Research Software Programs

Research software is the collection of tools, codes, libraries that allows a researcher to generate new data or analyze and make meaning of existing data. 

Some software is used across many disciplines, like MATLAB, R, python, whereas most are very domain specific.  The majority of software is provided by the researchers, however Harvard University's Research Computing groups have site or volume licenses for several packages for cluster and/or desktop use, which are provided at no cost to faculty and students.  Licenses are usually available upon request.  Desktops installation of software is self-service or can be done by your local HUIT Desktop support group. 

RC will also help you acquire any other software you may require for your research, or help you determine which packages are most appropriate for the types of analyses you want to do. These packages are purchased individually for each user and are charged to research accounts. 

Software Types: 

Open Source - software in which source code is released under a license in which the copyright holder grants users the rights to study, change, and distribute the software to anyone and for any purpose. Typically, open-source software is developed in a collaborative public manner. 

Commercial - any software or program that is designed and developed for licensing or sale to end users or that serves a commercial purpose. Commercial software was once considered to be proprietary software, but now a number of free and open-source software applications are licensed or sold to end users. Off-the-shelf software programs, to be used with little or no modification, are examples of commercial software. 

Custom - software solutions that are specially developed for a specific user or organization and may include solutions that have been designed to run on specific hardware (embedded software). Such software is used to address user needs that cannot be met by more traditional and widespread off-the-shelf software.  Custom software can also be modifications or extensions, for specific purposes, of Open Source and/or Commercial software. 

Licensing Types: 

Perpetual license - typically authorizes an individual to use an application indefinitely. Generally, outside of termination, a perpetual software license allows the holder to use a specific version of a given software program continually with payment of a single fee.  Along with a perpetual software license, the vendor typically provides a technical support period of one to three years. During this initial period, the vendor also provides software updates often. However, updates may or may not be provided for free in perpetuity. 

Subscription License - typically authorizes an individual to use an application for a defined a defined period. This might be 30 days (a monthly subscription) or 365 days (an annual subscription.) Subscriptions typically have no defined end or termination date and they automatically renew after the initial term. 

Individually Licensed – Individual Licenses can be based on per machine or per user and typically reflect the use of an application by an individual. 

Floating License - approach in which a limited number of licenses for a software application are shared among a larger number of users over time. When an authorized user wishes to run the application, they request a license from a central license server. 

Buying and Installing specific software.  Software can be purchased by an individual or through research computing.  Installation will typically occur by the research computing group either generally (to be available to all users) or within a specific user's space and be available to a limited number of individuals.  Responsibility of troubleshooting and the stability of an application will vary depending on the software title.  Software titles specifically supported by the research computing group are the ones we provide annual training for.  Ad-hoc installation requests will be supported as defined at the time of request. 

Eligibility information is outlined below based on providers with offerings that are available to the entire Harvard community or a specific unit/appointment. 

University-wide

Faculty of Arts and Sciences, Research Computing

Software Installation:   Existing software on the cluster can be found on our portal here

Software Downloads:  Distribution of desktop software for research can be found here. Requires FASRC VPN access. 

Licensed Software:  FASRC runs FlexLM software manager. 

Software purchasing:   FASRC has experience working with vendors and Harvard Procurement to navigate Terms & Conditions of software contracts for HPC Clusters.  FASRC does not need to be involved in SaaS contracts as those are hosted in vendor’s cloud platform.  Generally individual groups will purchase software for their Lab.  Whole departments might pool resources to purchase software for their domain.  Example: Chemistry and Chemical Biology purchase of Gaussian. General purpose software might be purchased by FAS with an institutional license (e.g. MATLAB, Mathematica, Stata, etc.)

Software Training:  See Training for current offerings.  Typical offerings include: 

  • MATLAB 
  • MPI 
  • Python 

Audience

Available to PIs with an active FASRC account from any Harvard School.  For more information see Account Requests

Service Provider

FAS Research Computing

Service Fee

None

Service Website

https://www.rc.fas.harvard.edu/services/software/

Contact Information

Contact Raminder Singh at rchelp@rc.fas.harvard.edu 

Institute for Quantitative Social Science

Audience

Available to social science researchers at Harvard.
For research, needs to be sponsored by Faculty.
For administration, needs to be sponsored by the responsible administrator.

Service Provider

IQSS

Service Fee

$75/hour (Tier 2)

Service Website

https://www.iq.harvard.edu/data-science-services

Contact Information

Steve Worthington
sworthington@iq.harvard.edu

 

 

 

Unit/Appointment-specific

Harvard Medical School

Software Installation:  

As of April 2021, the O2 cluster has 150+ applications and tools for computational analysis, including (partial examples of each category in parentheses).

