Grid computing impacts directly on the experimental scientific laboratory in the areas of monitoring and remote control of experiments, and the storage, processing and dissemination of the resulting data. 
We highlight some of the issues in extending the use of an MQ Telemetry Transport (MQTT) broker from facilitating the remote monitoring of an experiment and its environment to the remote control of an apparatus.
To demonstrate these techniques, an Intel-Play QX3 microscope has been "grid-enabled" using a combination of software to control the microscope imaging, and sample handling hardware built from LEGO Mindstorms. The whole system is controlled remotely by passing messages using an IBM WebSphere Message Broker. <br/

Bedi, Bharat V.

Conway-Jones, D.

De Roure, D. C.

Frey, Jeremy G.

Reynolds, Andrew D.

Robinson, Jamie M.

Stanford-Clark, Andrew J.

English

Southampton (e-Prints Soton)

The Combechem MQTT LEGO MicroscopeA grid enabled scientiﬁc apparatus demonstratorJ. M. Robinsona, J. G. Freya, D. C. DeRoureb, A. J. Stanford-Clarkc, A. D. Reynoldsc, B. V. Bedic,D. Conway-JonescEmail Contact : j.m.robinson@soton.ac.ukaUniversity of Southampton, School of Chemistry, Highﬁeld, Southampton, SO17 1BJ, United KingdombUniversity of Southampton, School of Electronics and Computer Science, Highﬁeld, Southampton, SO17 1BJ, UnitedKingdomcIBM UK Laboratories, Hursley Park, Winchester, SO21 2JN, United KingdomAbstractGrid computing impacts directly on the experimental scientiﬁc laboratory in the areas of monitoring andremote control of experiments, and the storage, processing and dissemination of the resulting data. Wehighlight some of the issues in extending the use of an MQ Telemetry Transport (MQTT) broker from facili-tating the remote monitoring of an experiment and its environment to the remote control of an apparatus. Todemonstrate these techniques, an Intel-Play QX3 microscope has been “grid-enabled” using a combination ofsoftware to control the microscope imaging, and sample handling hardware built from LEGO Mindstorms.The whole system is controlled remotely by passing messages using an IBM WebSphere Message Broker.1 BackgroundAs computer control becomes increasingly pervasivein the laboratory, it becomes easier to take advantageof automated and semi-automated experimental pro-cedures to enhance the safety, throughput, and qual-ity of data .An absent exprimenter’s expertise can be appliedretrospectively and to future experiments but not im-mediately, unless they have the the ability to moni-tor the experiment remotely (1). By adding remotecontrol to this monitoring, the experimenter can thensteer and modify the experiment without needingphysical access. Whilst being of use to the local ex-perimenter this technology opens the possibility ofremote, realtime, collaboration with researchers andexperts from beyond the local campus. In previouswork the use of middleware to support a Publish-Subscribe (or Pub-Sub) methodology(2) for experi-ment monitoring has been investigated(3). MQTT(4)messages were passed by an IBM MicroBroker to re-lay information on the laboratory environment to re-mote users. The same technology can be used to passmessages from the remote user to the laboratory.1.1 Safety and Physical SecurityRemote monitoring and control technologies such asMQTT and the message broker can be used to imple-ment "lights-out" operations of equipment. Thoughthis can be problematic for laboratory personel ifthe equipment or process is inherently dangerous.The use of local mechanical and electrical interlockscan help to avoid unintended local consequencesof a remote action, and by adding remote monitor-ing the operator is placed in a more knowledge-able position. Security devices such as PIR sensorsand door/pressure switches can be used to raise analert if anyone unexpectedly enters a room or build-ing. Identiﬁcation technology such as RFID taggingcan also be used to verify the identity of personnelwho enter or leave a controlled area, using the sameMQTT message channel to alert the appropriate par-ties. Similarly local operators can monitor the statusof remote controlers by similar means.2 Implementation2.1 Building the MQTT LEGO Mi-croscopeThe project can be broken down into three discretesections, Physical Construction (the LEGO bricks),RCX Software (the link between MQTT and theLEGO sensors and Motors), and Microscope Soft-ware (controlling the camera hardware).LEGO ConstructionThe LEGO construction around the microscopeneeds to support the microscope and sample, to pro-vide sample selection/movement and focusing abil-ity. The initial design involved focusing the sampleby translating the microscope vertically. The weightof the microscope, and quantity of available LEGOdictatedate that is was more approriate to move thesample vertically below the microscope, keeping themicroscope static. The sample platform was drivenvia a rack and pinion lift powered by a geared downMindstorms motor. A combination of gearing anddriving the motor for very short time periods, al-lowed the ﬁne control needed to bring the sampleinto focus even at the highest magniﬁcation settings.For protection the sample carriage was equippedwith vertical limit switches. Both limits (top and bot-tom of movement) were connected to the same sen-sor input (wired in parallel) and the limit reachedinferred from the current direction of travel. In afurther experiment the microsope was mounted ona LEGO tractor