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http://www.harvard.edu/

Institution of higher education in the United States. Private Ivy League research university in Cambridge, Massachusetts.

Proper citation: Harvard University; Cambridge; United States (RRID:SCR_011273) Copy   

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https://doi.org/10.7910/DVN/XD1A6B

Portal for cross sectional study where population based sample of adult cancer patients were recruited for mailed survey (with telephone follow-up of non-responders) to evaluate equivalence of PROMIS measures across socio-demographic and clinical sub-groups.

Proper citation: PROMIS 2 MY Health (RRID:SCR_021215) Copy   

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http://www.betacell.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented on August 1, 2015. Consortium that aims to facilitate interdisciplinary collaborations to advance the understanding of pancreatic islet development and function, with the goal of developing innovative therapies to correct the loss of beta cell mass in diabetes, including cell reprogramming, regeneration and replacement. They are responsible for collaboratively generating the necessary reagents, mouse strains, antibodies, assays, protocols, technologies and validation assays that are beyond the scope of any single research effort. The scientific goals for the BCBC are to: * Use cues from pancreatic development to directly differentiate pancreatic beta cells and islets from stem / progenitor cells for use in cell-replacement therapies for diabetes, * Determine how to stimulate beta cell regeneration in the adult pancreas as a basis for improving beta cell mass in diabetic patients, * Determine how to reprogram progenitor / adult cells into pancreatic beta-cells both in-vitro and in-vivo as a mean for developing cell-replacement therapies for diabetes, and * Investigate the progression of human type-1 diabetes using patient-derived cells and tissues transplanted in humanized mouse models. Many of the BCBC investigator-initiated projects involve reagent-generating activities that will benefit the larger scientific community. The combination of programs and activities should accelerate the pace of major new discoveries and progress within the field of beta cell biology.

Proper citation: Beta Cell Biology Consortium (RRID:SCR_005136) Copy   

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https://www.sharelatex.com/

An collaborative tool which allows users to edit LaTeX documents in their browser. Multiple users can simultaneously access and edit the same LaTeX document and see the changes in real time. The latest version is available online, and the built in chat helps communicate with others while editing.

Proper citation: ShareLaTeX (RRID:SCR_002652) Copy   

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https://CalRapp.org

A Web-based Analysis Tool for Indirect Calorimetry Experiments which measure physiological energy balance. It is a web application for indirect calorimetry analysis which generates customizable time, bar and regression plots for calorimetry data using two-, three-, and four-group templates.

Proper citation: CalR (RRID:SCR_015849) Copy   

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https://github.com/qiicr/dcmqi

Software library to help with the conversion between imaging research formats and the standard DICOM representation for image analysis results. Used to implement conversion of the data stored in commonly used research formats into the standard DICOM representation. Available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer.

Proper citation: dcmqi (RRID:SCR_016933) Copy   

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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   

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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   

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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   

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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   

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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   

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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   

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http://genetics.bwh.harvard.edu/pph2/

Software tool which predicts possible impact of amino acid substitution on structure and function of human protein using straightforward physical and comparative considerations. PolyPhen-2 is new development of PolyPhen tool for annotating coding nonsynonymous SNPs.

Proper citation: PolyPhen: Polymorphism Phenotyping (RRID:SCR_013189) 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   

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https://benchling.com

An online resource which helps researchers manage and organize labs and experimental results by supplying molecular biology software tools for experimental design and data analysis. Benchling provides tools for functions such as primer design and colony counting as well as CRISPR guide design and automated Gibson and Golden Gate cloning. Users can take notes in line with data, link data across entries, keep files and data in one place, and manage and keep track of team progress. An enterprise version of Benchling is available for scientists working within an organization with additional administrative, compliance, and security protocols.

Proper citation: Benchling (RRID:SCR_013955) Copy   

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http://direct2experts.org

An on-going project and collaboration tool where biomedical researchers can access to expertise and related resources across institutions, regardless of local platforms and tools. Users can work with participating institutions in order to connect to their existing research networking tools. Biomedical institutions that wish to participate must have a mature, deployed research networking tool and can commit resources to assessments.

Proper citation: DIRECT2experts (RRID:SCR_013958) Copy   

•   Source: SciCrunch Registry
  

http://www.genomecompiler.com

A software platform which enables users to conduct genetic engineering with genomic manipulation tools (provided in the platform). Genome Compiler includes multiple DNA synthesis providers, lab facility services, and advanced bioinformatics tools and genetic repositories. Data can be imported from VectorNTI, SnapGene, ApE, Clone Manager, and others. The Gibson Assembly and Restriction Ligation methods are supported by Genome Compiler.

Proper citation: GenomeCompiler (RRID:SCR_013988) Copy   

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