Onboarding Checklist: Faculty

• Familiarize yourself with FAS Research Computing Services
• Review Harvard policies and procedures
  • Research Data Ownership Policy
  • Harvard Research Data Security Policy (HRDSP)
  • Harvard University General Records Schedule
  • Harvard Data Security Levels
  • Retention and Maintenance of Research Records and Data Frequently Asked Questions (“FAQs”)
  • Harvard Data Safety Website
  • PI Responsibilities on the Cluster
    • Identify a data manager for the lab 
  • FASRC Data Ownership and Access Policy
• Get a FASRC account using the account request tool
  • Set your FASRC password
  • Set up OpenAuth for two-factor authentication (2FA)
  • Set up FASRC VPN
  • Link FASRC account to HarvardKey 
    • If you have a HarvardKey, but are denied access to approve new accounts, visit and complete the FAS Onboard tool for approvers. 
  • Faculty can sponsor FASRC accounts for any researcher working in their lab, including external collaborators. If a collaborator does not have a Harvardkey account, they may apply for an external FASRC account. External accounts need to be reenabled every 90 days. PIs will need to request an extension every 90 days to prevent the account from being suspended. 
• Learn how to utilize the High Performance Compute cluster 
  • User Quick Start Guide
  • Review Running Jobs
  • Review Cluster Customs and Responsibilities
  • Command line access with Terminal (login nodes)
  • Understand Fairshare on the cluster
• Review FASRC storage offerings 
  • Request a new storage allocation in Coldfront
    • Coldfront is a resource allocation management system FASRC adapted to manage allocations on the FASRC cluster. The platform enables the viewing and management of lab groups (Projects), and storage and cluster allocations (Allocations).
    • FAS Secure Environment
• Connect to your new storage folder from a desktop computer
• Transfer data to your new storage folder
• Create a well-defined storage workflow 
  • Develop streamlined directory structures
  • Establish consistent file naming conventions
• View information about storage folders associated with your group/lab
  • Utilize the Starfish Zones tool to view key information about your group’s storage folders. The Starfish Zone User Interface is a self-service visual tool that enables users to view group storage amounts and locations. Users can navigate folder structures to access detailed information about files and storage. Labs and groups are strongly recommended to utilize this tool to assist with their data organization and cleanup efforts.
• Installing and using software on FASRC cluster
• Attend FASRC introductory trainings 
  • Training calendar 
• Contact 
  • Email rchelp@fas.harvard.edu if you have any questions
  • Virtual Office Hours: Wednesdays 12-3PM 

Onboarding Checklist: Researchers

• Familiarize yourself with FAS Research Computing Services
• Review Harvard policies and procedures
  • Research Data Ownership Policy
  • Harvard Research Data Security Policy (HRDSP)
  • Harvard University General Records Schedule
  • Harvard Data Security Levels
  • Retention and Maintenance of Research Records and Data Frequently Asked Questions (“FAQs”)
  • Harvard Data Safety Website
• Get a FASRC account using the account request tool
  • Set your FASRC password
  • Set up OpenAuth for two-factor authentication (2FA)
  • Set up FASRC VPN
• Learn how to utilize the High Performance Compute cluster 
  • Introduction to Cluster Computing Docs and Video
  • Review Cluster Customs and Responsibilities
  • Command line access with Terminal (login nodes)
  • Understand Fairshare on the cluster
• Review FASRC storage offerings 
  • FAS Secure Environment
• Connect to your new storage folder from a desktop computer
• Transfer data to your new storage folder
• View information about storage folders associated with your group/lab
  • Utilize the Starfish Zones tool to view key information about your groups storage folders. The Starfish Zone User Interface is a self-service visual tool that enables users to view group storage amounts and locations. Users can navigate folder structures to access detailed information about files and storage. Labs and groups are strongly recommended to utilize this tool to assist with their data organization and cleanup efforts.
• Attend FASRC introductory trainings 
  • Training calendar 
• Contact 
  • Email rchelp@fas.harvard.edu if you have any questions 
  • Virtual Office Hours: Wednesdays 12-3PM

Each user is provided with a 100GiB Home Directory for individual use. Each PI or Lab Account also receives a 4TiB Lab Directory, for use by all members of the PI’s lab group and a 50TiB allotment of scratch (networked scratch). See the matrix below for more details.

