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http://www.people.fas.harvard.edu/~junliu/em/em.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A haplotype inference program.

Proper citation: EM-DECODER (RRID:SCR_000023) 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

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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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   

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http://HIVBrainSeqDB.org

The HIV Brain Sequence Database (HIVBrainSeqDB) is a public database of HIV envelope sequences, directly sequenced from brain and other tissues from the same patients. For inclusion in the database, sequences must: (i) be deposited in Genbank; (ii) include some portion of the HIV env region; (iii) be clonal, amplified directly from tissue; and (iv) be sampled from the brain, or sampled from a patient for which the database already contains brain sequence. Sequences are annotated with clinical data including viral load, CD4 count, antiretroviral status, neurocognitive impairment, and neuropathological diagnosis, all curated from the original publication. Tissue source is coded using an anatomical ontology, the Foundational Model of Anatomy, to capture the maximum level of detail available, while maintaining ontological relationships between tissues and their subparts. 44 tissue types are represented within the database, grouped into 4 categories: (i) brain, brainstem, and spinal cord; (ii) meninges, choroid plexus, and CSF; (iii) blood and lymphoid; and (iv) other (bone marrow, colon, lung, liver, etc). Currently, the database contains 2517 envelope sequences from 90 patients, obtained from 22 published studies. 1272 sequences are from brain; the remaining 1245 are from blood, lymph node, spleen, bone marrow, colon, lung and other non-brain tissues. The database interface utilizes a faceted interface, allowing real-time combination of multiple search parameters to assemble a meta-dataset, which can be downloaded for further analysis. This online resource will greatly facilitate analysis of the genetic aspects of HIV macrophage tropism, HIV compartmentalization and evolution within the brain and other tissue reservoirs, and the relationship of these findings to HIV-associated neurological disorders and other clinical consequences of HIV infection.

Proper citation: HIV Brain Sequence Database (RRID:SCR_008819) Copy   

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https://nar.oxfordjournals.org/content/35/suppl_1/D322.full-text-lowres.pdf

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The GO Partition Database was designed to feature ontology partitions with GO terms of similar specificity. The GO partitions comprise varying numbers of nodes and present relevant information theoretic statistics, so researchers can choose to analyze datasets at arbitrary levels of specificity. The GO Partition Database, featuring GO partition sets for functional analysis of genes from human and ten other commonly-studied organisms with a total of 131,972 genes.

Proper citation: Gene Ontology Partition Database (RRID:SCR_007693) Copy   

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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   

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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   

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https://www.dfhcc.harvard.edu/research/core-facilities/tumor-imaging-metrics

Core provides centralized, standardized, accurate, consistent, and timely longitudinal, multimodality anatomic, volumetric and functional tumor metrics including CT, MR, PET/CT and other nuclear medicine imaging studies to evaluate therapeutic response for patients enrolled in DF/HCC oncologic clinical trials. TIMC supports more than 30 tumor response assessment criteria including but not limited to RECIST 1.1, iRECIST, Lugano, LYRIC, IWCLL and RANO. Results of tumor metric analyses are offered on password-protected secure web-based report.

Proper citation: Harvard Tumor Imaging Metrics Core Facility (RRID:SCR_012298) Copy   

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http://www.schepens.harvard.edu/graphics

Core facility that provides the following services: Web and graphic services, Web design and content management service, Photography service. Peter Mallen is a designer and illustrator who manages a full-service web and graphics studio in a moderately sized scientific research facility, Schepens Eye Research Institute. He provides a full range of graphic design, scientific illustration, web design and development, content management, and general design and production services. His products are utilized by: faculty and scientific staff (books, scientific publications, slide shows, grant applications); professional staff (Administration, Development & Public Affairs; brochures, books, pamphlets); the general public (Institute websites) as well as clients of our 250-seat state-of-the-art conference center, Starr Center for Scientific Communications.

Proper citation: Harvard SERI Graphic Services Core (RRID:SCR_012309) Copy   

•   Source: SciCrunch Registry

https://hddc.hms.harvard.edu/gnotobiotics-microbiology-and-metagenomics

Core facility that assists investigators evaluating host microbiota and its role in normal physiology and disease. It includes a number of resources for groups studying the role of the microbiota in human health and disease.

