About CD-ROM:
Usage Information and Help Document

Data acknowledgement Policy

The data available from the CD-ROM data report are intended solely for scholarly use by the academic and scientific community, with the express understanding that any such use will properly acknowledge the originating investigator(s) as noted in the supporting documentation accompanying each individual data set. Anyone wishing to use U.S. JGOFS data in a presentation, report, thesis or publication is encouraged to contact the originating Principal Investigator. It is expected that all customary courtesies and privileges attached to data use will be strictly honored.

Suggested citation format

Suggested CD-ROM citation format from Modern Language Association Style Manual and Guide to Scholarly Publishing (2nd Edition [http://www.mla.org/set_stl.html ]):

Author or editor's name. "Document title." Publication information for printed source. Title of CD-ROM. CD-ROM. Edition, release or version (if relevant). Place of publication: Publisher's name, Date of publication.

Suggested general format for citing data or documents from this CD-ROM is:
PI name(s). "Data set title." United States JGOFS Final Data Report: Process Study Data 1989-1998. CD-ROM. volume 1, version 2, Woods Hole Oceanographic Institution, USA: U.S. JGOFS Data Management Office, April 2003.

For example, this would be the suggested format to cite Cindy Lee's Sediment Trap data set from the Arabian Sea cruises:
Lee, Cindy. "Arabian Sea deep sea sediment trap particle flux, amino acid and pigment data." United States JGOFS Final Data Report: Process Study Data 1989-1998. CD-ROM. volume 1, version 2, Woods Hole Oceanographic Institution, USA: U.S. JGOFS Data Management Office, April 2003.

To cite the CD-ROM (not a specific article):
United States JGOFS Final Data Report: Process Study Data 1989-1998. CD-ROM. volume 1, version 2, Woods Hole Oceanographic Institution, USA: U.S. JGOFS Data Management Office, April 2003.

In situations where a printed reference is required, it may be possible to cite an EOS (Transactions of the American Geophysical Union) paper (in progress). The citation will be listed in this document when avaiable.

Using web browser interface to U.S. JGOFS CD-ROM Data Report

The Data Directory page, accessed by clicking on the data button in the navigation bar at the top of each page, contains links to a vast number of data and supporting documentation files pertaining to each of the four U.S. JGOFS basin level process study programs. The links on the process study specific Data Directory pages fall into three major categories: Metadata, Merged Products and individual data sets listed by major science discipline (i.e. Biology, Chemistry, etc.). All files can be easily saved from the CD-ROM to a file, and then accessed using an application appropriate for that file's format.

Under the heading of 'Metadata' one will find cruise and project level files of information about the data sets (i.e. cruise event logs and data inventories). Supporting metadata including parameter description, units of measurement, analytical methodology, PI notes, etc., is linked via the info button for each Data Type listed on the Data Directory pages. The INVENTORY data entities for each cruise are included for those investigators who may find it easier to think of the data organized by cruise.

Merged Products
Merged data products are, as the name implies, the merging into a single file of an array of parameters having a common sampling methodology. These products are derived from the individual data files listed under the major science disciplines described below. The merged products available in this report are the consolidation of observations made from water column profiling CTD and bottle sampling instrumentation. These single file products are basin/project scale in scope. A separate merged data product is reported for each bottle sampling type used during a basin study: trace-metal-free (TM), Niskin, and GoFlo.

A merged basin scale bottle file contains all of the parameters for a given bottle type sorted by cruise, date, time, station, cast, and finally bottle number and sampling depth. The two-decibar sorted CTD data is organized according to the same metadata parameters with the exception that there is no bottle number.

Biological, Chemical, Physical, Optics, Particulates, Sediment core, Sediment trap
Individual data files received by the U.S. JGOFS Data Management Office from the submitting PI have each been assigned to one of the data categories listed above. Each of these files has been quality controlled and documented through the efforts of the PIs with support from the U.S. JGOFS DMO. The user community should use the Description field to aid in identifying data sets of interest. The cruise event log reported for each cruise should be consulted for date, time, and position information for each sampling event/station.

Using JGView (Java) interface to U.S. JGOFS CD-ROM Data Report

JGView, a custom Java application, permits user-specified selection of data from the CD-ROM. JGView provides a 'Search' function to help locate data of interest, the ability to subselect a dataset based on user-specified criteria and the option to export the subselected data in a variety of formats including Ocean Data View (ODV) and Matlab. Updates to JGView documentation will be posted here as they become available.

  JGView documentation (User Guide and Installation Instructions)

Accessing data

Most data file names are a combination of data type and cruise identification (i.e. bottle_nbp964 for Niskin bottle data from cruise NBP 96-4). Data which does not fit neatly into a single cruise or for which the collection technique might span several cruises, e.g. sediment trap data, are labeled with the process study name appended to the data type name (i.e. '_nabe'), because they are not associated with any single specific cruise.