which could be driven over a ﬂoormounted sample.RCX SoftwareThe LEGO RCX drive software is split into two parts.Both of these parts originate from IBM Hursley andwere modiﬁed for this project. The LEGO IR towerand the IR receiver on the RCX are used to link theRCX to the MQTT network in real-time however dueto the limited processing capabilities of the RCX afull MQTT protocol stack isn’t used. The implemen-tation used here uses single integers to trigger com-mands on the RCX and a two integer pair to receive atopic and message from the RCX for publishing overMQTT.This solution requires two bits of code. One thatruns on the RCX, and one running on a host PC,which bridges between the messages on IR link andMQTT messages over a TCP/IP network. To allowmore extensive programming of the RCX, the stan-dard LEGO ﬁrmware is removed and the “lejos” sys-tem installed instead(5). Lejos provides a basic Javabased programming environment on the RCX andPC side libraries to enable communication with theRCX over the IR link. This makes programming in-teractions between MQTT and the RCX easier as thestandard MQTT Java libraries can be used. The PCbased bridge subscribes to a topic from an MQTTbroker, and on receiving messages retransmits thepayload over the IR link (where the message payloadis assumed to only contain an integer). The softwareon the RCX receives messages over the IR link fromthe PC. If the integer received corresponds to one ofthe expected controls codes, the appropriate effec-tor is triggered, otherwise the message is ignored.On receiving a sensor event (the lejos code allowsevent triggers to be tied to changes in sensor state)the RCX may perform simple processing on the data,triggering effectors as required, and then transmitsa message over the IR link to the PC. This is shownschematically in Figure 1.In the case of the LEGO Microscope there ispresently one motor attached to motor control Awhich drives the focus position and two limitswitches (one for each end of travel) connected inparallel to sensor input 1. The RCX accepts codesto stop the motor, and to run it forwards and back-wards. It also accepts commands to “bump” the mo-tor in either direction - this drives the motor for 50msin the direction requested, then stops it. When thelimit switches are triggered, the code ﬁrstly stops themotors, then backs the motor off in the opposite di-rection for 200 ms (to release the limit condition),it then publishes a message over the IR link statingwhich limit switch has been triggered.Figure 2 shows this program ﬂow schematically.Microscope SoftwareThe IntelPlay Microscope is viewed from the com-puter as if it were a webcam. It uses a cpia chipset(6),which is driven by the cpia.ko Linux kernel module.The module writer made control of the camera inter-nal processing easy through the use of the Linux procinterface(7). Through this interface we are able toread and control Sample Lighting, and Image Bright-ness, Colour Saturation and Hue.Inthecurrentsystemimagesaretransmittedfromthe microscope using a simple webcam package(8).This presents images as either JPEG static frames, oras a multipart JPEG, moving them over a HTTP con-nection. It is planned to investigate other transmis-sion methods, including sending the images over theMQTT broker, at a later stage. Control of the camerasinternal processing and sample illuminators is pro-vided by a Linux proc interface to the camera driver.This interface is presented as a ﬁle within the procﬁle system on the Linux machine controlling the mi-croscope. Commands of the form “Toplight:on” arewritten into this ﬁle to control any of the parametersmentioned above. A Java MQTT client subscribes toa microscope control topic on the broker, and on re-ceivingcontrolmessageswritestheappropriatecom-mands into the camera’s control interface.2.2 Frontend Control.By using MQTT to pass messages within a remotecontrol system frontend interfaces can be developedusing a range of different programming languages,on a variety of platforms. For this demonstrator, theremotecontrolinterface was presentedas a webpage.Within this page the user is presentedwith apparatuscontrols using HTML form elements alongside im-ages from the microscopes camera.The use of a webpage also provided the beneﬁtthat the web browser dealt with transfer and displayof the images. The webcam server provided staticJPEG images and a javascript timer can then be usedto periodically refresh the image.MQTT control messages are generated using aPerl CGI script running on the webserver. When theend user triggers one of the control buttons on thewebform, the CGI script is called, which connects tothe broker and publishes messages as expected bythe RCX or microscope software.3 DiscussionThe use of LEGO components allows for the rapiddevelopment of mechanical solutions that may takeweeks to produce using traditional manufacturingprocesses. The use of LEGO Mindstorms provides uswith a convenient, robust, programmable controllerwhich whilst limited compared to some of its indus-trial counterparts is adequate for this initial proof ofconcept. The use of LEGO components does bringFigure 1: Software ﬂow within the RCX PC Bridge Agent.Figure 2: Procedure Flow within the RCX Code.some limits in terms of repeatabilty and toleranceof construction. For longer term use high spec in-dustrial components and indexed motion controllerswould produce a system with a much higher level ofreproducability. LEGO also has