Thursday, December 31, 2009

2009 Review

The end of the year is a good time to reflect, review accomplishments, and think about the year to come. 2009 was a good year for Geospiza’s customers, with many exciting accomplishments for the company. Highlights are reviewed below.

Two products form a complete genetic analysis system

Geospiza’s two core products, GeneSifter Laboratory Edition (GSLE) and GeneSifter Analysis Edition (GSAE), help laboratories do their work and scientists analyze their data. GSLE is the LIMS (Laboratory Information Management System) that laboratories, from service labs to high-throughput data production centers, use to collect information about samples, track and manage laboratory procedures, organize and process data, and deliver data and results back to researchers. GSLE supports traditional DNA sequencing (Sanger), fragment analysis, genotyping, microarrays, Next Generation Sequencing (NGS) and other technologies.

In 2008, Geospiza released the third version of the platform (back then it was known as FinchLab). This version launched a new way of providing LIMS solutions. Traditional LIMS systems require extensive programming and customization to meet a laboratory’s specific requirements. They include a very general framework designed to support a wide range of activities. Their advantage is that they are highly customizable. However, this advantage comes at the expense of very high acquisition costs accompanied by lengthy requirements planning and programming before they become operational.

In contrast, GSLE contains default settings that support genetic analysis out-of-the-box, while allowing laboratories to customize operations without programmer support. Default settings in GSLE suppport DNA sequencing, microarray, and genotyping services. The GSLE abstraction layer supports extensive configuration to meet specific needs as they arise. Through this design, the costs of acquiring and operating a high-quality advanced LIMS system are significantly reduced.

Throughout 2009, 100’s of features were added to GSLE to increase support for instruments and data types, and improve how laboratory procedures (workflows) are created, managed, and shared. Enhancements were made to features like experiment ordering, organization, and billing. We also added new application programming interfaces (APIs) to enable integration with enterprise software. Specific highlights included:
  • Extending microarray support to include sample sheet generation and automate uploading files
  • Improving NGS file and data browsing to simplify the process of searching and viewing the 1000’s of files produced in Next Gen sequencing runs
  • Making NGS data downloads, of very large gigabase files, robust and easy
  • Adding worksets to group DNA and RNA samples in customized ways that facilitate laboratory processing
  • Creating APIs to utilize external password servers and programmatically receive data using GSLE form objects
  • Enhancing ways for groups to add HTML to pages to customize their look and feel
In addition to the above features, we’ve also completed development on methods to multiplex NGS samples and track MIDs (molecular identifiers and molecular barcodes), enter laboratory data like OD values and bead counts in batches, create orders with multiple plates, and access SQL queries through an API. Look for these great features and more in the early part of 2010.


As noted, GSAE is Geospiza’s data analysis product. While GSLE is capable of running of running advanced data analysis pipelines, the primary focus of data analysis in GSLE is to provide quality control. Thus its data analyses and presentation focus on single samples. GSAE provides the infrastructure and tools to compare the results between samples. In the case of NGS, GSAE also provides more reports and data interactions. GSAE began as a web-based microarray data analysis platform making it well suited for NGS-based gene expression assays. Over 2009 many new features were added to extend its utility to NGS data analysis with a focus on whole transcriptome analysis. Highlights included:
  • Developing data analysis pipelines for RNA-Seq, Small RNA, ChIP-Seq, and other kinds of NGS assays
  • Adding tools to visualize and discover alternatively spliced transcripts in gene expression assays
  • Extending expression analysis tools to include interactive volcano plots, unbalanced two-way ANOVA computations
  • Increasing NGS transcriptome analysis capabilities to include variation detection and visualization
The above features fulfill the requirements needed to make a platform complete for both NGS and microarray-based gene expression analysis. And, the addition of variation detection and visualization lays the groundwork for GSAE to extend its market leadership to resequencing data analysis.

Geospiza Research

In 2009 Geospiza won two research awards in the form of Phase II STTR and Phase I SBIR grants. The STTR project is researching new ways to organize, compress, and access NGS data by adapting HDF technologies to bioinformatics. Through this work we are developing a robust data management infrastructure that supports our NGS sequencing analysis pipelines and interactive user interfaces. The second award targets NGS-based variation detection. This work began in the last quarter of the year, but is already delivering new ways to identify and visualize variants in RNA-Seq and whole transcriptome analysis.

To learn more about our progress in 2009, visit our news page. It includes our press releases and reports in the news, publications citing our software, and webinars where we have presented our latest and greatest.

As we close 2009, we especially want to thank our customers and collaborators for their support in making the year successful and we look forward to an exciting year ahead in 2010.

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