PICES Press, Vol. 10, No. 2, July 2002

International symposium on North Pacific transitional areas [pp. 1-4] [pdf, 0.8 Mb] PICES Volunteer Observing Ship (VOS) Workshop [pp. 5-7] [pdf, 0.3 Mb] Joint meeting on Causes of marine mortality of salmon [pp. 8-9] [pdf, 0.3 Mb] The state of the western North Pacific in the second half of 2001 [pp. 10-11] [pdf, 0.5 Mb] State of the eastern North Pacific in spring 2002 [pp. 12-13] [pdf. 0.4 Mb] The status of the Bering Sea in the second half of 2001 [pp. 14-15] [pdf. 0.3 Mb] PICES Workshop on “Perturbation analysis” on subarctic Pacific gyre ecosystem models [pp. 16-17] [pdf. 0.4 Mb] Status and future plans for SOLAS-Japan [pp. 18-20] [pdf. 0.5 Mb] China-Korea Joint Ocean Research Center: A bridge across the Yellow Sea to connect Chinese and Korean oceanographic institutes and scientists [pp. 21-22] [pdf. 0.3 Mb] Persistent changes in the California Current ecosystem [pp. 23-24] [pdf. 0.2 Mb] The Hokusei Maru: 53 years of research in the Pacific [pp. 25-28] [pdf. 0.5 Mb] First meeting of the CLIVAR Pacific Panel [pp. 29-30] [pdf. 0.3 Mb] Call for contributions to the North Pacific Ecosystem Status Report [p. 31] [pdf. 0.2 Mb] PICES announcements [p. 32] [pdf. 0.2 Mb]

Using forecasts to protect Federal facilities in the path of Hurricane Isabel

Hurricane Isabel made landfall as a Category 2 Hurricane on 18 September 2003, on the North Carolina Outer Banks between Cape Lookout and Cape Hatteras, then coursed northwestward through Pamlico Sound and west of Chesapeake Bay where it downgraded to a tropical storm. Wind damage on the west and southwest shores of Pamlico Sound and the western shore of Chesapeake Bay was moderate, but major damage resulted from the storm tide. The NOAA, National Ocean Service, National Centers for Coastal Ocean Sciences, Center for Coastal Fisheries and Habitat Research at Beaufort, North Carolina and the Center for Coastal Environmental Health and Biomedical Research Branch at Oxford, Maryland have hurricane preparedness plans in place. These plans call for tropical storms and hurricanes to be tracked carefully through NOAA National Weather Service (NWS) watches, warnings, and advisories. When a hurricane watch changes to a hurricane warning for the areas of Beaufort or Oxford, documented hurricane preparation plans are activated. Isabel exacted some wind damage at both Beaufort and Oxford. Storm tide caused damage at Oxford, where area-wide flooding isolated the laboratory for many hours. Storm tide also caused damage at Beaufort. Because of their geographic locations on or near the open ocean (Beaufort) or on or near large estuaries (Beaufort and Oxford), storm tide poses a major threat to these NOAA facilities and the safety of federal employees. Damage from storm surge and windblown water depends on the track and intensity of a storm. One tool used to predict storm surge is the Sea, Lake, and Overland Surges from Hurricanes (SLOSH) model of the NWS, which provides valuable surge forecasts that aid in hurricane preparation.

User’s Guide to ADMB2R: A Set of AD Model Builder Output Routines Compatible with the R Statistics Language

ADMB2R is a collection of AD Model Builder routines for saving complex data structures into a file that can be read in the R statistics environment with a single command.1 ADMB2R provides both the means to transfer data structures significantly more complex than simple tables, and an archive mechanism to store data for future reference. We developed this software because we write and run computationally intensive numerical models in Fortran, C++, and AD Model Builder. We then analyse results with R. We desired to automate data transfer to speed diagnostics during working-group meetings. We thus developed the ADMB2R interface to write an R data object (of type list) to a plain-text file. The master list can contain any number of matrices, values, dataframes, vectors or lists, all of which can be read into R with a single call to the dget function. This allows easy transfer of structured data from compiled models to R. Having the capacity to transfer model data, metadata, and results has sharply reduced the time spent on diagnostics, and at the same time, our diagnostic capabilities have improved tremendously. The simplicity of this interface and the capabilities of R have enabled us to automate graph and table creation for formal reports. Finally, the persistent storage in files makes it easier to treat model results in analyses or meta-analyses devised months—or even years—later. We offer ADMB2R to others in the hope that they will find it useful. (PDF contains 30 pages)