Proper citation: Harvard Digestive Diseases Center Biomedical CORE D: Gnotobiotic Mice, Microbiology and Metagenomics (RRID:SCR_012319) 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://www.readcube.com

A software resource application which organizes research literature. Users can import PDF articles into the application and create a searchable library. ReadCube enables users to perform keyword searches and provides references as well as note-taking tools. ReadCube also recommends articles to users based on library contents. For publishers, ReadCube enables interactive PDF versions of articles with tools for readers to make notes or perform author and keyword searches.

Proper citation: ReadCube (RRID:SCR_013777) Copy   

•   Source: SciCrunch Registry

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   

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http://compbio.mit.edu/cummeRbund/index.html

Software R package used for simplifying and analyzing Cufflink RNA-Seq output. This program takes various output files from a cuffdiff run and creates a SQLite database of the results that will describe the appropriate relationships between the genes, transcripts, transcription start sites and CDS regions.

Proper citation: CummeRbund (RRID:SCR_014568) Copy   

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

The Division of Medical Sciences was established at Harvard University in 1908. The Division was designed to provide students wishing to pursue careers in research and teaching with a broad education in basic biomedical science fields and specialization in one of them. Classroom and laboratory instruction are conducted primarily by the 450 faculty members of the basic sciences departments and affiliated hospital laboratories of the Harvard Medical School (HMS) in Boston. The Ph.D. degree is awarded by the Graduate School of Arts and Sciences (GSAS) of Harvard University. For 100 years, this fruitful collaboration has spawned research achievements across the spectrum from basic science to experimental medicine. Since 1909, over 2,000 Division graduates, including six Nobel Laureates, have gone on to distinguished careers in biomedical research, university teaching, and a number of increasingly diverse careers.

Proper citation: Harvard Medical School Division of Medical Sciences (RRID:SCR_007452) Copy   

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

GoFigure is a software platform for quantitating complex 4d in vivo microscopy based data in high-throughput at the level of the cell. A prime goal of GoFigure is the automatic segmentation of nuclei and cell membranes and in temporally tracking them across cell migration and division to create cell lineages. GoFigure v2.0 is a major new release of our software package for quantitative analysis of image data. The research focuses on analyzing cells in intact, whole zebrafish embryos using 4d (xyzt) imaging which tends to make automatic segmentation more difficult than with 2d or 2d+time imaging of cells in culture. This resource has developed an automatic segmentation pipeline that includes ICA based channel unmixing, membrane nuclear channel subtraction, Gaussian correlation, shape models, and level set based variational active contours. GoFigure was designed to meet the challenging requirements of in toto imaging. In toto imaging is a technology that we are developing in which we seek to track all the cell movements and divisions that form structures during embryonic development of zebrafish and to quantitate protein expression and localization on top of this digital lineage. For in toto imaging, GoFigure uses zebrafish embryos in which the nuclei and cell membranes have been marked with 2 different color fluorescent proteins to allow cells to be segmented and tracked. A transgenic line in a third color can be used to mark protein expression and localization using a genetic approach that this resource developed called FlipTraps or using traditional transgenic approaches. Embryos are imaged using confocal or 2-photon microscopy to capture high-resolution xyzt image sets used for cell tracking. The GoFigure GUI will provide many tools for visualization and analysis of bioimages. Since fully automatic segmentation of cells is never perfect, GoFigure will provide easy to use tools for semi-automatically and manually adding, deleting, and editing traces in 2d (figures-xy, xz, or yz), 3d (meshes- xyz), 4d (tracks- xyzt) and 4d+cell division (lineages). GoFigure will also provide a number of views into complex image data sets including 3d XYZ and XYT image views, tabular list views of traces, histograms, and scattergrams. Importantly, all these views will be linked together to allow the user to explore their data from multiple angles. Data will be easily sorted and color-coded in many ways to explore correlations in higher dimensional data. The GoFigure architecture is designed to allow additional segmentation, visualization, and analysis filters to be plugged in. Sponsors: GoFigure is developed by Harvard University., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Harvard Medical School, Department of Systems Biology: The Megason Lab -GoFigure Software (RRID:SCR_008037) Copy   

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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