Shared Facilities

Columbia's physical facilities, instruments, and online platforms reflect the quality and quantity of collaborations that prove so integral to our research enterprise. We strongly encourage all Columbia researchers to take advantage of the extensive spectrum of shared resources listed on this page. If you have suggestions for new entries on this page, please contact marley.bauce@columbia.edu. To be included on this website, shared facilities must be open for use by any researcher from any department or school across Columbia University.


Medical Center Shared Facilities

Responding to requests from facility administrators, the catalogue below contains some entries for facilities based at the Columbia University Medical Center. For a full and complete listing of shared facilities across the Medical Center, please click here: http://ps.columbia.edu/research/research-shared-facilities-name


 

Internal Resources

The AGES (Argon Geochronology for Earth Sciences) lab, located in the Gary C. Comer Geochemistry building at Lamont-Doherty Earth Observatory, is currently equipped with a operating mass spectrometer system, and one on the way. The AGES lab is overseen by Sidney Hemming and Tanzhuo Liu and is primarily dedicated to using the 40Ar/39Ar approach to dating potassium-bearing minerals. We collaborate on projects across the Earth and Planetary Sciences, but our particular foci are on sedimentary tracer studies and high precision geochronology for sequencing Earth history. We use sedimentary provenance studies to understand past changes in ice sheets, ocean currents, and other climatically relevant processes. Additionally, we use the 40Ar/39Ar system to precisely date igneous rocks to constrain the timing and rates of important geological processes.

http://www.ldeo.columbia.edu/research/geochemistry/argon-geochronology-earth-sciences-ages-lab

Contact: Dr. Sidney Hemming, Director, sidney@ldeo.columbia.edu

The Chemical Probe Synthesis (CPS) Facility in the Northwest Corner Building on Morningside campus is a state-of-the-art resource that offers expertise and services in design and synthesis of small molecules. The CPS Facility is staffed by scientists with expertise in computer-aided drug discovery, organic and medicinal chemistry, drug metabolism, and pharmacokinetics. The CPS facility offers services in the following areas: (1) Virtual screening and docking to biological targets and computational design of small molecules; (2) Organic synthesis of small molecules, building blocks, or compound libraries; (3) Medicinal chemistry and lead optimization of biologically active compounds; and (4) Drug metabolism/pharmacokinetic (DMPK) and metabolic profiling of organic compounds.

http://cps.bio.columbia.edu/

Contacts: Dr. Brent Stockwell, Director, BStockwell@columbia.edu
                 Dr. Arie Zask, Manager, AZ2280@columbia.edu

The shared facilities at Columbia Nano Initiative consist of a renovated and expanded Nanofabrication Cleanroom, an advanced Materials Characterization Laboratory, and a brand new Electron Microscopy Laboratory. The CNI shared labs are user facilities managed by professional staff who assist the members of the Columbia nanoscience community with their research. Users from Columbia University, outside academic departments, and industry are all welcome. The shared facilities include a wide range of instruments for advanced micro and nano fabrication, processing, characterization, and imaging. The facilities are supported by user fees. For more information, please contact:

Cleanroom: http://nano.columbia.edu/columbia-university-clean-room
Contact: James Vichiconti, Senior Staff Associate, jv2534@columbia.edu

Shared Materials Characterization Lab:

The Shared Materials Characterization Laboratory at Columbia Nano Initiative provides microscopy, spectroscopy and x-ray diffraction instruments for materials researchers in chemistry, physics, and engineering. The facility specializes in the characterization of surfaces, films, magnetic materials, layered materials and other nanostructures, and crystalline/polycrystalline materials. Notably, users can fabricate and characterize air-sensitive materials in a nitrogen-filled glovebox containing an AFM, micro-Raman spectrometer, and optical autowinder.

http://nano.columbia.edu/shared-materials-characterization-laboratory-smcl

Contact: Dr. Daniel Paley, Director, dwp2111@columbia.edu

Electron Microscopy: http://nano.columbia.edu/electron-microscopy
Contact: Dr. Chris Goulbourne, Director, cg2929@columbia.edu

For general questions about the CNI shared facilities, please contact Dr. Nava Ariel-Sternberg, Director of Shared Laboratory Facilities, na2661@columbia.edu or cnilabs@columbia.edu.

