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

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