*Snapshots are copies of a directory taken at a specific moment in time. They offer labs a self-service recovery option for overwritten or deleted files within the specific time period. Disaster recovery is a copy of an entire file system that can be used internally by FASRC in case of system-wide failure.

Home Directory

• Description: Individual user folder intended for other types of data (code, scripts, documentation, analysis data)
• Moderate performance
• Size: 100GiB (cannot be expanded)
• Mount: /n/homeNN/username
• Daily snapshots for 7 days and weekly snapshots for 4 weeks. Includes disaster recovery.
• Cost: Free
• Security level: Up to Level 2 (Level 3 with FASSE)
• Automatically generated when granted cluster access.
• Is not visible to anyone but the owner. Not intended for sharing.

Lab Directory

• Description: General lab folder intended for data, scripts with version control and documentation.
• Moderate performance
• Size: 4TiB (cannot be expanded)
• Mount: /n/holylabs
• No snapshots. No disaster recovery.
• Cost: Free
• Security level: Up to Level 2
• Automatically generated for approved PIs with two subfolders:
  • Lab: Subfolders are visible to everyone in the lab. We recommend housing most of the data in this subfolder.
  • Everyone: Subfolders visible to anyone on the cluster, great for collaboration between labs.

netscratch

• Description: Temporary storage location for high performance data analysis.
• High performance.
• Size: 50TiB per group, 100 million inodes
• Mount: /n/netscratch
• No snapshots. No disaster recovery.
• Retention: 90-day retention policy.
• Cost: Free
• Security level: Up to Level 2 (Level 3 with FASSE)
• Automatically accessible if a member of the lab group with two subfolders:
  • Lab: Subfolders are visible to everyone in the lab. We recommend housing most of the data in this subfolder.
  • Everyone: Subfolders visible to anyone on the cluster, great for collaboration between labs.

Active Lab Storage for Compute (Tier 0)

• Description: Storage folder intended for active analysis research data connected to the high-performance compute cluster.
• High performance.
• Size: 1-1024TiB
• Mount:/n/server/LABS/folder
• No snapshots. No disaster recovery.
• Cost: $50/yr per TiB
• Security level: Up to Level 2
• Request storage allocation

Active Lab Storage with Snapshots (Tier 1)

• Description: General purpose storage location for data analysis and project data. Best for irrecoverable data like raw datasets as it comes with backups.
• Moderate performance.
• Size: 1-1024TiB
• Mount: /rc_labs/folder
• Daily snapshots for 7 days and weekly snapshots for 4 weeks. Includes disaster recovery.
• Cost: $250/yr per TiB
• Security level: Up to Level 2
• Request storage allocation

Active Lab Storage with Disaster Recovery (Tier 2)

• Description: Intended for intermediary storage of research data for ongoing and recent projects. Not designed for frequent increases/decreases in allocation size. 
• Low/moderate performance.
• Size: 1-306TiB
• Mount: /n/pi_lab
• No snapshots. Includes disaster recovery.
• Cost: $100/yr per TiB
• Security level: Up to Level 2
• Request storage allocation

Cold Storage (Tape)

• Description: Long-term storage of inactive research data after project completion for data retention purposes.
• No performance or access.
• Size: 20TB increments. Ten thousand files per folder. File sizes between 1GiB to 100 GiB.
• Access: Tape-based access with Globus or S3
• No snapshots. Includes disaster recovery.
• Cost: $5/yr per TB
• Security level: Up to Level 2
• Request storage allocation

FASSE (Secure Enclave) 

• Description: Secure storage environment for analysis or sensitive data, such as data generated using Data Use Agreements (DUAs) or IRB
• Can be applied to Cluster Storage, Lab Storage, or Tier 2 based on project need.
• Security level: Up to Level 3

Default Directory Structure

Two subdirectories will be created by default within the parent directory for most storage on the cluster. This helps enable Globus transfers and provide initial guidance for how to organize storage. The directories are:

Lab: This directory is intended as the primary working directory. It is also the directory shared out via Globus. By default, folders in this subdirectory are visible to the whole lab. Individual users may update their permissions to adjust access as they like though we highly recommend keeping access open to all lab members to allow for easier collaboration and data cleanup after you leave the university.

