Life science laboratory processes vary widely and often generate large, disparate datasets. Effective data capture, management, and analysis require that the unique characteristics of different scientific platforms be reflected in their corresponding process and data management applications.

GraphLogic creates custom life sciences applications designed specifically for each process, fully integrating workflow and data management capabilities. Scientists can access microarray, proteomic, sequencing, genotyping, and clinical data all within the same web-based system. Analysis results can be stored locally or on a designated server for multi-site collaborations.

GraphLogic enterprise applications are just as adept at managing workflows and data for leading technologies such as microarrays (e.g. DNA, CGH, tissue, antibody) as they are for emerging technologies that require specialized workflows and analytics.

Scientific Workflows and Applications:

• Microarrays
• Data Visualization
• Proteomics (Mass Spectrometry, Protein Microarrays, 2D-gel)
• Sequencing (traditional and next generation)
• GS20/FLX™ LIMS
• Operations Management (e.g. tracking costs, reagent use)
• Genotyping
• R & D
• Next generation applications: RNAi, DNA methylation, synthetic biology, glycomics Let us know and we'll build it for you!

The modular nature of our custom application lets customers acquire only those systems currently needed and to add more as laboratory operations change or expand. Since all systems are built on the same technology, new modules are easily and efficiently integrated. Additionally, all GraphLogic systems are highly-scalable and run on Windows, Unix and MacOS.

Microarrays

Microarray projects require a significant investment in equipment, personnel and software. Therefore, our microarray systems are fully integrated, providing the full range of comprehensive management tools available in PointDragon LIMS systems along with the added features of data analysis and visualization. GraphLogic provides a complete microarray solution which is customized to meet our customers' specific microarray workflow, data storage, and data analysis needs.

Our web-based enterprise microarray solutions support all microarray technologies: including commercial, in-house, one and two color platforms. Users have complete control over the workflow, from sample acquisition to data analysis, and also have full access to comparison data for identifying differentially expressed genes and patterns of gene expression. Data is easily integrated with proprietary and public databases, including gene annotation information. Data processing can run automatically over the web or allow for intervention at user specified steps. The pipeline is a fully MIAME compliant, browser-based thin client solution, which enables scientific collaboration regardless of investigator location.

Through the integration of web-services technology with either the open source BioConductor suite of modules or customer developed algorithms, GraphLogic's microarray enterprise solution provides multiple methods for data normalization, filtering, clustering, and analysis. Users can upload raw data files from any microarray platform, including .CEL files from Affymetrix, and then process the data through RMA, gcRMA or other algorithms. Data transformation and preprocessing results can be visualized through a number of methods, including M vs A plots, box plots, or correlation matrices. The microarray pipeline also contains fully integrated statistical, 2D and 3D interactive data visualization capabilities. This unique feature greatly simplifies the maintenance and overhead typically associated with patching together multiple third party data analysis and visualization applications. Scientists can now choose among various options, including self-organizing maps (SOM), hierarchical and K mean clustering, principal component analysis (PCA), and ANOVA. New user defined methods and algorithms can be easily added. Some of the key features of our microarray applications are summarized here.

Microarray and Process Tracking

PointDragon can manage every aspect of microarray projects.

• Manage in-house microarray printing operations
• Monitor sample processing status
• Track microarray use and reagent inventory
• Check robot, hybridization and wash chamber performance
• Store and access image files
• Provide customer access over the web

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Data Analysis and Visualization

Perform data analysis directly in the web-browser and collaborate in real-time.

• Automated pipeline via web-service integration
• Integrate with Bioconductor or proprietary algorithms
• Filter data using one or multiple criteria
• Choose among various analysis methods (clustering, PCA, SOM, etc.)
• Choose among various visualization methods (charts, graphs, 2D, 3D)
• Store and manage gene lists and annotation
• Query on experimental data and metadata

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Proteomics

The proteomics field is experiencing tremendous growth and innovation, leading to new applications in the fields of discovery, development, diagnostics, and clinical practice. GraphLogic's enterprise proteomics solutions can manage all current proteomics technologies, including 2D-gel/LC/HPLC/mass spectrometry, protein microarrays, protein screening technologies, and tissue microarrays. GraphLogic enterprise solutions are uniquely positioned to integrate new and emerging technology platforms. Scientists know that proteomics studies generate very large datasets. PointDragon systems are designed to track every detail of proteomics projects, including complete sample tracking, data capture, storage, retrieval and sharing. PointDragon systems are easily customized to accommodate biomarker discovery, drug screening, and pharmacogenomics/toxicogenomics. Some of the key features of our proteomics applications are summarized here.

Gel and Process Tracking

PointDragon can manage every aspect of DIGE and 2D gel electrophoresis.

