Action triggering protocol


#1

I am a current student studying at the University of York in the UK. I have built a DropBot and I intend to use it for my project. I am looking at hybrid bio-electronic devices. My project involves implementing the use of a Flourometer to detect whether something has occurred.

I was wondering if there is any support for taking the data from another device and using it to control the DropBot software, basically making decisions based on another devices output?

What I am trying to do is measure luminescence of a droplet in order to ascertain whether a reaction has taken place, and if it has then move onto the next stage of the experiment. I have designed a photo-detector set-up with an LED, and I can get the data into the computer, but my issue is translating this data to an action within MicroDrop.

Any help would be greatly appreciated.

Thanks


#2

Hi Henry,

Conditional programming (e.g., making decisions in a protocol based on input from a sensor) isn’t currently supported in MicroDrop protocols; however, we’ve put together a bit of a hack-ish way to do this in another custom plugin that we’ve used to make a pseudo chemostat. It basically checks the state of a OD sensor on a particular step and based on that reading, it conditionally executes one of two “sub”-protocols. It may provide a good starting point for you to write your own plugin.

We’re planning to implement official support for conditionals as part of a new protocol standard, but don’t currently have the resources to throw at it right now. If anyone out there is interested in working on this, we’d be happy to provide some direction. As part of this effort, it would be helpful if you could put together a detailed use case for exactly what you want to do.

Thanks,
-Ryan

···

On Wed, Jan 11, 2017 at 6:29 AM, Henry Bissell henryb...@gmail.com wrote:

I am a current student studying at the University of York in the UK. I have built a DropBot and I intend to use it for my project. I am looking at hybrid bio-electronic devices. My project involves implementing the use of a Flourometer to detect whether something has occurred.

I was wondering if there is any support for taking the data from another device and using it to control the DropBot software, basically making decisions based on another devices output?

What I am trying to do is measure luminescence of a droplet in order to ascertain whether a reaction has taken place, and if it has then move onto the next stage of the experiment. I have designed a photo-detector set-up with an LED, and I can get the data into the computer, but my issue is translating this data to an action within MicroDrop.

Any help would be greatly appreciated.

Thanks

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#3

Ryan,

I cant seem to install that plugin in MicroDrop 2.4, do you have any instructions for installing custom plugins?

Henry

···

On Friday, 13 January 2017 14:17:11 UTC, Ryan Fobel wrote:

Hi Henry,

Conditional programming (e.g., making decisions in a protocol based on input from a sensor) isn’t currently supported in MicroDrop protocols; however, we’ve put together a bit of a hack-ish way to do this in another custom plugin that we’ve used to make a pseudo chemostat. It basically checks the state of a OD sensor on a particular step and based on that reading, it conditionally executes one of two “sub”-protocols. It may provide a good starting point for you to write your own plugin.

We’re planning to implement official support for conditionals as part of a new protocol standard, but don’t currently have the resources to throw at it right now. If anyone out there is interested in working on this, we’d be happy to provide some direction. As part of this effort, it would be helpful if you could put together a detailed use case for exactly what you want to do.

Thanks,
-Ryan

On Wed, Jan 11, 2017 at 6:29 AM, Henry Bissell henr...@gmail.com wrote:

I am a current student studying at the University of York in the UK. I have built a DropBot and I intend to use it for my project. I am looking at hybrid bio-electronic devices. My project involves implementing the use of a Flourometer to detect whether something has occurred.

I was wondering if there is any support for taking the data from another device and using it to control the DropBot software, basically making decisions based on another devices output?

What I am trying to do is measure luminescence of a droplet in order to ascertain whether a reaction has taken place, and if it has then move onto the next stage of the experiment. I have designed a photo-detector set-up with an LED, and I can get the data into the computer, but my issue is translating this data to an action within MicroDrop.

Any help would be greatly appreciated.

Thanks

You received this message because you are subscribed to the Google Groups “dropbot-dev” group.

To unsubscribe from this group and stop receiving emails from it, send an email to dropbot-dev...@googlegroups.com.

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#4

You’re right, sorry. I’ll take a look at updating it for compatibility with v2.x…

···

On Mon, Jan 16, 2017 at 8:33 AM, Henry Bissell henryb...@gmail.com wrote:

Ryan,

I cant seem to install that plugin in MicroDrop 2.4, do you have any instructions for installing custom plugins?

Henry

On Friday, 13 January 2017 14:17:11 UTC, Ryan Fobel wrote:

Hi Henry,

Conditional programming (e.g., making decisions in a protocol based on input from a sensor) isn’t currently supported in MicroDrop protocols; however, we’ve put together a bit of a hack-ish way to do this in another custom plugin that we’ve used to make a pseudo chemostat. It basically checks the state of a OD sensor on a particular step and based on that reading, it conditionally executes one of two “sub”-protocols. It may provide a good starting point for you to write your own plugin.

We’re planning to implement official support for conditionals as part of a new protocol standard, but don’t currently have the resources to throw at it right now. If anyone out there is interested in working on this, we’d be happy to provide some direction. As part of this effort, it would be helpful if you could put together a detailed use case for exactly what you want to do.

Thanks,
-Ryan

On Wed, Jan 11, 2017 at 6:29 AM, Henry Bissell henr...@gmail.com wrote:

I am a current student studying at the University of York in the UK. I have built a DropBot and I intend to use it for my project. I am looking at hybrid bio-electronic devices. My project involves implementing the use of a Flourometer to detect whether something has occurred.

I was wondering if there is any support for taking the data from another device and using it to control the DropBot software, basically making decisions based on another devices output?

