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http://harvard.eagle-i.net/i/00000139-928e-36d0-f016-703c80000000

The Biostatistics Core serves the needs of the HIV/AIDS researchers within the Ragon Institute and its affiliates. In particular, members of the Biostatistics Core provide expertise in the planning, conduct and analysis of research with the goal of enhancing the scientific quality of HIV-related research at the institute. The primary objective of the core is to ensure that studies are well designed, correctly analyzed, clearly presented, and correctly interpreted.

Proper citation: Ragon Institute Biostatistics Core (RRID:SCR_010055) Copy   

•   Source: SciCrunch Registry
  

http://harvard.eagle-i.net/i/0000012e-5eed-e0fd-55da-381e80000000

Core facility that provides the following services: Coulter XL flow analysis, Cytomation MoFlo cell sorting, LaserScan Cytometry, BD Biosciences LSR II flow cytometry analysis, Flow cytometry data analysis. The Flow Cytometry Facility is a core facility of Schepens Eye Research Institute that provides fluorescent-based cell analysis and sorting to Boston area biomedical researchers.

Proper citation: SERI Flow Cytometry Core Facility (RRID:SCR_010059) Copy   

•   Source: SciCrunch Registry
  

https://github.com/dattalab/moseq2-app

Software application as starting point to MoSeq2 package suite. Unsupervised machine learning method which takes inputs from depth cameras in 3D and transforms them into different behavioral motifs which called syllables. Used to extract mouse pose from depth video and model how pose evolves over time.

Proper citation: moseq2-app (RRID:SCR_025031) Copy   

•   Source: SciCrunch Registry
  

https://bioinformatics.sph.harvard.edu/

Provides single point of contact for Harvard researchers interested in bioinformatics support, applying genomic approaches together with established and developing methodologies from epidemiology, environmental health, biostatistics and bioinformatics to improve human health.Services include analysis all types of next-generation sequencing data from RNA-seq and single cell RNA-seq to variant sequencing (exome or whole genome), to ChIP-seq or bisulfite sequencing. Offers bioinformatics training program for Harvard researchers interested in learning basic data skills and analysis of high-throughput sequencing data.

Proper citation: Harvard University Chan School of Public Health Bioinformatics Core Facility (RRID:SCR_025373) Copy   

•   Source: SciCrunch Registry
  

http://writefullapp.com

A software application which provides feedback on writing, wording, and frequency of text by checking against databases of correct language. Users can highlight a chunk of text and use Writefull to see how often the specific text appears in different language databases. Writefull can also offer synonyms and suggestions for wording. Writefull is supported by numerous writing tools which include MS Word and Gmail.

Proper citation: Writefull (RRID:SCR_014006) Copy   

•   Source: SciCrunch Registry
  

https://github.com/QTIM-Lab/DeepNeuro

Software Python package for neuroimaging data. Framework to design and train neural network architectures. Used in medical imaging community to ensure consistent performance of networks across variable users, institutions, and scanners.

Proper citation: DeepNeuro (RRID:SCR_016911) Copy   

•   Source: SciCrunch Registry
  

https://github.com/DReichLab/AdmixTools

Software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates.

Proper citation: ADMIXTOOLS (RRID:SCR_018495) Copy   

•   Source: SciCrunch Registry
  

http://harvard.eagle-i.net/i/0000012c-7441-2a90-c437-ff0b80000000

Core facility that provides the following services: Tissue trimming, cassetting, processing, and embedding, Cutting and staining of paraffin-embedded and cryostat sections, Immunohistochemistry for both routine and novel markers, In situ hybridization, using chromogenic or radioactive detection methods, Laser capture microdissection.

Tissue analysis is critical to validation and evaluation of animal models of human cancer, and human cancer tissues serve as the operating system for translational research. The facility supports a wide spectrum of cancer-relevant research, from basic studies on pathogenic mechanisms in cancer to translational research focused on the development of new tests for biomarkers that stratify patients and direct therapy. The Specialized Histopathology (SHP) Core, was created in 2005 by consolidating five histopathology cores into a single unit with two performance sites: Longwood, Directed by Jon Aster and based at the Brigham and Women?s Hospital and MGH, Directed by Anat Stemmer-Rachamimov and based at Massachusetts General Hospital East in Charlestown. The SHP Core provides professional and technical research pathology services to DF/HCC investigators working in diverse organisms (e.g., rodents, fish, and monkeys) or human tissues. The Core also assists in experimental design and the development and interpretation of tests and their results. As of July 2012, the Longwood site offers CLIA Certified services.

Proper citation: DF/HCC Specialized Histopathology Services Core (RRID:SCR_000872) Copy   

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http://wyss.harvard.edu/viewpage/594/

A core facility with access to imaging equipment and analysis software such as wide-field light microscopy, Total Internal Reflection Fluorescence microscopy (TIRF), confocal microscopy, Atomic Force Microscopy (AFM), Transmission Electron Microscopy (TEM), small animal imaging, spectroscopy, and flow cytometry.

Proper citation: Wyss Institute Imaging Core (RRID:SCR_000898) Copy   

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http://harvard.eagle-i.net/i/00000137-e19e-59a0-d807-77a880000000

Microscopists at Weld Hill will find a range of tools from the simple hand lens to the confocal microscope for 3-D reconstructions.