The scientific mission of Comparative Pathology Laboratory (CPL) is to serve Columbia biomedical researchers by providing accurate, timely and high quality veterinary pathology service so as to translate the knowledge of disease process, diagnosis, treatment and prevention in research animals to improve diagnostic and clinical applications in veterinary and human medicine. The Comparative Pathology Laboratory provides a complete range of diagnostic services, including anatomic pathology, clinical chemistry panels, complete blood count, coagulation panels, blood gas panels, parasitology examinations, microbiology testing, rodent pathogen cell line testing, and research services related to histopathology, molecular biology and histomorphometry. The ICM maintains a collaborative research relationships with several national and international biomedical research centers and commercial laboratories and can outsource services if they are not done at Columbia University.  

http://vesta.cumc.columbia.edu/dept/icm/cpl/index.html

Contact: Dr. Andrea Hubbard, Head of Diagnostic Lab, h2911@columbia.edu

The Confocal and Specialized Microscopy Shared Resource (CSMSR) provides advanced microscope systems for multidimensional optical imaging of living and fixed cells and tissues. The CSMSR offers a wide range of state-of-the-art microscopy technologies, including fluorescence, confocal, multiphoton, and super-resolution microscopy, as well as laser capture and microirradiation.

Our full-time staff provide assistance using the microscopes, technical support, and training for independent use. Trained in cell biology, biophysics, microbiology and image analysis, with in-depth expertise in light microscopy, the staff can help with experimental design, image acquisition, and data analysis.

http://www.hiccc.columbia.edu/research/sharedresources/confocal

Contact: Dr. Theresa Swayne, Manager, tcs6@cumc.columbia.edu

The DataBase Shared Resource (DBSR) is a core within the Cancer Center, whose central function is to provide oversight and infrastructure for the development and maintenance of cancer-related clinical databases and link them to existing biospecimens. DBSR disseminate information about the clinical databases and biobanks to the research and lay community to support research projects in any cancer-related area. Our overall objective is to stimulate multi-disciplinary clinical and translational research utilizing these databases and biobanks.

http://www.hiccc.columbia.edu/research/sharedresources/database

Contact: dbsr@columbia.edu 

Human CD34+ hematopoietic stem cell-engrafted NSG™ mice develop multi-lineage human immune cells, and are a validated platform for translational and preclinical researches. We, as the renowned experts in developing and characterizing hu-mice, provide the standard hu-mice grafted with human fetal thymus/CD34+ stem cells for in vivo studies in human immune system development, cancer models/tumor immunotherapy, human infectious diseases, drug screening, etc. We also offer a unique “Personalized Immune (PI)” mouse model, which reconstituted with adult bone marrow stem cells, and in coordination with investigators who will obtain the patient specimens to fit various needs.

http://www.cumc.columbia.edu/ccti/research/cores/humanized-mouse-core

Contact: Dr. Hui Wang, Manager, hw2334@cumc.columbia.edu

The Lamont-Doherty Core Repository (LDCR) contains one of the world’s most unique and important collection of scientific samples from the deep sea. Tens of thousands of sediment cores from every major ocean basin are archived at the Core Repository, as well as thousands of dredge and grab samples, including a large collection of manganese nodules.  In addition to physical samples, an open database of the Lamont core collection has been maintained for nearly 50 years. We provide long-term curation and archiving of samples and cores collected by the geoscience community, fulfill sample and data requests from around the world, assist investigators from any institution in the planning and execution of sample collection activities, including sea-going expeditions, and educate teachers, students, and the public about the important role science and the Core Repository play in building a better understanding of Earth processes such as climate change, ocean acidification, evolution, and tectonics. 

http://www.ldeo.columbia.edu/core-repository

Contact: Dr. Maureen Raymo, Director, raymo@ldeo.columbia.edu

The Columbia Maker Space is a user-managed facility dedicated to design and hands-on prototyping and fabrication. The space provides a variety of materials and equipment including 3D printers, laser cutters, sewing machines, and gear for electronics prototyping and testing. In addition to providing space, materials, and equipment, the Maker Space also conducts training and outreach programming throughout the year to train new users and engage the community. The Maker Space is available for all interested faculty, students, and staff across the University.

http://make.columbia.edu

Contact: Ioannis (John) Kymissis, Associate Professor of Electrical Engineering, johnkym@ee.columbia.edu

The MS core facility in the Chemistry Department consists of four instruments. A Waters Xevo QTOF is run by staff personnel and provides high resolution, exact mass determination as well as optional MS/MS and SFC separations. A Bruker MALDI Ultra Flex Extreme offers high resolution on large molecules including proteins. A Waters SFC-MS and an Advion CMS offer low resolution walk-up usage for routine unit resolution analysis with either SFC separation or direct injection. MS analysis is available for corporate users. 