What I am trying to do is measure luminescence of a droplet in order to ascertain whether a reaction has taken place, and if it has then move onto the next stage of the experiment. I have designed a photo-detector set-up with an LED, and I can get the data into the computer, but my issue is translating this data to an action within MicroDrop.

Any help would be greatly appreciated.

Thanks

You received this message because you are subscribed to the Google Groups “dropbot-dev” group.

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#5

I’ve updated the optical-detector-plugin code for compatibility with MicroDrop v2.0.

To build the python package, just clone the github repository and run the command:

python release.py

This should build the package optical_detector_plugin-2.x.tar.gz which you can install with from MicroDrop’s plugin manager by clicking on the Install plugin... button.

-Ryan

···

On Mon, Jan 16, 2017 at 9:27 AM, Ryan Fobel ry...@fobel.net wrote:

You’re right, sorry. I’ll take a look at updating it for compatibility with v2.x…

On Mon, Jan 16, 2017 at 8:33 AM, Henry Bissell henryb...@gmail.com wrote:

Ryan,

I cant seem to install that plugin in MicroDrop 2.4, do you have any instructions for installing custom plugins?

Henry

On Friday, 13 January 2017 14:17:11 UTC, Ryan Fobel wrote:

Hi Henry,

Conditional programming (e.g., making decisions in a protocol based on input from a sensor) isn’t currently supported in MicroDrop protocols; however, we’ve put together a bit of a hack-ish way to do this in another custom plugin that we’ve used to make a pseudo chemostat. It basically checks the state of a OD sensor on a particular step and based on that reading, it conditionally executes one of two “sub”-protocols. It may provide a good starting point for you to write your own plugin.

We’re planning to implement official support for conditionals as part of a new protocol standard, but don’t currently have the resources to throw at it right now. If anyone out there is interested in working on this, we’d be happy to provide some direction. As part of this effort, it would be helpful if you could put together a detailed use case for exactly what you want to do.

Thanks,
-Ryan

On Wed, Jan 11, 2017 at 6:29 AM, Henry Bissell henr...@gmail.com wrote:

I am a current student studying at the University of York in the UK. I have built a DropBot and I intend to use it for my project. I am looking at hybrid bio-electronic devices. My project involves implementing the use of a Flourometer to detect whether something has occurred.

I was wondering if there is any support for taking the data from another device and using it to control the DropBot software, basically making decisions based on another devices output?

What I am trying to do is measure luminescence of a droplet in order to ascertain whether a reaction has taken place, and if it has then move onto the next stage of the experiment. I have designed a photo-detector set-up with an LED, and I can get the data into the computer, but my issue is translating this data to an action within MicroDrop.

Any help would be greatly appreciated.

Thanks

You received this message because you are subscribed to the Google Groups “dropbot-dev” group.

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#6

Thanks Ryan,

I’ve managed to get it installed perfectly. I was wondering if you might be able to briefly describe the operation of the plugin? I don’t want to get anything wrong and damage experiments!

Thanks again,

Henry

···

On Monday, 16 January 2017 21:24:48 UTC, Ryan Fobel wrote:

I’ve updated the optical-detector-plugin code for compatibility with MicroDrop v2.0.

To build the python package, just clone the github repository and run the command:

python release.py

This should build the package optical_detector_plugin-2.x.tar.gz which you can install with from MicroDrop’s plugin manager by clicking on the Install plugin... button.

-Ryan

On Mon, Jan 16, 2017 at 9:27 AM, Ryan Fobel ry...@fobel.net wrote:

You’re right, sorry. I’ll take a look at updating it for compatibility with v2.x…

On Mon, Jan 16, 2017 at 8:33 AM, Henry Bissell henr...@gmail.com wrote:

Ryan,

I cant seem to install that plugin in MicroDrop 2.4, do you have any instructions for installing custom plugins?

Henry

On Friday, 13 January 2017 14:17:11 UTC, Ryan Fobel wrote:

Hi Henry,

Conditional programming (e.g., making decisions in a protocol based on input from a sensor) isn’t currently supported in MicroDrop protocols; however, we’ve put together a bit of a hack-ish way to do this in another custom plugin that we’ve used to make a pseudo chemostat. It basically checks the state of a OD sensor on a particular step and based on that reading, it conditionally executes one of two “sub”-protocols. It may provide a good starting point for you to write your own plugin.

We’re planning to implement official support for conditionals as part of a new protocol standard, but don’t currently have the resources to throw at it right now. If anyone out there is interested in working on this, we’d be happy to provide some direction. As part of this effort, it would be helpful if you could put together a detailed use case for exactly what you want to do.

Thanks,
-Ryan

On Wed, Jan 11, 2017 at 6:29 AM, Henry Bissell henr...@gmail.com wrote:

I am a current student studying at the University of York in the UK. I have built a DropBot and I intend to use it for my project. I am looking at hybrid bio-electronic devices. My project involves implementing the use of a Flourometer to detect whether something has occurred.

I was wondering if there is any support for taking the data from another device and using it to control the DropBot software, basically making decisions based on another devices output?

What I am trying to do is measure luminescence of a droplet in order to ascertain whether a reaction has taken place, and if it has then move onto the next stage of the experiment. I have designed a photo-detector set-up with an LED, and I can get the data into the computer, but my issue is translating this data to an action within MicroDrop.

Any help would be greatly appreciated.

Thanks

You received this message because you are subscribed to the Google Groups “dropbot-dev” group.

To unsubscribe from this group and stop receiving emails from it, send an email to dropbot-dev...@googlegroups.com.

