User feedback on Schedulers

Schedulers
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Hi everyone,

I am looking into possibilities for orchestration and scheduling (both open-source / script-based and commercial). For commercial solutions, Green Button Go, Cellario and Overlord seem to come up quite often. These software (or scripts) would be mostly used for larger automated workflows with multiple devices (Liquid handlers from all size and brands, cobots, etc…). I am especially interested in the deployment speed, breadth of device integration, and end-user experience.

Is there other solutions that you know work well for your automation workflows, or do you have some feedback (+/-) relative to the use of GBG, Cellario or Overlord ?

Cheers !

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In my opinion the moat these companies have is mostly around licensing device drivers. I would like to see open-source scheduler solutions that allow for more flexibility and customizability. There’s such a wide range of scientific workflows (which are themselves continuously changing and advancing) that closed-source solutions are not really able to keep up. There is a reason that basically every popular software development tool is open source, and that all big tech companies invest heavily into open source.

Other companies that invest into open source are Toyota, McDonalds, and Walmart, so it is not just a tech thing. Of course, there has to be strategy associated with the approach, it is not just giving away free stuff. There are some companies that would benefit massively from an open source model in automation and some companies that would lose out if that model becomes the standard.

I don’t really think every automation engineer should have to become a software developer for this to work. Automation code should be easier for software devs to work with and understand, so they can create tools that help automation engineers. This is easiest when automation scripts are in the same language/ universe as dev tools familiar to software people, like Python.

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Before we go off on this matter, some of the folks over at BiB put together this spreadsheet with TechBio Tools in mind. Note that the section for Automation is missing a lot of players… with that said, it’s still handy.

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Hi @Jeremy,
When it comes to “Orchestration” Biosero is defiantly a market leader in that regard and has a wide array of software tools that provide connectivity of devices at an integrated workcell level and orchestrated solutions at a laboratory level. I am not on this forum to make sales pitches but to answer the questions above:

Green Button Go Scheduler and Orchestrator:
-We routinely deploy large complex integrations featuring multiple integrated workstations, stores, etc.

-Biosero is 100% hardware agnostic, we work with the best devices from robotic arms, liquid handlers, and peripheral equipment.

-Biosero has 400+ existing device drivers and a team dedicated to creating new as customer needs requires. We can develop a green button go driver as long as there is an API, and the device is robot friendly (loadable with a robotic arm).

-Deployment time depends on the scale of the project and ability to get components needed. A standard workcell can be delivered in 4-6 months.

-As far as references happy to connect with current users, but at SLAS, several of our customers are speaking at “Adapting to Demand by Orchestrating Your Lab”. This talk is on Monday Febuary 27 at 12:00PM. It will feature speakers from Biosero, Invitate, DeepCure, and Metagenomi. If you can attend this would be a great showcase to show you a wide array of integrated solutions Biosero has deployed.

-Easy to use low code/no code interface, but have capability of easily integrating scripts from C#, Python, VBA, etc. It can be easy as a drag and drop interface or some people prefer to make things more complex implementing custom solutions using scripts.

@Jeremy if you are interested in a Demo or learning more, please send me a DM and I can connect you with the correct regional team. I am also happy to connect in person at SLAS if you will be attendance next week.

Take Care,
Derek

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Stefan,

I’m sure you saw this blog but it’s a great starting point for discussion around the current landscape of open-source development in the life sciences.

Open Development of Scientific Software

There are some good examples of projects, pitfalls of the realities of open source but also a shout out to PyLabRobot.

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Yeah! I did see it, good stuff. I’m actually writing a perspective paper about it as well so my gears have been turning on the topic.

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Oh interesting, I’m definitely curious about your thoughts on the matter.

Maybe there’s a good opportunity for an open discussion (a virtual round table of sorts), I’m sure people in the community will listen in and participate in such a conversation.

