Limnology, Aquatic Ecology, Phytoplankton Resources

Below are some resources for doing work with limnology (the study of inland waters) /oceanography, aquatic ecology and just plain water! If you have any files that you would like me to post here, send 'em to me!

I banged on these tools for my thesis work and I'd hate to see all of this hard work go to waste. If you can use these tools, they are free for the taking. If you used them or learned something from them, please shoot me a note!

Please note, unless otherwise stated these are Windows files. If you are clever, you might find ways to make them cross platform though. If your browser starts to read the files, shift-click on them to save to files.

Update: As part of a hobby, I am contemplating creating a virtual aquatic ecology/physical limnology lab planner on this website. This will be a database where lesson plans and teaching materials are stored, queried and submitted. Maybe this resource would be useful for people presenting these classes, especially TAs. If you're interested, lemme know and I'll get off my fanny and build it sooner than later. Until then, here are some useful links:
  • Example of a data entry website using PHP and probably some open source DB
  • An excellent online lab manual

  • My online lab guidelines
  • Another online syllabus with guideline for each lab. The links are not underlined.
  • Another syllabus. No links
  • Ditto
  • UC-Davis online PDF lab manual

Here are tools for Everett Fee's (, 1993) phytoplankton production modeling applications.   
  • File generators in M$ Excel us Plus, DOS batch files for automation. The excel files will create the input files properly formatted for direct input into the applications. I have some 'controller' sheets that allow you input data as monthly averages for ALL input parameters. Included is a spreadsheet for the Great Lakes region that will create half-hour solar files for the entire year based upon percent of monthly cloud cover.
Here are some EndNote (bibliographic software, the best $100 you'll ever spend!) resources. These sources focus primarily on: Photoacclimation, diatoms, photosynthesis modeling, Lake Michigan, Asterionella, light history studies, remote sensing and methods in the study of phytoplankton.  
  • An import filter for importing references from the site (formerly CARL Uncover). I hacked this one together to import the 'download' format that you can mail yourself after a search
  • This is a slight derivation of the above where the RECORD identifiers are slightly different in the version that you can copy-n-paste from a view. Both seem require that you save a text file with the first line beginning with RECORD and each record separated by RECORD.
Here are some files that are useful for calculating photosynthetic parameters such Pmax (PM or PBm) and Alpha according to Jassby and Platt 1976 using the nonlinear capabilities of the stat program SYSTAT. Some time saving features have been implemented. There are many ways to make these more user friendly.   
Actions for Photoshop 5 that create water (not mine) WaterSet.atn
Actions that create better clouds (a work in progress) CloudSet.atn
A link to a page with lotsa limno links on it
Excel formula for calculating Julian day of the year from a date field
An Excel spreadsheet for calculating the Langelier Saturation Index used in the balancing of pool and spa waters. SaturationIndex.xls

A table of links with useful summaries of threads from various newgroups and listservs relating to the following topics:

  1. Phytoplankton/microscopy
  2. Geographical information science
  3. Linux and *NIX
Topic Click here Date Details Source Source-type


2001-12-23 Quality assurance and quality control in visual counts of phytoplankton abundance ALGAE-L listerv


2000-12-01 Summary of thread about using consumer digital cameras for digital microscopy. Additional resources inserted by me ALGAE-L listerv


2000-09-22 A thread regarding the philosophy of 'nuisance' algae and how to treat it ALGAE-L listserv


2001-11-29 A small list of freshwater algal taxonomy books/keys ALGAE-L listserv

j o h n z a s t r o w
updated 2001-Dec-26