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#7

Hi Henry,

I’ve added a high-level overview to the github page. You will probably need to comment out most of the content in that plugin since you don’t have the required hardware. Basically, it just shows an outline of how to run a “sub-protocol” on a given step dependent on a sensor reading.

-Ryan

···

On Tue, Jan 17, 2017 at 10:24 AM, Henry Bissell henryb...@gmail.com wrote:

Thanks Ryan,

I’ve managed to get it installed perfectly. I was wondering if you might be able to briefly describe the operation of the plugin? I don’t want to get anything wrong and damage experiments!

Thanks again,

Henry

On Monday, 16 January 2017 21:24:48 UTC, Ryan Fobel wrote:

I’ve updated the optical-detector-plugin code for compatibility with MicroDrop v2.0.

To build the python package, just clone the github repository and run the command:

python release.py

This should build the package optical_detector_plugin-2.x.tar.gz which you can install with from MicroDrop’s plugin manager by clicking on the Install plugin... button.

-Ryan

On Mon, Jan 16, 2017 at 9:27 AM, Ryan Fobel ry...@fobel.net wrote:

You’re right, sorry. I’ll take a look at updating it for compatibility with v2.x…

On Mon, Jan 16, 2017 at 8:33 AM, Henry Bissell henr...@gmail.com wrote:

Ryan,

I cant seem to install that plugin in MicroDrop 2.4, do you have any instructions for installing custom plugins?

Henry

On Friday, 13 January 2017 14:17:11 UTC, Ryan Fobel wrote:

Hi Henry,

Conditional programming (e.g., making decisions in a protocol based on input from a sensor) isn’t currently supported in MicroDrop protocols; however, we’ve put together a bit of a hack-ish way to do this in another custom plugin that we’ve used to make a pseudo chemostat. It basically checks the state of a OD sensor on a particular step and based on that reading, it conditionally executes one of two “sub”-protocols. It may provide a good starting point for you to write your own plugin.

We’re planning to implement official support for conditionals as part of a new protocol standard, but don’t currently have the resources to throw at it right now. If anyone out there is interested in working on this, we’d be happy to provide some direction. As part of this effort, it would be helpful if you could put together a detailed use case for exactly what you want to do.

Thanks,
-Ryan

On Wed, Jan 11, 2017 at 6:29 AM, Henry Bissell henr...@gmail.com wrote:

I am a current student studying at the University of York in the UK. I have built a DropBot and I intend to use it for my project. I am looking at hybrid bio-electronic devices. My project involves implementing the use of a Flourometer to detect whether something has occurred.

I was wondering if there is any support for taking the data from another device and using it to control the DropBot software, basically making decisions based on another devices output?

What I am trying to do is measure luminescence of a droplet in order to ascertain whether a reaction has taken place, and if it has then move onto the next stage of the experiment. I have designed a photo-detector set-up with an LED, and I can get the data into the computer, but my issue is translating this data to an action within MicroDrop.

Any help would be greatly appreciated.

Thanks

You received this message because you are subscribed to the Google Groups “dropbot-dev” group.

To unsubscribe from this group and stop receiving emails from it, send an email to dropbot...@googlegroups.com.

For more options, visit https://groups.google.com/d/optout.

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#8

Hi Ryan (and others)

I’ve taken over from Henry and have also managed to get the plug-in built and installed. I’ve also manged to comment out anything cause incompatibility with missing hardware. However, when I try to run the plug-in and the sub-protocol I consistently get an error saying "AttributeError: ‘NoneType’ object has no attribute ‘state_of_channels’. This is caused by line 403 in the plug-in which reads:

state = dmf_options.state_of_channels

dmf_options are defined as (line 400):

dmf_options = step.get_data('microdrop.gui.dmf_device_controller')

I’ve checked dmf-device-controller.py and can find no reference to state_of_channels, so I was wondering if something has gone wrong in an update and the array is actually named differently now? I found a function called “channel_states” in “dmf-control-board.py” which looks like the right thing but I’m unsure about how to call this in my plugin code.

Hope this makes sense and thanks in advance if anyone can help.

···

On Saturday, 21 January 2017 19:11:34 UTC, Ryan Fobel wrote:

Hi Henry,

I’ve added a high-level overview to the github page. You will probably need to comment out most of the content in that plugin since you don’t have the required hardware. Basically, it just shows an outline of how to run a “sub-protocol” on a given step dependent on a sensor reading.

-Ryan

On Tue, Jan 17, 2017 at 10:24 AM, Henry Bissell henr...@gmail.com wrote:

Thanks Ryan,

I’ve managed to get it installed perfectly. I was wondering if you might be able to briefly describe the operation of the plugin? I don’t want to get anything wrong and damage experiments!

Thanks again,

Henry

On Monday, 16 January 2017 21:24:48 UTC, Ryan Fobel wrote:

I’ve updated the optical-detector-plugin code for compatibility with MicroDrop v2.0.

To build the python package, just clone the github repository and run the command:

python release.py

This should build the package optical_detector_plugin-2.x.tar.gz which you can install with from MicroDrop’s plugin manager by clicking on the Install plugin... button.

-Ryan

On Mon, Jan 16, 2017 at 9:27 AM, Ryan Fobel ry...@fobel.net wrote:

You’re right, sorry. I’ll take a look at updating it for compatibility with v2.x…

On Mon, Jan 16, 2017 at 8:33 AM, Henry Bissell henr...@gmail.com wrote:

Ryan,

I cant seem to install that plugin in MicroDrop 2.4, do you have any instructions for installing custom plugins?