Everyone: This directory is visible to any one on the HPC cluster and is intended for collaboration with other labs on the cluster. Data in this directory is by default owned by the lab who hosts the data. Note that this directory is not available on Globus and is intended only for internal sharing.

While this is the default structure, labs may request additional folders be set up. Please email rchelp@rc.fas.harvard.edu if you have questions.

Directory structures on the cluster may differ depending on when they were created. Some older storage folders may have a third subdirectory called Users. We have deprecated use of this folder due to issues related to data access by the lab and PI’s, especially after users have left the university. If you are migrating data from a storage system that has a Users subdirectory we recommend moving that data into the Lab directory and making it available to the lab to view and access.

If you have questions regarding the data storage options at FASRC, please email the Research Data Manager at rdm@rc.fas.harvard.edu.

Offboarding Checklist: Leaving Harvard University

Researchers:

1. General: 

   1. Inform FASRC via email prior to leaving the university, and provide us with an estimated departure date. 

2. Storage: 

   1. Please review all research data prior to your departure (FAS Storage, Google Drive, Dropbox etc.). Confirm with your PI and department what data can be deleted or moved to long-term storage. 
      1. Review and receive approval from your PI what data can be removed. 
         1. Delete any data approved by your PI. 
         2. Please ensure a record of what data was deleted is available to your PI, if needed.
         3. For protected data (Level 3), PIs are responsible for informing FAS RC if and when the data requires disposal. Please email FAS RC to discuss destruction options.
      2. If research data stored on FASRC storage is ready to be moved to long-term storage, work with FASRC’s Research Data Manager and your PI to migrate the data. 
         1. An FASRC account is required to access FASRC storage; please ensure you have an account prior to moving data via rclone or Globus. 
      3. Ensure your research data is available to your PI and other collaborators, moving all research data to a shared storage location prior to your departure. Please ensure a record of what data was migrated is available to your PI, if needed.
      4. If you would like to take data with you following your departure from the university, you will need approval from your PI and department. Research data generated at the university is owned and maintained by the university. 

3. Accounts 

   1. We will be closing your FASRC account when your appointment ends and your Harvard email account is closed. 
   2. If you need to maintain a FASRC account, please have your PI or authorized lab member (general manager or access manager) email us directly, prior to your departure, so we can convert the account to an external account and extend it by 90 days. 
      1. If you require an extension longer than 90 days, your PI will need to email us again prior to the end of the 90 day extension. We will also need an external email address for the account, as your Harvard email will be disabled automatically. 
   3. Disabling the account will automatically remove you from associated groups, including secure groups (FASSE), administrative groups, and project groups. 

Faculty/PIs:

1. General: 

   1. Inform FASRC via email when you will be leaving the university. 
   2. Please inform FASRC if you will be returning or compensating FASRC for any physical resources (compute notes and storage servers).  

2. Software: 

   1. All purchased software will remain on the cluster. Please delegate the software license responsibility to another entity (lab or department) or inform FASRC when the license will expire. 

3. Storage: 

   1. Please review all research data prior to your departure. Confirm what data can be deleted or moved to long-term storage.
      1. Please review Harvard’s Data Retention FAQs, to ensure you are in compliance with the university’s policy around data retention.
      2. Collaborate with FASRC’s Research Data Manager to migrate remaining data to long-term storage. 
   2. If you would like to take research data with you following your departure from the university, ownership of the original data may be transferred from Harvard to your new institution upon request. The University asserts ownership over research data for all projects conducted at the University, under the auspices of the University, or with University resources.
      1. Requirements:
         1. Prior written approval from the Vice Provost for Research;
         2. A written agreement from your new institution that guarantees its acceptance of ongoing custodial responsibilities for the data and allowing Harvard access to the original data, should such access become necessary for any reason;
         3. Relevant confidentiality restrictions, where appropriate.

4. Accounts 

   1. Inform FASRC via email when you will be leaving the university so they can disable your account. Your FASRC account will be closed when your appointment ends and your Harvard email account is closed. If you attain a different appointment at Harvard after your primary appointment ends, please notify FASRC as soon as possible.
   2. All lab members will need a new sponsor for their accounts. Please inform FASRC who the new sponsor will be for any remaining lab members. 
   3. Disabling your account will automatically remove you from associated groups, including secure groups (FASSE),  administrative groups, and project groups. 

