Standardization in Lab Automation: Difference between revisions

Revision as of 16:50, 12 December 2019

Revision as of 16:17, 18 December 2019

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Such technical obstacles impede the development of higher level autonomous experimentation systems.

SiLA enables researchers to focus on their scientific questions by reducing equipment connectivity effort to a minimum. This is achieved by using proven, tested and maintained documentation and code.

There are 2 SiLA Versions: SiLA 2 and SiLA 1.x.

===SiLA 2===

SiLA 2 considers every entity in the modern laboratory as a service. Focus on behaviour and service oriented design structures leads to the Feature Definition Language (FDL). SiLA is built to connect systems in a laboratory, such as [[Laboratory information management system]]s, [[electronic lab notebook]]s, [[chromatography software]] and laboratory devices such as balances, pipettors and various other analytical instruments.

SiLA's basic structure consists of a client – server communication model. The SiLA Server (≙[[web server]]) exposes all it's capabilities to the SiLA Client (≙[[web client]]). Capabilities of the SiLA Server are grouped together as SiLA Features. The concept of Features serves as a common communication base for subject matter experts (SME), IT experts and end users. Each Feature is described by its Feature Definition, an [[XML]]-file containing information about parameters, interactions, data types, return values, etc. SiLA 2 is based on a microservice architecture. Relying on [[HTTP/2]], SiLA uses [[Protocol Buffers]] to serialize payload data. Furthermore, SiLA 2 uses the wire format provided by [[gRPC]].

===SiLA 1.x - Device Interface Standard===

[[File:SiLA.Integration level.full.png|thumb|SiLA 1.x - Three supported integration levels]]

The SiLA device interface standard covers all ISO/OSI levels of the device control interface from physical to application layer.

The interface standard is based on web service/[[SOAP]] communication with the devices. Commands are generally executed in asynchronous manner with an immediate response and a delayed event after completion of the command processing or after an error. Error recovery procedures are also supported and the general behavior of the devices is managed by a state machine. The state machine enables also complex behaviors like parallel processing of commands and command queuing.

By supporting three different integration levels, SiLA provides a unique, standardized interface between lab automation devices and process management systems so that also legacy devices can be integrated in SiLA compliant systems. SiLA compliance can be achieved by providing native, directly embedded SiLA device interfaces or by software only SiLA drivers and/or interface converters. The SiLA Device Control and Data Interface Standard eases and accelerates the integration and adaptation of systems through generic Device Class Interfaces providing Common Command Sets.

===SiLA 1.x - Common Command Dictionary===

By grouping devices of the same functionality device classes can be created. SiLA Common Command Sets define commands for these device classes. SiLA defines the command names, the number of parameters and their names as well as the return data. Since commands and parameters are described in the WSDL documentation tag of the commands web service, a process management software (PMS) can automatically generate a list available commands for each device.

SiLA has defined about 30 device classes and a command library with about 100 commands. Commands range from mandatory commands that are needed to make transitions in the state machine, over required commands for the specific device class, to optional commands for which not every device in the device class might provide the functionality. In addition guidelines for the implementation of supplier-specific device commands and parameters are provided.

Some commands are applicable for almost every device class. For example, the commands SetParameter, GetParameter, ExecuteMethod are widely used. Also PrepareForOutput and PrepareForInput are common because they enable the transport mechanisms to transfer labware items from device to device. The mandatory commands include operations like Reset, Initialize, Abort and Pause. In addition also locking a device for exclusive use is provided.

==History==

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| 2007 || Successful Proof of Concept (PoC) of the Common Command Set concept by Hamilton and Novartis.

|}

===SiLA 2===

SiLA 2 considersaddresses everycontrol entityand indata theinterfaces modernbetween laboratorydevices asand aprocess service.management, Focus on behaviourLIMS and service oriented design structures leads to the Feature Definition LanguageEnterprise (FDL)Systems. SiLAIt is built to connect systems in a laboratory, such as [[Laboratory information management system]]s, [[electronic lab notebook]]s, [[chromatography software]] and laboratory devices such as balances, pipettors and various other analytical instruments.

Enhancing the first standard SiLA 1.x by adopting proven concepts and applying already existing open standards and protocols in a "lean and mean" manner, SiLA 2 is designed to enable plug-and-play operations in the laboratory.

===Technical Background===

SiLA 2 considers every entity in the modern laboratory as a service. Focus on behaviour and service oriented design structures leads to the Feature Definition Language (FDL). SiLA 2 is based on a microservice architecture. Relying on [[HTTP/2]], SiLA uses [[Protocol Buffers]] to serialize payload data. Furthermore, SiLA 2 uses the wire format provided by [[gRPC]].

===Structures===

SiLA 2 can split up into a Core and Feature level. The SiLA Core is written and maintained by the SiLA 2 Working group. SiLA Features are specific extensions that may change and evolve in any way.

