BIOINFORMATICS Supporting competencies for the pharma industry

Transcription

1 BIOINFORMATICS Supporting competencies for the pharma industry

2 ABOUT QFAB QFAB is a bioinformatics service provider based in Brisbane, Australia operating nationwide and internationally. QFAB was established in 2007, and provides bioinformatics services to industry and academic researchers. Our specialties include the integration of hetergeneous biological datasets, interpretation and visualization of omics data, and statistical integrative analysis of complex data. Our staff have a strong background in the pharma and biotech industries and the application of omics technologies and advanced statistics for biomarker selection, drug discovery and development. With a demonstrated track record in delivering business and research relevant outcomes, QFAB has become one of Australia s leading bioinformatics service organizations. We are well positioned to help you recover the maximum value from your data. MODELS OF ENGAGEMENT We have developed core competencies in the management and analysis of very large and diverse datasets to support life science research, and complement the capabilities of omics and clinical facilities with bioinformatics and biostatistics support. QFAB provides its bioinformatics and biostatistics services through several models of engagement, which include: > Fee for service / project - For specific projects with a defined scope, timeline and deliverables. > Pre-paid FTE days - Exploratory analysis and long-term support. Ex: 1 day per week, 40 days per year... > Embedded personnel on site and HelpDesks - Get a flexible %FTE bioinformatician or biostatistician embedded within your organisation. > Training - We organise bioinformatics and biostatistics workshops all throughout the year, and can organise customised training within your organisation. > Co-applicant on grants

3 DATA MANAGEMENT AND INTEGRATION We have developed core competencies in the management and mining of very large and diverse datasets to support life science research. These include data capture, curation and integration through cross-references, metadata and ontologies. QFAB can develop, provide and manage databases to store and integrate a diverse range of complex data types, which include: > DNA/RNA sequence > Expression data > Metabolomic data > Proteomic data > Clinical data QFAB recognizes that the nature, structure and uses of data will change over time, and so provides maintainable database architectures that are robust and extensible to accommodate such changes. The databases can be coupled to web applications offering ongoing curation functions, intuitive upload interfaces, search, visualization and download tools, and direct integration into analysis functions. QFAB provides expertise in experimental design to ensure that the produced data will match commercial standards to optimize clinical trials, including statistical and genotype-specific dimensions. CHEMINFORMATICS QFAB supports drug discovery projects using cheminformatics approaches: > Prioritization of compounds and assays (Efficacy, Toxicity, ADME) > Design of compound libraries (diverse, focused or targeted) > Combinatorial library design and library enumeration > Quantitative Structure-Activity Relationships (QSAR) > Integrative analysis of genomics and cheminformatics datasets

4 STATISTICAL SELECTION AND VALIDATION OF RESEARCH DATA AND BIOMARKERS Even when collected under ideal circumstances, research and clinical data can be noisy or incomplete. QFAB s statistics team can help maximizing value from data acquisition programs by assessing data quality and rigorous statistical validity of results. In particular, QFAB can help to: > Design meaningful and statistically robust validation or pilot studies > Screen early research data for outliers and low-reliability data points, and to flag these for manual or automated removal from subsequent analyses > Compensate for missing data through specialized statistical imputation techniques > Reveal relationships between different datasets, conditions, platforms and time points > Develop integrative approaches with statistics and pathway analysis for patient stratification (responder/ non-responder, sensitive and resistant populations...) or treatment effect monitoring... mixomics motion chart Heatmap - transcripts and metabolites

5 DATA VISUALIZATION : TAKE CONTROL OF YOUR DATA > UCSC Genome Browser QFAB can provide access to secure web servers hosting an up-to-date version of your choice of genomes and associated publicly available annotations. These platforms enable you to analyze, visualize and share private data in the context of public databases without exposing any Intellectual Property externally. > Customized Galaxy Platforms QFAB offers the development and implementation of Galaxy platforms with the tools necessary for creating and executing customized analysis workflows. > Development of pipelines and workflows The QFAB Team is skilled in the development of data processing and analytical pipelines for the Galaxy or Pipeline Pilot platforms. > MixOmics by QFAB QFAB provides access and support to mixomics, an R package dedicated to the statistical analyses of large biological data sets such as omics data or highly dimensional data sets. mixomics offers a wide range of statistical methodologies to enable data exploration, visualization, and integration of data from different platforms, as well as prediction of categorical or continuous responses. > Interact with your data QFAB has expertise in interactive web technologies such as Shiny for R, GoogleCharts or Pipeline Pilot to build interactive web applications that let the user explore and visualize research data. These applications provide the ability to interact with the variables and parameters and to instantaneously see how the system reacts, enabling associations to be made. Shiny Interface Pipeline Pilot Interactive Graphics

6 QFAB Bioinformatics Level 6, Queensland Bioscience Precinct The University of Queensland 306 Carmody Road St Lucia QLD 4067 Australia T +61 (0) F +61 (0) E [email protected]