Henry

On Friday, 13 January 2017 14:17:11 UTC, Ryan Fobel wrote:

Hi Henry,

Conditional programming (e.g., making decisions in a protocol based on input from a sensor) isn’t currently supported in MicroDrop protocols; however, we’ve put together a bit of a hack-ish way to do this in another custom plugin that we’ve used to make a pseudo chemostat. It basically checks the state of a OD sensor on a particular step and based on that reading, it conditionally executes one of two “sub”-protocols. It may provide a good starting point for you to write your own plugin.

We’re planning to implement official support for conditionals as part of a new protocol standard, but don’t currently have the resources to throw at it right now. If anyone out there is interested in working on this, we’d be happy to provide some direction. As part of this effort, it would be helpful if you could put together a detailed use case for exactly what you want to do.

Thanks,
-Ryan

On Wed, Jan 11, 2017 at 6:29 AM, Henry Bissell henr...@gmail.com wrote:

I am a current student studying at the University of York in the UK. I have built a DropBot and I intend to use it for my project. I am looking at hybrid bio-electronic devices. My project involves implementing the use of a Flourometer to detect whether something has occurred.

I was wondering if there is any support for taking the data from another device and using it to control the DropBot software, basically making decisions based on another devices output?

What I am trying to do is measure luminescence of a droplet in order to ascertain whether a reaction has taken place, and if it has then move onto the next stage of the experiment. I have designed a photo-detector set-up with an LED, and I can get the data into the computer, but my issue is translating this data to an action within MicroDrop.

Any help would be greatly appreciated.

Thanks

You received this message because you are subscribed to the Google Groups “dropbot-dev” group.

To unsubscribe from this group and stop receiving emails from it, send an email to dropbot-dev...@googlegroups.com.

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#9

Hi Caspar,

Sorry, it’s been a while since we started this thread and the MicroDrop code has changed significantly in the meantime. Can you please remind me exactly what you are trying to achieve? You mentioned that you are doing some kind of measurement (luminescence), but what is the action you are trying to control? Do you want to wait until a condition is met before proceeding with a set protocol, or do you need to execute a different set of steps depending on the measurement result?

If you can provide a high level overview of what you are trying to achieve, we can hopefully suggest the easiest way forward.

Thanks,

-Ryan

···

On Mon, Jan 14, 2019 at 11:10 AM casper.kunstmann via dropbot-dev dropb...@googlegroups.com wrote:

Hi Ryan (and others)

I’ve taken over from Henry and have also managed to get the plug-in built and installed. I’ve also manged to comment out anything cause incompatibility with missing hardware. However, when I try to run the plug-in and the sub-protocol I consistently get an error saying "AttributeError: ‘NoneType’ object has no attribute ‘state_of_channels’. This is caused by line 403 in the plug-in which reads:

state = dmf_options.state_of_channels

dmf_options are defined as (line 400):

dmf_options = step.get_data('microdrop.gui.dmf_device_controller')

I’ve checked dmf-device-controller.py and can find no reference to state_of_channels, so I was wondering if something has gone wrong in an update and the array is actually named differently now? I found a function called “channel_states” in “dmf-control-board.py” which looks like the right thing but I’m unsure about how to call this in my plugin code.

Hope this makes sense and thanks in advance if anyone can help.

On Saturday, 21 January 2017 19:11:34 UTC, Ryan Fobel wrote:

Hi Henry,

I’ve added a high-level overview to the github page. You will probably need to comment out most of the content in that plugin since you don’t have the required hardware. Basically, it just shows an outline of how to run a “sub-protocol” on a given step dependent on a sensor reading.

-Ryan

On Tue, Jan 17, 2017 at 10:24 AM, Henry Bissell henr...@gmail.com wrote:

Thanks Ryan,

I’ve managed to get it installed perfectly. I was wondering if you might be able to briefly describe the operation of the plugin? I don’t want to get anything wrong and damage experiments!

Thanks again,

Henry

On Monday, 16 January 2017 21:24:48 UTC, Ryan Fobel wrote:

I’ve updated the optical-detector-plugin code for compatibility with MicroDrop v2.0.

To build the python package, just clone the github repository and run the command:

python release.py

This should build the package optical_detector_plugin-2.x.tar.gz which you can install with from MicroDrop’s plugin manager by clicking on the Install plugin... button.

-Ryan

On Mon, Jan 16, 2017 at 9:27 AM, Ryan Fobel ry...@fobel.net wrote:

You’re right, sorry. I’ll take a look at updating it for compatibility with v2.x…

On Mon, Jan 16, 2017 at 8:33 AM, Henry Bissell henr...@gmail.com wrote:

Ryan,

I cant seem to install that plugin in MicroDrop 2.4, do you have any instructions for installing custom plugins?

Henry

On Friday, 13 January 2017 14:17:11 UTC, Ryan Fobel wrote:

Hi Henry,

Conditional programming (e.g., making decisions in a protocol based on input from a sensor) isn’t currently supported in MicroDrop protocols; however, we’ve put together a bit of a hack-ish way to do this in another custom plugin that we’ve used to make a pseudo chemostat. It basically checks the state of a OD sensor on a particular step and based on that reading, it conditionally executes one of two “sub”-protocols. It may provide a good starting point for you to write your own plugin.

We’re planning to implement official support for conditionals as part of a new protocol standard, but don’t currently have the resources to throw at it right now. If anyone out there is interested in working on this, we’d be happy to provide some direction. As part of this effort, it would be helpful if you could put together a detailed use case for exactly what you want to do.

