Sensing only: optical sensor (photodiode, phototransistor) for new spectra, pH sensor
Actuation only: optical stimulation w/ new LED
Both: fluorescence measurements (LED/optical sensor pair), feedback driven optical stimulation
Can new hardware be fitted onto vial?
Hardware CAD files can be found here.
Can the eVOLVER provide necessary power to control actuator?
The base eVOLVER can provide 5V or 12V PWM signal to the vials.
Otherwise, look into changing the power supply.
Is the signal you are sensing strong enough to be sensed using the components you will use?
The best way to answer these questions is to go through the datasheets of components you are interested in integrating and breadboarding with the eVOLVER Motherboard. This will help you also establish and tune dynamic ranges for new sensing capabilities. Additionally, you can explore swapping in new power supplies for components with higher power consumption specs. Once you've established compatibility and feasibility, you can begin integrating a new experimental parameter for eVOLVER.
Each Arduino is connected to 2 SA slots so that culture parameters that require sensing/actuation can share data, but Arduino is still capable of controlling each SA slot individually.
If parameter requires only sensing or actuation, then its best to pair with parameters that also require sensing or actuation (i.e. stir) for efficient usage of Arduinos
If the experimental parameter is sensing a culture condition, plug in a ADC Board
If the experimental parameter is applying a stimulus to the culture, plug in a PWM Board
All Arduinos communicate with Raspberry Pi along same serial line and either look for tags/add tags associated with the parameter they’re responsible for controlling
Smart Sleeve 3D printed housing may need to be redesigned to fit components
Solder component leads to correct Component Mount Board (CMB) pins, which is set by slot position of SA slot(s)
E.g. If using SA slot 8, make sure that components leads are wired to position 8 on CMB
If parameter is for actuating, 'fields_outgoing' set to 17 (see example below):
If parameter is for sensing, fields_outgoing set to 2 (see example below):
DPU section of wiki goes in more depth on how to create culture control algorthms
Basically, you need to create a new method in the EvolverNamespace class
, which can be called in your custom control code
Example below using default stir parameter:
Make sure that the name you are using for the experimental parameter is consistent throughout this process. eVOLVER will pull a list of experimental parameters from the conf.yml to sort through incoming serial data and tag outgoing serial commands. Inconsistencies with naming will lead to issues later on!
Adding pH and Dissolved Oxygen Sensors
Light inducible protein domains have been used to dynamically control and rapidly prototype genetic networks24,52. Hardware for light inducible systems typically rely on batch culture, limiting experiments to a narrow time window in which all cells across an experiment are in exponential phase. Attempts at coupling continuous culture to light induction have been limited by throughput (1-2 cultures) and reconfigurability. Equipped with components for light induction, eVOLVER would uniquely enable long-term optogenetic perturbations in finely controlled growth phases across a large number of culture vessels. Due to the modularity of eVOLVER hardware components, integrating optogenetic control is straight forward and requires minor modifications to the system. Details on integrating LEDs into eVOLVER is described in more detail as the example modification in Supplementary Note 4.
Bulk fluorescence measurements have previously been demonstrated by Takahashi et al. during continuous culture, without the use of a photomultiplier tube (PMT)7. To recapitulate this setup in eVOLVER, an extra LED-diode pair would be added to the 6th and 7th S/A Slots, similar to adding LEDs for light induction. Additionally, the 3D printed part would be modified to house optical filters for better detection of any fluorescence signal. Potential setbacks in this setup (without a PMT) include potentially a low signal to noise ratio.
This can be solved by multiplexing signal from all cultures into a single PMT via fiber optics. The electronics controlling the PMT would communicate back to the same RS485 line to be controlled by the same Raspberry Pi, similar to the auxiliary board. Alternatively, single cell fluorescence measurements would also be made possible by interfacing eVOLVER with a pipetting robot, droplet microfluidics, or using the native pump from the flow cytometer sample directly from the cultures. These systems could interface serially with the Raspberry Pi via RS485/USB or the lab computer via USB.