SiLA's basic structure consists of a client – server communication model. The SiLA Server (≙[[web server]]) exposes all it's capabilities to the SiLA Client (≙[[web client]]). Capabilities of the SiLA Server are grouped together as SiLA Features.

===Features===

The Feature concept serves as a common communication base for subject matter experts (SME), IT experts and end users. Each Feature is described by its Feature Definition, an XML-file containing information about parameters, interactions, data types, return values, etc. It exposes a certain number of Commands which model actions that can be performed by the SiLA Server.

==SiLA 1.x ==

SiLA 1.x has been used from 2009 until 2018. But getting started with SiLA 1.x is not an easy process. Furthermore, As SiLA 1.x is based on XML/Soap which is considered outdated. It is now replaced by SiLA 2.

===SiLA 1.x - Device Interface Standard===

[[File:SiLA.Integration level.full.png|thumb|SiLA 1.x - Three supported integration levels]]

The SiLA device interface standard covers all ISO/OSI levels of the device control interface from physical to application layer.

The interface standard is based on web service/[[SOAP]] communication with the devices. Commands are generally executed in asynchronous manner with an immediate response and a delayed event after completion of the command processing or after an error. Error recovery procedures are also supported and the general behavior of the devices is managed by a state machine. The state machine enables also complex behaviors like parallel processing of commands and command queuing.

By supporting three different integration levels, SiLA provides a unique, standardized interface between lab automation devices and process management systems so that also legacy devices can be integrated in SiLA compliant systems. SiLA compliance can be achieved by providing native, directly embedded SiLA device interfaces or by software only SiLA drivers and/or interface converters. The SiLA Device Control and Data Interface Standard eases and accelerates the integration and adaptation of systems through generic Device Class Interfaces providing Common Command Sets.

===SiLA 1.x - Common Command Dictionary===

By grouping devices of the same functionality device classes can be created. SiLA Common Command Sets define commands for these device classes. SiLA defines the command names, the number of parameters and their names as well as the return data. Since commands and parameters are described in the WSDL documentation tag of the commands web service, a process management software (PMS) can automatically generate a list available commands for each device.

SiLA has defined about 30 device classes and a command library with about 100 commands. Commands range from mandatory commands that are needed to make transitions in the state machine, over required commands for the specific device class, to optional commands for which not every device in the device class might provide the functionality. In addition guidelines for the implementation of supplier-specific device commands and parameters are provided.

Some commands are applicable for almost every device class. For example, the commands SetParameter, GetParameter, ExecuteMethod are widely used. Also PrepareForOutput and PrepareForInput are common because they enable the transport mechanisms to transfer labware items from device to device. The mandatory commands include operations like Reset, Initialize, Abort and Pause. In addition also locking a device for exclusive use is provided.

==Membership==

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SiLA is a not-for-profit membership corporation with global footprint. Membership is open for institutions, corporations and individuals active in the life science lab automation industry.

The SiLA consortium provides professional training, support and certification services to suppliers and system integrators implementing SiLA compliant interfaces.

==Scope of Standardization==

[[File:SiLA.Scope of Standardization.full.png|thumb|SiLA 1.x - Main scope]]

The SiLA foundation of standards addresses control and data interfaces between devices and process management, LIMS and Enterprise Systems.

==External links==

* [http://www.sila-standard.org/ SiLA homepage]

* [https://gitlab.com/SiLA2/sila_base/wikis/home SiLA 2 GitLab]

* [https://ilt.hsr.ch/Standardisation-in-Lab-Automat.12357.0.html ILT on Standardisation in Lab Automation]

* [http://unitelabs.ch/technology/control-software Camunda as component in control software]

* [https://www.ncbi.nlm.nih.gov/pubmed/22357556 NIH on SiLA: Basic standards for rapid integration in laboratory automation.]

* [https://www.researchgate.net/publication/221854198_SiLA_Basic_Standards_for_Rapid_Integration_in_Laboratory_Automation Researchgate on SiLA: Basic Standards for Rapid Integration in Laboratory Automation]

* [http://www.labautopedia.org/mw/SiLA Labautopedia on SiLA]

* [https://medium.com/@matthieu.croissant/sila-2-hands-on-bringing-automation-to-the-laboratory-dacc12df7152 SiLA 2 Hands-on]

* [https://www.linkedin.com/posts/bryn-roberts-685171_labautomation-robotic-autonomous-activity-6582897402808676353-b4TK Autonomous Robot running with SiLA]

* [https://www.youtube.com/watch?v=B-LU1Tq7qYw Roche's Camunda-based AutoLab software]

==Sources==

* [http://www.sila-standard.org/ SiLA homepage]

* [https://gitlab.com/SiLA2/sila_base/wikis/home SiLA 2 GitLab]

* [http://www.labautopedia.org/mw/SiLA Labautopedia on SiLA]

[[Category:Automation]]