Harvard Medical School
Research Computing



Status


To check for outages or planned maintenance windows, see the status page.





News

Research Computing and O2 Cluster contributes to radical HMS deep-learning protein prediction advances

Mohammed AlQuraishi’s recent publication in Cell (April 17, 2019) demonstrated a deep-learning method to determine protein structure that is up to one million times faster than previous methods. This groundbreaking research was undertaken in partnership with the HMS-IT Research Computing group and using HMS’s O2 high performance computing cluster, where the model was trained against thousands of proteins and then tested against the Critical Assessment of Protein Structure Prediction. For more info see: https://www.eurekalert.org/pub_releases/2019-04/hms-fr041619.php.

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As of December 3, 2018, all logins to O2 from outside of the HMS network will require two factor authentication. For more information, please see our documentation on two factor authentication.

As of March 31, 2018, the Orchestra cluster is officially retired. Please try using our new cluster, O2!

If you are interested in obtaining an O2 account, please fill out the Account Request form below.

Are you looking for text describing O2, Orchestra, or Research Computing for a grant application? See our grant page or contact us if you need something different.




HPC Cluster Account


NOTE: for after hours emergency support please contact the IT service desk and let them know you have a research computing issue by calling (617) 432-2000 or e-mailing itservicedesk@hms.harvard.edu.

The O2 cluster is a shared high-performance computing environment serving a large research community with diverse research requirements and workflows, including dedicated hardware available for high-memory and GPU-intensive tasks. Tens of thousands of jobs run on the cluster every day, and we are constantly improving the job handling software and configuration to balance throughput between our many users.

Hundreds of HMS-affiliated researchers use RC's high-performance computing environment for big and small projects in next-gen sequencing analysis, molecular dynamics, mathematical modeling, image analysis, proteomics, and other areas. Click the Account Request button below to get an account for O2. For more information, please view the O2 documentation.





Support


Helping beginners and experts get research done on computers.

Computational research is an increasingly important part of any life science research project. Research computing staff help researchers get access to software and hardware resources and provide advice on how to use those resources. Ask us big or small, beginner or expert questions.

We can help you ...

  • access the O2 cluster to analyze data
  • Run RNA-Seq, ChIP-Seq, or your favorite other -Seq pipeline
  • install or use a particular bioinformatics program
  • make your programs run faster
  • filter and reformat data so that a particular program (or you) can read it
  • run MPI parallel jobs on a cluster
  • run Matlab or Mathematica interactively or in batch
  • download exon sequences for genes, with 100 bp on either side
  • run your analysis 5000+ times using a simple script

Research computing consultants with a life science background can talk with you about your project, help you decide an effective strategy for the computational part of your research, and acting as liaisons to other parts of IT to access the necessary resources. If we can't help with a particular problem, we'll try to find somebody who can.

All services are offered free of charge.





Storage


The thousands of researchers we support generate a tremendous amount of data. Some of our group resources and time go towards evaluating future storage products for cost, performance, and suitability for our researchers. There are multiple petabytes of network attached storage, in several different storage tiers available to HMS-affiliated researchers.

For data management needs, we collaborate with Research Data Management to provide consulting for groups that would like to plan out their storage requirements on a more granular level.

Due to current storage shortages, we are unable to honor storage requests from groups that do not have a primary appointment with a Harvard Medical School Quad-based pre-clinical department. We are working to develop a sustainable solution to address this issue. If you are not eligible for this storage, contact Research Computing to talk about other options.





User Training


Members of our group are also pro-active in the Quad community and teach classes every semester and summer. Courses include an introduction to using the cluster, Perl, R/Bioconductor, RNAseq, and others. Slides from classes are posted on our User Training page.




Cloud Computing


The computational resources needed by our community wax and wane with the academic year and the funding deadlines. We are looking towards the future and evaluating cloud computing as a possible solution to provide surge compute capacity during times of high need.




Downloads


We do have some code available through our Github.

There are many research applications installed on the cluster. If you don't see a program you want and are having trouble setting it up yourself, just ask us.

The following licensed desktop research applications are distributed by Research Computing; all downloads require either HMS eCommons ID or Harvard Key authentication. Please note that the HMS Affinity ID will not work.

  • ChemOffice is a suite of chemistry tools available to all Quad-based faculty, staff, and students of HMS/HSDM, and licensed for use on or off the HMS network. [installation notes]
  • FlowJo is a software package for analyzing flow cytometry data. FlowJo is only licensed to specific departments within HMS. [info]
  • Geneious is a bioinformatics software platform that is licensed for use on the Harvard Medical School network. Licenses are restricted to HMS Quad-based Staff/Faculty/PostDocs. HMS affiliates are not eligible. [installation notes]
  • GraphPad Prism combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Licenses are restricted to HMS Quad-based Staff/Faculty/PostDocs. HMS affiliates are not eligible. [download page]
  • JMP is statistical discovery software that is licensed to all members and affiliates of Harvard Medical School. [download page]
  • Lasergene is a suite of sequence analysis software by DNAStar for Windows and Mac, with analysis tools including alignments, contig assembly, gene discovery, primer design, restriction mapping, protein structure prediction, and more. Lasergene is available for use only on the HMS network. [download page]
  • Mathematica is licensed to all members and affiliates of Harvard University. Mathematica can also be run on the O2 environment in addition to the desktop versions. [download page]
  • MATLAB is available under a site license to all Quad-based faculty, staff, and students of HMS. Harvard FAS users can obtain MATLAB from FAS directly. Members of HMS affiliates, such as MGH, BIDMC, Children's Hospital, etc., should seek MATLAB licensing through their primary institution. MATLAB can also be run in the HPC environment in addition to the desktop versions. [download page]



People


Andy Bergman

Research Systems Administrator

After supporting UNIX systems and network services in the software and health care industries, I joined Harvard Medical School to focus on IT for scientific computing and helped design and implement the first shared computing cluster at HMS (Orchestra) as well as its successor (O2). I currently provide Linux server and application support and work with the HMS user community to better use our HPC, web hosting, and software licensing services.

