New Mexico Molecular Libraries Screening Center

New Mexico MLSC Inventory/Capabilities

Space

The NM MLSC occupies and has available the following contiguous space on the second floor of UNM Cancer Research Facility (~ 2500 sq ft):

• 2 x 650 sq ft laboratories (CRF219 and 221) for sample preparation and physical screening
• 200 sq ft of laboratory space for assay development and implementation (CRF 229)
• 200 sq ft of laboratory space for flow cytometry analysis (CRF 217)
• 2 x 200sq ft office space (CRF219a and 221a)
• 150 sq ft tissue culture facilities (CRF 216)
• 300 sq ft shared confocal microscopy facilities (CRF212/216)

Also available is a 400 sq ft laboratory space in the basement of the CRF. Informatics has available 1400 sq ft in the Research Incubator Building.

Equipment

1. Assay Development / Adaptation (AD/A):

• 2 custom designed HyperCyt® high-throughput flow cytometry instrument clusters for sample delivery from microplate to flow cytometer with custom software to control operational and analytical functions
• 4 BD Biosciences FACScan Flow Cytometers dedicated to assay development
• Wallac 1420-040 Victor 3V multilabel plate reader with 2 injectors for plate-based readings of fluorescence, time-resolved fluorescence, luminescence, absorbance, fluorescence polarization; capable of single point and kinetic measurements
• Beckman Coulter Biomek NX Span-8 Workstation with integrated gripper, Span-8 tip-wash station and 4 x 3 Automated Labware Positioners
• Beckman Coulter Biomek NX Multichannel Workstation with integrated gripper, P30/384 dispense head, P20/96 well dispense head, 384 tip-wash station, disposable tip loader station and 4 x 3 Automated Labware Positioners, integrated pintools (V&P Scientific) for transfer of nL scale volumes
• Titertek MAP-C2 pipetting instrument custom modified for dispensing cells into microwell plates
• Eppendorf epMotion 5070 liquid dispenser with single and eight channel tools for delivery of 1-1000 mL
• Biotek Nanoquot dispenser for non-contact dispensing into 96-, 384-, and 1536-well microplates; equipped with microplate stacker for increased throughput (also available for screening applications)

2. High Throughput Screening / Implementation (HTS/I):

• 3 HyperCyt® HT flow cytometry instrument clusters for sample delivery from microplate to flow cytometer with custom software to control operational and analytical functions
• 1 Accuri® C6 benchtop flow cytometer; 2 laser / 4 fluorescence parameters / 2 light scatter detectors
• 2 Dako Cyan® flow cytometers capable of 10 million events / data file; 3 laser / 9 fluorescence parameters and 2 laser / 7 fluorescence parameters, respectively
• Beckman Coulter Biomek FXp workstation with integrated gripper; Span-8 and multichannel heads, Span-8 and 384 tip-wash stations, 4 x 3 and 1 x 1 automated labware positioners, static peltier labware positioner, and shaking labware positioner; integrated pintools (V&P Scientific) for transfer of nL scale volumes
• 1 4titute® controlled atmosphere modular compound storage sstem for up to 320 plates and six -30 freezers for storage of several copies of the MLSMR
• 1 Cytomat® 24 compound plate storage for up to 504 compound plates
• 1 Cytomat® 44 compound plate storage for up to 924 compound plates
• 1 Cytomat® 2: cell incubator for up to 42 plates; Cytomat Hotel (63 tip boxes/252 plates) with conveyors
• Beckman Coulter Data Aquisition  and Reporting Tool for tracking usage on Biomek instruments including capture of all barcoded plates, reagent volume and labware tracking (also available for AD/A instruments)

The NMMLSC is located adjacent to the UNM Shared Flow Cytometry Resource. The SFCR is equipped with a Cytomation Mo Flo 4-laser, 9-detector, high-speed sorter, capable of 4-way sorting and single cell deposition; a Beckman Coulter Epics Elite 3-laser cell sorter for operator-assisted routine cell sorting, analysis, and sample handling applications; and BD Biosciences FACScan and FACSCalibur benchtop flow cytometers for unassisted 3- and 4-color fluorescence analysis, respectively. Also available are an SLM 8000 Spectrofluorometer for cell and solution based fluorescence analysis, a Zeiss fluorescence, phase-contrast microscope for visual inspection of cells and beads, and a Beckman Coulter Z2 particle counter for quantifying cell/bead size distributions (Coulter volume) and concentrations.


3. Screening Informatics (SI):
Computational resources - the machines are named after chili peppers:

• "Chilaca" - 16x2 AMD Opteron processors with 1MB L2 Cache, 16x2 GB RAM memory and 16x250 GB SATA (4 TB) hard drives on master plus 15x80 GB on each node
• "Chiltepin" - 4 AMD Opteron 846 processors, 32 GB RAM memory, 12x400 GB SATA 7200 RPM hard drives
• "Poblano" - 16-way IBM 590 AIX, 256 GB RAM memory (remote cluster for backup)
• "Pequin" - 4 Power 5 processors IBM 570, AIX with 16 GB RAM memory
• HSC-Backup - 10 TB Dell server with 2 Dual Core Xeon Procesors 5130 + 4 LTO-3 tape drives and ML6000 tape library, which can hold up to 402 400 GB cartridges (remote backup system)

Poblano and Pequin are available through the Center for High Performance Computing at the University of  New Mexico (HPC@UNM).

Informatics Software:

• IDLeQuery, RoadRunner (HTS data and curve fitting) 
• Weka (non-linear modeling)
• SIMCA from Umetrics (linear multivariate analysis)
• MatLab (general mathematical modeling)

Chemistry Software:

• OpenEye Scientific programs for chemical library filtering, docking, conformer generation, similarity searching, electrostatic scoring and substructure search programming
• Mesa Analytics & Computing LLC software for 2D fingerprinting, similarity searches, and fingerprint studies
• Accelrys and Tripos programs for molecular modeling framework studies
• Chemical database systems from various vendors (Elsevier-MDL, Cambridgesoft, and Chemaxon) for storage, retrieval and analysis of bio-activity data

This wide array of software, specifically optimized for intensive computing, can and is currently being used for large-scale data analysis, data archiving, massively parallel computing, related to bioinformatics and cheminformatics.

Center Expertise

Cellular Assays:

G protein-coupled receptors; Integrins and adhesion molecules; Proteases/proteasome; Cell cycle; Apoptosis

Bead-based assays:

Protein-protein interactions; Protein-nucleic acid interactions; Kinase assays

Informatics:

State-of-the-art, innovative tools for ligand-based and structure-based virtual screening; Unique tools for post-HTS analyses, clustering and in silico profiling; High performance tools for bioinformatics analyses; Unique data archiving and data mining capabilities; Tools to evaluate post-HTS analyses

Capacity

Projected: 5,000-10,000 wells per day per detector

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