9,292
edits
BISC209/F13: Lab3: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
→Community Carbon Source Utilization Profiling:
Tucker Crum (talk | contribs) |
Tucker Crum (talk | contribs) |
||
| Line 212: | Line 212: | ||
The data should be saved automatically in softmax pro, but please also save to our BISC209 folder on the desktop, labeling clearly with your group letter and the date. | The data should be saved automatically in softmax pro, but please also save to our BISC209 folder on the desktop, labeling clearly with your group letter and the date. | ||
Because the instrument computer is not networked, you will have to Save the data to a FLASH DRIVE. <BR> | Because the instrument computer is not networked, you will have to Save the data to a FLASH DRIVE to export it to your Sakai data file. <BR> | ||
Export the labeled data to the Flash drive | Export the labeled data to the Flash drive by clicking on the blue image of the plate in the upper left of the screen. From the menu that appears, click Export. Then Choose Plate1 and Output format PLATE raw (.txt). Click OK. Then SAVE AS with your site and date AND change the file type to .xls (not the default!). Save to the USB (D:) drive. | ||
Close the Spectromax software. DON'T SAVE! (You have already saved and exported adequately.)<BR> | Close the Spectromax software. DON'T SAVE! (You have already saved and exported adequately.)<BR> | ||
Shut off the SpectraMax spectrophotometer unless you know another group is waiting. DO '''NOT''' SHUT DOWN THE COMPUTER!!!<BR> | Shut off the SpectraMax spectrophotometer unless you know another group is waiting. DO '''NOT''' SHUT DOWN THE COMPUTER!!!<BR> | ||
Eject the Flash drive hardware properly by right clicking on the left image on the bottom of the computer's tool bar. If that doesn't work, go to Computer--USB (D:) Eject<BR> | |||
Remove Flash drive and take it to the lab computer facing the Spectromax and plug it into a USB port. | |||
<BR> | |||
'''DATA STORAGE:'''<BR> | |||
Open your team's Data folder from Sakai and download and open your group's Biolog data sheet. The file is called: BIOLOG-CMD_calc&GraphGroup__2013fa. <BR> | |||
Then EDIT: PASTE SPECIAL: TEXT the data carefully to your team's Excel spreadsheet making SURE that you are on the appropriate day (found in tabs on the bottom of the workbook). Note that each day that you collect data has a separate page in this spreadsheet.<BR> | |||
Copy and paste one column in the spectrophotometer 96 well format at time into your group's spreadsheet. After pasting column 1, 2 and 3 you will begin the next set of replicates (columns 4-6 then 7-9). <BR> | |||
'''This is a very important step because it aligns the replicate cells properly. '''<BR> | '''This is a very important step because it aligns the replicate cells properly. '''<BR> | ||
| Line 227: | Line 230: | ||
[[Image: Read2.jpg]] | [[Image: Read2.jpg]] | ||
When you have finished, | When you have finished, go to Finder and eject the Flashdrive from Devices. Wait for it to disappear. Please store the flash drive in the USB port in the computer on the Spectromax. If it is not there, send a message to the class to see if someone took it home by mistake and email your instructor. You can still transfer your data to your Sakai data folder if the disk is missing by reading off the data from the Spectromax computer to your open data Spreadsheet. (The 2 computer screens are close enough to allow that.) If you need to look at the Biolog template to see if you are transferring the appropriate cells you can pull it up from the Powerpoint intro for Lab 3 found in Resources in Sakai. It is crucially important that you align the right carbon source to its value (don't forget water) and get the right well numbers transferred to the appropriate position on the Worksheet DAY (1, 2,etc) in the template workbook. Note that the Template contains a separate worksheet (tabs on the bottom) for each day within the full workbook. Make sure that you fill out the appropriate day (DAY 0, 1, 2 etc). If you miss a day, leave that page blank. | ||
PRECAUTION: If you haven’t saved your data and another group reads their plate, your data will be overwritten and lost.<BR><BR> | PRECAUTION: If you haven’t saved your data and another group reads their plate, your data will be overwritten and lost.<BR><BR> | ||
DATA ANALYSIS:<BR> | |||
The Spreadsheet is pre-formatted with the calculations for these data. It includes the formulas to average replicate measurements each day and it will automatically subtract the background (readings in the water wells). There is a normalization for background that will be subtracted automatically (this threshold absorbance is 0.25 for each carbon source). We hope that including these pre-made calculations in the template will make your calculation of community metabolic diversity (CMD) and the data analysis of carbon source utilization patterns relatively uncomplicated. Please make sure you understand the EXCEL performed calculations. When you are sure that your data has been copied correctly into the appropriate template day, you will notice that the built in calculations will provide a final average absorbance reading for each substrate. | The Spreadsheet is pre-formatted with the calculations for these data. It includes the formulas to average replicate measurements each day and it will automatically subtract the background (readings in the water wells). There is a normalization for background that will be subtracted automatically (this threshold absorbance is 0.25 for each carbon source). We hope that including these pre-made calculations in the template will make your calculation of community metabolic diversity (CMD) and the data analysis of carbon source utilization patterns relatively uncomplicated. Please make sure you understand the EXCEL performed calculations. When you are sure that your data has been copied correctly into the appropriate template day, you will notice that the built in calculations will provide a final average absorbance reading for each substrate. | ||
