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.
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.
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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 email@example.com.
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.
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 ...
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.
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.
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.
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.
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.
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.
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.
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's focus is on the web-hosting service and base infrastructure of the O2 cluster.
I deal with O2 hardware and Configuration Management.
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.
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.
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.
Helping users with O2 and beyond.
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.
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.
Research Computing works together closely with a number of other organizations in order to provide the most complete research experience possible.
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.
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.
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.
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.
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.
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