Research Application Platforms

Images and illustrations can be imported and the service includes the creation of new custom icons on demand. In addition to saving on expensive illustration software, the goal of this solution is to reduce the amount of time required by researchers to create illustrative figures.

 

Eligibility

• Available to anyone working at Harvard University (Faculty, Staff, Postdocs, and Students)
• 33-digit Harvard billing number required for payment
• A valid and active HarvardKey account
• Hospital Affiliates are not eligible

 

Licensing

• Starting November 1, 2022, pricing per user per year will be $154.26
• Harvard Departmental 33-digit billing code required
• License term is November 1- October 31
• To opt-out of automatic renewal, send an email to rchelp@hms.harvard.edu
• No prorated pricing available for this software

 

How to request

• Request a BioRender license via PPMS RC Core
  • Detailed instructions on how to create a PPMS RC Core account and order research software

 

BioRender access

• Portal for currently registered users

 

Support

• Issues with the BioRender application
• Setup and account issues contact us at rchelp@hms.harvard.edu

 

System Requirements

BioRender is a web-based tool that supports Mac OS, Windows, and Linux browsers.

Platform Overview 

eLABJournal is a fully compliant Electronic Lab Notebook (ELN), offering an intuitive and flexible solution to documenting, organizing, searching, and archiving research data. You can upload and annotate images, upload and edit excel files and link to your larger data files. You can upload files of any type and view or edit those files through associated desktop applications. You can also link to samples and reagents stored in eLABInventory. 

With eLABInventory you can efficiently track any sample, specimen, chemical, or instrument in the lab. You can setup templates to track any information about any item in your lab inventory. You can also centralize orders by keeping track of quantities, and receive notifications when chemicals, samples, and consumables run out of stock. 

eLabProtocols is a web-based protocol management system to design protocol templates and Standard Operating Procedures (SOPs). You can create a step-by-step experimental procedure and define the output parameters to be collected in your experiment.

 

Eligibility 

• HMS On-quad Labs, Departments, and Cores approved by HMS ELN steering committee. 

 

Features 

• Integrated with HMS Authentication with 2FA.  HMS account ID required

• Application is available via the HMS network and externally

• Intuitive User Interface 

• Integration with HMS Office 365 Excel 

• Supports Experiment Templates, Protocols & SOP management, including version support 

• Sign and Witness experiments 

• Automatically synchronize uploaded data (eLABSync)  

• Upload files of any type, and open with associated desktop software (eLABWebEdit) 

• Collaborate with colleagues 

• Customizable User Roles and Permissions  

• Sample & Inventory Barcoding 

• Keep track of quantities, and centralize ordering 

• Schedule lab devices 

• Mobile app and other add-ons 

• Secure and Compliant (ISO 27001 certified, FDA 21 CPR part 11, GLP) 

• Fully documented API and SDK 

 

Limitations 

• Currently limited to Harvard Data Security Level 3 

 

Compatibility 

• Brower-based system, compatible with all major web browsers on Linux, Mac OS, and Windows, Mac systems. 

• Mobile app available for iOS and Android devices. 

 

Cost 

• There is no cost for HMS on-quad users during the pilot. 

 

Request an account 

• HMS Principal Investigators or core directors who would like their groups to participate in the eLabNext Pilot should contact rchelp@hms.harvard.edu for further information about eligibility. 

 

Getting started with eLabNext 

• During the Pilot, training will be provided to new groups as needed. Email us at rchelp@hms.harvard.edu for further details 

  

Research Computing will assist HMS Researchers with setting up a GitHub space to store your code/scripts in Git.  There is no cost for this service.

This service is NOT HIPAA compliant.

Eligibility

• Available to anyone working at Harvard University (faculty, staff, postdoctoral researchers, and students),  
• HMS-affiliated hospitals do not qualify for this license

If you are interested, please email us at rchelp@hms.harvard.edu

Description

The HMS Globus platform enables users to share large volumes of data with collaborators. It allows researchers to efficiently, reliably, and securely transfer large data sets to and from O2-accessible storage and folders or local workstations. Files can be exchanged with external collaborators who have access to the Globus.org platform.

Features

• Optimized for large file transfer (Gigabytes or Terabytes).

• Enables collaboration with external HMS Researchers.

• Bidirectional transfers to and from O2 accessible storage and folders and local file storage.

• Transfers run in the background. You don’t need to stay connected for the transfer node to complete.

• Accommodates scheduled transfers.

• Web Console that provides transfer monitoring and sharing status.

• Command line feature available on the platform via the Globus CLI application allowing users to automate file transfers.

• Globus Desktop Client “Connect Personal Client' that supports Linux, macOS, and Windows.

Eligibility

• Available to HMS Quad-based faculty, staff, postdocs, and graduate students. Also available to externally sponsored collaborators who are working with HMS Labs or Cores.

Requirements

• The user must have a Harvard Key. You will also need an HMS account if you intend to use O2-accessible storage.

  • O2 accessible storage includes Active Compute, Scatch, and Standy.

Cost

• No Cost

Limitations

• At this time, HMS Active Collaborations i.e. Research.Files storage areas cannot be accessed through Globus system.

