• Just passed 3,000 members in the group

  • John Jones answered to the question “Disease5 days, 13 hours ago

    Do you have a question related to this information that you are looking for feedback on?

  • Rachel, I will check with my connections that have done validation of the LabLynx implementation and my other connections as well.

  • John Jones posted an update in the group Laboratory Management 1 week, 2 days ago

    We have passed the 10,000 member mark.

  • John Jones answered to the question “Labware Data extraction2 weeks, 2 days ago

    No doubt about it if you have login access to the database. Pretty much any data can be extracted if you have login access to the database. If you can get the login to the db then just use Excel to attach to the db and attach to the view that best fits the query you want to execute. Here is a set of instructions for attaching to a database with Excel: https://www.erpsoftwareblog.com/2017/01/microsoft-excel-connections-sql-databases/

  • John Jones answered to the question “health care analytics2 weeks, 2 days ago

    Thanks for posting this course. I hope those that take it will post some feedback here. I see that Jupyter will be one of the tools in the course. For those not familiar with jupyter, I think you will find it be an excellent and well supported community tool. It is free without any sort of restriction. Here is an example of real time healthcare analytics using Jupyter: https://360digitmg.com/india/life-sciences-and-healthcare-analytics-certification-programme

  • Niall, the rpi is not inherently insecure because the rpi is purely hardware. What will make the device secure or insecure of course is the OS installed on the rpi. If you go simple and use NOOBS, you will also need to go through a process of hardening the device. There are articles to help you through this. In our case, we created our own OS stack configuration custom that was very, very minimal in terms of footprint and that allowed us to do some very solid hardening of the device. Further, by using the ZeroTier app, we were able to create an isolated network and secure it with a 2 factor authentication so that the devices cannot be accessed without 2fa. I think zerotier (ZT) is the key ingredient for you. I think ZT will actually install on even Windows xp and 7. As you can see: https://www.zerotier.com/download/ there is an x86 installer for those old versions of windows but it may or may not work. Just try it. Once you have created a ZT network of all your instrument PC’s and devices, the world opens up for you in terms of integration and it will be as secure as you can get given the tech.

  • Hi Marcin, To start with you will want to post the link to your product website and make sure it is in English as well as other languages. After that you will want to make sure it gets listed on the LIMSwiki.org LIMS product page: https://www.limswiki.org/index.php/LIMS_vendor As you can see there are no shortage of LIMS companies and the list is growing every year. Also please be sure to post full product demo videos and pricing on your product site. I think that will make a good start for your new LIMS. If you are able to release it as open source that will give it a huge market advantage. Your business model with Open Source can be to provide customization and implementation services and of course support and maintenance service. You can provide a community edition and enterprise edition.

  • Niall, We handle all instrument interfaces with a Rasberry Pi with NodeRed installed on the Pi device. With this arrangement we are able to interface to serial instruments, file based, api based, USB based, TCP based and pretty much everything. The Pi devices are headless and are running zerotier so that we have created an isolated instrument network and then with Nodered we make calls to our LIMS api. Doing this allows for the LIMS to be local or hosted in the cloud. Here are the links to the components mentioned: Raspberry Pi Kit: https://www.amazon.com/CanaKit-Raspberry-4GB-Starter-MAX/dp/B07XPHWPRB?ref_=ast_sto_dp&th=1&psc=1 NodeRed is included on the NOOBS Chip: https://nodered.org/ ZeroTier: https://www.zerotier.com/ NOOBS for RPi: https://www.amazon.com/Raspberry-Pi-32GB-Preloaded-NOOBS/dp/B01LXR6EOA?ref_=ast_bbp_dp My company, LabLynx, has created our own packaged system that contains all of these components along with the cloud services that make it all work with our LIMS and other systems as well. If you want us to help you with this, just contact me: jhjones@lablynx.com

  • Welcome to our Data Science group on LiMSforum.

  • Karen, given the facts you have listed and your desires, you need to find out how many cannabis testing labs there are in your area. Many labs are startups and their revenue and income will be dicey at best. Many go in and out of business. It is just the nature of a new and growing industry. Given the facts you have stated, you will not get a lab manager position, you will have to start at the bottom and work your way up by taking initiatives and solving problems that others are not willing to take on. All the usual stuff that endears you to the owner of the lab. Hard work and care for the company will be rewarded with more work and if it is not, then you need to hold on to the job for 2 years before you move to the next job that hopefully provides the rewards that hard work and care deserves. Cannabis is a risky business but I think it is worth the risk. My company is investing heavily into software to serve the industry and we are working as hard as we can to serve that industry. If you really want to be in that industry, you will simply have to do the same.

