It’s not every day that a LIMS vendor admits that a product is inadequate, but Matthew Frome, bioinformatics business development manager at Amersham Biosciences, says that for high-throughput research, LIMS “are not collecting enough information.” To address this shortcoming, the instrumentation giant recommends a third-party software product that plugs into its LIMS to monitor and track the process flow through the system.
The software, Focus, is sold by a tiny, San Jose-based company called BergenShaw, and Amersham is not the only large life science player to notice the low-profile firm. BergenShaw also boasts Incyte Genomics, Celera Genomics, the Joint Genome Institute, and Applied Biosystems among its loyal customers.
Focus runs on top of an existing LIMS to closely monitor the sample yield across every step in the research process. While the LIMS tracks various factors at each of these steps, such as the date, time, operator, temperature, flow rate, reagent lot number, and the like, Focus adds a new level of capability by assessing and comparing the performance of each one of these factors — both individually as well as in combination with every other process factor in the system. The result is a table that ranks combinations of process factors according to their performance. Users can then pinpoint which factors or combinations of factors contributed to low yield, high yield, or other performance results of interest, and act accordingly.
Jim Shaw, president of the company, said that when he demonstrated the software at Incyte and picked up a process flaw in 20 minutes, he was surprised at the response — a stony silence. After assuming the worst, Shaw said the project manager told him that his team was able to find the same flaw, but it took two months. Incyte purchased the software on the spot.
According to Frome, the alternative for most companies running high-throughput sequencing pipelines is to backtrack manually, step by step, machine by machine, to find a stuck capillary or other bottleneck that the Focus software can locate automatically. “By that time, five days have gone by, and you’ve lost your availability to keep the throughput high.”
Focus can be set up to perform its analysis automatically on a daily or weekly basis, with certain performance thresholds, Shaw said. It then sends out an e-mail when user-defined conditions appear in the analysis results.
Shaw said the company has focused its efforts on sequencing pipelines so far, but has already modified Focus to analyze genotyping process data and is working on a new version for microarray experiments. Long-term, Shaw said he expects the company to expand into proteomics, high-throughput screening, and other specialized research pipelines.