The majority of data entities have an obvious association with a particular oceanographic discipline. However, because some include a variety of parameters, their 'Data Type' category is less clear. For example, CTD data has been placed in the 'Physical' data category. While the CTD data entities predominantly include parameters having a relationship to physical oceanography, they may also include parameters such as dissolved oxygen, beam attenuation, PAR or fluorescence, which have associations to other oceanographic disciplines. Likewise, the CTD/Niskin bottle data file is predominantly Chemistry data and has been listed in the 'Chemical' data category.

If you are having difficulty locating a particular type of data, try using the browser's 'Find in Page' function (usually available as an Edit menu item), while viewing the Data Directory page for a basin study. You may want to try JGView, the custom JAVA application, which provides a 'Search' function to locate data sets that include a user-specified keyword or parameter name.

Descriptions of the data and any notes from the Principal Investigator are found in documents listed on the right side of the Data Directory table under 'Description' and are accessed by clicking on the adjacent info button.

Most links refer to documents included on the CD-ROM. Linked documents which are not physically included on this disc are indicated by a blue arrow and will open a new browser window.

Additional applications that may be required:
Acrobat Reader is required to read PDF files. Click on the logo, to download the free reader now.

Other information available in this data report

Additional information can be accessed by clicking on the buttons in the navigation bar appearing atop most pages of this report.

  for general information about the U.S. JGOFS program

  to access this page of instructions for using this data report

  for a description of the U.S. JGOFS scientific research program

  for a list of U.S. JGOFS publications

  to go directly to the U.S. JGOFS data directory page (complete explanation above)

The 'sub-nav' bar provides access to supplementary information contained in this report.

HOME   returns to the first page (back to where you started)
CONTACTS   lists U.S. JGOFS contact information (addresses)
RELATED LINKS   lists web pages of sites related to U.S. JGOFS
SITE INDEX   is a navigable table of contents for this report
HELP   is a link to this page of instructions

Platforms tested

This CD-ROM is ISO-9660 compliant with Rock Ridge (anonymous), 30 character filename and Joliet (Windows) extensions. The file content was developed using Macromedia Dreamweaver 4.0 (HTML 4.0 Transitional//EN syntax) on a Windows 2000 system with Internet Explorer 6.0 and Netscape 4.76.

This CD-ROM has been tested on and can be viewed using the following combinations of operating systems and web browser clients:
Windows 2000 v5.0 SP3, IE 6.0, Netscape 4.76, Netscape 7.0.2, JRE: J2RE 1.4.0
(2GHz with 512 MB RAM and 1GHz with 256 MB RAM)
Windows XP, IE 6.0, Netscape 6.2, Netscape 4.79, JRE: J2RE 1.4.0
Windows 98, IE 5.0, Netscape 4.5, JRE v1.3.1 (128 and 192 MB RAM)
Macintosh OS 9, IE 4.5, IE 5.2, Netscape 4.78
Macintosh OS X v10.2.4, IE 5.2.2 Netscape 4.78 and 7.02, Java 1.4.1
(867 MHz PowerPC G4, 512 MB RAM)
Linux Red Hat 7.2, Netscape 4.79
Linux Red Hat 7.3, Netscape 4.79
Solaris 7 (SunOS 5.7), Netscape 4.75, JRE: J2SE 1.4.1 (Sparc 10, 96 MB RAM !)
Solaris 8 (SunOS 5.8), Netscape 4.78, JRE: J2SE 1.4.1 (Ultra Sparc 5, 512 MB RAM)
IRIX 6.5, Netscape 4.78, Java2 JRE 1.3.1_02
(Origin 200/dual 180 MHz with 640 MB RAM and O2/250 MHz with 256 MB RAM)

Known Issues

The pages of this report are content-rich and are best viewed at a high screen resolution. The documents were developed using a 1600 x 1200 display setting and are best viewed on a screen set to at least 1280 x 1024 with 16 bit color.

In some configurations one receives a message when opening welcome.htm: "Cannot find welcome.htm or one of it's components" (or a variation of same). The file will most likely open anyway and you may continue navigating the CD-ROM without serious side-effects.

Sometimes after clicking on a link from the data directory pages, a page is returned which lists the file system contents of a data directory. If this happens, simply use the browser [Back] button to return to the previous page and try clicking the same link again. The second try usually returns the desired page.

IE 6 on Windows 2000: can not right-click or SHIFT-Click to download the data or supporting documentation files from the Data Directory pages. Click on the link to view the file and then use 'File->Save As' to copy the file to your local disk.

For some pages, Netscape 4.7x on Windows 2000 does not change the color for links that have already been visited, because it is not using the style sheet specifications. This behavior has been fixed in Netscape 7.0.

Mac OS sometimes 'disappears folders from the CD-ROM'. If you suddenly receive error messages about files not found, try ejecting the CD-ROM from the drive and then reinserting the disc and trying again.

Internet Explorer on MacOS may not be able to open the .tsv format data files until you have specified the appropriate Helper Application.

  MacOS/IE: specifying helper applications