5. Virtual Machines 

   1. Remove any data you would like to retain from virtual machines prior to your departure; please inform FASRC once the data has been removed 
   2. Virtual Machines will be decommissioned shortly after your departure, once it is no longer aligned with an active account.

Offboarding Checklist: Changing Labs/Groups

Researchers:

1. Request to be added to the new group using Portal. Your PI can also utilize Coldfront to add users to their group. 
2. Review your research data to determine what data will need to remain in your previous lab folder(s) and what data needs to be migrated to your new lab folder. 
   1. Discuss the data migration with your former PI and get approval for the move.
   2. If you plan to continue to store research data in your previous lab folder, confirm this with your former PI, as there will be associated storage costs. 
   3. Delete any research data that will not be useful to either lab. Confirm with your former PI what data can be removed.
   4. Ensure your research data is available to your former PI and other collaborators, moving your research data to a shared storage location prior to your departure. Please ensure a record of what data was migrated is available, if needed.
   5. Review data in your group’s Scratch environment, as the data will be removed.
3. Your new PI must inform FASRC via email that they will be sponsoring your account, so they can be assigned as your primary group. Provide the date of transition. 
4. FASRC will then modify your FASRC account information.
   1. Add you to the new lab group/department
   2. Add your new PI as your manager
   3. Modify your Slurm group to be associated with the new lab
   4. Remove you from your previous lab and Slurm group. 
      1. If you require access to your previous lab, your former PI can re-add you to their group using the Coldfront application. 
5. Storage
   1. Home directory data will always remain with the user account. The data will not need to be transferred. 

Additional information:

1. Harvard Human Resources Offboarding Information 
2. Harvard IT Offboarding Information 

Contact:

If you have questions regarding the offboarding process, please email the FAS Research Data Manager at rdm@rc.fas.harvard.edu.

Benefits of Data Sharing

• Compliance with research funding organizations that require data management plans and data accessibility
• Compliance with journals that require submission of research data alongside publications
• Recognition for your contribution to the creation of research data, with academic citations
• Encourages additional research opportunities, as others can replicate or reuse the data for new analyses

Data Sharing Recommendations

• Deposit research data and code in open access data repositories
• Use persistent links between publications and data repositories
• Thoroughly document contextual information related to data, code, workflows and the computational environment and include the information with your dataset submission
• Encourage reproducibility of your research results by publishing in an open access journal

Policies

• NIH Data Sharing Policy and Public Access Policy
• NSF Data Sharing Policy
• Harvard’s Intellectual Property Statement
• Harvard FAS Open Access Policy

Journals

Many journals now require that published articles include the associated research data as part of the submission. To determine whether your journal requires your data be shared, review the journal’s data sharing policy.

• Science
• Springer Nature

Intellectual Property

Review any intellectual property and copyright restrictions. In general, raw data cannot be copyrighted, but some expressions of data like databases can be copyrighted or licensed.

• Promote data sharing and reuse by assigning an appropriate license
  • Open Data Commons License
  • Creative Commons License
• If you assign a license that restricts the sharing of data, provide detailed information about how to generate and analyze the data, so others can reproduce your results.
• If you have questions about how to protect your work as an inventor, consider filing a Report of Innovation(ROI) with Harvard OTD.

Data Use Agreements

Data Use Agreements (DUAs) are binding contracts between organizations that govern how research data will be transferred and utilized. The terms and conditions vary depending on the laws and regulations around the data type (i.e. personally identifiable information), as well as the policies or requirements of the Provider. The Office for Sponsored Programs (OSP) and Office of Research Administration (ORA) are the authorized signatories for Harvard and can help facilitate the DUA process for Harvard researchers. If you have any questions, please contact the Harvard DUA team.

Data Repositories

Data repositories offer the necessary infrastructure to host research data as required by institutions, funders, and journals. They can assist with the maintenance, organization, access, and curation of your research data. They also provide a persistent identifier and citation for your data, generally in the form of a DOI.

