements needed. Or, perhaps, nobody cares and nobody actually reads it. If that is the case then perhaps we don't need the Newsletter at all. To check out which is the case, 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 . 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 is running the Ecological Modeling Lab at SERC. The Lab applies quantitative tools of spatial modeling and statistics to explore ecological questions about the factors controlling nutrient discharges from watersheds, the role of wetlands in moderating nutrient transport, and the relationships between watershed geography and the health of wetland or stream ecosystems.
Don was part of the Linden Group that has brought the CCMP into being. He is still one the major players in CCMP, serving on the Steering Committee since the very beginning of the program.
6. Featured Model: Chesapeake Bay Program's Watershed Model
Our featured model in this issue of the newsletter is:
Chesapeake Bay Program's Watershed Model
The Chesapeake Bay Watershed Model was developed to empower state and local governments, academics, and other interested parties to run their own decision scenarios for how the Chesapeake Bay Watershed can impact the Bay. Using this model, a group can determine the nutrient and sediment loads delivered to the Bay under various management strategies. By installing this model, supplying data on management practices, land use, and/or other relevant factors, and following the step to run the model, users can determine the loads that result.
The system is also meant as a jumping-off point for other types of investigations. For example, users may be interested in using a calibrated watershed model to investigate the effects of climate change on the Chesapeake Bay or a local region.
The CBP Watershed model was one of the first to endorse the "community" approach and the model became the Chesapeake Bay Community Watershed Model already several years ago. At it's core, the model is an implementation of a well known model called HSPF (Hydrological Simulation Program--Fortran) applied to and calibrated for the Chesapeake Bay watershed. The model went through many development cycles and currently is available as "Phase 5". Phase 5 Chesapeake Bay Watershed Model has been intentionally designed to be made available through the web and has the following community model features:
- Can be easily broken into smaller watersheds
- All open source (except MatLab postprocessor). Should be available from SourceForge shortly. Currently can be downloaded from the CCMP web site
- Broad user community during development
With Phase 5 the model went far beyond the HSPF application, focusing on pre- and post-processing, calibration, more detailed spatial implementation, and computational efficiency.
Very much through the watershed model, the CBP has become a strong supporter of the CCMP efforts. Lewis Linker and Gary Shenk are very active players in CCMP and do a lot to promote the ideas of open research and modeling.
7. Position announcement at CCMP
Applications are being sought for a technical assistant with stong IT skills to work with the Chesapeake Community Modeling Porgam (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 dutires include facilitating communications and assisting with logistical planning of workshops and presentations.
The position offers great opportunity to network with teams of outstanding scientists working in the Bay area, particiapte in research projects, and could be a great bridge position to prepare for graduate school.
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/resume to A. Voinov, at avoinov_at_uvm_dot_edu .
Chesapeake Community Model Program
http://ches.communitymodeling.org/
Chesapeake Research Consortium
Edgewater, MD
410-798-1283