Proper citation: Arnold Arboretum of Harvard University: Weld Hill Microscopy Lab (RRID:SCR_004485) Copy   

•   Source: SciCrunch Registry
  

https://bauercore.fas.harvard.edu/

Helps to advance research efforts in life sciences that cannot readily be accomplished in the traditional academic laboratory because of need for expensive instrumentation or automation, scientific or organizational infrastructure, or multidisciplinary expertise. Provides expertise and hands-on training and use of instrumentation for nominal fee. Researchers can sign up to use instrumentation through on-line scheduling system and conduct their experiments independently.

Proper citation: Harvard University Bauer Core Facility (RRID:SCR_022656) Copy   

•   Source: SciCrunch Registry
  

https://venomsbase-dashboard.shinyapps.io/VenomLanding/

Open-access, browser-based visualization and summary tool for venom transcriptomic and proteomic data. R Shiny–based interactive application designed as visualization and reporting interface for venom transcriptomic and proteomic data. It enables users to explore annotation metrics, toxin gene families, and quality-control summaries generated by analysis pipelines. While it will eventually serve as part of the VenomsBase front end, VenomView currently operates as standalone prototype. Provides interactive dashboards showing assembly quality, annotation scores, toxin gene families, and functional domains generated by the VenomFlow analysis pipeline. Connected to VenomLanding, VenomView currently features Doryteuthis pealeii (Squid), linking metadata with detailed annotation summaries. The expanded version will include Sepia bandensis (Cuttlefish), Octopus bimaculoides, and arachnid species.

Proper citation: VenomView (RRID:SCR_027588) Copy   

•   Source: SciCrunch Registry
  

https://wiki.med.harvard.edu/SysBio/Megason/MegaCapture

MegaCapture is a VisualBasic macro developed for automating the acquisition of in toto image sets. It is useable on Zeiss microscopes using LSM v4.x software (pre-Zen). MegaCapture can automatically acquire image sets across any combination of dimensions including x, y, z, time, color, x-tile, y-tile, row, and column. Images are exported on the fly and can be compressed allowing very large (100,000 images) image sets to be captured. Sponsors: MegaCapture is supported by Harvard University.

Proper citation: Harvard Medical School, Department of Systems Biology: The Megason Lab - MegaCapture Software (RRID:SCR_001732) Copy   

•   Source: SciCrunch Registry
  

https://www.writelatex.com

A collaboration tool which allows users to edit and publish scientific articles and papers. Overleaf utilizes the convenience of an easy-to-use WYSIWYG manuscript editor with real-time collaboration and structured, fully typeset output produced automatically. Authors can publish immediately and directly to their journal of choice while publishers can reduce their editorial and review turnaround times with powerful change tracking, commenting, and project lifecycle management features. It was formerly known as writeLaTex but changed its name to Overleaf in 2015.

Proper citation: Overleaf (RRID:SCR_003232) Copy   

•   Source: SciCrunch Registry
  

http://www.nitrc.org/

Software repository for comparing structural (MRI) and functional neuroimaging (fMRI, PET, EEG, MEG) software tools and resources. NITRC collects and points to standardized information about structural or functional neuroimaging tool or resource.

Proper citation: NeuroImaging Tools and Resources Collaboratory (NITRC) (RRID:SCR_003430) Copy   

•   Source: SciCrunch Registry
  

http://cistrome.org

Web based integrative platform for transcriptional regulation studies.

Proper citation: Cistrome (RRID:SCR_000242) Copy   

•   Source: SciCrunch Registry
  

http://flybase.org/

Database of Drosophila genetic and genomic information with information about stock collections and fly genetic tools. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. Additionally, FlyBase accepts data submissions. FlyBase can be searched for genes, alleles, aberrations and other genetic objects, phenotypes, sequences, stocks, images and movies, controlled terms, and Drosophila researchers using the tools available from the "Tools" drop-down menu in the Navigation bar.

Proper citation: FlyBase (RRID:SCR_006549) Copy   

•   Source: SciCrunch Registry
  

http://www.hms.harvard.edu/NEPRC/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. A center that focuses on performing bio-medical research on nonhuman primates to aid in human health research. The center also focuses on training young scientists for professional careers in bio-medical research and primate biology. One of the New England Primate Research School's main accomplishments was the creation of an animal model for AIDS that first demonstrated that vaccine protection could be possible. Recent research has led to the development of novel agents for brain imaging that will aid in the diagnosis and treatment of Parkinson's disease.

Proper citation: New England Primate Research School (RRID:SCR_008290) Copy   

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http://www.hsph.harvard.edu/cli/complab/dchip/

Sponsor:
support is NIH grant R01 GM077122
National Institutes of Health, Claudia Adams Barr Program, and Friends of DFCI.
We are interested in how genomics changes promote cancer progression. Through collaboration with biomedical researchers, we analyze high-throughput microarray and sequencing data to study genomics, expression, and network changes in cancer cells. New methods are packaged into widely-used software such as dChip, which has been cited more than 1600 times.

Proper citation: Cheng Li Lab of Computational Genomics (RRID:SCR_008613) Copy   

•   Source: SciCrunch Registry
  

https://joslinresearch.org

Diabetes research center which provides patient care and performs diabetes research. Its primary aim is to provide a facilitating framework for conducting multi-disciplinary basic and clinical research and to encourage the scientific development of young investigators.

Proper citation: Joslin Diabetes Center (RRID:SCR_009019) Copy   

•   Source: SciCrunch Registry