  • Harjit, there is no correct answer to the question but your question is very good. I would personally use this as an opportunity to evaluate the vendors in many dimensions. The one that answers the questions in the most meaningful way for you, you may find easier to work with and the ones that have made it difficult for you to understand may well be difficult to work with. I would be disinclined to accept a URS response that is tied off to the manual. I would want the vendor to provide a high level explanation of the system works with a drill down to each individual requirement. Referencing the manual is fine but only as a footnote to the actual response.

  • Hi Matt, thanks for posting this. My company, LabLynx, is interested in what you have. We have been looking for a patient portal platform to integrate with. While we provide a physician portal for our clinical lab customers, we do not provide a patient portal and we have had to steer our clients to patient portal providers. We are not willing to bear the risks associated with consumer grade relationships like patients. We are always looking for patient data access solutions to steer our clients to and we are happy to integrate with.

  • John Jones posted a new activity comment 3 months, 3 weeks ago

    In reply to: John Jones posted an update in the group Laboratory Informatics & Automation
    Does anyone in the group use BPMN 2.0 to manage lab workflows? I am looking at a number of products for modeling workflows […]
    View

    Joe Liscouski, you may not know this but there is BPEL for People.  That is an interesting concept of applying automated controlled workflows to human processes: https://docs.oasis-open.org/bpel4people/bpel4people-1.1.html

    Also, you will want to look at these open source apps that would make up a complete solution suite for workflow automation.  You need of course the bpmn engine and designer, then you need the forms for human and automated data collection points in the flow and then you need the rules engine for the custom processes that are inevitably a part of the bpmn flow.  Finally, you need a flow based integration tool to pull in data from external systems and instruments.  So the tool set is as follows:
    1. https://camunda.com/ –  BPMN
    2. 
    https://www.form.io/  – Forms
    3.
    https://www.drools.org/  – Business Rules
    4. 
    https://nodered.org/ – Integration & Automation

    At LabLynx we package most of this to run through an IoT device when we do lab automation through our LabVia product.

  • Speaking as a LIMS software vendor, we would prefer that your instrument provide a REST based API. That is not typical for any instrument vendors because of how legacy most are but if you are starting from scratch, go REST based api. Other than that go with flat text files that can be easily parsed by the LIMS and then LIMS can put back a text file of your specified format. All the other stuff like animl, HL7, ASTM, etc. is really just noise and of little use to a host system like a LIMS/LIS/ELN.

  • Does anyone in the group use BPMN 2.0 to manage lab workflows?

    I am looking at a number of products for modeling workflows specific to different types of testing. I am wondering if we can build workflows and share them for Open Access use. Are there any LIMS/ELN/LES/SDMS that currently utilize BPMN to manage/execute workflows?

    #workflows #bpmn #lims

    Source: https://www.linkedin.com/feed/update/urn:li:activity:6609545232793034753/

    • This is a link to the REST APIs and sample code: https://chalex.smartflo.biz/SmartFloAPI/index.html

    • CHALEX sells a DAM enabled BPM sandbox that imports an XPDL file. Currently that engine is BPMN 1 compliant. The rules engine supports a broad range of actions associated with conditional routing.  The drag & drop workflow modeller uses a swimlane metaphor.  Training is through interactive e-book.

    • Thanks Murray Oles, can you please post some links that could be of help?  Also, do you have any use cases you can share that apply to lab processes?

    • I am citing some of my contacts that may want to weigh in on this discussion:  Jeff Vannest John Newtown Joe Liscouski  Avrum Goodblatt Rich Lysakowski, Ph.D. Leon Kopelev  Shameek Ray, MS, TOGAF, PSM Herbert Schwarz

      I hope that some of you might have some first hand experience in applying BPMN to lab processes and describe what tools were used and how.

