Monday, November 22, 2010

GeneSifter Lab Edition 3.16

Recently, we released GeneSifter Laboratory Edition (GSLE) 3.16. Over 40 new features were added to improve laboratory workflow support, enhance multiplexing, make orders and their data easier to manage, and extend the system's application programming interfaces (APIs).

Laboratory Workflow Support

Several new features will make working in the lab easier and improve data tracking and how GSLE is used. Workflows now include the ability to validate data using data ranges, and use laboratory defined lists to track the details about how samples are processed.  For Next Gen Sequencing (NGS), sample multiplexing has been extended to make it possible to define multiplexes and associate Barcodes, MIDs, or Indexes (or whatever else you like to call the little adapter tags) at any step of your process. Also, for those who use specific naming conventions to track process steps, sample naming conventions can be defined for process steps.  Finally, to use the above features and view data, the workflow editor has been streamlined to simplify data entry, workflows can be versioned to track your lab's process improvements, and a new report builder makes workflow data easy to access and view.

To better track samples organized in tubes, plates, slides, flowcells, freezers, buildings, and the universe, we have introduce a new tool called containers. Containers can be defined by the laboratory and are used to link samples to specific actions like sample storage or a data collection run. For example, Illumina flowcells can be created and have samples added. The flowcell can be run immediately or stored following cluster generation.  When samples are added to a flowcell, a new visual interface simplifies adding mixtures of multiplexed samples, single samples in individual lanes, or single samples spread over several lanes. Other kinds of containers track sample storage and can be updated with bed scanners to track the arrangement of samples as they move through the lab. And, containers can contain workflows to manage more complex procedures.

Order and Sample Management

Details matter, and GSLE 3.16 improves how you view them. Lab samples (templates) views now show all laboratory data associated with a sample on a single page. These data are organized in sections that can be collapsed so you can see the big picture, or focus on specific details. We also updated views of orders to make it easier to view their progress and made the orders easier to access when viewing data for release.

API Support

Some groups use GSLE as a stand alone system, others use GSLE in conjunction with external systems in commercial and very high-throughput production environments.  To support the later case, GSLE has a set of rich data-driven APIs that enable system to system communication. In 3.16, the APIs have been extended to edit certain kinds of stored data, add large batches of laboratory samples, upload container maps  to track samples, and manipulate charge codes with accounting systems.

Contact to learn more.

Wednesday, November 3, 2010

Samples to Knowledge

Today Geospiza and Ingenuity announced a collaboration to integrate our respective GeneSifter Analysis Edition (GSAE) and Ingenuity Pathway Analysis (IPA) software systems. 

Why is this important?

Geospiza has always been committed to providing our customers the most complete software systems for genetic analysis. Our LIMS [GeneSifter Laboratory Edition] and GSAE have worked together to form a comprehensive samples to results platform. From core labs, to individual research groups, to large scale sequencing centers, GSLE is used for collecting sample information, tracking sample processing, and organizing the resulting DNA sequences, microarray files, and other data. Advanced quality reports keep projects on track and within budget.  

For many years, GSAE has provided a robust and scalable way to scientifically analyze the data collected for many samples. Complex datasets are reduced and normalized to produce quantitative values that can be compared between samples and within groups of samples. Additionally, GSAE has integrated open-source tools like Gene Ontologies and KEGG pathways to explore the biology associated with lists of differentially expressed genes. In the case of Next Generation Sequencing, GSAE has had the most comprehensive and integrated support for the entire data analysis workflow from basic quality assessment to sequence alignment and comparative analysis. 

With Ingenuity we will be able to take data-driven biology exploration to a whole new level.  The IPA system is a leading platform for discovering pathways and finding the relevant literature associated with genes and lists of genes that show differential expression in microarray analysis. Ingenuity's approach focuses on combining software curation with expert review to create a state-of-the-art system that gets scientists to actionable information more quickly than conventional methods.  

Through this collaboration two leading companies will be working together to extend their support for NGS applications. GeneSifter's pathway analysis capabilities will increase and IPA's support will extend to NGS. Our customers will benefit by having access to the most advanced tools for turning vast amounts of data into biologically meaningful results to derive new knowledge.

Samples to ResultsTM becomes Samples to KnowledgeTM