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http://bionumbers.hms.harvard.edu/

Database of key numbers in molecular and cell biology--the quantitative properties of biological systems of interest to computational, systems and molecular cell biologists. Contents of the database range from cell sizes to metabolite concentrations, from reaction rates to generation times, from genome sizes to the number of mitochondria in a cell. Along with the numbers, you'll find the relevant references to the original literature, useful comments, and related numbers. While always of importance to biologists, having numbers in hand is becoming increasingly critical for experimenting, modeling, and analyzing biological systems. BioNumbers was motivated by an appreciation of how long it can take to find even the simplest number in the vast biological literature. All numbers are taken directly from a literature source and that reference is provided with the number. BioNumbers is designed to be highly searchable and queries can be performed by keywords or browsed by menus. BioNumbers is a collaborative community platform where registered users can add content and make comments on existing data. All new entries and commentary are curated to maintain high quality.

Proper citation: BioNumbers (RRID:SCR_002782) Copy   

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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   

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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   

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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   

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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   

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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   

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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   

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https://www.eagle-i.net/

Web application to discover resources available at participating networked universities. This distributed platform for creating and sharing semantically rich data is built around semantic web technologies and follows linked open data principles.

Proper citation: Eagle I (RRID:SCR_013153) Copy   

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http://harvard.eagle-i.net/i/0000012c-6032-ce8f-c437-ff0b80000000

A lab facility that aims to accelerate research in the stem cell field by facilitating the derivation and distribution of induced pluripotent stem cell lines. Disease-specific pluripotent stem cell lines can provide the opportunity to study the mechanisms of disease and develop treatments. The core facility serves as a repository for iPS cells produced by HSCI scientists.

Proper citation: Harvard HSCI iPS Cell Core Facility (RRID:SCR_000880) Copy   

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https://github.com/IQSS/DataTaggingLibrary

Software tool to help humans interactively assess artifacts or situations against set of rules. Model consists of n-dimensional space and decision graph that guides users through that space using questions. Open source software tool for DataTags Decision Graph language, used to create questionnaires and tag spaces. Can be used to perform interactive interviews which yield concrete treatment that is both human readable and machine actionable. Models can also be visualized, and can be analyzed to find caveats or loopholes.

Proper citation: PolicyModels (RRID:SCR_019084) Copy   

•   Source: SciCrunch Registry
  

http://harvard.eagle-i.net/i/0000012e-6e60-8691-55da-381e80000000

Core facility that provides the following services: Website development and hosting for research labs and studies requiring an online presence, interactive functionality, or site traffic tracking.

The Health Communication Core offers a full range of creative communication services to support evidence-based recruitment and retention of study participants and intervention research. HCC serves researchers from diverse disciplines who need websites, logos, brochures, social media campaigns, publications, and interactive media targeted to the needs and preferences of specific audiences.

Proper citation: DF/HCC Health Communication Core (RRID:SCR_000871) Copy   

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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   

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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   

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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   

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http://harvard.eagle-i.net/i/0000012e-5977-000a-55da-381e80000000

The Community Practice Research Core (CPRC) provides DF/HCC investigators access to a racially diverse population of over 11,000,000 patients within the community-based clinical practices of Harvard Vanguard Medical Associates (HVMA)/ Atrius Health, a Boston-based medical specialty group comprised of over 20 office locations across eastern Massachusetts providing care to more than 510,000 adult and pediatric patients; Harvard Pilgrim Health Care (HPHC), one of the largest health maintenance organizations in New England with close to 1,000,000 members and an extensive provider network that includes physicians who practice in a variety of settings; the Cancer Research Network is comprised of 9 health care systems and 6 affiliate sites across the nation with a total membership of 11,000,000 patients. The populations of HVMA/Atrius, HPHC, and the CRN are particularly ideal for studies: (1) involving basic, clinical, and population sciences; (2) addressing diverse communities; (3) investigating dissemination of proven technologies and interventions; (4) requiring large samples of patients and/or providers; (5) involving rare cancers; and (6) of cancer prevention.

