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Software & Databases

Function and Purpose Brand Lab
MALDI mass spectra viewing and processing Data Explorer by Applied Biosystems Analytical Proteomics
Bone density calculation Carestream Experimental and Preclinical Imaging
Flow cytometry data analysis Flowjo Immunology
ELISpot experiments analysis Biospot Immunology
ELISpot experiments analysis Immunospot Immunology
Multispectral imaging Carestream Experimental and Preclinical Imaging
ICP-RIE Instrument Control PC 2000 (proprietary) by Oxford Instruments Microfabrication and Microfluidics
PECVD Instrument Control PC 2000 (proprietary) by Oxford Instruments Microfabrication and Microfluidics
General Instrument Control and Automation LabVIEW by National Instruments Microfabrication and Microfluidics
Micorarray and NGS data analysis and visualization GeneSpring by Agilent Genomics Facility
Microarray data management GeneTraffic by Iobion Genomics Facility
Gene regulation networks and protein interaction map analysis PathwayAssist by Ariadne Genomics Facility
Network data integration, analysis, and visualization Cytoscape Genomics Facility
Gene expression and SNP microarrays analysis and visualization dChip Genomics Facility
Gene map annotator and pathway profiler GenMAPP Genomics Facility
High-throughput genomic data analysis and comprehension Bioconductor Genomics Facility
Gene expression computation RMAExpress Genomics Facility
Photomask design AutoCAD by Autodesk Microfabrication and Microfluidics
3D object design Inventor by Autodesk Microfabrication and Microfluidics
Computer Aided Manufacturing (CAM) HSM by Autodesk Microfabrication and Microfluidics
SEM interface software SEMTech Solutions Microfabrication and Microfluidics
Next-generation sequencing data primare analysis Illumina RTA Genome Sequencing
Next generation sequencing real-time monitoring and secondary analysis Illumina BaseSpace Genome Sequencing
1D,2D,3D-NMR data acquisition, processing and analysis Topspin Biomolecular NMR
1D,2D,3D-NMR data processing NMRpipe Biomolecular NMR
1D,2D,3D-NMR data analysis Sparky Biomolecular NMR
Mojo 3D Printer Control Mojo Control Panel; Print Wizard 1.1 by Stratasys Microfabrication and Microfluidics
CNC Mill Control Mach3 by ArtSoft Microfabrication and Microfluidics
Microscope Video and Still Image Capture 2.2 by Capture IC Imaging Microfabrication and Microfluidics
Device Modeling Software COMSOL Multiphysics 5.0 Microfabrication and Microfluidics
MS data acquisition, analysis, managing, sharing MassLynx, Biopharmalynx, ProteinLynx PLGS by Waters Analytical Proteomics
Database search, protein sequence mapping Mascot Server by Matrix Science Analytical Proteomics
De novo sequencing for identifying novel peptides of unsequenced organisms PEAKS by Bioinformatics Solutions Analytical Proteomics
FPGA Development Xilinx ISE Design Suite 14 Instrumentation Design
Electronics CAD Eagle Electronics Design Suite 6 Instrumentation Design
Graphical user interface development Microsoft Visual Studio Instrumentation Design
Mechanical CAD AutoCad, AutoDesk Inventor Professional Instrumentation Design
Drawing CAD package Corel Graphics Suite, Adobe Creative Suite Instrumentation Design
Microcontroller Development Systems Various Instrumentation Design
Statistical analysis of protein/peptide identifications, data sharing Scaffold by Proteome Software Analytical Proteomics
Proteomics data raw file processing and search XCalibur & Proteome Discoverer by Thermo Fisher Scientific Analytical Proteomics
Chemical database JChem by ChemAxon CMLD
Next generation sequencing data visualization and analysis CLC Genomics Workbench Applied Bioinformatics
Comprehensive platform for drug discovery and protein/molecular modeling and simulation MOE by Chemical Computing Group Applied Bioinformatics
Advanced data analysis and visualization (bioinformatics and statistics modules available) MATLAB by MathWorks Applied Bioinformatics
Genomic expression data visualization and analysis GeneSpring by Agilent Technologies Applied Bioinformatics
