Andrew J. Davies, Kim S. Last, Karl Attard, Vicki J. Hendrick

Many aquatic organisms rely on the suspension of particulate matter for food or for building materials, yet these conditions are difficult to replicate in laboratory mesocosms. Consequently, husbandry and experimental conditions may often be sub-optimal. The VOrtex Resuspension Tank (VORT) is a simple and reliable system for the resuspension of food or sediments using an enclosed airlift. The particle rain from the lift is mixed in the tank by two water inputs that provide directional current flow across the study organism(s). The vortex mixing creates a turbulent lateral water flow that allows the distribution of particulate matter outwards from the sediment outflow. By calibrating a VORT it is possible to control sedimentation rate by manipulating water and air flow rates. As an example application, three VORTs were maintained under different sediment loading to assess the sediment fraction utilisation and tube growth rates of the tube-building polychaete worm Sabellaria spinulosa. S. spinulosa consistently utilised a lower mean particle size than that of the background sediment when provided with well sorted medium sands. Under sediment starved conditions, there was net erosion of colonies whereas under intermediate and high sediment rates there was consistent cumulative growth throughout a 15 d experiment. This highlights the importance of suspended sediment for S. spinulosa and also the suitability of the VORT system for maintaining organisms with suspended matter requirements.

Publication in Journal of Experimental Marine Biology and Ecology 370.

Request PDF

Full citation

Davies, A.J., Last, K.S., Attard, K. & Hendrick, V.J. (accepted) “Maintaining turbidity and current flow in laboratory aquarium studies, a case study using Sabellaria spinulosa” Journal of Experimental Marine Biology and Ecology 370, 35-40.

http://dx.doi.org/10.1016/j.jembe.2008.11.015

Just been working with my favourite language to change a space delimited file into a comma delimited file (CSV). With large files, even good file editors like JujuEdit take forever. For the first time I have actually crashed this program whilst searching and replacing a 250mb file. Maybe it’s me?!

To avoid this problem reoccuring, and because I have not updated my site in a while, here is a nifty perl one-liner to search and replace spaces with comma-space.

First install a perl package, I use ActivePerl. Its free and easy to install on Windows (there are many different OS versions available).

Second, after the install has completed, open up the Windows command prompt (Start > Run > cmd). Change the directory to your working directory that contains the files that you wish to search and replace. For example (in blue):

C:\>cd c:\perl\myworkingdir

Now your in your working directory, you need to type the following (in blue):

c:\perl\myworkingdir>c:\perl\bin\perl.exe -p -i.bak -e “s/ /, /g” filename.csv

Here is the breakdown:

• c:\perl\bin\perl.exe: Calls the perl program
• -p: Loops the search and replace through the file.
• -i.bak: Creates a backup file incase you make a mistake.
• -e: Makes the script directly executable.
• “s/ /, /g”: The expression to pattern match, in this case s means start of line / / is the space, , / is the string to replace it and g is to tell perl to run it on all the file, not just the first instance.
• filename.csv: The name of the file to search and replace.