• Maximum of 5 million files per directory

• Only Active Compute, Scatch, and Standy storage mounted to O2 transfer nodes can be accessed by Globus. 

How to request the service

• Current O2 users have access via the Globus Web Console.

• Sign up and sign in for the service at https://app.globus.org

Support

• If you need help or have questions, contact us at rchelp@hms.harvard.edu.

• Please see our HMS Globus getting start guide for step-by-step instructions.

Overview

OMERO is a visualization platform for the management of microscope images and metadata, available for use across the HMS research community. 

Eligibility

Available to HMS Quad-based faculty, staff, postdocs, and graduate students. External sponsored collaborators who are working with HMS Labs or Cores.

Requirements

The user must have an HMS account.

Cost

No Cost for HMS Quad-based faculty, staff, postdocs, and graduate students. No Cost for external sponsored collaborators who are working with HMS Labs or Cores.

Storage Limitation:

Reference HMS storage and quota policies.

Request HMS OMERO account

Account Request Form. 

Client Software

Download and install OMERO.insight, which is necessary to import data into OMERO. 

Support

• If you having issues, contact us at rchelp@hms.harvard.edu.

• Guides for using OMERO.insight are maintained on the openmicroscopy.org website. Go to Adding image data for instructions on how to import data into OMERO. 

• More information on getting started is available in the FAQ.

Eligibility

• For HMS IRB studies in REDcap,  users must be listed on your active approved IRB.
• Available to all HMS, HSDM, and HSPH quad-based staff, faculty, and postdoctoral researchers. Other HMS affiliates do not qualify for this license.
• Students who work in HMS-based research labs are also eligible, with Lab or Departmental approval.
• Survey subjects do not need an HMS account ID to take a REDCap survey.

 

Features

• Online or offline project design: Use the Online Designer or offline using a “data dictionary” template in Microsoft Excel that can be uploaded later into REDCap.
• Secure and web-based: Input data or build an online survey or database from anywhere in the world over a secure web connection with authentication and data logging.
• Fast and flexible: Conception to production-level database or survey in less than one day.
• Fully customizable
• Audit trails: For tracking data manipulation and user activity.
• Automated export procedures: For seamless data downloads to Excel, PDF, and common statistical packages (SPSS, SAS, Stata, R).
• A built-in project calendar
• A scheduling module
• Ad hoc reporting tools
• Advanced features such as branching logic, file uploading, and calculated fields.
• Available in multiple languages
• HMS REDCAP is approved for use with Harvard Data Security Level 4 data
• Preview or Test Projects can be created in our REDCap Sandbox environment.

 

Limitations

• HMS REDCap is not a HIPAA-compliant service.
• Provide functional support for Survey (Project) creation, import, conversion, or publication.

 

Compatibility

• A browser-based system,  compatible with all major web browsers on Linux, macOS, and Windows, Mac systems.
• REDCap mobile app for iOS and Android

 

Cost

• There is no cost to eligible users of this HMS service.

 

Request an account

• HMS REDCap website sign in page 
• Complete the request form to get an account and a REDCap project 

 

Getting started with REDCap

• Brief Overview of REDCap (5 min)
• REDCap essential resources.
• Support and training are available via the REDCap Consortium Community Website.

Note: once you submit your request, it can take up to 10 business days to provision the Posit (RStudio) Connect instance

Features

• Support for hosting and publishing Shiny developed applications, like the shinyapps.io service.

• Support for custom content URL per app so researchers can easily brand their work.

• Highly available cloud infrastructure designed to ensure your application is up and running.

• Ability to publish apps that are available to the public or can be secured, requiring users to use their Harvard Key to view the data.

• Use the  Posit (RStudio) Desktop IDE application to create, upload, and publish your Shiny apps.

Eligibility

• Available to HMS Quad-based faculty, staff, postdocs, and graduate students.

• HSDM, HSPH and Hospital Affiliates, and hospital-based labs are not eligible.

Requirements

• You must have a Harvard Key account and have been provided access to the instance.

• Your lab must be located on the HMS Quad.

Cost

• During the pilot phase, there is no cost to use this service however in the future based on demand there could be an annual fee to use this platform.

Limitations

• Applicants must have a faculty member or research staff member as a sponsor. (Faculty and research staff may sponsor themselves.)

• Shiny Application limit: 100 MB per app.

• Data size limit: 5 GB per application.

• Maximum number of authenticated users per lab: 10

• Access to HMS Posit/RStudio Connect is restricted to faculty, staff, and students who are on-quad at HMS.

• This system is approved for use with Harvard Data Security Level 3 data if Harvard Accounts are used for authentication.

• This system is NOT a HIPAA-compliant service.

• RDVP service is provided for the distribution of lightweight apps.

• Currently, there is no integration with the HMS O2 Cluster.

• Shiny app performance can be impacted by code design.

• If you need additional resources or larger amounts of local storage please contact us at

  rchelp@hms.harvard.edu

How to request the service

• Please complete this form to request an RDVP Posit (RStudio) Connect instance