The Company

Sigma-Aldrich is a leading Life Science and High Technology company committed to Enabling Science to Improve the Quality of Life. Its chemical and biochemical products and kits are used in scientific research, including genomic and proteomic research, biotechnology, pharmaceutical development and as key components in pharmaceutical, diagnostic and other high technology manufacturing. The company has customers in life science companies, university and government institutions, hospitals, and in industry. Over one million scientists and technologists use its products. Sigma-Aldrich operates in 40 countries and has 7,900 employees providing excellent service worldwide.

Need for a Software Solution

The client was looking for an efficient real-time primer and probe design tool for offering value-added services to its customers. Sigma wanted to offer an online application for its customers to design specific and efficient oligonucleotides adhering to quantitative real-time PCR design guidelines. The need was to offer a best-in-class product with proven algorithms that could be integrated into Sigma’s eCommerce systems. Sigma also wanted a “Customer Relationship Manager” working behind the tool to track customer registrations,to record user engagement, and to offer personalized support. The solution needed to include product deployment, website hosting, and maintenance assuring zero downtime.

The Challenge

Although the tool was expected to be based on Beacon Designer, the user experience and interface needed to be created online. HTML templates were embedded with primer / probe design modules and search options.The tool had to be designed to meet all of the oligo design requirements of the user along with keeping the interface apparent. The application also needed the development of a scalable database management system to integrate the many facets and systems of the organization while providing the business team with the tools it needed for customer profiling and engagement.

Expected Benefits

The client has been a long-time customer of PREMIER Biosoft and has been successfully using Beacon Designer for its qPCR assay design services. Sigma has also been recommending Beacon Designer to its customers for their assay design needs. By providing free online primer and probe design software, especially for quantitative assays, Sigma-Aldrich expects to offer its existing customers value-added services and most importantly, generate sales leads to meet business expansion objectives. Using the expertise of PREMIER Biosoft in developing best-in-class quantitative real-time PCR design software products such as Beacon Designer and AlleleID, the client expects to provide its customers a sophisticated, yet easy-to-use tool for qPCR assay design needs. "After years of successful use internally by our technical support team, we wanted to offer Beacon Designer functionality directly to our customers. We chose to use this powerful tool because it offers best-in-class performance and is highly regarded by the research community." says Tom Russell, Ph.D., Product Manager, Sigma Life Science. Close collaboration between the Sigma-Aldrich's business team and PBI's development team, coupled with superior project management, enabled the successful launch of OligoArchitect™ Online.

The Company

DxTerity Diagnostics has developed the NEAT™ platform for nucleic acid-based testing applications in molecular diagnostics and personalized medicine. NEAT or Non-Enzymatic Amplification Technology is a robust and widely-applicable genomic testing platform that replaces expensive enzymatic amplification techniques, enabling the development of simple and affordable diagnostic tests.

Need for a Software Solution

The popularity of a nucleic acid amplification platform depends on its performance and ease of use. A technique that requires a significant investment in time and money has few takers. An easy to use software system that allows customers to design probes for specific targets can increase the market penetration of the technology.

However, the automatic design of probes that are highly efficient can be challenging. Designing probes for more complicated assays such as multiplex mRNA detection and in-situ/in-vitro imaging adds further challenges.

"We wanted to make this robust technology popular in companies and labs working on personalized medicine. An easy to use software system that efficiently designs NEAT and QUAL™ (Quenched Auto- Ligation) probes is essential for this. The NEAT software program developed in conjunction with Premier Biosoft allows users to quickly design probes which conform to the specific guidelines that we developed, without compromising on the flexibility that the users of this platform may need," says Bob Terbrueggen, President and CEO, DxTerity Diagnostics.

The Challenge

The client outlined a comprehensive set of criteria to be fulfilled. The possibility of a large user base necessitated a generic and stable design. At the same time, the design needed to be highly customizable to allow the user to control all their design parameters. This meant that the requirements must be understood correctly from the client’s perspective, and the product must be designed for the users' needs.

Expected Benefits

By providing a software solution to the probe design needs of NEAT, DxTerity expects to make the technology more popular by minimizing (or removing) the barriers for adopting a new platform for diagnosis. NEAT is an easy to use system developed to replace the traditional enzymatic amplification techniques that are key to most nucleic acid detection technologies. The software provides two primary benefits, increased assay success and ease of use. The use of sophisticated algorithms ensures that each base is interrogated to find a suitable probe that passes all the set design parameters. The tags are checked for uniqueness and the designed probes must conform to all guidelines, increasing the probability of assay success. Without a software system, customers would need to design probes manually by trial-and-error, or rely on DxTerity for all designs, even in cases where security of early-stage IP is critical. With the biologist designed interface and short learning curve, it is possible for customers to design assays in their own facility with just a click of a button, with a high probability of successful results.

The Company

PrimerDesign Ltd. is an innovative biotechnology company focused on developing improved solutions for gene quantitation by real-time PCR. Founded within Southampton University's School of Medicine and in partnership with ATDbio, PrimerDesign specializes in developing gene quantitation assays validated and manufactured to the very highest standard.

Need for a Software Solution

The client was looking for a robust solution for their gene quantitation primer design needs. They have been customers of Beacon Designer for over the last three years and understood that with a little bit of tweaking to the Beacon Designer algorithm, they would get solutions very specific to their business and research needs. A high throughput application was needed to help design numerous assays for validating microarray data. The also had a need for forcing the design of compatible oligos, given a partial set of predesigned oligos. This meant designing strong search and ranking algorithms to help choose the best possible assay. The client wanted a team that could quickly get up to speed on their technologies and deliver a concrete mechanism that would enable their internal design team to focus on offering next generation services.

The Challenge

The client spelled out what was needed. It was imperative for the product to offer results that the client was expecting which included making a Beacon Designer-like program but faster and more powerful and at the same time give more options to choose from. The solution had to be cost effective and yet complement the client's future business road map.

Expected Benefits

By providing a software solution to real time PCR primer design especially for quantitation assays, PrimerDesign expects to increase their assay design business by offering a better solution to their customers. Leveraging PREMIER Biosoft's strong domain expertise in real time PCR, the client expects to design better and more robust assays in less time. In addition, the client expects to meet their business goals to generate consistent revenues. Based on the services offered, they expect to get repeat orders. “We wanted a software product that could meet our specific requirements. We have been using Beacon Designer for more than three years now and I was convinced that PREMIER Biosoft could offer a solution for my current needs, given their considerable expertise in real time PCR and their strength in designing programs that were both, intuitive and powerful. My faith in them was not misplaced; I got exactly what I was looking for, in the budgeted time and in the budgeted cost. PREMIER Biosoft International is a competent partner for algorithmically challenging bioinformatics projects." says Dr. Robert Powell, Managing Director, PrimerDesign Ltd.