    • John, SmartFlo is a Sandbox, and as such it is designed to support any business process use case.  The workflows are expressed in XML format. The DAM supports the workflow by indexing assets with project / job & task metadata. The rules engine is highly configurable, so if you want to drive devices, query external systems, and make routing decisions based on analytics the rules engine doc explains how. https://chalex.smartflo.biz/3/?2i83
      CHALEX seeks OEM partners with specialized domain expertise and the desire to solve complex process management challenges through the application of BPM and DAM practices.  
      Murray

    • The LabVantage Workflow Manager supports both import and export from BPMN. This is useful when drafting workflows offline or in a format that’s portable outside the LIMS. There are advanced integrations that can only be done inside of LabVantage, of course.

    • That is excellent Jeff Vannest.  All LIMS products should do exactly the same.  I am hoping to put in an Open Access BPMN workflow repository into LiMSforum for folks to share workflow processes and then to provide a workflow engine such as Camunda to execute the flows along with Form.io for the data collection forms.  Eventually will add IoT resources with NodeRed so we can also have integration flows.  At LabLynx we use BPMN for workflows but the ones we have are pretty specific to each client.  

      We have many integration flows using NodeRed and are happy to share those to an Open Access repository.  One I know will be useful to most people will be the ASTM serial interface standard (deprecated but widely used).  We have a nice packaged set of interfaces for clinical instruments that use that standard.

      Can you share a small narrative on how you have used BPMN for lab workflows?

    • Thanks for bringing this to my attention, I did some reading last night and it looks like it should be really useful along with the BPEL (execution language).  Labs are full of processes, but one place it should work well is in Lab Execution Systems as a means fo prototyping the process before it is coded.

    • Joe Liscouski, you may not know this but there is BPEL for People.  That is an interesting concept of applying automated controlled workflows to human processes: https://docs.oasis-open.org/bpel4people/bpel4people-1.1.html

      Also, you will want to look at these open source apps that would make up a complete solution suite for workflow automation.  You need of course the bpmn engine and designer, then you need the forms for human and automated data collection points in the flow and then you need the rules engine for the custom processes that are inevitably a part of the bpmn flow.  Finally, you need a flow based integration tool to pull in data from external systems and instruments.  So the tool set is as follows:
      1. https://camunda.com/ –  BPMN
      2. 
      https://www.form.io/  – Forms
      3.
      https://www.drools.org/  – Business Rules
      4. 
      https://nodered.org/ – Integration & Automation

      At LabLynx we package most of this to run through an IoT device when we do lab automation through our LabVia product.

  • Jon, that is an excellent question and I think your observations about the organizations is spot on. The laboratory and scientific industry is very, very conservative and very focused. They are not swayed by tech innovations. The organizations are focused on the work they do and everything that does not directly deal with the work they do is a distraction. So when they need something they talk to their peers for guidance. So what does that mean for you? It means that if you are going to make Kolabtree successful, you will have a long hockey stick base or you will have to invest a lot upfront in order to build momentum. This industry changes very slowly and makes extensive use of peer recommendations. All of that being said, my company makes extensive use of freelancers all the time using Upwork. One suggestion is that your company offer traditional recruiting and staffing services along with freelancing. This is going a bit retro but you will have more short term success and as long as you use it as a technique to push the freelancer model and let the client choose what is best for them, I would think you would be successful. If you are VC or PE funded, try to get yourself some funds to acquire a scientific staffing company and build it into a NextGen scientific staffing firm.

  • John Jones posted a new activity comment 3 months, 3 weeks ago

    In reply to: John Jones posted an update in the group Laboratory Informatics & Automation
    Does anyone in the group use BPMN 2.0 to manage lab workflows? I am looking at a number of products for modeling workflows […]
    View

    That is excellent Jeff Vannest.  All LIMS products should do exactly the same.  I am hoping to put in an Open Access BPMN workflow repository into LiMSforum for folks to share workflow processes and then to provide a workflow engine such as Camunda to execute the flows along with Form.io for the data collection forms.  Eventually will add IoT resources with NodeRed so we can also have integration flows.  At LabLynx we use BPMN for workflows but the ones we have are pretty specific to each client.  

    We have many integration flows using NodeRed and are happy to share those to an Open Access repository.  One I know will be useful to most people will be the ASTM serial interface standard (deprecated but widely used).  We have a nice packaged set of interfaces for clinical instruments that use that standard.

    Can you share a small narrative on how you have used BPMN for lab workflows?

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