Biological sequence manipulation DS Gene by Accelrys Applied Bioinformatics
Next-generation sequencing data analysis and visualization CLC Genomics Workbench Genomics and Bioinformatics
X-ray diffraction data processing XDS Protein Structure Lab
Graphical interface for XDS XDSAPP Protein Structure Lab
Macromolecule diffraction data processing MOSFLM Protein Structure Lab
X-ray diffraction data processing HKL-2000 Protein Structure Lab
X-ray diffraction data processing d*TREK by Rigaku Protein Structure Lab
Automated data processing using XDS autoPROC Protein Structure Lab
Automated data processing using XDS or Moslfm Xia2 Protein Structure Lab
Macromolecular x-ray crystallography suite CCP4 Protein Structure Lab
Macromolecular x-ray crystallography suite Phenix Protein Structure Lab
Molecular replacement EPMR Protein Structure Lab
Molecular replacement Phaser Protein Structure Lab
Molecular replacement MolRep Protein Structure Lab
Experimental phasing Shelx C/D/E Protein Structure Lab
Graphical Interface for Shelx C/D/E HKL2MAP Protein Structure Lab
Macromolecular structure refinement BUSTER Protein Structure Lab
Macromolecular structure refinement Refmac Protein Structure Lab
Macromolecular model building Coot Protein Structure Lab
Macromolecular model building and refinement-automated Arp/wARP Protein Structure Lab
Macromolecular model building and refinement-automated Buccaneer Protein Structure Lab
Preparation of publication quality graphics and structure analysis CCP4mg Protein Structure Lab
NMR data acquisition and processing Bruker Topspin Nuclear Magnetic Resonance
NMR data processing ACD NMR by ACD/Labs Nuclear Magnetic Resonance
Molecular structure determination Xplor-NIH Nuclear Magnetic Resonance
NMR data processing, analysis, managing and reporting MestreNova by Mestrelab Nuclear Magnetic Resonance
Molecular dynamics force field simulator AMBER Molecular Graphics & Modeling
MacroModel Schrodinger 5 Molecular Graphics & Modeling
Macromolecular simulations CHARMM Molecular Graphics & Modeling
Molecular surface calculator DMS Molecular Graphics & Modeling
Binding-modes of small molecules DOCK Molecular Graphics & Modeling
Molecular electronic structures calculator GAMESS Molecular Graphics & Modeling
Electronic structure modeling Gaussian Molecular Graphics & Modeling
Protein docking GRAMM Molecular Graphics & Modeling
Molecular dynamics LAMMPS Molecular Graphics & Modeling
Comprehensive platform for drug discovery and protein/molecular modeling and simulation MOE by Chemical Computing Group Molecular Graphics & Modeling
Computational chemistry tools NWChem Molecular Graphics & Modeling
Protein binding site prediction PASS by Computational Chemistry List Molecular Graphics & Modeling
Molecular structure cavity detection VOIDOO by Uppsala Software Factory Molecular Graphics & Modeling
Graphical molecular modeling Cerius 2 by Accelrys Molecular Graphics & Modeling
Repository of experimentally determined organic and metal-organic crystal structures Cambridge Crystallographic Database by CCDC Molecular Graphics & Modeling
Chemistry computation, management, analysis and visualization system CACTVS Molecular Graphics & Modeling
Molecular structure information interchange hub Babel Molecular Graphics & Modeling
Small molecule binding prediction tool AutoDock Molecular Graphics & Modeling
Graphing tool Gnuplot Molecular Graphics & Modeling
Molecular biology and bioinformatics analysis EMBOSS Molecular Graphics & Modeling
Offline processing and analysis of NMR spectra Felix by Accelrys Molecular Graphics & Modeling
Molecular visualization gOpenMol Molecular Graphics & Modeling
2D plotting tool Grace Molecular Graphics & Modeling
Biological molecule visualization Insight II by Accelrys Molecular Graphics & Modeling
Intermolecular interactions library IsoStar by CCDC Molecular Graphics & Modeling
Comparative protein structure modelling MODELLER Molecular Graphics & Modeling
Molecular and electronic structure visualization MOLDEN Molecular Graphics & Modeling
