User Training

Registrations are now managed through the Harvard Training Portal, which requires a Harvard ID (HUID). Those members of the extensive HMS community who do not currently have HUIDs - such as employees at affiliate hospitals, or collaborators from other institutions - may self-register for one as a "Person of Interest" with their faculty member's sponsorship. This form may take several days to process, please visit this page for details: https://it.hms.harvard.edu/our-services/accounts-and-user-access/person-interest-poi

Spring 2022 (Part 1) Registration is open!

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Important Notice: After registration, you should receive an confirmation email from the Harvard Training Portal with a Zoom link. If you do not have your email address on file in the Training Portal, such messages cannot be be sent to you. Please contact us for the Zoom meeting details if you did not get a confirmation email.

Optimizing O2 Jobs

Description:
In this short seminar we cover some simple but essential rules to use the O2 cluster in the most efficient (and inexpensive ) way.
Audience:
Anyone running jobs in the O2 cluster
Prerequisites:
Familiarity with the O2 cluster and the Slurm scheduler.

RCBio: easy and quick HPC pipeline builder & runner

RCBio is a HPC pipeline runner and workflow tool supported by HMS RC consultants. It was first designed for a Neubiology lab and later opened to all O2 users. RCBio helps users to quickly build and run multiple steps data analysis pipeline on a computer cluster. RCBio automatically keeps logs on all job status and use email to notify user. When re-run the same pipeline, RCBio automatically submit failed jobs and ask user if she/he want to re-run the successful jobs. Here is our wiki page about the RCBio project: RC workflows

BioGrids Academic Software Platform: No Installation Required

Academic Software Platform (ASP) integrates two major stacks of scientific software: BioGrids stack of ~400 biomedical applications (https://biogrids.org/software/) as well as SBGrid stack of ~500 structural biology applications. Multiple versions of applications are maintained, and users can also easily install the same stack of software on laptops, research workstations or cloud resources, under Linux or Mac OS X operating systems. More information about this resource is available on O2 wiki: https://harvardmed.atlassian.net/wiki/spaces/O2/pages/1630994700/Using+Software+Provided+by+BioGrids

Intro to O2

O2 for New Users addresses the needs of users who have very little linux experience, and are just getting started with HPC. More time will be devoted to covering linux basics, and the concepts of schedulers and jobs, and data management best practices. The lecture portion of this class is one hour, the second hour will be spent clinic-style with HMS RC staff to address workflow-specific questions and help convert commands to O2 SLURM syntax.

Intro to Python

Python is a popular scripting language for scientific computing and available across all computer platforms. The course will introduce you to some of the basics of the Python language as well as some of the nuances involved with its use specific to the O2 environment. The goal is to provide users with a foundational level of familiarity. Topics covered include basic data types and declaration, flow control (if/else), loops, a brief introduction to constructing a script, and a briefer introduction to modules. The course will be taught on O2, but general concepts are easily translatable to desktop and local installations.

Intro to R/Bioconductor

Intro to using R and Bioconductor. R is a powerful, open-source, highly adaptable statistical language useful for crunching numbers to datasets like those produced by next-gen sequencing. This class covers R basics and learning to think like/understand R. Users will learn how to set up personal R libraries on O2, and use O2 R for its high memory allocations and parallelization. Topics include how to install packages, learn about variables, data types. data manipulation, flow control, and functions, perform simple statistical tests, and create a variety of plots. Laptops are encouraged.

Intro to MATLAB

Matlab has become the “language of science” in the past few decades. It is simple to use, yet powerful enough to be productive on large computing infrastructures. If you need: 1) Fast prototyping of research ideas; or 2) avoid spending too much time in coding instead of doing real science by taking advantage of Matlab’s built-in functions; 3) User friendly graphical interface and educational documentation; 4) Simplicity of code; 5) Easy access to GPU computing power; 6) Easy plotting and presentation of data; you will find this introduction course useful. This course will introduce the basics of the MATLAB coding language with O2-scalability and data presentation.

Intro to Parallel Computing

This is a short introduction to Parallel Computing that will include an overview of the basic concepts of parallel programming: from running your job in an embarrassingly parallel way to writing simple shared and distributed memory parallelization codes in different languages. The seminar will cover several examples of actual parallel codes however it will not have any "hands on" components. A basic programming experience (of any language, no parallelization) is preferred in order to better follow the topics presented during the seminar.

Intermediate O2

Intermediate O2 is for current O2 users who would like to brush up on their bash skills, learn more advanced file transfer techniques, and unleash some of the powerful features of the SLURM scheduler.

Intro to Git and GitHub

This course introduces Git and GitHub and covers topics including: Getting Started with Git for version control, Using GitHub Desktop effectively, Collaborating with others on GitHub, and Utilizing GitHub Flow for better workflow. No previous exposure is assumed. We hope attendees will leave the class with the knowledge and tools necessary to start integrating Git into their workflows and excited to begin collaborating on GitHub.

Introduction to Globus Data Transfer and Data Collaboration on O2

This course is designed to showcase the Globus specific data transfer and sharing functionality that is available to anyone with o2 access. We will be going over not only how to share data with collaborators outside of HMS, but also how to receive data from outside collaborators. The class will delve into the Globus features that are available via the Globus website at first and eventually transition into the functionality provided by the globus cli.

Additional computational trainings are available through other groups:

• Training from the Harvard Chan Bioinformatics Core
  

• Training from the Harvard Longwood Medical Area Research Data Management Working Group

• Training from the SBGrid Consortium 

• Training from BioGrids

Please reach out directly to the above groups if you are interested in attending their trainings.