Calvin Cox

Research Computing Support Specialist

I have 5+ years of research computing experience, and about the same amount in IT Support. I have constructed NGS pipelines using open source software while doing research at Clemson University, and at Agios Pharmaceuticals. Most of my IT support experience comes from my time at Clemson Computing and Information Technology (CCIT) and the Metropolitan Area Planning Council (MAPC). Currently, I provide support for routine issues that come into our ticket system, as well as assisting other RCCs when needed. Python is my preferred programming language, but I can hack together code in a few other languages too.

Lingsheng Dong

Senior Research Computing Consultant

I have a MD degree in Clinical Medicine, a Master's degree in Information Systems, 6+ years wet lab cancer research experience and 8+ years bioinformatics experience. For the last 5 years I have been working in the Harvard Medical School Research Computing Group to help researchers with their research computing needs.


Doug Feldmann

Senior Research Systems Architect

Doug's focus is on the web-hosting service and base infrastructure of the O2 cluster.

Bhanu Prasad Ganguru

Systems Administrator

I deal with O2 hardware and Configuration Management.

Amir Karger

Associate Director of Research Computing

I have a PhD in Computational Chemistry and over a decade of experience supporting research computing at Harvard Faculty of Arts & Sciences and Harvard Medical School. I love talking to scientists about their research and helping catalyze their way over computational barriers. "perl" is one of my favorite verbs.


Michael McClellan

DevOps Engineer

I am a member of the team that maintains and operates the O2 cluster. I also maintain the Football Players Health Study infrastructure. I have broad experience in High Performance Computing (HPC), Modeling, Simulation & Analysis (MS&A) and Data Science. I enjoy working on challenging problems and facilitating computational research.

Kathleen Keating

Research Computing Consultant

I have a Master's degree in Bioinformatics, and over 7 years experience in the realm of computational biology, 3 of which were as an analyst working on de novo genome assemblies. I enjoy helping researchers become fluent in bioinformatics analyses, enabling them to independently process their data and achieve their research goals. Perl 5 is my preferred programming language.

Jason McDonald

DevOps Team Lead

Helping users with O2 and beyond.


Raffaele Potami

Senior Research Computing Consultant

I have a Master's in Aerospace Engineering, a PhD in Mechanical Engineering and more than seven years of experience working with research computing, the last 3 at Harvard Medical School. I collaborate with the DevOps team to maintain the O2 cluster and help our users run and optimize their code. I specialize in Matlab and programs parallelization.

Alex Truong

Research Computing Consultant

I have a Master's in Bioinformatics and experience with HPC, with primary emphasis on Python-related applications. Recently I've taken up software infrastructure and deployment, and work with my colleagues and members of the community to make the O2 cluster as friendly to use as possible.





Partnerships

Research Computing works together closely with a number of other organizations in order to provide the most complete research experience possible.


Research IT Solutions (RITS)

The Research IT Solutions group works collaboratively with researchers at HMS to identify, design, and deliver a wide range of technological solutions at the ever-changing forefront of biomedical research.


Research Data Management (RDM)

The Research Data Management group supports the research community with short, medium, and long term storage requirement planning, and works with researchers and groups to implement best practices in storing, accessing, and tracking data generated by their work in a sustainable and appropriate manner.


SBGrid

The Structural Biology Grid (SBGrid) support structural biologists by providing structural biology laboratories with a tested and refined software infrastructure that includes a large library of scientific applications, as well as support for High Performance Computing and training.


SPH Bioinformatics Core

The Harvard Chan School of Public Health Bioinformatics Core provides consulting, training, tools, databases and best practices for high-throughput biological data, focusing on next-generation sequencing support. Their consulting services for HMS researchers have been subsidized for by TNT and the Harvard NeuroDiscovery Center.




About


History

By recommendation of the CIO, The Research Information Technology Group (RITG) was founded in July 2003 by the Information Technology department to support research computing on the Quad that falls beyond the scope of local system administrators or the existing HMS IT department's desktop support.

In 2011, by recommendation of the Research Computing Governing Council, RITG was expanded with the addition of a Director and Research Computing Consultants. The new organization was named the Research Computing group (RC).

Besides augmenting research IT support on the Quad, RC works with other departmental administrators to pool resources, efforts, and expertise. We aim to foster collaboration within the community of systems administrators at HMS to share knowledge and establish common best practices.




Contact


You are more than welcome to visit us at the following address at any time. However, we may not always be there so it's best to send us an e-mail/ticket to confirm first. We do have weekly office Hours on Wednesdays from 1-3pm. Stop by to chat about anything, or bring your data and questions. It's safest to schedule an appointment, so we can guarantee that someone is available to meet with you, since office hours tend to be first come, first served. Also, a ticket helps so that we can have more background information on your problem!

Gordon Hall #500
25 Shattuck Street
Boston, MA 02115
(617) 432-2000
rchelp@hms.harvard.edu
We also have a fledgling online social presence on Twitter and Github.


Contact
HMS Research Computing
Gordon Hall #500
25 Shattuck Street
Boston, MA 02115
P: (617) 432-2000
E: rchelp@hms.harvard.edu