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http://compbio.dfci.harvard.edu/tgi/ego/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. EGO is a database of eukaryotic gene orthologs generated by pair-wise comparison between the Tentative Consensus (TC) sequences that comprise the Dana Farber Gene Indices from individual organisms.

Proper citation: EGO - Eukaryotic Gene Orthologs (RRID:SCR_000732) Copy   

•   Source: SciCrunch Registry

https://fgr.hms.harvard.edu/

Database that provides free online tools to users to allow the retrieval of information related to the Drosophila genome and allows access to genome-wide and related cell-based screening of Drosophila at Harvard Medical School (for a fee) . Tools available include SnapDragon, and RNAi designer, a heat map tool for viewing screen data, and gene and amplicon search and download tools. The DRSC mainly exists to provide Drosophila genome screening services, including help with assay development and optimization, data and image analysis, and planning of follow-up assays.

Proper citation: Drosophila RNAi Screening Center (RRID:SCR_000733) Copy   

•   Source: SciCrunch Registry

https://www.authorea.com/

Online word processor for scientific and scholarly papers. Write, share, cite, comment, export, and track changes of articles in one place.

Proper citation: Authorea (RRID:SCR_002547) Copy   

•   Source: SciCrunch Registry

https://kleintools.hms.harvard.edu/tools/spring.html

Interactive web tool to visualize single cell data using force directed graph layouts. Kinetic interface for visualizing high dimensional single cell expression data. Collection of pre-processing scripts and web browser based tool for visualizing and interacting with high dimensional data.

Proper citation: SPRING (RRID:SCR_023578) Copy   

•   Source: SciCrunch Registry

http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases

Probabilistic atlases covering 48 cortical and 21 subcortical structural areas, derived from structural data and segmentations kindly provided by the Harvard Center for Morphometric Analysis. T1-weighted images of 21 healthy male and 16 healthy female subjects (ages 18-50) were individually segmented by the CMA using semi-automated tools developed in-house. The T1-weighted images were affine-registered to MNI152 space using FLIRT (FSL), and the transforms then applied to the individual labels. Finally, these were combined across subjects to form population probability maps for each label. Segmentations used to create these atlases were provided by: David Kennedy and Christian Haselgrove, Centre for Morphometric Analysis, Harvard; Bruce Fischl, the Martinos Center for Biomedical Imaging, MGH; Janis Breeze and Jean Frazier from the Child and Adolescent Neuropsychiatric Research Program, Cambridge Health Alliance; Larry Seidman and Jill Goldstein from the Department of Psychiatry of Harvard Medical School.

Proper citation: Harvard - Oxford Cortical Structural Atlas (RRID:SCR_001476) Copy   

•   Source: SciCrunch Registry

http://www.hms.harvard.edu/research/brain/atlas.html

2D mouse brain atlas of high quality coronal Nissl- and myelin-stained sections with labels, 3D images of hippocampal formation and limited other brain structures. The data for this digital atlas are based on the Atlas of the Mouse Brain and Spinal Cord, authored by Richard L. Sidman, Jay. B. Angevine and Elizabeth Taber Pierce, published as a hard cover book by Harvard University Press in 1971 and currently out of print. C57BL/6J strain adult specimens were used in creating the atlas.

Proper citation: High Resolution Mouse Brain Atlas (RRID:SCR_006063) Copy   

•   Source: SciCrunch Registry

http://antibodyregistry.org

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. It was integrated with Antibody Registry. The JCN antibody database is a listing of all antibodies used in JCN papers from 2006 onward. The catalog numbers and vendor information is included for all antibodies listed, and with a new collaboration with NIF''''s AntibodyRegistry, a unique identifier is also listed for each antibody. The Journal of Comparative Neurology requires rigorous characterization for all antibodies that are used in JCN papers. The antibodies in the The Journal of Comparative Neurology antibody database have in nearly all cases been described and characterized adequately according to the provided guidelines. This information can be used to identify a particular target immunohistochemically or to design an experiment using the antibody information. If you are looking for an antibody to identify a particular target immunohistochemically, this list is a good place to begin your search. We suggest you then look up the paper in which the antibody was used, to make sure that it will meet your needs and to verify its characterization. (The characterization of antibodies in JCN papers often goes well beyond the material published by the manufacturer, so that examining this information before you order an antibody can be very useful.) While we do not guarantee that these antibodies will identify only the intended target (that is a function of the actual experiment and controls), this is the most carefully verified list of antibodies that we are aware of, and we wanted to share this resource with our readers and authors.

