THE FIRST OF ITS KIND
The Lab7 Enterprise Science Platform (ESP) is the first complete sample-to-answer software platform for data-intensive laboratory operations.
THE HEART OF ESP:
A FULLY CUSTOMIZABLE WORKFLOW ENGINE
ESP's workflow engine organizes your lab around different data-rich workflows. ESP Workflows encompass not only wet lab operations but support full integration of analysis and reporting, drastically reducing the amount of IT "machinery" required to manage, process, and analyze samples. ESP's Resource Manager maintains data provenance throughout
HOW DOES ESP...
- TRACK SAMPLES AND MANAGE WORKflOWS
- DEVELOP PIPELINES AND AUTOMATE ANALYSIS
- GENERATE REPORTS AND SHARE RESULTS
- KEEP TRACK OF ALL THE DATA IN THE SYSTEM - RESOURCE MANAGER
LIMS: SAMPLE AND PROTOCOL MANAGEMENT
The Lab7 ESP's LIMS tools are designed to provide full transparency into your operations. Whether running as a complete LIMS solution or complementing your existing LIMS, the Lab7 ESP streamlines sample tracking and communication between lab technicians, managers, and scientists
The Lab7 ESP’s LIMS functionality gives your laboratory the tools it needs to maintain critical records, and forms the basis for the provenance that will be required for downstream reports.
Sample & Experiment Tracking
The Lab7 ESP gives stakeholders a detailed view of a sample’s status in its workflow. As samples move from the lab into analysis, users can view results as they become available directly from the Lab7 ESP; no more hunting around for spreadsheets or emailing technicians for status reports.
In the lab, efficient protocol management and data entry are key for maintaining quality and throughput goals. A typical NGS lab will have a Protocol, LIMS, Data management, bioinformatics variety of protocols it will run to prepare samples for its sequencers. As the laboratory moves into more clinical or other regulated environments, accurate record keeping, along with tracking a sample’s progression through the preparation, become stringent requirements
Protocols in our LIMS functionality are built around customizable spreadsheet views for fast data entry. Spreadsheets are created for each lab technician, giving them a concise view into their daily workflow.
ANALYSIS PIPELINE MANAGER
The Lab7 ESP's Analysis Pipeline Manager is a comprehensive set of pipeline creation and management tools designed to seamlessly integrate into your existing bioinformatics environment. The pipeline engine is accessible via Web interface, command line, or via RESTful API calls.
The core of our Analysis Pipeline Manager is a task graph execution engine that provides maximum flexibility for creating complex pipelines. Our pipeline manager sits on top of your IT environment and supports parallel execution with all major job schedulers and integrated file tracking on any file system.
The Lab7 ESP's detailed monitoring interface gives you real time visibility into your pipeline's status and makes it easy to monitor many pipelines in a high-throughput environment.
Tasks can be any shell script that can execute on the target compute resource. No plugins or custom wrappers are required; simply take your current shell-based pipelines and migrate them directly to the Lab7 ESP.
Tasks leverage a flexible templating engine that allows shell scripts to be fully parameterized. Our templating language provides a rich set of operations that can be used to modify parameters as they are used by different tasks in a pipeline.
REPORTS, ANNOTATIONS, AND VISUALIZATIONS
The Lab7 ESP’s reporting and visualization engine allows scientists to view reports from pipelines as they are executing, giving them unprecedented access to their data during the analysis phase.
Customized Report Generation
Reports in the Lab7 ESP can be created from any data generated within a Lab7 Workflow, including any file that is registered with the system during the execution of a pipeline. The Lab7 ESP includes a variety of data visualizations, such as plots and charts, text and table tools, and heatmaps, but since the ESP is a web application, you also have the flexibility to utilize any other HTML content or tools. You can also pull in external files and data to include the necessary level of data reporting and content that your audience requires.
Integrated Genome Browsing
The Lab7 ESP includes a genome browser that can be integrated into reports to interactively display genomic content and annotations. The browser includes support for all common sequencing file formats, including FASTA, BAM, BED, GFF, VCF, Wig/bigWig. Display tracks can combine data registered from pipelines, local data on the user’s computer, or remote data supplied by DAS (Distributed Annotation System) services.
Variant Annotation Management
The Lab7 ESP’s Annotation Manager is a complete data management and visualization tool that ties together third-party variant annotation databases with in-house annotations and allows Lab7 ESP users to quickly build ACMG-style reports from their VCF files. Incorporate any annotation database, including commercial ones, to leverage as much information as you need to develop your actionable reports.
LAB7 RESOURCE MANAGER: DATA PROVENANCE & SECURITY
The Lab7 ESP is designed to run in research, production, and regulated environments. In each environment, ready access to the “5 Ws and an H” of your data (who, what, when, where, why, how) is essential for increased productivity, quality assurance, and regulatory compliance.
We track the full provenance of sequencing data, from the instrument to QC and mapping pipelines and to experiment specific analyses. Scientists have full access to the provenance chain and all the data associated with each step, enabling complex queries that allow scientists to fully explore their results.
The Lab7 ESP’s monitoring tools provide multiple views into in-flight analyses and workflows, giving scientists complete transparency.
With our security model, scientists can control access to all aspects of their experimental environment. Fine-grained access control lists enable read, write, and execute permissions for all data and pipelines.