Blistering Covid LIMS performance. Virologist testers required

Any LIMS worth its salt should perform well under the light loads of single test Covid analysis requests, no big deal. Open Source LIMS does it with the very best, and with much more freedom, less outlay


Double quick configuration After a previous sprint showed that the minimalist Covid screening SOP makes it possible to configure Bika LIMS in just over an hour, Bika LIMS for Covid screening, we set out to see about performance itself - not only the LIMS but the UIX. How can it be improved (and who is going to pay:) As an intermittent experiment, interrupted by making notes towards the Gap Analysis and documenting progress in Bika Covid at Full Tilt, we threw a batch of 500 Samples at it and timed LIMS processing through each workflow step Use Case We are still not 100% sure about our use case - Virologists are hard to come by - but opted for a workflow that includes preparation steps for Sample Inactivation, Plating and Nucleic Acid Extraction before a final outcome is determined with and RT-PCR analysis We included results capture for RNA extraction, and kept Sample Rejection enabled for the lab to dispose of poor quality RNA samples before they get to the PCRs Analysis Specifications are used to alert analysts to these Samples, and finally of any Positive and Indeterminable results	Blistering performance We expected it to go well, these sample objects are smaller by a factor 100 compared to 120 test Cannabis analysis requests, but were nevertheless pleasantly surprised: Excluding physical sample handling and instrument work, the LIMS spent little more than half an hour of aggregated processing time to complete receive, label and prepare samples for PCR Good enough to get this out there already for labs needing new viral screening LIMS that is easy to configure and affordable. We still have to complete results verification and publication steps for which we are resurrecting a simple CSV exporter for tabled results publication, also in PDF Gap Analysis Check back soon. We'll also be publishing a gap analysis, listing customisations toward an even better fit Most obvious are instrument interfaces for any one of those your lab uses, CSV parsers are dirt cheap And maybe a LIMS function to Push results across the Bika API to downstream EMR or DHIS. These systems if configurable and using a RESTful interface architecture, can already be authorised to read the Bika DB using the CSID (Client Sample ID) to reference results	Assistance new labs We did not expect labs to come running after publishing Bika Covid at first, LIMS acquisition is a slow process. It seems however that testing just for Covid v.19 will continue for many more months, especially in resource poor regions Capacity building should once more become prominent post outbreak, as was the case earlier when the more traditional Case centric Bika Health was used in Liberia. Bika will gladly assist deserving labs to get going, with installations and then these very lightweight configurations. Nobody has to pay outrageous proprietary LIMS prices in a time of crisis Bika Covid Demo Please take some time to evaluate the Bika Covid demo. Request lab manager access

Double quick configuration

After a previous sprint showed that the minimalist Covid screening SOP makes it possible to configure Bika LIMS in just over an hour, Bika LIMS for Covid screening, we set out to see about performance itself - not only the LIMS but the UIX. How can it be improved (and who is going to pay:)

As an intermittent experiment, interrupted by making notes towards the Gap Analysis and documenting progress in Bika Covid at Full Tilt, we threw a batch of 500 Samples at it and timed LIMS processing through each workflow step

Use Case

We are still not 100% sure about our use case - Virologists are hard to come by - but opted for a workflow that includes preparation steps for Sample Inactivation, Plating and Nucleic Acid Extraction before a final outcome is determined with and RT-PCR analysis

We included results capture for RNA extraction, and kept Sample Rejection enabled for the lab to dispose of poor quality RNA samples before they get to the PCRs

Analysis Specifications are used to alert analysts to these Samples, and finally of any Positive and Indeterminable results

Blistering performance

We expected it to go well, these sample objects are smaller by a factor 100 compared to 120 test Cannabis analysis requests, but were nevertheless pleasantly surprised: Excluding physical sample handling and instrument work, the LIMS spent little more than half an hour of aggregated processing time to complete receive, label and prepare samples for PCR

Good enough to get this out there already for labs needing new viral screening LIMS that is easy to configure and affordable. We still have to complete results verification and publication steps for which we are resurrecting a simple CSV exporter for tabled results publication, also in PDF

Gap Analysis

Check back soon. We'll also be publishing a gap analysis, listing customisations toward an even better fit

Most obvious are instrument interfaces for any one of those your lab uses, CSV parsers are dirt cheap

And maybe a LIMS function to Push results across the Bika API to downstream EMR or DHIS. These systems if configurable and using a RESTful interface architecture, can already be authorised to read the Bika DB using the CSID (Client Sample ID) to reference results

Assistance new labs

We did not expect labs to come running after publishing Bika Covid at first, LIMS acquisition is a slow process.

It seems however that testing just for Covid v.19 will continue for many more months, especially in resource poor regions

Capacity building should once more become prominent post outbreak, as was the case earlier when the more traditional Case centric Bika Health was used in Liberia.

Bika will gladly assist deserving labs to get going, with installations and then these very lightweight configurations. Nobody has to pay outrageous proprietary LIMS prices in a time of crisis

Bika Covid Demo

Please take some time to evaluate the Bika Covid demo. Request lab manager access