Proper citation: Journal of Comparative Neurology Antibody database (RRID:SCR_006470) Copy   

•   Source: SciCrunch Registry

http://www.strokedatabase.org/

Database and associated software tools providing access to clinical and research data on stroke, including deidentified patient data. Data types include imaging (e.g. CT, MRI, PET), clinical demographic data, genetic data, simulation perfusion data for verifying deconvolution algorithms used in bolus-tracking perfusion-weighted imaging (PWI). Also available are programs for performing deconvolution of bolus-tracking PWI, DTI tractography and an automated program for etiologic classification of ischemic stroke -- Causative Classification System for Ischemic Stroke (CCS)

Proper citation: International Stroke Database (RRID:SCR_007347) Copy   

•   Source: SciCrunch Registry

https://data.broadinstitute.org/chembank/assay

ChemBank is a public, web-based informatics environment that includes freely available data derived from small molecules and small-molecule screens, and resources for studying the data so that biological and medical insights can be gained. ChemBank is intended to guide chemists synthesizing novel compounds or libraries, to assist biologists searching for small molecules that perturb specific biological pathways, and to catalyze the process by which drug hunters discover new and effective medicines. ChemBank stores an increasingly varied set of cell measurements derived from, among other biological objects, cell lines treated with small molecules. Analysis tools are available and are being developed that allow the relationships between cell states, cell measurements and small molecules to be determined. Currently, ChemBank stores information on hundreds of thousands of small molecules and hundreds of biomedically relevant assays that have been performed at the ICG in collaborations involving biomedical researchers worldwide. These scientists have agreed to perform their experiments in an open data-sharing environment. The goals of ChemBank are to provide life scientists unfettered access to biomedically relevant data and tools heretofore available almost exclusively in the private sector. We intend for ChemBank to be a planning and discovery tool for chemists, biologists, and drug hunters anywhere, with the only necessities being a computer, access to the Internet, and a desire to extract knowledge from public experiments whose greatest value is likely to reside in their collective sum.

Proper citation: ChemBank (RRID:SCR_007592) Copy   

•   Source: SciCrunch Registry

http://arep.med.harvard.edu/dpinteract/

DPInteract is a database of DNA-binding site matrices. This dataset is being collected with several purposes in mind: 1. Cataloging demonstrated sites and non-sites for E.coli DNA-binding proteins; 2. Aiding the annotation of such sites in other E.coli databases and sequence entries; 3. Interpreting the results of whole-genome in vivo methylation protection experiments; 4. Developing better computational tools for recognizing DNA binding proteins in sequence data.

Proper citation: DPInteract (RRID:SCR_007627) Copy   

•   Source: SciCrunch Registry

http://bio.dfci.harvard.edu/DFRMLI/

This repository contains full data from MHCPEP database, and selected data including independent data sets of proteins and protein fragments, non-binding peptides, lists of T-cell epitopes, and recommendations for scaling and comparison of performance of prediction systems. It can be used in conjunction with IEDB data sets for the development of advanced machine learning and pattern recognition solutions.

Proper citation: MHCPEP (RRID:SCR_007786) Copy   

•   Source: SciCrunch Registry

http://paradox.harvard.edu/sdr

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. A database of predicted specificity-determining residues in protein families. Predicted positions may have been used during evolution to change the function of proteins within a protein family. These positions are excellent targets for mutational studies and should lead to a better understading of protein function. SDR uses the PFAM database of protein domains for sequence alignments and domain definitions as well as the GPCR database for G-protein coupled receptors.

Proper citation: SDR: Specificity-Determining Residues in Protein Families (RRID:SCR_007917) Copy   

•   Source: SciCrunch Registry

http://harvard.eagle-i.net/i/00000139-53f7-02d1-9072-1e4280000000

Core facility that provides the following services: Flow Cytometric Cell Sorting. The mission of Ragon Institute Imaging Core, Flow Cytometry Division is to provide training and access to flow cytometers with up to 18 parameters, as well as cell sorting of biohazardous samples. As an MGH Core Facility, the Ragon Institute Imaging Core serves the greater MGH community. Since the Ragon Institute is also a collaboration between MGH, Harvard, and MIT, so too does the facility welcome members of the MIT and Harvard communities. The facility is equipped with three LSR2?s, an LSR Fortessa, a FACSCalibur, and a FACSAria IIu cell sorter in a biosafety cabinet. The core also serves as a resource for addressing a variety of flow cytometry needs including consultation on topics related to experimental design and sample preparation.

Proper citation: Ragon Institute Imaging Core Flow Cytometry (RRID:SCR_010056) Copy   

•   Source: SciCrunch Registry

http://harvard.eagle-i.net/i/00000139-4f2c-8328-4d8e-943b80000000

Core facility that provides the following services: Microscopy Instrumentation Access, Training in Microscopy/Imaging, Assisted Microscopy. The mission of Ragon Institute Imaging Core, Microscopy Division is to bring the latest imaging modalities and technology to bear on fundamental molecular and cell biological questions pertaining to infectious diseases. As an MGH Core Facility, the Ragon Institute Imaging Core also serves the MGH greater MGH community. Since the Ragon Institute is also a collaboration between MGH, Harvard, and MIT, so too does the facility welcome members of the MIT and Harvard communities as we are now located in Cambridge at MIT. The facility encompasses five imaging systems, including a Zeiss LSM510 laser scanning confocal microscope and a fully automated Zeiss Axio Observer microscope, both housed in BL2+ compliant facilities. These imaging systems are therefore fully equipped for both fixed and live cell imaging. In addition, the facility has two slide scanning systems (MIRAX MIDI and TissueFAXS) for high speed automated imaging and cellular screening of tissue sections and cultured cells on glass slides. In the Flow Cytometry section of the Imaging Core, we also have an ImageStream X Mark II by Amnis. The core also serves as a resource for addressing a variety of imaging needs including consultation on a topics related to imaging applications, experimental design, and sample preparation.

