Harvard Medical School
Research Computing



Status


For more information on cluster or storage downtimes, see the Orchestra status page. HMS Research Computing Grid

Visit our News Page for current events.





News

Visit our News Page for Research Computing Current Happenings!

  • Research Computing will be temporarily moving offices to HIM 147 (first floor of HIM, connected to NRB) 3/6/15: We have moved back to Gordon Hall 500!
  • The HMS Data Center Move/Network Upgrade is complete! We started the Core and Campus Network upgrades planned for 2015.
  • We are teaching computing and bioinformatics classes this semester (https://wiki.med.harvard.edu/Orchestra/UserTraining). Unfortunately, all classes are full. Stay tuned for more classes.
  • Welcome to new Research Computing Consultant Jimi Chu
  • BioGrids software collection on Orchestra



Orchestra


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

The Orchestra cluster is a shared high-performance computing environment serving a large research community with diverse research requirements and workflows. 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 the Orchestra high-performance computing cluster for big and small projects in next-gen sequencing analysis, molecular dynamics, mathematical modeling, image analysis, proteomics, and other areas. Click the big button below to get an account on the Orchestra cluster. The Orchestra wiki has lots of information on using the cluster, including an Introduction to using Orchestra and a Frequently Asked Questions page..





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 Orchestra 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.

We currently have several petabytes of network attached storage, between the various file servers. Storage is available to Orchestra users on our system.





User Training


Members of our group are also pro-active in the Quad community and teach classes every semester and summer. Courses include UNIX, introduction to using Orchestra, Perl/bioPerl, 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 Orchestra. If you don't see a program you want, just ask us.

The following licensed desktop research applications are distributed by research computing; all downloads require HMS eCommons ID authentication. Please note that the HMS Affinity ID and Harvard PIN will not work for this.

  • 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. [installation notes]
  • GraphPad Prism combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. [info]
  • 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 Orchestra HPC 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 on the Orchestra HPC in addition to the desktop versions. [download page]

See the HMS Software Wiki for links to other Harvard organizations with software licensing resources.




People


Andy Bergman

Research Systems Administrator

I help support the HMS user community to better use our HPC, web hosting, and software licensing services.

Chris Botka

Director of Research Computing

I strategically visualize things. Ask me about the future of Orchestra. Suggestions welcome.

Tom Chittenden

Senior Biostatistics & Mathematical Biology Consultant

I develop mathematical and statistical models to further understanding of complex biological systems.


Ruilin (Jimi) Chu

Senior Research Computing Consultant

I specialize in parallelization and optimization of programs for cluster computing.

Lingsheng Dong

Senior Research Computing Consultant

Helping biomedical researchers with their computational needs. Any feedback is welcomed.

Doug Feldmann

Senior Research Systems Architect

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


Kris Holton

Research Computing Consultant

I make bioinformatics accessible, and interpret results back to the biology.

Amir Karger

Senior Research Computing Consultant

I love talking to scientists about their research and helping catalyze their way over the computational barriers. "perl" is one of my favorite verbs.

Byoung-Do (BD) Kim

Associate Director of Research Computing

Enabling scientific breakthroughs at scales with high performance computing.


Nam Pho

Senior Research Computing Consultant

#bigdata #science #hpc #bioinformatics

Alex Truong

Research Computing Consultant

Taming pythons for bioinformatics research.

We are hiring!

Senior DevOps Engineer - Team Lead

This could be be you. Join us as Lead DevOps Engineer in the HMS Research Computing Group. Read more and apply online: Job ID: 34454BR


We are hiring!

HPCC Storage Engineer

Help us manage tens of PBs of Research Data Storage. Read more and apply online: Job ID: 34417BR

Current Opening

DevOps Engineer

We have an exciting position open to do some automation of systems administration for HPC. Any parallel file system experience is a plus.




About


Orchestra

Orchestra is a shared high-performance computing (HPC) environment maintained by our group. It has over 5000 compute cores and several Petabytes of network attached storage. Although it was originally designed to enable computationally intensive bioinformatics research, it has evolved to support other IT solutions including web hosting. You can read more about the Orchestra hardware here.


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 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.

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, Facebook, and Github.


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

24/7/365 :)