November 12, 2013

Lab7 ESP™

The Lab7 Enterprise Science Platform

The Lab7 Enterprise Science Platform (ESP) is the first complete sample-to-answer software platform for data-intensive laboratory operations. It is a centralized lab data management platform that helps organizations and individual researchers track samples, process data, produce reports, and manage workflows and analysis pipelines – increasing sample throughput and freeing space for new opportunities in the lab.

The heart of the Lab7 ESP is a fully customizable workflow engine that organizes your lab around different sequencing workflows. Lab7 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.

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.Better LIMS, data management, bioinformatics

Protocol Management

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.

Pipelines

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.Pipeline, NGS pipeline, bioinformatics

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

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.Tasks, command line, ngs pipeline, bioinformatics

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.ACMG Report, clinical data, data management, analysis, bioinformatics

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.Browser Annotation, genomics, ngs informatics, bioinformatics, data management, ClinVar, COSMIC, dbSNP

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.

Provenance

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.Sample Provenance, data provenance, audit trail, bioinformatics, data management

Monitoring

The Lab7 ESP’s monitoring tools provide multiple views into in-flight analyses and workflows, giving scientists complete transparency.Pipeline Monitor, pipelines, ngs pipelines, bioinformatics, data management

Security

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.

Deployment and Administration

Our core development team has over 60 years combined experience developing and deploying scientific software in complex, high-performance environments. As a result, the Lab7 ESP has been designed from the ground up to work in many different deployment scenarios, from single workstations to bench-side compute clusters to supercomputers and on to the cloud.

Deployment

The Lab7 ESP is designed to not only be platform agnostic but also to be self contained and to deploy quickly in most environments. A basic installation is as simple as extracting a tarball (or unzipping a zip file, if that’s how you roll) and adjusting a few configuration settings. The client side is even simpler. As a Web-based application, the Lab7 ESP requires nothing more than a recent, HTML5 compliant Web browser such as Safari, Chrome, or Internet Explorer 9.data management software, bioinformatics, LIMS, pipelines, ngs

Developer Tools

The Lab7 ESP provides administrative access from the Web, command-line tools, and RESTful APIs. Our command-line tools can be used to launch and monitor pipelines, allowing the Lab7 ESP to integrate with existing job management systems.

HPC Integration

We leverage your existing job scheduler, file systems, and user models to integrate seamlessly into existing compute environments. The Lab7 ESP supports all major job schedulers, including PBS, SLURM, SGE/OGE, and Platform LSF. Our core pipeline engine is built on a task graph engine that uses shell scripts as the main unit of execution: any executable or file visible from the job scheduler’s execution environment can be used.

The Lab7 ESP works with job schedulers and user databases via a secure user model that allows Lab7 users to be mapped to users on the compute nodes. All pipelines execute as the user who submitted them and root access is never required while running the software.

  • Operating Systems:  Linux and OS X
  • Compute Infrastructure:  Scales from single workstations to large clusters or clouds
  • Job Schedulers:  Compatible with all major job schedulers (SLURM, SGE/OGE, PBS, LSF)
  • Browser Support:  Any HTML5-compliant browser, including mobile
  • Environment:  Self-contained runtime environment (No external dependencies)
  • Pipelines:  Pipeline tasks can be any shell script and run as the submitting user
  • Security:  Built on existing OS security with additional access controls, root access not required
  • Versioning:  Annual licenses include all updates and upgrades
  • Auditing Capabilities:  Built-in tools to provide compliance with any regulatory requirements (e.g. CLIA, GxP, 21 CFR Part 11)
  • Analysis Agnosticism:  Run any NGS analysis (DNA, RNA)…or, frankly, any analysis pipeline.  Remember, it’s customizable to your requirements.