http://chem.columbia.edu/resources/facilities/mass-spec/

Contact: Dr. Brandon Fowler, Manager of Mass Spectrometry, brandon.fowler@columbia.edu

The primary goal of the Microbiome Core is to facilitate microbiome studies for researchers at CUMC. The facility is a centralized and cost-effective resource for receiving, handling, and storing biological specimens that are collected as part of research studies in molecular epidemiology or studies of disease in model systems. The core provides consultation on study design and protocols for sample collection and analysis, and fosters informal interactions of investigators from varied backgrounds to enhance microbiome studies at CUMC. Sequencing can also be carried out through the core or in collaboration with select sequencing centers for larger samples volumes.

http://blogs.cuit.columbia.edu/microbiome/

Contact: Dr. Anne-Catrin Uhlemann, Director, au2110@columbia.edu

The Mouse NeuroBehavior Core (MNBC) is a newly-established and centralized mouse behavioral testing facility conveniently located in the William Black Building of the CUMC campus. The MNBC strives to become an intellectual and technical resource for the CUMC community and for PIs across other neuroscience research institutions. Qualified users have access to state-of-the art behavioral equipment in the 8-room testing suite. We provide full testing services, as well as extensive training to users who want to conduct their own experiments. Our team of experts additionally provides assistance with breeding, tissue harvesting, experimental design, data analysis and interpretation, and publication of results.

http://www.igm.columbia.edu/resources/mouse-neurobehavior-core-mnbc

Contact: Dr. Mu Yang, Co-Director, my2524@cumc.columbia.edu

The Nevis Labs machine shop consists of one machinist with experience in an assortment of modern CNC equipment. The shop prides itself on quality work, innovative solutions to difficult problems, and fast turnaround on projects. The shop provides both conventional and CNC milling (52" x 30" maximum X ∓ Y travel), turning (15" swing), precision grinding, and sheet metal fabrication and welding (Tungsten Inert Gas). The shop works with ferrous and non-ferrous metals, plastics, Teflon, scintillator, and a variety of other materials. There is extensive experience in the manufacture, welding and Helium leak testing of high vacuum systems. The current rate for use of the machine shop is $75/hour.

https://www.nevis.columbia.edu/machine/

Contact: Dr. David Thomas, Experimental Machinist, dpt2@columbia.edu

The NMR core facility in the Chemistry Department consists of six Bruker instruments with fields ranging from 300 to 500 MHz. The core supports all experiments for small molecule structure determination. One instrument supports solid-state CPMAS experiments as well. Academic users are trained by facility staff to take their own spectra. A full range of service spectra are available for corporate users. 

http://www.columbia.edu/cu/chemistry/groups/nmr/introduction.html

Contact: Dr. John Decatur, Director of Chemical Instrumentation, jdd13@columbia.edu

The Proteomics Shared Resource supports both discovery-based and targeted proteomic analysis. The facility provides cancer researchers access to the state-of-the-art mass spectrometers and software for qualitative (e.g. protein identification), quantitative (e.g. relative quantification), and post-translational modification (PTM) analyses. Services include (1) mass determination of purified proteins/peptides; (2) identification of purified protein complexes; (3) site-targeted PTM mapping on purified proteins, targeted MRM quantification; (4) global proteome analysis, subproteome isolation and identification; and (5) large-scale PTM characterization. The facility director and technical personnel have extensive expertise in mass spectrometry-based techniques, and will provide consultation on experimental design, data analysis, and troubleshooting. We encourage researchers to contact us prior to submission of samples to discuss sample preparation, experimental design, and potential outcomes of research projects.

http://www.hiccc.columbia.edu/research/sharedresources/proteomics

Contact: Dr. Emily Chen, Director, ec2974@cumc.columbia.edu

The proteome is the expressed protein complement of a cell, matrix, organelle, tissue, organ, or organism. Similarly, metabolomics is the large-scale study of the global sets of small molecules in cell and tissues. We specialize in quantitative proteomics and metabolomics using mass spectrometry to define differences in expression among different biological states (e.g., control vs. treatment, healthy vs. disease, specific genotype vs. wild type). A wide variety of sample types can be processed including cells, tissues, organelles, biofluids, and affinity preparations (animal, plant, bacterial, protest, yeast, insect, and patient samples are routinely studied). We welcome collaborations with academic and industry partners leading to new scientific opportunities and funding.