• Harvard Dataverse
  • All file formats accepted
  • Files cannot exceed 2.5GB, but larger files can be uploaded by Harvard Dataverse upon request.
  • Dataset size set to 1TB per researcher, but larger datasets can be uploaded by Harvard Dataverse upon request.
  • Strongly encourages use of the Creative Commons Zero (CC0) license for all public datasets
  • Assigns a DOI for each dataset
  • Tiered level access (administrator, collaborator, curator)
  • Comprehensive data and metadata search capabilities
  • Data downloading via API
  • Free for all researchers worldwide (up to 1TB), with no maintenance fees

Manuscript Repositories

• Harvard Library DASH
• PubMed_Central
• NSF Public Access Repository

Other Data Sharing Information and Resources at Harvard

• Harvard Research Support
• Harvard University Digital Scholarship Group
• Harvard HUIT Cloud Program

Starfish Zones is a self-service visual interface that allows groups to view folder storage amounts and locations. Users can navigate through the folder structures in the dashboard to explore directory and file level details, including storage amounts, last accessed and modified times, file owners, and file counts. The tool is still under development and may experience short downtimes to accommodate modifications.

Login

To access the dashboard, navigate to https://starfish.rc.fas.harvard.edu/. You will need to be on Harvard VPN, FASRC VPN, or a wired on-campus connection. See VPN Setup for how to connect to FASRC VPN.

After navigating to the website, input your FASRC account name and password. If you have issues with your FASRC password, please visit the FASRC website.

If you are unable to access the Starfish dashboard, please email FASRC Help. If you are a new faculty or group owner, it may take some time before your information is fully populated in FASRC systems. You will also need an active FASRC supported storage folder to receive a Starfish Zone.

Navigation

Once logged in, you will be able to view storage folders associated with your group. Note: If you notice a storage folder is missing from your dashboard, please email FASRC’s Research Data Manager. While a majority of storage folders supported by FASRC are now viewable in Starfish, some filesystems still need to be added.

By double-clicking on the selected folder path, you can drill down into the folder down to the file level. Group members can modify what information is displayed on the dashboard by right-clicking on the column headers. All available column selections will be shown.

The dashboard is updated on a consistent basis. You can view when the Zone was last updated on the upper right-hand corner of the dashboard, where a date and time will be listed. If no modifications have been made to the folder contents, the updated time will reflect the last time changes were made to the folder.

Data Cleanup

Starfish can be used to identify files and directories that might no longer be useful to a group. There are several ways to use Starfish to identify folders and files that have not recently been modified or accessed or are owned by a group member who is no longer part of the team.

Browsing

1. After logging in, navigate to the group’s storage folder.
2. Navigate to the top of the dashboard and select the “Sunburst” map or the radial chart symbol to generate a visualization of directory contents.
3. The Sunburst map helps visualize data based on the last accessed and modified times of the files. The map can also showcase files based on file type.
4. You can mouse over the map for more information about the visualized directories.

Please note that directory access times are often updated when a user or process lists a directory (ls or dir), which means that access time may be later than the last time a file was actually accessed.

At the bottom of the sunburst graph is an option to select “Users” – select this option in order to see a breakdown of allocation data by user.

Export

The dashboard allows users to export the information as a CSV file. At the top of the zone is a “Download CSV” option. Users can select which columns they would like included in the downloaded spreadsheet. Some of our suggested columns include:

• Count (number of files)
• Path (folder path)
• Logical size (dataset size)
• Newest accessed (tree)
• Newest modified (tree)

Depending on the number of files and folders listed, the CSV file may be too large to download. We recommend selecting the specific subfolder that you would like to view as an export, to decrease the size of the downloaded file.

Contact

If you have any additional questions about how to login or utilize the Starfish Zones dashboard, please email Sarah Marchese, FASRC Research Data Manager.

Accessing Coldfront

To access Coldfront, connect to the @fasrc VPN and log in using FASRC credentials.

https://coldfront.rc.fas.harvard.edu/

After logging in you will see your home page, which has sections for your projects, your allocations, and any pending requests or change requests for your allocations. Click the project link or Allocation status button to view details about a given project or allocation.

Project Pages:

A Project page allows all project members to:

• view the project’s allocations
• view the project’s users
• adjust their project notification settings.

Additionally, from the project page, project managers and PIs can:

• request new storage allocations
• request changes to existing storage allocations
• add users to the project
• remove or request to remove users from the project
• edit the roles of project users (i.e., assign or remove Manager status)
• send an email to project users that have elected to receive notifications.

The project page’s allocation section allows you to view storage and cluster allocations for your lab. Managers can also click the “Request New Storage Allocation” button on this table’s header to… yes, that’s right, submit a request for a new storage allocation.