Proper citation: DF/HCC Community Practice Research Core (RRID:SCR_009735) Copy   

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http://harvard.eagle-i.net/i/0000012e-5d8c-a118-55da-381e80000000

Core provides all of the tools of modern functional proteomics. Equipped with technologies for proteomics; protein profiling, protein identification, protein and peptide fractionation, and quantization. Personalized experimental design consultation, comprehensive individualized bioinformatics support. The mission of the DF/HCC Cancer Proteomics Core is to develop a comprehensive and interdisciplinary proteomics core for High Sensitivity, High Resolution and High Throughput Proteomics with particular emphasis on in depth proteomic consultation, referral to the optimal proteomics facility and a strong focus on clinical sample analysis. The core combines consultation, service and education into a comprehensive, translationally and clinically oriented proteomics core.

Proper citation: Dana Farber and Harvard Cancer Center Cancer Proteomics Center (RRID:SCR_009733) Copy   

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http://harvard.eagle-i.net/i/0000012c-9d60-89cb-b977-103480000000

Core facility that provides the following services: Scientific computing for data analysis and scientific graphics, Advice and consultation regarding grant applications and management of clinical trials data, Training in study design, data collection, computerization, and statistical methods.

The Biostatistics Core facility is a shared resource supporting consultation on biostatistics and epidemiology throughout the Dana-Farber/Harvard Cancer Center (DF/HCC). The mission of the core is to ensure that experimental designs, study monitoring and data analyses take advantage of robust, efficient methods that reflect ''best practices'' in biostatistics and epidemiology; to support NIH-funded peer reviewed grants that do not contain salary support for statisticians; and to enable pilot and small scale studies to become part of successful applications for peer-reviewed funding. These services are available to Dana-Farber / Harvard Cancer Center members only. The Biostatistics Core is located across several of the member institutions of the DF/HCC. To contact the Core, please email or call the statistician associated with your disease site.

Proper citation: DF/HCC Biostatistics Core Facility (RRID:SCR_009730) Copy   

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http://www.dfhcc.harvard.edu/core-facilities/tissue-microarray-and-imaging-pathology/

Core facility that provides the following services: Construction of standard and custom TMA service, Nucleic acid isolation from paraffin embedded tissue service, Immunofluorescent staining service, Access to the Automated Quantitative Analysis (AQUA) system, Tissue microarray consultation service.

The mission of the Tissue Microarray and Imaging Core is to generate tissue microarrays by allowing placement of up to 480 0.6 mm diameter tissue samples into a single standard tissue block, allowing hundreds of tumors and samples to be evaluated on a single slide. The DF/HCC Tissue Microarray & Imaging (TMI) Core is dedicated to the construction and evaluation of high quality TMAs for cancer research. In addition, the Core performs high-throughput isolation of DNA and RNA from formalin-fixed paraffin-embedded tissues. The Core also provides web-based digital pathology services using the Aperio system. These services include slide scanning, image viewing and storage, and quantitative image analysis, which facilitate tissue-based research. Finally, the Core provides access to the Automated Quantitative Analysis (AQUA) system.

Proper citation: DF/HCC Tissue Microarray and Imaging Core Facility (RRID:SCR_009743) Copy   

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http://harvard.eagle-i.net/i/0000012c-6056-ed57-c437-ff0b80000000

Core facility that provides the following services: Protein development/cloning, Western blot service, ELISA service, Flow cytometry service.

The mission of the DF/HCC Monoclonal Antibody Core (MAC) is to produce novel monoclonal antibodies that are directed against antigens of interest to Dana-Farber, the Harvard Cancer Center, and affiliated investigators. These monoclonal antibodies may be useful for basic research, drug discovery and clinical applications including diagnosis, surrogate markers for disease status, response to therapy or drug toxicity. Given the diverse research needs of investigators at DFCI and the Harvard Community, the MAC should strive to support a wide range of antibody requests. A key component of the DF/HCC MAC is the ability to explore and develop new technologies that facilitate generation of monoclonal antibodies. The DF/HCC MAC should be capable of supporting all basic functions of generating, screening, storing and producing monoclonal antibodies.

Proper citation: DF/HCC Monoclonal Antibody Core (RRID:SCR_009740) Copy   

•   Source: SciCrunch Registry