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I agree Stefan, open source is the way to go, both for for-profit and non-profit projects. I struggle at the moment to find alternative able to keep up with big names in the scheduling space though.
A PyLabRobot sister project on Scheduling and device integration would be nice indeed !!!
Out of curiosity, if or when you integrate multiple devices, what do you go for ? some particular Python libraries or routines that work best in your applications?

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Thank you for the resource, Luis, that’s very helpful (not only for the scheduling actually!)

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Here is a small guide on how to integrate 3rd party (ie non-Hamilton) equipment into PyHamilton. The best case is a .NET dll that you can import with pythonnet.

https://forums.pylabrobot.org/t/getting-started-with-pyhamilton/28/5?u=stefan

As far as a scheduler project, it sounds interesting but I’d want to be more clear on what the needs are. To my knowledge, schedulers provide control logic around the operation of different pieces of equipment and software resources. When I write a Python script that talks to a robot and other integrated equipment, that seems to fulfill the basic use-case of a scheduler as I understand it.

If there’s additional functionality in commercial schedulers now that is not available as a Python package but that you’d like to be, I’d love to know about it. We’re always trying to come up with useful tools like that.

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So I can only speak to end user experience here for the GBG product.
Like any it has had its ups and downs. The set up is pretty easy - we did this in Europe in 2018, before they had very much happening here. So there was some misses as talking to west coast USA from Denmark was kind of messy. But, that has been fixed and they have a full service team here in Europe. So from the point they come to install - depending on the complexity of the system this will take a few days. It is worth having one of your staff around to follow, help out, learn while they do this. Plan for at least a week.
Ours is hooked to 2 Echo’s , incubator, FACS machine, plate washer, dispenser, shaker, and plate reader (colour and flouresence), and centrifuge. That would be 7 different source manufactorers. This has not been really much of an issue. The drivers have worked for this well. The one exeption is the Echo’s - this is not fully smooth as they do not like being a slave, so in the most recent version of GBG we have had issues around the system being ‘stuck’ when the echo is running, with the arm now being stalled at the echo until the run is complete. But I have heard they are working to fix it, and it was not the case in the older version.
From a user standpoint, this is an easy software to get your head around. There is no need for coding - but there is space for that if you want to. So you can run this with pretty much a graphical interface and never do a line of code and run through multi-machine protocols easily.
There is also a set up where the user has access to only pre-made protocols and cannot mess with the behind the curtain stuff. This can be handy if you have techs that are a little put off by all the background stuff - or students you just want to prevent then from fucking stuff up.

So for our system there was hickups. But I would expect that you can have a moderate system set up and the users fairly comfortable with using the system and creating protocols in something like 4-6 months (obviously depending on your users comfort with automation, more if this is ‘scary’ for them).

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I’m a Cellario user. I’ve also used VWorks to run a BioCel system. I don’t have experience with GBG or Overlord. Brooks (now Azenta) used to offer a scheduler called Sprint6; not sure if they still offer it. It was nice when I demoed it. Wako automation might offer scheduler as well.

We use our Cellario systems for high throughput screening. At last count our newest system has about 50 devices including Echos, a PheraStar and a Yokogawa CV8000 high content imager. I like a lot of things about Cellario. For many protocols you can drag-and-drop to create the workflow. We hired a new automation engineer and he was comfortable running Cellario in a few months and was creating protocols in a year or so. More complicated protocols often require scripting (which is C#) and that has a steeper learning curve.

I’m not sure if you are trying to buy the software alone, but I don’t think HighRes licenses Cellario apart from a system purchase.

My installs have all been mostly on schedule, setting up Cellario on a system takes time - if I recall correctly it was on the order of about 6 weeks from build to pre-FAT. I usually budget about 10-12 months from sending a PO to commissioning. Our last system upgrade suffered from 3rd party device build times due to component shortages.

There have not been many devices I was told I could not integrate. If it has an API they can probably build a driver. Not all the drivers work the way you think they might, and documentation on drivers is lacking. You can always open a ticket with the helpdesk to ask for help, though.

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