Molecular visualization Molekel Molecular Graphics & Modeling
Molecular visualization- large biomolecular systems using 3-D graphics and built-in scripting VMD Molecular Graphics & Modeling
Molecular graphics- 3-D structures of biological macromolecules MolMol Molecular Graphics & Modeling
Molecular graphics- 3-D structures MolScript Molecular Graphics & Modeling
Multiple protein sequence analysis MPSA Molecular Graphics & Modeling
Molecular visualization PyMOL Molecular Graphics & Modeling
Molecular visualization RasMol Molecular Graphics & Modeling
Comparative protein modeling Swiss-PdbViewer Molecular Graphics & Modeling
Molecular modeling from sequence through lead optimization SYBYL by Tripos Molecular Graphics & Modeling
Protein fold recognition Threader Molecular Graphics & Modeling
Computational structural biology X-PLOR Molecular Graphics & Modeling
Chemical drawing package ChemSketch by ACD Molecular Graphics & Modeling
Protein molecule modeling and graphics MOLDA Molecular Graphics & Modeling
Chemical database JChem by ChemAxon Molecular Graphics & Modeling
Chemical structures drawing tools Marvin by ChemAxon Molecular Graphics & Modeling
Grid computing database Oracle 10g Molecular Graphics & Modeling
Molecular structural analysis of large biomolecular systems O Molecular Graphics & Modeling
High throughput screening data management and analysis K-Screen by Kansas University High Throughput Screening
Image analysis ImageJ by NIH Microscopy and Analytical Imaging
Image processing and data analysis Slidebook by 3i Microscopy and Analytical Imaging
Image analysis CellProfiler Microscopy and Analytical Imaging
Data analysis CellProfiler Analyst Microscopy and Analytical Imaging
Image analysis ImageQuant by GE Healthcare Life Sciences Microscopy and Analytical Imaging
2D DIGE analysis Progenesis PG 220 by Nonlinear Dynamics Microscopy and Analytical Imaging
Data analysis, high dimensional, non-linear, complex Visumap Microscopy and Analytical Imaging
Image and spectrum acquisition and analysis TIA (TEM Image and Analysis) Microscopy and Analytical Imaging
Flow cytometry data analysis FlowJo Microscopy and Analytical Imaging
Image data analysis and management Attovision by BD Biosciences Microscopy and Analytical Imaging
Image acquisition and processing DigitalMicrograph by Gatan Microscopy and Analytical Imaging
In-house macromolecular x-ray data acquisition and processing Proteum2 by Bruker X-Ray Crystallography
Macromolecular x-ray data processing; structure solution and refinement CCP4 X-Ray Crystallography
Powder diffraction data acquisition and processing DiffracPlus.SUITE by Bruker X-Ray Crystallography
Powder diffraction data analysis; identification of crystalline phases Eva by Bruker X-Ray Crystallography
Rietveld analysis and structure refinement Topas by Bruker X-Ray Crystallography
Small-molecule crystal structure search Cambridge Structural Database X-Ray Crystallography
Small-molecule and macromolecular crystal structure solution and refinement SHELXTL by Bruker X-Ray Crystallography
Small-molecule structure validation Platon X-Ray Crystallography
Small-molecule x-ray diffraction data acquistion and processing SMART, SAINT by Bruker X-Ray Crystallography
Small-molecule x-ray diffraction data acquistion and processing APEX2 by Bruker X-Ray Crystallography
 

LINKS TO LAB WEBSITES

Biochemistry & Protein Science

Bioinformatics & Modeling

Cross-Disciplinary

Materials Characterization

Molecular Structures

Translational Biology

EVENTS
Ability to set up 24 NMR experiments at one time and eliminate periodic user intervention
Screen up to 100,000 compounds in two days for endpoint assays
Next-generation genome sequencing
Near-infrared and bioluminescence imaging instrumentation to track gene of interest and/or tumor growth
Expertise in the design and stability of various pharmaceutical dosage forms
More than 40 computational chemistry software programs and databases
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