Project Membership and Roles

The project page contains a users table that lists all the users in the lab group. PIs, Access Managers, and and General Managers will also see options to add users to the project, and remove or request to remove users from the project. PIs and General Managers can additionally edit the roles of project users or send an email to project users that have elected to receive notifications.

Project user roles correspond to the roles described in FASRC Roles and Responsibilities:

• PI. This role is automatically assigned to the lab’s PI and cannot be assigned to another Project user. The PI can:
  • Request new allocations
  • Request changes to the size of existing allocations
  • Add and remove project users
  • Change the roles of existing project users
• General Manager. General Managers can be assigned by PIs. They have all the permissions of a PI, save the ability to assign General Manager status to other project members.
• Storage Manager. Storage Managers can be assigned by PIs and General Managers. Storage Managers can:
  • Request new allocations
  • Request changes to the size of existing allocations
• Access Manager. Access Managers can be assigned by PIs and General Managers. Access Managers can:
  • Add and remove project users
• User. Project users can view project and allocation information. They cannot change or request changes to the project or its allocations.

Allocations:

The Allocation Page provides a comprehensive view of details about the allocation, presenting key information such as the total allocation size, overall usage, and the estimated monthly cost. This page also features a table that illustrates usage per user, with data sourced and updated daily from our data management system, Starfish.

Making an Allocation Request:

PIs and users with General Manager or Storage Manager status can make a new allocation request or request changes to project allocations.

To request a new allocation:

1. Go to the page of the project the new allocation is for and click the Request New Storage Allocation button.
2. Fill out and submit the allocation request form.
3. You will be notified via email when your new allocation is ready to use.

Allocations can be requested on storage tiers 0-3. To explore and understand the specifics of each storage tier, please refer to our detailed documentation on storage tiers here.

Making an Allocation Change Request:

PIs and project managers can request to change the size of an allocation associated with their project. Follow these steps to initiate the process:

1. Navigate to the allocation page corresponding to the allocation you wish to modify.
2. Click the “Request Change” button at the top of the “Allocation Information” table.
3. In the resulting form, shown below, enter the desired size of the allocation and the justification for those changes and click submit.
4. You will be notified via email when the allocation is updated and ready to use. Space permitting, we try to fulfil change requests within 3 business days.

For storage features and updates, please review the Data Storage Workflow documentation on our website.

For information about ColdFront’s dataflow, check the Storage Service Center page.

If you have any questions, please feel free to reach us here: rchelp@rc.fas.harvard.edu

RSpace (ResearchSpace) is an open-source electronic lab notebook (ELN) supported by Harvard IT that can help researchers organize, store, and share protocols, analysis and experimental notes in a centralized and secure platform. RSpace has been developed in close consultation with researchers and research data professionals at leading global research institutions to meet expanding researcher needs.

Benefits

Tailored for academic environments and the research workflow, ELNs help manage and track research data throughout the data lifecycle. They facilitate good data management practices, support data review and oversight, enable group collaboration, and manage inventories of samples and other equipment.

Features

Researchers:

• Capture and organize research data to maintain a record of work
• Collaborate with lab groups and lab members
• Simplify data inventory and sample management
• Integrate with popular research tools
  • Harvard Dataverse, protocols.io, OneDrive, Google Drive, Dropbox, S3 Cloud, DMPTool, GitHub, Jupyter Notebook, Slack and more!
• Link to research data stored in institutional storage
• Store research data up to Harvard Security Level 3
• Login with HarvardKey authentication

Principal Investigators (PIs):

• Delegate administration of group access to a manager
• Open or restricted data sharing capabilities available
• Real time visibility of researcher communication
• Data ownership stays with the PI and the university
• Export data in HTML, XML, DOC and PDF formats
• Data backups retained by RSpace to prevent data loss

Additional information available on the RSpace website. An overview of the RSpace ELN for prospective users is also provided by Harvard IT (HarvardKey login required).

Eligibility

• Available to Principal Investigators (PIs) with a Harvard appointment. Members of the labs can be added as users.
• To request RSpace for your Lab, please complete the Harvard RSpace ELN Onboarding Request Form.

Contact

Please direct additional questions to Sarah Marchese, Research Data Manager with FAS Research Computing: rdm@rc.fas.harvard.edu