  • Major computational tools (MATLAB)  
  • Computer languages (R, Python, Perl)  
  • Next-generation sequencing analysis tools (STAR, kallisto, cellranger and libraries (vcflib) 
  • Structural biology (Gromacs, relion) 
  • Deep learning (Tensorflow) 
  • Performance libraries (openmpi, Boost, openblas) 
  • Image analysis and management (OMERO, ImageMagick, CellProfiler, Fiji) 
  • And tools for other life science research disciplines 

Software Downloads:  HMS IT RC provides access the following software packages at charge.  

ChemOffice – a scientifically intelligent, integrated suite of personal productivity tools that helps scientists to efficiently keep track of their work, gain a deeper understanding of their data and produce scientific reports professionally and efficiently. 

DNAStar LaserGene – a bioinformatics software solution for complete analysis, from cloning to next-gen sequencing.  The software includes all of the applications in Lasergene Molecular Biology, Lasergene Protein, and Lasergene Genomics to provide powerful and accurate results. 

JMP Pro – a statistical discovery software with advanced features for more sophisticated analysis including predictive modeling and cross-validation techniques. Understand data in an easy-to-use interface using a desktop software. 

JMP Genomics – a unique integrated analysis software used for biological experiments. It can detect differential expression patterns, find signals in next-generation sequencing data, discover reliable biomarker profiles, perform single-cell sequencing analysis or increase genetic diversity for plant traits in silico. 

LabView – a system engineering software for applications that require test, measurement, and control with rapid access to hardware and data insights. The software is a graphical programming platform that helps engineers visualize, create, and code engineering systems with scale from design to test and from small to large systems. 

MATLAB – a software for developing high-level programming language consisting of an interactive environment mainly used for numeric computation, programming, and visualization.  The software is used for mathematical computation, algorithm development, modeling, simulations, and data analyzing. 

Licensed Software:  HMS IT RC provides access the follow software solutions via charge back. 

BioRender – a web solution for creating and sharing illustrative scientific figures for publication and communication using a scientifically accurate image library.  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. 

FlowJo – a software package for analyzing flow cytometry data. Files produced by modern flow cytometers are written in the Flow Cytometry Standard format with an .fcs file extension. FlowJo will import and analyze cytometry data regardless of which flow cytometer is used to collect the data. 

GraphPad Prism – a commercial scientific 2D graphing and statistics software available for both Windows and Macintosh computers.  Features include analysis of quantitative and categorical data. This makes it easier to enter data correctly, choose suitable analyses, and create graphs.   

SnapGene – a software application that enables an easy and secure way to plan, visualize, and document everyday molecular biology procedures. The software has an intuitive interface, enables DNA sequence visualization, sequence annotation, sequence editing, cloning, protein visualization, and simulating common cloning methods. The software also enables documentation and sharing of data. 

Software purchasing:   FASRC has experience working with vendors and Harvard Procurement to navigate Terms & Conditions of software contracts for HPC Clusters.  FASRC does not need to be involved in SaaS contracts as those are hosted in vendor’s cloud platform.  Generally individual groups will purchase software for their Lab.  Whole departments might pool resources to purchase software for their domain.  Example: Chemistry and Chemical Biology purchase of Gaussian. General purpose software might be purchased by FAS with an institutional license (e.g. MATLAB, Mathematica, Stata, etc.)

Audience

Almost all software on the cluster is available to all users with an O2 account. A few groups have specially licensed software.  

Service Provider

HMS

Service Fee

Software-specific

Service Website

https://it.hms.harvard.edu/our-services/research-computing/services/research-applications-software/research-software

Contact Information

Contact Amir Karger at rchelp@hms.harvard.edu 

Harvard Business School

Licensed Software 

  • Abbyy FineReader
  • AMOS
  • ARCGIS
  • Data Desk
  • EViews
  • FileMaker Pro
  • GAUSS
  • Gurobi
  • KNITRO
  • LIWC
  • MathType
  • Cortex (MatchIt)
  • NAVICAT
  • Scientific Workplace
  • Scientific Word
  • Tableau
  • UCINET
  • WINEDT

Software Training

  • Python
  • R

Audience

HBS Faculty, Doctoral Students and staff conducting research at HBS

Service Provider

HBS

Service Fee

None

Service Website

https://www.hbs.edu/research-computing-services/resources/compute-cluster/selectingsoftware.aspx

Contact Information

Contact Bob Freeman at research@hbs.edu