User’s Guide to C2R: A Set of C Language Output Routines Compatible with the R Statistics Language

C2R is a collection of C routines for saving complex data structures into a file that can be read in the R statistics environment with a single command.1 C2R provides both the means to transfer data structures significantly more complex than simple tables, and an archive mechanism to store data for future reference. We developed this software because we write and run computationally intensive numerical models in Fortran, C++, and AD Model Builder. We then analyse results with R. We desired to automate data transfer to speed diagnostics during working-group meetings. We thus developed the C2R interface to write an R data object (of type list) to a plain-text file. The master list can contain any number of matrices, values, dataframes, vectors or lists, all of which can be read into R with a single call to the dget function. This allows easy transfer of structured data from compiled models to R. Having the capacity to transfer model data, metadata, and results has sharply reduced the time spent on diagnostics, and at the same time, our diagnostic capabilities have improved tremendously. The simplicity of this interface and the capabilities of R have enabled us to automate graph and table creation for formal reports. Finally, the persistent storage in files makes it easier to treat model results in analyses or meta-analyses devised months—or even years—later. We offer C2R to others in the hope that they will find it useful. (PDF contains 27 pages)

User’s Guide to For2R: A Module of Fortran 95 Output Routines Compatible with the R Statistics Language

For2R is a collection of Fortran routines for saving complex data structures into a file that can be read in the R statistics environment with a single command.1 For2R provides both the means to transfer data structures significantly more complex than simple tables, and an archive mechanism to store data for future reference. We developed this software because we write and run computationally intensive numerical models in Fortran, C++, and AD Model Builder. We then analyse results with R. We desired to automate data transfer to speed diagnostics during working-group meetings. We thus developed the For2R interface to write an R data object (of type list) to a plain-text file. The master list can contain any number of matrices, values, dataframes, vectors or lists, all of which can be read into R with a single call to the dget function. This allows easy transfer of structured data from compiled models to R. Having the capacity to transfer model data, metadata, and results has sharply reduced the time spent on diagnostics, and at the same time, our diagnostic capabilities have improved tremendously. The simplicity of this interface and the capabilities of R have enabled us to automate graph and table creation for formal reports. Finally, the persistent storage in files makes it easier to treat model results in analyses or meta-analyses devised months—or even years—later. We offer For2R to others in the hope that they will find it useful. (PDF contains 31 pages)

A scientific forum on the Gulf of Mexico: The Islands in the Stream Concept. Proceedings of the Forum: 23 January 2008, Keating Education Center, Mote Marine Laboratory, Sarasota, Florida

The Scientific Forum on the Gulf of Mexico: The Islands in the Stream Concept took place in January 2008 in Sarasota, Florida. The purpose of the meeting was to bring together scientists and managers from around the Gulf of Mexico to discuss a range of topics on our knowledge of the Gulf of Mexico, from its geology to larger-scale connectivity to the Caribbean region, and their applications to the concept of a more integrated approach to area-based management. The forum included six panels of invited experts who spoke on the oceanographic and biological features in the Gulf of Mexico, including connections with Mexico and the Mesoamerican barrier reef system, and the legal and regulatory structure currently in place. The charge to the group was to share information, identify gaps in our knowledge, identify additional potential areas for protection, and discuss available science about connectivity and the potential value of establishing a marine protected area network in the Gulf of Mexico. (PDF has 108 pages.)

Atlas of abundance and distribution patterns of ichthyoplankton from the Northeast Pacific Ocean and Bering Sea ecosystems: based on research conducted by the Alaska Fisheries Science Center (1972–1996)