• Access third party pick lists, manage associated metadata
• Manage images, access in real-time access
• Import and export files to analysis applications
• View upstream and downstream (mass spec) processes

Mass Spectrometry and Proteomic Analysis

Manage multi-step mass spectrometry workflows and data output.

• Manage sample processing - from submission to data output
• Handle any plating and re-arraying throughout processing
• Manage sample metadata and associated spectra
• Efficiently handle mzXML data
• Store and manage results from database searches
• View data analysis and visualization in a browser-based environment
• Create custom queries on spectra, gels, treatments and other data.

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Sequencing

The generation of sequence data is rapidly advancing, and whole bacterial genomes are now sequenced in days. This deluge of data creates a corresponding downstream data management and analysis bottleneck. GraphLogic enterprise solutions for sequencing are ideally suited for the evolving needs of scientists working with new sequencing technology that deliver tremendous quantities of data. Some of the key features of our sequencing applications are summarized here.

Sample Processing

• Manage library preparation, plating and tracking
• Track all subsequent cloning or amplification steps
• Design primers - track, order and receive them online

Data Management

• Primer walking, colony picking and microplate tracking
• Whole genome shotgun sequencing and assembly
• De novo assembly and resequencing
• Single molecule sequencing
• Calculate and display quality scores

Web-enabled Sequence Analysis

• Identify ORFs, start and stop signals, splice variants and also annotate within an application
• Automatically incorporate standard (BLAST family of applications, Glimmer, GeneMark, tRNAscan, or other) or proprietary analysis programs
• Perform surveys on conserved regions and genetic hotspots
• Execute comparative analyses, within and between organisms
• Examine sequence data alongside drug and antibiotic resistance data
• Contig assembly and trace viewer is fully integrated within workflow

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Next Generation Sequencing - GraphLogic LIMS for GS20/FLX™

The GraphLogic GS20/FLX™ LIMS is a web-based system that streamlines operations and enhances productivity through a comprehensive integrated workflow, detailed production reporting, improved data management, and secure data sharing. GraphLogic maintains a close relationship with 454 Life Sciences, acquired by Roche, to continue to provide the most up-to-date management of new kits and preparation methods. Whether interested in a LIMS to support your Genome Sequencer FLX™ system or an integrated solution for all of your next generation sequencing operations, GraphLogic has the experience and technology to deliver your customized solution and fast. Contact us for a free trial version and demonstration.

Streamline Your GS20/FLX™ LIMS Sequencing Operations

Integrated Modules

• GS20/FLX™ LIMS Sequencing Operations
• Management Systems
• System Administration

Comprehensive Workflows Designed Specifically for GS20/FLX™ LIMS Process

• Sample Management (Submission, Tracking, Pooling)
• Genome Sequencer Management (Plate Layout, Setup, Run, QC)
• Emulsion PCR (Setup, Breaking, and Enrichment)
• Project Management and Reporting

System Features

• Web-based (any browser)
• Role-based access & security
• Runs on any system architecture (Windows, Unix, Linux, MacOS)
• Interfaces with any database (Oracle, SQL)

System Benefits

• Streamlined lab operations
• Improved data management
• Simplified data sharing
• Seamless data flow between steps

Implementation

• 48 hours installation
• On-line training

Customization

• Customization available on a fixed project fee basis

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Operations Management

• Add operation costs for individual steps
• Edit operation costs for individual steps
• View overall project costs and cost breakdown by reagents or supplies
• Input different cost rates for different customers
• Generate billing reports for internal or external customers

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Genotyping

Completion of the HapMap project has created an unprecedented opportunity for genetic analysis. Insight into disease origin, progression, and treatment will increase significantly in the coming years. Managing and integrating this new SNP, mutation, and haplotype data with other "omic" type data presents a formidable challenge. PointDragon technology is ideally suited for creating custom applications and fully integrating genotyping data with microarray, proteomic and sequencing data.

Pinpoint SNPs and Mutations

• Select chromosome of interest
• Select genomic region of interest
• Select gene of interest by name of gene identifier
• Select by internal identifier
• Display haplotypes
• Zoom in or out on the region of interest
• Overlay SNP and haplotype data onto genomic and protein information

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R & D

Research and Development is a highly mutable environment that requires a lean software solution. Collaborating with lead scientists in this demanding area, GraphLogic has developed a cutting edge solution that focuses on flexibility, security, and elucidated results.

Highlights

• Instrument Definition
• Flexible Experimental Design
• SOP Tracking
• Reporting
• PDA Integration

Samples are optionally grouped within an experimental set and integrated with an Inventory system as desired. An experimental design is defined for an experimental set by adding instruments on the fly and refining parameter values. New SOPs are tracked for later use and reporting as instrument parameters are added and modified. Data capture is streamlined with easy one-click button entries and PDA interfaces for scanning experimental set barcodes. GraphLogic's R&D solution is designed to meet the needs of any GxP laboratory.

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