Proper citation: Ragon Institute Imaging Core Microscopy (RRID:SCR_010058) Copy   

•   Source: SciCrunch Registry

http://harvard.eagle-i.net/i/0000013e-5708-120e-7db7-114480000000

The Core''s capabilities include six Computer Numerical Control (CNC) milling centers (one of which is a five-axis micro-milling machine), two 3D printers, a waterjet cutter, a laser cutter, and a sinker Electrical Discharge Machining (EDM) tool. The Core has three full time machinists with experience in both industrial and academic machine shops, creating prototypes for varied applications. In addition to fabrication, these experts help researchers during the design phase, enabling development from a simple concept into real prototypes.

Proper citation: Wyss Institute Machine Shop / 3D Prototyping Core (RRID:SCR_010212) Copy   

•   Source: SciCrunch Registry

http://harvard.eagle-i.net/i/00000137-b920-a047-d807-77a880000000

The Wyss Institute Materials Characterization Core is dedicated to promoting leading edge biologically inspired research by providing users with a wide range of state-of-the-art materials characterization equipment and analysis software. These tools help support the characterization of a material?s unique physical, chemical, and mechanical properties. The Materials Characterization Core team provides exceptional hands on training, method development, and technical expertise. We also proactively stride to introduce the latest innovations in materials characterization to the Wyss Institute community and our affiliated partners. Our current techniques include chromatography, mass spectrometry, UV-Vis spectroscopy, particle sizing, quartz crystal microbalance, electrochemical testing, rheology, and nanoindentation.

Proper citation: Wyss Institute Materials Characterization Core (RRID:SCR_010213) Copy   

•   Source: SciCrunch Registry

http://www.neurodiscovery.harvard.edu/research/lddn_2.html

Core facility that provides the following services: Assay design and development service. The NeuroDiscovery Center''''s Laboratory for Drug Discovery in Neurodegeneration (LDDN) was established to discover chemical agents from which we and others will develop a new generation of drugs to treat neurodegenerative diseases (including degenerative diseases of the eye and ear). To accomplish this goal, LDDN has recruited a permanent staff of industry-seasoned scientists with expertise in assay development, laboratory automation, informatics, and medicinal chemistry, to work in close collaboration with principal investigators from the academic neuroscience community. In this way, LDDN helps transform discoveries in the basic biology of neurodegeneration into opportunities for drug discovery. (While priority is given to members investigating neurodegenerative diseases and the central nervous system, we welcome inquiries from all investigators.)

Proper citation: HNDC Drug Discovery in Neurodegeneration (RRID:SCR_012680) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/bauer-core-laboratory-fas-harvard

Core facility that provides the following services: Liquid handling, Long read sequencing, Cell sorting service, Cell analysis service, Imaging systems service, Microarrays service, Sequencing service, Genotyping service, Fragment analysis, Solexa DNA sequencing service, Solexa gene expression service, Solexa small RNA service, Solexa ChIP-Seq service, Real-time quantitative PCR service, Protein-molecule interaction service, Library replication service, Nucleic acid isolation service, Nucleic acid shearing service, DNA, RNA and protein sample analysis service. Their goal is to advance research efforts in the life sciences that cannot readily be accomplished in the traditional academic laboratory because of a need for expensive instrumentation or automation, scientific or organizational infrastructure, or multidisciplinary expertise. To promote cutting-edge research and to foster scientific collaborations, we make our extensive laboratory and computational resources available to scientists at Harvard. Our technical staff provide expertise and hands-on training in protocols and the use of instrumentation for a nominal fee. Researchers can sign up to use the instrumentation through an on-line scheduling system and conduct their experiments independently.

Proper citation: Harvard FAS Bauer Core Laboratory (RRID:SCR_001031) Copy   

•   Source: SciCrunch Registry

http://harvard.eagle-i.net/i/00000137-e19f-9e69-d807-77a880000000

The molecular lab at Weld Hill is well equipped for modern molecular studies, from RNA expression studies to phylogenetic analyses.

Proper citation: Arnold Arboretum of Harvard University: Weld Hill Molecular Lab (RRID:SCR_004781) Copy   

•   Source: SciCrunch Registry

http://harvard.eagle-i.net/i/0000012b-00c4-1614-db6e-7a3f80000000

Core facility that provides the following services: Magnetic resonance spectrometer training service, Magnetic Resonance Instrument Access. Welcome to the Magnetic Resonance Facility of the Department of Chemistry and Chemical Biology, Harvard University, in the Laukien-Purcell Instrumentation Center.

Proper citation: Harvard FAS Magnetic Resonance Laboratory (RRID:SCR_008476) Copy   

•   Source: SciCrunch Registry