This regional atlas summarizes and illustrates the distribution and abundance patterns of fish eggs and larvae of 102 taxa within 34 families found in the Northeast Pacific Ocean including the Bering Sea, Gulf of Alaska, and U.S. west coast ecosystems. Data were collected over a 20+ year period (1972–1996) by the Recruitment Processes Program of the Alaska Fisheries Science Center (AFSC). Ichthyoplankton catch records used in this atlas were generated from 11,379 tows taken during 100 cruises. For each taxon, general life history data are briefly summarized from the literature. Published information on distribution patterns of eggs and larvae are reviewed for the study area. Data from AFSC ichthyoplankton collections were combined to produce an average spatial distribution for each taxon. These data were also used to estimate mean abundance and percent occurrence by year and month, and relative abundance by larval length and season. Abundance from each tow was measured as catch per 10 m2 surface area. A larval distribution and abundance map was produced with a geographic information system using ArcInfo software. For taxa with identifiable pelagic eggs, distribution maps showing presence or absence of eggs are presented. Presence or absence of adults in the study area is mapped based on recent literature and data from AFSC groundfish surveys. Distributional records for adults and early life history stages revealed several new range extensions. (PDF file contains 288 pages.)

The Marine Science Library, Resource Center : poster presentation

The first concept of a new library was introduced in 2001 by a faculty member at the University of Texas Marine Science Institute. The suggestion for the construction of a new library was based on two specific reasons: existing library is located in one of the most vulnerable buildings to hurricane damage and the library has outgrown its current space. This presentation provides a general overview of the current status and changing needs of the Marine Science Library and how the idea of a new library finally became a reality

Impact pathway analysis for research planning: the case of aquatic resources research in the WorldFish Center

In line with its mandate of poverty reduction and sustainable development, the WorldFish Center is orienting its research towards high impact scientific activity. Identifying such activities is the task of prospective impact assessment, in turn based on impact pathway analysis. The paper describes a framework for analyzing benefits from aquatic resources research, the relevant research categories, pathways to impact by category, and indicators along each pathway that can be estimated in order to quantify probable research impact.

Investing in Africa: the WorldFish Center's African strategy in summary

Across much of Africa, freshwater and coastal fisheries provide an important source of food and livelihood for many millions of people. In addition, the aquaculture potential of the continent has only recently begun to be developed. To help sustain these capture fisheries, support the emergence of aquaculture and foster the contribution of both to sustainable livelihoods and improved food security, the WorldFish Center is increasing its investment in Africa. The framework for this investment is provided by a new Strategy for Africa and West Asia 2002-2006 that identifies priorities for the Center’s work in rivers and floodplains, lakes and reservoirs, coastal fisheries, aquaculture, policy research and capacity building. The present article summarizes the issues being addressed by the Center and describes initial research priorities.

Catching and rearing postlarval cleaner shrimp for the aquarium trade: results from a WorldFish Center project in Solomon Islands

Between 1999 and 2003, the WorldFish Center in Solomon Islands conducted research into the feasibility of a new fishery based on the capture and culture of postlarval coral reef fish for the live fish trade. The work was carried out in two phases: a research phase from late 1999 to the end of 2002; and a “finetuning” phase in 2003. Most of the species were of value to the marine aquarium trade, with very few live reef food fish recorded. The most valuable ornamentals were the banded cleaner shrimp, Stenopus species. Cleaner shrimp were harvested using crest nets, the method being modified with the addition of a solid, water-retaining cod-end designed to increase survival at capture. Grow-out techniques were improved by rearing the shrimp separately in jars to prevent aggression. The jars were painted black to protect the shrimp from sunlight. An economic model using experimental catch data and farm gate prices indicates that the fishery based on shrimp, supplemented with small numbers of lobster and fish is economically viable. The next step will be setting up a demonstration farm in a village in the Western Province of Solomon Islands.

A History of Benthic Research in the NMFS Northeast Fisheries Science Center

The Northeast Fisheries Science Center of NOAA's National Marine Fisheries Service has a long history of research on benthic invertebrates and habitats in support of the management of living marine resources. These studies began in the 1870's under Spencer F. Baird's guidance as part of an effort to characterize the Nation's fisheries and living marine resources and their ecological interactions. This century and a quarter of research has included many benthic invertebrate studies, including community characterizations, shellfish biology and culture, pathology, ecosystem energy budget modeling, habitat evaluations, assessments of human impacts, toxic chemical bioaccumulation in demersal food webs, habitat or endangered species management, benthic autecology, systematics (to define new species and species population boundaries), and other benthic studies. Here we review the scope of past and current studies as a background for strategic research planning and suggest areas for further research to support NOAA's goals of sustainable fisheries management, healthy coastal ecosystems, and protected species populations.