http://proteomics.bio.columbia.edu/

Contact: Dr. Lewis M. Brown, Director, lb2425@columbia.edu

The Radiological Research Accelerator Facility is a dedicated radiobiology research center offering irradiation services using protons, alpha particles, and neutrons as well as X rays. The centerpiece of the RARAF irradiation facilities are our high-throughput single-cell/single-particle microbeams, which can deliver defined amounts of ionizing radiation (down to a single particle) into specified locations in individual cells with micron or sub-micron resolution. The ability to specifically irradiate cellular targets while guaranteeing that neighboring cells or organelles do not receive any ionization allows for the study of intra- and intercellular communication and damage response. In addition to the microbeam, broad beam particle and X-ray irradiation facilities are available on site for comparison of the microbeam systems to standard irradiation methods. Our facilities support a broad range of applications and we encourage prospective users to contact us for system specifications and discussion of experimental possibilities.

http://www.raraf.org

Contact: Dr. Andrew Harken, Associate Research Scientist, adh2121@cumc.columbia.edu, Dr. Guy Garty, Associate Director, gyg2101@cumc.columbia.edu

The Radiation Research Core Facility, located within and maintained by the Center for Radiological Research, provides a comprehensive irradiation service.  The facility provides the capability to expose small animals, mammalian cells in culture, microorganisms and macromolecules to gamma-rays, x-rays and 254 nm UV light. Research goals are diverse and include such tasks as creating double strand breaks or bulky lesions in DNA, irradiating mice before injection of cells to test tumorigenicity, creating transformed cells, preparing feeder layers for tissue culture, irradiating mice specifically in their eyes to analyze cataractogenesis, and measuring radiosensitivity of yeast, mouse, hamster or human cells. Arrangements can also be made to fabricate custom-designed shielding to expose animals only at specific anatomical sites. The Facility currently has six irradiators, including one with combined CT imaging and irradiation capabilities.

http://www.hiccc.columbia.edu/research/sharedresources/radiation

Contact: Dr. Howard Lieberman, Director, hbl1@cumc.columbia.edu
               Dr. Kevin M. Hopkins, Manager, kh16@cumc.columbia.edu

The ReaDI program is a new program to enhance data management and research integrity at Columbia University. The ReaDI program provides resources, outreach and consultation services to researchers at all stages in their careers.

https://research.columbia.edu/ReaDI-Program

Contact: Michelle Benson, Assistant Director for Research Integrity and Compliance, mb3852@columbia.edu

Columbia's centrally-managed High Performance Computing (HPC) resources on the Morningside campus are housed in the Shared Research Computing Facility (SRCF). The University's machine - Habanero - is comprised of 200 computer systems, a high speed local network, and a parallel storage server. One dozen systems include GPU hardware accelerators, allowing certain highly parallelized applications to achieve performance levels far beyond what would be possible on conventional hardware. The service is managed by CUIT's Research Computing Services staff under the guidance of a faculty-led committee responsible for overseeing operations.

31 groups are active buyers and users of the Habanero machine, representing disciplinary investigations spanning astronomy, biochemistry, data science, engineering, neuroscience, oceanography, physics, statistics, and many others.

www.columbia.edu/srcpac

Contact: srcpac@columbia.edu

The stable isotope laboratory houses mass spectrometers for the analysis of carbonates, water, and organic compounds. Four mass spectrometers are currently in use: 1) one Elementar Isoprime 100 w/ dual inlet and multiprep for oxygen isotope (d18O) and carbonate isotope (d13C) analysis of larger carbonate samples, d18O and dD (hydrogen isotopes) of water, and a 10 collector isotopologue array for the analysis of multiply substituted isotopes of CO2. 2) A Thermo Delta V+ w/ dual inlet and Kiel IV, and Gasbench II continuous flow operating modes to analyze smaller carbonate samples and water samples requiring high precision; 3) A Thermo Delta V+ w/ Conflo IV, Trace GC and Isolink, TC/EA, Costech EA w/autosampler and configured for the stable isotopic (d18O, d13C, d15N, dD) analysis of bulk and compound-specific organics and tree ring samples; 4) one VG Optima dual-inlet mass spectrometer for the analysis of carbonates. The laboratory is located in climate-controlled room 212 of the New Core Lab on the Lamont campus.