Thanks,
-Ryan

On Wed, Jan 11, 2017 at 6:29 AM, Henry Bissell henr...@gmail.com wrote:

I am a current student studying at the University of York in the UK. I have built a DropBot and I intend to use it for my project. I am looking at hybrid bio-electronic devices. My project involves implementing the use of a Flourometer to detect whether something has occurred.

I was wondering if there is any support for taking the data from another device and using it to control the DropBot software, basically making decisions based on another devices output?

What I am trying to do is measure luminescence of a droplet in order to ascertain whether a reaction has taken place, and if it has then move onto the next stage of the experiment. I have designed a photo-detector set-up with an LED, and I can get the data into the computer, but my issue is translating this data to an action within MicroDrop.

Any help would be greatly appreciated.

Thanks

You received this message because you are subscribed to the Google Groups “dropbot-dev” group.

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#10

Hi Ryan

Quite contrary, thanks for replying so quickly. Yes, I can imagine, and that would explain why so many references in the code come up empty…

Very briefly I want to be able to do some kind of conditional programming, but initially I’d be more than happy being able to simply run a protocol and then at a certain step have a “measurement” (in our case fluorescence via a PMT). Based on the readout and compared with a threshold one of two sub-protocols could be run. So really very similar to what was described here earlier. I’ve managed to read in the optical signal from a second Arduino Mega using the base-node-rpc plugin you guys have made, it’s simply a matter of controlling the sub-protocols and getting them to execute.

I’ll be happy to provide more details. Thanks again and look forward to hearing from you again,

\Casper

···

On Tuesday, 15 January 2019 19:16:45 UTC, Ryan Fobel wrote:

Hi Caspar,

Sorry, it’s been a while since we started this thread and the MicroDrop code has changed significantly in the meantime. Can you please remind me exactly what you are trying to achieve? You mentioned that you are doing some kind of measurement (luminescence), but what is the action you are trying to control? Do you want to wait until a condition is met before proceeding with a set protocol, or do you need to execute a different set of steps depending on the measurement result?

If you can provide a high level overview of what you are trying to achieve, we can hopefully suggest the easiest way forward.

Thanks,

-Ryan

On Mon, Jan 14, 2019 at 11:10 AM casper.kunstmann via dropbot-dev drop...@googlegroups.com wrote:

Hi Ryan (and others)

I’ve taken over from Henry and have also managed to get the plug-in built and installed. I’ve also manged to comment out anything cause incompatibility with missing hardware. However, when I try to run the plug-in and the sub-protocol I consistently get an error saying "AttributeError: ‘NoneType’ object has no attribute ‘state_of_channels’. This is caused by line 403 in the plug-in which reads:

state = dmf_options.state_of_channels

dmf_options are defined as (line 400):

dmf_options = step.get_data('microdrop.gui.dmf_device_controller')

I’ve checked dmf-device-controller.py and can find no reference to state_of_channels, so I was wondering if something has gone wrong in an update and the array is actually named differently now? I found a function called “channel_states” in “dmf-control-board.py” which looks like the right thing but I’m unsure about how to call this in my plugin code.

Hope this makes sense and thanks in advance if anyone can help.

On Saturday, 21 January 2017 19:11:34 UTC, Ryan Fobel wrote:

Hi Henry,

I’ve added a high-level overview to the github page. You will probably need to comment out most of the content in that plugin since you don’t have the required hardware. Basically, it just shows an outline of how to run a “sub-protocol” on a given step dependent on a sensor reading.

-Ryan

On Tue, Jan 17, 2017 at 10:24 AM, Henry Bissell henr...@gmail.com wrote:

Thanks Ryan,

I’ve managed to get it installed perfectly. I was wondering if you might be able to briefly describe the operation of the plugin? I don’t want to get anything wrong and damage experiments!

Thanks again,

Henry

On Monday, 16 January 2017 21:24:48 UTC, Ryan Fobel wrote:

I’ve updated the optical-detector-plugin code for compatibility with MicroDrop v2.0.

To build the python package, just clone the github repository and run the command:

python release.py

This should build the package optical_detector_plugin-2.x.tar.gz which you can install with from MicroDrop’s plugin manager by clicking on the Install plugin... button.

-Ryan

On Mon, Jan 16, 2017 at 9:27 AM, Ryan Fobel ry...@fobel.net wrote:

You’re right, sorry. I’ll take a look at updating it for compatibility with v2.x…

On Mon, Jan 16, 2017 at 8:33 AM, Henry Bissell henr...@gmail.com wrote:

Ryan,

I cant seem to install that plugin in MicroDrop 2.4, do you have any instructions for installing custom plugins?

Henry

On Friday, 13 January 2017 14:17:11 UTC, Ryan Fobel wrote:

Hi Henry,

Conditional programming (e.g., making decisions in a protocol based on input from a sensor) isn’t currently supported in MicroDrop protocols; however, we’ve put together a bit of a hack-ish way to do this in another custom plugin that we’ve used to make a pseudo chemostat. It basically checks the state of a OD sensor on a particular step and based on that reading, it conditionally executes one of two “sub”-protocols. It may provide a good starting point for you to write your own plugin.

We’re planning to implement official support for conditionals as part of a new protocol standard, but don’t currently have the resources to throw at it right now. If anyone out there is interested in working on this, we’d be happy to provide some direction. As part of this effort, it would be helpful if you could put together a detailed use case for exactly what you want to do.