a limited maximumload capacity (it is after all designed as a toy).The use of MQTT as a remote control protocolbrings some beneﬁts and some unexpected features.By using existing libraries the software developmentcan be extremely rapid, which when producing ademonstrator is important. MQTT also provides asolution to some of the traditional network prob-lems, for example dealing with broken or unreliableconnections, and making sure that the message al-ways gets through. However, with remote control itis necessary to consider if messages should alwaysget through, if the end effector is unable to recievethe control signal straight away, should the systemthen queue it for later delivery? It was found withthis work that the reliability of the IR link betweenthe PC and the RCX was somewhat variable, some-times it was necessary to manually move the RCX toregain signal. When the link was regained, MQTTthen ensured that waiting messages were delivered,often resulting in unpredictable behaviour. In thecase of the LEGO model this was unexpected, but notdangerous. However, with another system the un-predictable behaviour from delayed messages couldcause a dangerous situation, hence control hardwareand software should be designed to avoid this, inparticular using the non persistent messaging modeof MQTT.4 Extensions and Future work4.1 Sample HandlingAs part of automating an apparatus in a laboratorymoving physical samples onto and off the appara-tus needs addressing. Some existing apparatus areﬁtted with auto samplers and sample batching han-dlers which allow the operator to preload a num-ber of samples, usually into a grid or carousel thatthen sequentially presents the samples to the mea-surement position. By combining sample selectionhardware with a scheduling and notiﬁcation systemthe remote user could arrange a time on the appara-tus during which their sample would be mounted,and they would be given control of the apparatus.4.2 Inclusion of Remote MonitoringWork on remote environment and apparatus mon-itoring has previously reported that MQTT can beused to monitor sensors in realtime(1; 3; 9). Whenimplementing automation on a real-laboratory sce-nario, it is important to provide the operator with asmuch information about the apparatus, and person-nel in the vicinity of the apparatus as possible, bothfor reasons of safety and result reliabilty. By usingcommon technologies adding this data becomes a fareasier task.4.3 Authorisation over MQTTMQTT deliberately has a very minimalist approachto security, enabling appropriate security to be lay-ered on top of it as required for any given applica-tion. In this demonstrator, security was purpouslyoverlooked as the equipment is relativly safe, anddata trafﬁc limited to the campus network. Beforeusing this type of system to allow control over ahostile network (such as the internet) an appropri-ate security scheme would need to be implemented.This could include; Encrypting the message pay-load (which could use PKI certiﬁcates to addition-ally provide signing for authentication and non-repudiation), Challenge/response security (by send-ing the challenge/response ﬂows as MQTT messagesover pub/sub), or TCP/IP trafﬁc protection (such asstandard VPN or SSH tunnels).References[1] J. M. Robinson, J. G. Frey, A. J. Stanford-Clark, A. D. Reynolds, B. V. Bedi, Sensor networks and grid mid-dleware for laboratory monitoring, in: First International Conference on e-Science and Grid Computing(e-Science’05), pp. 562 – 569, pages.URL http://doi.ieeecomputersociety.org/10.1109/E-SCIENCE.2005.73[2] A. Stanford-Clark, Integrating monitoring and telemetry devices as part of enterprise informationresources, Tech. rep., IBM (2002).URLhttp://www-306.ibm.com/software/integration/mqfamily/integrator/telemetry/pdfs/telemetry_integration_ws.pdf[3] J. M. Robinson, J. G. Frey, A. J. Stanford-Clark, A. D. Reynolds, B. V. Bedi, Chemistry by mobile phone(or how to justify more time at the bar), in: Proceedings of the UK e-Science All Hands Meeting 2005, ,pages.URL http://www.allhands.org.uk/2005/proceedings/papers/481.pdf[4] IBM, WebSphere MQ Telemetry Transport Speciﬁcation.URL http://publib.boulder.ibm.com/infocenter/wbihelp/index.jsp?topic=/com.ibm.etools.mft.doc/ac10840_.htm[5] Lejos : Java for the rcx, accessed 24 April 2006.URL http://lejos.sourceforge.net/[6] Cpia webcam driver for linux, accessed 24 April 2006.URL http://webcam.sourceforge.net/[7] A. Nirendra, Exploring procfs, Linux Gazette 115.URL http://linuxgazette.net/115/nirendra.html[8] jtravis@p00p.org, Ofﬁcial camserv home page, accessed 28 April 2006.URL http://cserv.sourceforge.net[9] Floodnet: Pervasive computing in the environmment, accessed 24 April 2006.URL http://envisense.org/floodnet/floodnet.htmIBM and WebSphere are trademarks of IBM Corporation in the United States, other countries or both.Java is a trademark of Sun Microsystems Inc. in the United States, other countries or both.LEGO and Mindstorms are trademarks of The LEGO Group in the United Kingdom, and other countries.Intel is a trademark of Intel Corporation in the United States and other countries.

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Sensor networks and grid middleware for laboratory monitoring, in:

The Combechem MQTT LEGO microscope: a grid enabled scientific apparatus demonstrator

The Combechem MQTT LEGO microscope: a grid enabled scientific apparatus demonstrator

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