Scientific Expertise

• High throughput large-scale computing for systems biology data processing and knowledge generation
• Information management for sequence analysis and Next Generation Sequencing technology
• Microarray Analysis, Genome-Wide Association Studies (GWAS), Biomarker Discovery, Gene Set Analysis
• Numerical Methods and Biostatistics
• Cheminformatics, QSAR, ADMET modeling for drug discovery
• Computer-assisted molecular modeling, simulation and drug design (CADD)
• Regulated information systems
• Laboratory Informatics, automation, robotics, LIMS, ELN
• Electronic Health Records, clinical knowledge management and telemedicine systems

Technology Capabilities

Sequence analysis methods and software: BLAST, FASTA, Smith-Waterman, multiple alignment methods, HMMer, sequence assembly, Phred/Phrap/Consed, protein identification and function prediction, SignalP, Vector NTI

Genomics, Transcriptomics, Next Generation Sequencing: TGICL, SSAKE, SHARCGS, VCAKE, Newbler, Celera Assembler, Euler, Velvet, ABySS, AllPaths

Protein 3d modeling and MD simulation: Accelrys tools (Discovery Studio, Insight II, QUANTA, CHARMm), Xplor, Felix, MODELER, GROMOS, ChemAxon

Cheminformatics, compound registration and computer-assisted drug design: Accelrys, CambridgeSoft, Molsoft, MDL ISIS, ACD software; QSPR, ADME property prediction, virtual screening; PK/PD: Pharsight WinNonLin

Scientific data management, Electronic Lab Notebook (ELN), Laboratory Information Management (LIMS) software:Thermo Scientific LIMS (SampleManager); LabVantage SQl*LIMS; Waters (formerly NuGenesis) SDMS, ELN, Empower Chromatography Data System; CambridgeSoft ELN; SciTegic Pipeline Pilot; Agilent ChemStation, GeneSpring, Cerity CDS, OpenLab; Labtronics LimsLink, Collect, iLab, Nexxis ELN; Spotfire DecisionSite; Activity Base; Nautilus

Dynamic systems modeling for business processes, chemical reactions and metabolic pathways

Business process mapping and engineering: UML, Sparx Systems Enterprise Architect, Business Process Management (BPM), BPEL, Orchestra; SOA, WSDL, web services

Project management and SDLC: Rational Unified Process (RUP), Extreme Programming (XP), Scrum, Stage Gate process, SDLC

Workflow, collaboration, versioning and change control: Documentum; MS Sharepoint; Sparta Systems Trackwise quality and change management; MS VSS, CVS, RCS, Subversion, Serena Systems PVCS

Regulated and validated systems: development of requirements (URS), functional design specifications (FSDS), risk assessment, Master Validation Plans, IQ, OQ, PQ

Data warehousing, database development, reporting and business intelligence:
Oracle; MySQL; PostreSQL; Sybase; Illustra; SQL, PL/SQL; Quest TOAD; Versant OODBMS; ERwin; Pro*C, Pro*C++; Cognos; Business Objects; Crystal Reports

Programming: J2EE, Perl, Python, Ruby, C/C++, VBA, ASP.NET, VB Script, JavaScript, XML, PHP, Fortran; IIS, Tomcat, Apache, Gauche Resin AS

Statistics: pattern recognition, optimization algorithms, genetic algorithms, regression models, principal component analysis, factor analysis, discrimination and classification, clustering, multidimensional scaling; Matlab, R, S+, SAS, JMP, R, Bioconductor

OS: UNIX (all flavors and distributions of Linux, Solaris, SGI IRIX); Windows from NT to Vista; VAX VMS

Automation and control systems: Emerson DeltaV; OSIsoft PI Historian; Northwest Analytics process monitoring

Information Technology Services

• Expert project and program management
• Data modeling and database design
• Evaluation, recommendation and independent benchmarking of computational methods and applications
• Integration of scientific computing tools, applications and databases
• Heterogeneous knowledge mining
• Automated analysis pipelines
• Validation of regulated computer systems
• Education and training in scientific computing
• Interim information systems leadership
• Assistance in international and domestic project sourcing
• Custom algorithm and application development
  • Business systems analysis
  • Functional and engineering specification
  • Multi-platform implementation
  • Continuous system testing
  • Complete documentation and support