Thanks,
-Ryan

On Wed, Jan 11, 2017 at 6:29 AM, Henry Bissell henr...@gmail.com wrote:

I am a current student studying at the University of York in the UK. I have built a DropBot and I intend to use it for my project. I am looking at hybrid bio-electronic devices. My project involves implementing the use of a Flourometer to detect whether something has occurred.

I was wondering if there is any support for taking the data from another device and using it to control the DropBot software, basically making decisions based on another devices output?

What I am trying to do is measure luminescence of a droplet in order to ascertain whether a reaction has taken place, and if it has then move onto the next stage of the experiment. I have designed a photo-detector set-up with an LED, and I can get the data into the computer, but my issue is translating this data to an action within MicroDrop.

Any help would be greatly appreciated.

Thanks

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#11

Hi Ryan

Sorry to pester you about this but I would love a few hints on how to move forward with this. I’ll be more than happy to provide more details, but all I essentially need the “subprotocol” functionality from the optical-detector-plugin you originally wrote MicroDrop v. 1.0. Thanks again! :slight_smile:

···

On Tuesday, 15 January 2019 19:16:45 UTC, Ryan Fobel wrote:

Hi Caspar,

Sorry, it’s been a while since we started this thread and the MicroDrop code has changed significantly in the meantime. Can you please remind me exactly what you are trying to achieve? You mentioned that you are doing some kind of measurement (luminescence), but what is the action you are trying to control? Do you want to wait until a condition is met before proceeding with a set protocol, or do you need to execute a different set of steps depending on the measurement result?

If you can provide a high level overview of what you are trying to achieve, we can hopefully suggest the easiest way forward.

Thanks,

-Ryan

On Mon, Jan 14, 2019 at 11:10 AM casper.kunstmann via dropbot-dev drop...@googlegroups.com wrote:

Hi Ryan (and others)

I’ve taken over from Henry and have also managed to get the plug-in built and installed. I’ve also manged to comment out anything cause incompatibility with missing hardware. However, when I try to run the plug-in and the sub-protocol I consistently get an error saying "AttributeError: ‘NoneType’ object has no attribute ‘state_of_channels’. This is caused by line 403 in the plug-in which reads:

state = dmf_options.state_of_channels

dmf_options are defined as (line 400):

dmf_options = step.get_data('microdrop.gui.dmf_device_controller')

I’ve checked dmf-device-controller.py and can find no reference to state_of_channels, so I was wondering if something has gone wrong in an update and the array is actually named differently now? I found a function called “channel_states” in “dmf-control-board.py” which looks like the right thing but I’m unsure about how to call this in my plugin code.

Hope this makes sense and thanks in advance if anyone can help.

On Saturday, 21 January 2017 19:11:34 UTC, Ryan Fobel wrote:

Hi Henry,

I’ve added a high-level overview to the github page. You will probably need to comment out most of the content in that plugin since you don’t have the required hardware. Basically, it just shows an outline of how to run a “sub-protocol” on a given step dependent on a sensor reading.

-Ryan

On Tue, Jan 17, 2017 at 10:24 AM, Henry Bissell henr...@gmail.com wrote:

Thanks Ryan,

I’ve managed to get it installed perfectly. I was wondering if you might be able to briefly describe the operation of the plugin? I don’t want to get anything wrong and damage experiments!

Thanks again,

Henry

On Monday, 16 January 2017 21:24:48 UTC, Ryan Fobel wrote:

I’ve updated the optical-detector-plugin code for compatibility with MicroDrop v2.0.

To build the python package, just clone the github repository and run the command:

python release.py

This should build the package optical_detector_plugin-2.x.tar.gz which you can install with from MicroDrop’s plugin manager by clicking on the Install plugin... button.

-Ryan

On Mon, Jan 16, 2017 at 9:27 AM, Ryan Fobel ry...@fobel.net wrote:

You’re right, sorry. I’ll take a look at updating it for compatibility with v2.x…

On Mon, Jan 16, 2017 at 8:33 AM, Henry Bissell henr...@gmail.com wrote:

Ryan,

I cant seem to install that plugin in MicroDrop 2.4, do you have any instructions for installing custom plugins?

Henry

On Friday, 13 January 2017 14:17:11 UTC, Ryan Fobel wrote:

Hi Henry,

Conditional programming (e.g., making decisions in a protocol based on input from a sensor) isn’t currently supported in MicroDrop protocols; however, we’ve put together a bit of a hack-ish way to do this in another custom plugin that we’ve used to make a pseudo chemostat. It basically checks the state of a OD sensor on a particular step and based on that reading, it conditionally executes one of two “sub”-protocols. It may provide a good starting point for you to write your own plugin.

We’re planning to implement official support for conditionals as part of a new protocol standard, but don’t currently have the resources to throw at it right now. If anyone out there is interested in working on this, we’d be happy to provide some direction. As part of this effort, it would be helpful if you could put together a detailed use case for exactly what you want to do.

Thanks,
-Ryan

On Wed, Jan 11, 2017 at 6:29 AM, Henry Bissell henr...@gmail.com wrote:

I am a current student studying at the University of York in the UK. I have built a DropBot and I intend to use it for my project. I am looking at hybrid bio-electronic devices. My project involves implementing the use of a Flourometer to detect whether something has occurred.

I was wondering if there is any support for taking the data from another device and using it to control the DropBot software, basically making decisions based on another devices output?

What I am trying to do is measure luminescence of a droplet in order to ascertain whether a reaction has taken place, and if it has then move onto the next stage of the experiment. I have designed a photo-detector set-up with an LED, and I can get the data into the computer, but my issue is translating this data to an action within MicroDrop.

Any help would be greatly appreciated.