Contact: Dr. Braddock Linsley, Lamont Research Professor, blinsley@ldeo.columbia.edu; Dr. Wei Huang, Senior Staff Associate, weih@ldeo.columbia.edu

Stan is a flexible and scalable open-source probabilistic programming language that allows users to specify custom statistical models and then perform estimation and prediction based on data. Stan was originally developed at Columbia University. Many of the core developers are housed in the Columbia Statistics Department and available to provide consulting in statistical methodology, modeling, and computing. Stan's modeling framework is general enough to account for both scientific processes and measurement, including noisy, unbalanced, censored, and missing data, linear, non-linear and dynamic spatio-temporal relationships, as well as dynamic models expressed as differential equations. Stan has been applied to hundreds of application areas across the the physical, biological, and social sciences, engineering, and business. There is a vibrant user community outside of the core project who have produced several books about Stan and hundreds of peer-reviewed papers based on statistical models fit with Stan.

http://mc-stan.org

Contact: Dr. Andrew Gelman, Professor of Statistics and Political Science, gelman@stat.columbia.edu

The Structural and Mechanical Characterization Facility is a shared facility of the Materials Science and Engineering (MSE) program of the Department of Applied Physics and Applied Mathematics (APAM) in the School of Engineering and Applied Science (SEAS) at Columbia University.  The facility houses a suite of modern instruments for sample preparation for microstructural characterization by visible light microscopy, surface characterization by atomic force microscopy, structural analysis by X-ray diffraction with associated crystallographic software, macroscale mechanical property characterization using Instron instruments and hardness testers, and microscale mechanical behavior characterization using a microindenter.

www.mseshared.apam.columbia.edu

Contact: Adrian Chitu, Facility Engineer, ac2224@columbia.edu

The Thermo Scientific Triton at the Lamont-Doherty Earth Observatory is a thermal ionization mass spectrometer with positive and negative ion capabilities. With 9 Faraday cups, one 10^10, six 10^11 and three 10^12 Ohm resistors, as well as a secondary electron multiplier, it is currently set up to measure Boron, Strontium, Osmium and Neodymium isotopes. Analytical methods for additional isotope systems can easily be adopted, but require dedicated user participation. The facility is not supported by a technician, and users will have to perform the analyses by themselves, albeit under the guidance of the PI.

http://www.ldeo.columbia.edu/~hoenisch/TIMS_facility.html

Contact: Dr. Bärbel Hönisch, Associate Professor of Earth and Environmental Sciences, hoenisch@ldeo.columbia.edu

External Resources

The City University of New York’s Advanced Science Research Center (ASRC) is a University-wide venture that elevates CUNY’s legacy of scientific research and education through initiatives in five distinctive, but increasingly interconnected disciplines: Nanoscience, Photonics, Structural Biology, Neuroscience and Environmental Sciences. The center is designed to promote a unique, interdisciplinary research culture with researchers from each of the initiatives working side by side in the ASRC’s core facilities, sharing equipment that is among the most advanced available.

http://www.asrc.cuny.edu/facilities/

Contact: Eric Shipp, Deputy Executive Director, eric.shipp@asrc.cuny.edu

The New York Genome Center is an independent, nonprofit academic research organization at the forefront of transforming biomedical research and clinical care with the mission of saving lives. A collaboration of renowned academic, medical and industry leaders in New York and other partners throughout the country, the New York Genome Center focuses on translating genomic research into clinical solutions for serious diseases. New York Genome Center member institutions (including Columbia) and partners are united in this unprecedented collaboration of technology, science, and medicine. The Center advocates and educates, sharing its findings and discoveries with the scientific, medical, and thought leadership communities. It integrates genomic research with cutting-edge technologies and leading physician-scientists so that patients around the world can benefit from more effective clinical treatments.

http://www.nygenome.org/

Contact: service@nygenome.org

The New York Structural Biology Center (NYSBC) is an extraordinary consortium representing nine renowned academic research institutions that is recognized as the most comprehensive center for structural biology in the US. NYSBC conducts research, offers educational symposia and classes, and provides access to its advanced instrumentation and expertise in Cryoelectron Microscopy, NMR and X-Ray Crystallography to faculty and students from its member institutions. Its resources include: seven microscopes, including three Krios microscopes with direct detectors, and a dual beam scanning FIB/SEM microscope; eight NMRs with cryoprobes, including two at 900 MHz, a dynamic nuclear polarization magnet and 800 MHz magnets for both solution- and solid-state work; and a new microdiffraction beamline, NYX, located at NSLS-II at the Brookhaven National Laboratory (BNL). Its fully accredited graduate-level courses include: NMR Spectroscopy of Macromolecules; Cryoelectron Microscopy of Macromolecular Assemblies; and Biomolecular NMR Spectroscopy. Columbia University was a founding member of NYSBC which opened its 45,000 square foot facility at 133rd Street and Convent Avenue in 2002, and the CU faculty has full access to NYSBC.

http://nysbc.org/

Contact: Crystal Love, clove@nysbc.org