TITLE: Feedstocks-to-Fuels Labman solid biomass dispensing protocol
AUTHORS: Tad Ogorzalek, Jennifer Gin, Christopher J Petzold

[DESCRIPTION]
This protocol details the steps necessary for aliquoting biomass for the Feedstocks-to-Fuels pipeline. Samples must be ground and put in scintillation or Sarstedt tubes prior to dispensing into the Micronic48 tubes. The tolerance is typically below 10%, but check the settings for the dispensing method you are using. Be sure to grind the biomass thoroughly to minimize clogs

[BEFORE_START]
You will need:
Dispensing method for your type of biomass
Input and mapping files
Ground biomass distributed into scintillation vials or Sarstedt tubes 


[GUIDELINES]
This protocol requires dispensing methods that are specific to a particular biomass and a particular distribution amount.  Confirm that the correct dispensing method is available prior to running this protocol.

A 2mm grind or smaller is recommended for all biomass to prevent the robot from clogging.

If the biomass of interest has a tendency to form needles or a tendancy to “clump”, performing a grinding protocol on the Labman prior to running this method is recommended.

As a general rule of thumb, a full scintillation tube can hold ~4.5g of biomass.  To ensure success, do not map more than 4g of biomass from a full scintillation tube to destination tubes. This means, for example, If you are adding ~0.2 g per destination tube, then each source tube should map to no more than 10 destination tubes.

It takes ~ 1 min to distribute ~0.2 g of biomass into each Micronic48 tube.  This means that it will take ~ 1 hour to complete a full plate.

[STEPS]
SECTION: Run Configuration - Process Parameters (middle left side)
3. 
Process Parameters:

Input Filename - Input csv file
Manual Mapping Filename - manual mapping csv file
Output File Path -  Output file path
Input filename - The input file ('Input Filename' option) is a csv file that tells the robot where the source vials will be located.  It has four columns.

 

SECTION: Starting a Run
6. Setting up the deck:

Place all source and destination tubes on the deck in the designated positions. 
Once the deck is set, close the doors completely.  They are all magnetic, and should click into place.  
Then click the big green button - located next to the FRONT emergency stop button.  

 

SECTION: Software Layout and Start Up
1. The graphical layout of this user interface (UI) is intended to resemble the deck of the Labman if you were facing the deck on the same side as the monitor.


If the software is already open when you start your run: click on the “Clear Racks” button of the “Function Buttons”. This will clear out settings from the previous run

If you opened the software yourself, click on the “Initialize” button of the “Function Buttons”.  This will allow all electronics to calibrate prior to the run.

 

SECTION: Run Configuration - Process Parameters (middle left side)
4. Manual Mapping filename - The “Manual Mapping” file is a csv file that assigns a source (or input) vial to a destination (or output) vial.  Note that these columns have labels, while the input file does not.

      OutputRack  OutputRackPosition  InputRack  InputRackPosition  DispenseWeight (g)  LiquidVolume (uL)    1  1  1  1  0.4  0    1  2  1  1  0.4  0    1  3  1  1  0.4  0    1  4  1  1  0.4  0    1  5  1  1  0.4  0    1  6  1  1  0.4  0    1  7  1  1  0.4  0    1  8  1  2  0.4  0    1  9  1  2  0.4  0    1  10  1  2  0.4  0    1  11  1  2  0.4  0    1  12  1  2  0.4  0    1  13  1  2  0.4  0    1  14  1  2  0.4  0    1  15  1  3  0.4  0  

SECTION: Run Configuration - Process Parameters (middle left side)
5. Output file path - Create a new file prior to each run with the date in the name.

 

SECTION: Run Configuration - Process Mode (top left corner)
2. Process Mode: - Select "FeedingOnly"
Mapping Mode - Select “Manual”
Input Vial Type - Select "Scintillation tube" or "Sarstedt tube" depending on the format of your samples
Output Vial Type - Select “Micronic 48”
SECTION: Starting a Run
7. Click the “Setup Run” button in the “Function Buttons” portion of the screen. 
 

SECTION: Starting a Run
8. Once this is complete, click the “Start” button of the “Function Buttons”.  You should see the following checkbox:
  

 

Clicking on 'OK' will initiate the run.