Thanks

You received this message because you are subscribed to the Google Groups “dropbot-dev” group.

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#12

Hi Casper,

We’re in the process of writing up some documentation on this (e.g., how to write a plugin compatible with recent versions of MicroDrop). Should have something to share by the end of next week.

-Ryan

···

On Fri, Jan 25, 2019 at 5:30 AM casper.kunstmann via dropbot-dev dropb...@googlegroups.com wrote:

Hi Ryan

Sorry to pester you about this but I would love a few hints on how to move forward with this. I’ll be more than happy to provide more details, but all I essentially need the “subprotocol” functionality from the optical-detector-plugin you originally wrote MicroDrop v. 1.0. Thanks again! :slight_smile:

On Tuesday, 15 January 2019 19:16:45 UTC, Ryan Fobel wrote:

Hi Caspar,

Sorry, it’s been a while since we started this thread and the MicroDrop code has changed significantly in the meantime. Can you please remind me exactly what you are trying to achieve? You mentioned that you are doing some kind of measurement (luminescence), but what is the action you are trying to control? Do you want to wait until a condition is met before proceeding with a set protocol, or do you need to execute a different set of steps depending on the measurement result?

If you can provide a high level overview of what you are trying to achieve, we can hopefully suggest the easiest way forward.

Thanks,

-Ryan

On Mon, Jan 14, 2019 at 11:10 AM casper.kunstmann via dropbot-dev drop...@googlegroups.com wrote:

Hi Ryan (and others)

I’ve taken over from Henry and have also managed to get the plug-in built and installed. I’ve also manged to comment out anything cause incompatibility with missing hardware. However, when I try to run the plug-in and the sub-protocol I consistently get an error saying "AttributeError: ‘NoneType’ object has no attribute ‘state_of_channels’. This is caused by line 403 in the plug-in which reads:

state = dmf_options.state_of_channels

dmf_options are defined as (line 400):

dmf_options = step.get_data('microdrop.gui.dmf_device_controller')

I’ve checked dmf-device-controller.py and can find no reference to state_of_channels, so I was wondering if something has gone wrong in an update and the array is actually named differently now? I found a function called “channel_states” in “dmf-control-board.py” which looks like the right thing but I’m unsure about how to call this in my plugin code.

Hope this makes sense and thanks in advance if anyone can help.

On Saturday, 21 January 2017 19:11:34 UTC, Ryan Fobel wrote:

Hi Henry,

I’ve added a high-level overview to the github page. You will probably need to comment out most of the content in that plugin since you don’t have the required hardware. Basically, it just shows an outline of how to run a “sub-protocol” on a given step dependent on a sensor reading.

-Ryan

On Tue, Jan 17, 2017 at 10:24 AM, Henry Bissell henr...@gmail.com wrote:

Thanks Ryan,

I’ve managed to get it installed perfectly. I was wondering if you might be able to briefly describe the operation of the plugin? I don’t want to get anything wrong and damage experiments!

Thanks again,

Henry

On Monday, 16 January 2017 21:24:48 UTC, Ryan Fobel wrote:

I’ve updated the optical-detector-plugin code for compatibility with MicroDrop v2.0.

To build the python package, just clone the github repository and run the command:

python release.py

This should build the package optical_detector_plugin-2.x.tar.gz which you can install with from MicroDrop’s plugin manager by clicking on the Install plugin... button.

-Ryan

On Mon, Jan 16, 2017 at 9:27 AM, Ryan Fobel ry...@fobel.net wrote:

You’re right, sorry. I’ll take a look at updating it for compatibility with v2.x…

On Mon, Jan 16, 2017 at 8:33 AM, Henry Bissell henr...@gmail.com wrote:

Ryan,

I cant seem to install that plugin in MicroDrop 2.4, do you have any instructions for installing custom plugins?

Henry

On Friday, 13 January 2017 14:17:11 UTC, Ryan Fobel wrote:

Hi Henry,

Conditional programming (e.g., making decisions in a protocol based on input from a sensor) isn’t currently supported in MicroDrop protocols; however, we’ve put together a bit of a hack-ish way to do this in another custom plugin that we’ve used to make a pseudo chemostat. It basically checks the state of a OD sensor on a particular step and based on that reading, it conditionally executes one of two “sub”-protocols. It may provide a good starting point for you to write your own plugin.

We’re planning to implement official support for conditionals as part of a new protocol standard, but don’t currently have the resources to throw at it right now. If anyone out there is interested in working on this, we’d be happy to provide some direction. As part of this effort, it would be helpful if you could put together a detailed use case for exactly what you want to do.

Thanks,
-Ryan

On Wed, Jan 11, 2017 at 6:29 AM, Henry Bissell henr...@gmail.com wrote:

I am a current student studying at the University of York in the UK. I have built a DropBot and I intend to use it for my project. I am looking at hybrid bio-electronic devices. My project involves implementing the use of a Flourometer to detect whether something has occurred.

I was wondering if there is any support for taking the data from another device and using it to control the DropBot software, basically making decisions based on another devices output?

What I am trying to do is measure luminescence of a droplet in order to ascertain whether a reaction has taken place, and if it has then move onto the next stage of the experiment. I have designed a photo-detector set-up with an LED, and I can get the data into the computer, but my issue is translating this data to an action within MicroDrop.

Any help would be greatly appreciated.

Thanks

You received this message because you are subscribed to the Google Groups “dropbot-dev” group.

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#13

Sounds great Ryan, many thanks and look forward to seeing it.

