Using BioSoftLab to perform experiments

In order to run a physical experiment using the BioSoftlab interface to the physical lab, select the Physical Experiment scenario from the BioSoftlab main menu. BioSoftlab presents you with a software view of the physical lab and its equipment. The functionality of each virtual instrument is identical to that of its physical counterpart.

Entering the physical experimentation scenario

In order to setup and run a physical experiment, the user has to set up the physical lab: this includes filling up the reservoirs and the injection with the solutions used in the experiment. Now scientists may perform the rest of the set up remotely using the BioSoftlab interface to the physical laboratory. There are various types of information required by BioSoftlab:

  1. Enabling the equipment. Enabling the detector, enabling the controller, deciding whether to clear the loop or to perform an experiment.
  2. Programming the equipment. Programming the (virtual) controller in the same way one would program the physical Waters 600E Controller in the lab; selecting the operating mode of the (virtual) controller, specifying the flow rate of each solvent for each time step, etc.
  3. Setting up the PC for data acquisition. Running the data acquisition software on the (virtual) PC, specifying how the data should be gathered during the experiment.
This information is identical to the information the user would input to the actual equipment in the physical lab in order to set up a physical experiment. Since this input is sufficient to setup and run a physical experiment in the lab, it should also be sufficient to run a physical experiment using BioSoftlab. This is indeed the case.

Given this input, BioSoftlab has all the information required to run a physical experiment. After the experiment is started, BioSoftlab displays an animation of what is happening in the physical lab: the reservoirs empty, liquid flows through the column, etc. Currently, this animation information is calculated given the controller flow rate information. As the next step, we would like to communicate with the controller to acquire this information and display it in the same way on the BioSoftlab virtual instruments.

When the experiment is complete, BioSoftlab can be used to connect to the Waters PC and access the data which was collected. This data is displayed on BioSoftLab's virtual PC. After reviewing the data, the scientist can choose to record the experiment in an experiment database for later retrieval. The information saved in the database includes both the experimental input and output. For the information to be complete (so that we can re-create the experiment or compare it to some other experiment) we ask the user to provide the following information:

  1. Description of the physical makeup of the input solutions. In order to save the experiment in the database, information like the quantity of each solution used and a description of the chemical composition of each solution is required to fully describe the experiment.
  2. Physical description of the equipment used. Equipment like the tube connecting the column to the controller and the detector are non-standard, and different tubes could result in different data being generated. We request that the user provide all information relative to the tube, so that re- creating the exact experiment is possible.
The above data is information that an experimental scientist would need to record (in a notebook) to identify or re-create an experiment in the physical lab. Therefore, the information is also required here to fully identify an experiment within the database. Thus, BioSoftLab's database also becomes an "electronic notebook" or experiment depository.

During the implementation of this scenario, we encountered various problems related to the passing of information between the controller and BioSoftlab. This was particularly hard, since the Waters equipment was not designed to allow for remote control. Therefore, control via the virtual instruments was possible only by translating the user's input to the actual controller language. The ease of implementing a physical scenario, therefore, is directly related to the design and functionality of the actual physical equipment.

Another problem was more specific to interaction with the user. The virtual environment must be able to request the necessary information in such a way that even novice bioseparation scientists could supply the required input. The interaction between physical equipment is automatic, and we had to simulate the same inter-connection. If the user inputs a certain piece of information then we should be able to derive from it as much as possible, without asking the user to supply more than is absolutely necessary.