\Casper

···

On Saturday, 26 January 2019 00:20:31 UTC, Ryan Fobel wrote:

Hi Casper,

We’re in the process of writing up some documentation on this (e.g., how to write a plugin compatible with recent versions of MicroDrop). Should have something to share by the end of next week.

-Ryan

On Fri, Jan 25, 2019 at 5:30 AM casper.kunstmann via dropbot-dev drop...@googlegroups.com wrote:

Hi Ryan

Hi Caspar,

Sorry, it’s been a while since we started this thread and the MicroDrop code has changed significantly in the meantime. Can you please remind me exactly what you are trying to achieve? You mentioned that you are doing some kind of measurement (luminescence), but what is the action you are trying to control? Do you want to wait until a condition is met before proceeding with a set protocol, or do you need to execute a different set of steps depending on the measurement result?

If you can provide a high level overview of what you are trying to achieve, we can hopefully suggest the easiest way forward.

Thanks,

-Ryan

On Mon, Jan 14, 2019 at 11:10 AM casper.kunstmann via dropbot-dev drop...@googlegroups.com wrote:

Hi Ryan (and others)

I’ve taken over from Henry and have also managed to get the plug-in built and installed. I’ve also manged to comment out anything cause incompatibility with missing hardware. However, when I try to run the plug-in and the sub-protocol I consistently get an error saying "AttributeError: ‘NoneType’ object has no attribute ‘state_of_channels’. This is caused by line 403 in the plug-in which reads:

state = dmf_options.state_of_channels

dmf_options are defined as (line 400):

dmf_options = step.get_data('microdrop.gui.dmf_device_controller')

I’ve checked dmf-device-controller.py and can find no reference to state_of_channels, so I was wondering if something has gone wrong in an update and the array is actually named differently now? I found a function called “channel_states” in “dmf-control-board.py” which looks like the right thing but I’m unsure about how to call this in my plugin code.

Hope this makes sense and thanks in advance if anyone can help.

On Saturday, 21 January 2017 19:11:34 UTC, Ryan Fobel wrote:

Hi Henry,

I’ve added a high-level overview to the github page. You will probably need to comment out most of the content in that plugin since you don’t have the required hardware. Basically, it just shows an outline of how to run a “sub-protocol” on a given step dependent on a sensor reading.

-Ryan

On Tue, Jan 17, 2017 at 10:24 AM, Henry Bissell henr...@gmail.com wrote:

Thanks Ryan,

I’ve managed to get it installed perfectly. I was wondering if you might be able to briefly describe the operation of the plugin? I don’t want to get anything wrong and damage experiments!

Thanks again,

Henry

On Monday, 16 January 2017 21:24:48 UTC, Ryan Fobel wrote:

I’ve updated the optical-detector-plugin code for compatibility with MicroDrop v2.0.

To build the python package, just clone the github repository and run the command:

python release.py

This should build the package optical_detector_plugin-2.x.tar.gz which you can install with from MicroDrop’s plugin manager by clicking on the Install plugin... button.

-Ryan

On Mon, Jan 16, 2017 at 9:27 AM, Ryan Fobel ry...@fobel.net wrote:

You’re right, sorry. I’ll take a look at updating it for compatibility with v2.x…

On Mon, Jan 16, 2017 at 8:33 AM, Henry Bissell henr...@gmail.com wrote:

Ryan,

I cant seem to install that plugin in MicroDrop 2.4, do you have any instructions for installing custom plugins?

Henry

On Friday, 13 January 2017 14:17:11 UTC, Ryan Fobel wrote:

Hi Henry,

Conditional programming (e.g., making decisions in a protocol based on input from a sensor) isn’t currently supported in MicroDrop protocols; however, we’ve put together a bit of a hack-ish way to do this in another custom plugin that we’ve used to make a pseudo chemostat. It basically checks the state of a OD sensor on a particular step and based on that reading, it conditionally executes one of two “sub”-protocols. It may provide a good starting point for you to write your own plugin.

We’re planning to implement official support for conditionals as part of a new protocol standard, but don’t currently have the resources to throw at it right now. If anyone out there is interested in working on this, we’d be happy to provide some direction. As part of this effort, it would be helpful if you could put together a detailed use case for exactly what you want to do.

Thanks,
-Ryan

On Wed, Jan 11, 2017 at 6:29 AM, Henry Bissell henr...@gmail.com wrote:

I am a current student studying at the University of York in the UK. I have built a DropBot and I intend to use it for my project. I am looking at hybrid bio-electronic devices. My project involves implementing the use of a Flourometer to detect whether something has occurred.

I was wondering if there is any support for taking the data from another device and using it to control the DropBot software, basically making decisions based on another devices output?

What I am trying to do is measure luminescence of a droplet in order to ascertain whether a reaction has taken place, and if it has then move onto the next stage of the experiment. I have designed a photo-detector set-up with an LED, and I can get the data into the computer, but my issue is translating this data to an action within MicroDrop.

Any help would be greatly appreciated.

Thanks

You received this message because you are subscribed to the Google Groups “dropbot-dev” group.

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Sorry to pester you about this but I would love a few hints on how to move forward with this. I’ll be more than happy to provide more details, but all I essentially need the “subprotocol” functionality from the optical-detector-plugin you originally wrote MicroDrop v. 1.0. Thanks again! :slight_smile:

On Tuesday, 15 January 2019 19:16:45 UTC, Ryan Fobel wrote:

You received this message because you are subscribed to the Google Groups “dropbot-dev” group.

To unsubscribe from this group and stop receiving emails from it, send an email to dropbot-dev...@googlegroups.com.

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