Fall 2018 Tutorial Series

September 6, 2018 – October 5, 2018

The Research Computing Services (RCS) group, part of Boston University Information Services & Technology, will offer a series of tutorials on programming, high performance computing, and scientific visualization. These tutorials are free and open to all members of the Boston University community.

Please note that the RCS offices and IS&T training space are now located at 2 Cummington Mall. All Charles River Campus tutorials will be held in room 107, the IS&T Training Room. The BUMC tutorials will continue to be held at 72 E. Concord St., room L1110.

There is one brand new tutorial this Fall in addition to our usual offerings,. The new tutorial is part of our series of tutorials on R and is called Data Wrangling in R.

The RCS tutorials cover concepts, techniques, and tools which researchers can use in their own computing environments. Many are designed to help you make effective use of the Boston University Shared Computing Cluster. The RCS staff can also deliver extra, or customized, tutorial sessions to your group or lab. Please contact us at rcs@bu.edu if you are interested.

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Charles River Campus Tutorials


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BU Medical Campus (BUMC) Tutorials

You may register for as many tutorials as you like. Registration is required and is accessed with your BU Kerberos password.

If you don’t have a Kerberos password, or if you find that a tutorial is full, or have any other questions, please send email to rcs-tutorial@bu.edu.

Tutorial Locations and Directions

Charles River Campus (CRC)

All CRC sessions will be held in the IS&T Training Room 107 at 2 Cummington Mall.

BU Medical Campus (BUMC)

The BUMC sessions will be held in the “L” building at 72 E Concord St using room number L1110. The “L” building is the BUMC main instructional building and the 11th floor is accessible by elevator. The tutorial room is at the end of the hall on the left.


Tutorial Descriptions and Times

Research Computing Basics Tutorials

Introduction to Linux (Hands‐on)

Instructor: Augustine Abaris (augustin@bu.edu)

Thursday, September 6, 10:00am – 12:00pm
Friday, September 7, 12:15pm – 2:15pm
Monday, September 10, 10:00am – 12:00pm, BUMC L1110

This tutorial will give attendees a hands-on introduction to Linux. Topics covered will include a short history of Linux, logging in with ssh, the Bash shell and shell scripts, I/O redirection (pipes), file system navigation, and job control. Time permitting, attendees will edit, compile, and run a simple C program.

Introduction to BU’s Shared Computing Cluster (Hands‐on)

Instructor: Aaron Fuegi (aarondf@bu.edu)

Thursday, September 6, 12:15pm – 2:15pm
Friday, September 7, 10:00am – 12:00pm
Monday, September 10, 2:00pm – 4:00pm, BUMC L1110

This tutorial will introduce Boston University’s Shared Computing Cluster (SCC) in Holyoke, MA. This Linux cluster has more than 16,000 processors and over 4.2 petabytes of storage available for Research Computing by students and faculty on the Charles River and BUMC campuses. A very large number of software packages for programming, mathematics, data analysis, plotting, statistics, visualization, and domain-specific disciplines are available as well on the SCC. You will get a general overview of the SCC and the facility that houses it and then a hands-on introduction covering connecting to and using the SCC for new users. This tutorial will cover a few basic Linux commands but we strongly encourage people to also take our more extensive “Introduction to Linux” tutorial.

There will also be ample time for questions of all types about the SCC. Those who wish can bring their own laptops and we will help you with installing the software you need to effectively connect to and use the SCC. Others will use the Windows machines in the room.

Intermediate Usage of the SCC

Instructor: Katia Oleinik (koleinik@bu.edu)

Tuesday, September 11, 10:00am – 12:00pm
Friday, September 14, 10:00am – 12:00pm, BUMC L1110

This tutorial will provide some more advanced techniques and common strategies used for interacting with the Shared Computing Cluster and its resources.

The topics discussed during the tutorial include:

  • Customizing your environment
  • Parallel computing on the SCC
  • Jobs monitoring (CPU and memory usage)
  • Profiling programs for performance optimization
  • General optimization strategies

Recommended prerequisite: some prior experience with high performance computing or attendance of our “Introduction to BU’s Shared Computing Cluster” tutorial.

Managing Projects on the SCC for LPIs

Instructor: Charlie Jahnke (cjahnke@bu.edu)

Friday, September 21, 2:00pm – 4:00pm, BUMC L1110
Tuesday, September 25, 2:30pm – 4:30pm

Intended for Lead Project Investigators (LPI) and Administrative Contacts, this tutorial covers a high level overview and best practices for managing projects on the Shared Computing Cluster (SCC). Topics include compute resources, project creation, project management, storage/SU allocation management, and the Buy-In Program.

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Computer Programming Tutorials

Introduction to Python, Part One (Hands‐on)

Instructor: Brian Gregor (bgregor@bu.edu)

Monday, September 10, 12:15pm – 2:15pm
Thursday, September 13, 2:00pm – 4:00pm, BUMC L11110
Tuesday, September 18, 10:00am – 12:00pm

Recommended but not required: some programming experience. For example, you should understand concepts like loops and functions.

This is an introduction to the essential features of Python. This first part of the tutorial includes an introduction to basic types, if-statements, functions, lists, dictionaries, loops, and modules. The tutorial includes the use of a popular Python development environment and covers setting up Python on your own computer in addition to using Python on the SCC. This is a two-part tutorial so please remember to sign up for both parts.

Introduction to Python, Part Two (Hands‐on)

Instructor: Brian Gregor (bgregor@bu.edu)

Wednesday, September 12, 12:15pm – 2:15pm
Friday, September 14, 2:00pm – 4:00pm, BUMC L11110
Thursday, September 20, 10:00am – 12:00pm

This tutorial is a continuation of Introduction to Python, Part One and introduces more features of the language, common libraries such as numpy and matplotlib, and the basics of debugging Python programs. Please make sure you sign up for part one as well.

Perl with Pipeline Example, Part One (Hands-on)

Instructor: Yun Shen (yshen16@bu.edu)

Tuesday, September 18, 2:00pm – 4:00pm, BUMC L1110

This tutorial will give you an introduction to the Perl language through code snips and examples. In order to help put Perl in a more relevant context, we will share a real life research pipeline for cancer research, which demonstrates Perl’s many powerful features. The pipeline is able to support the bioinformatical data management of the entire life cycle of research, including data acquisition and consolidation, NGS sequence alignment and data analysis, as well as the result bookkeeping, etc.

You do not need to have any prior Perl or other programming language experience to take this tutorial. All levels are welcome.

This first part of the tutorial will start by sharing the basics of a pipeline example to showcase what Perl can do. Then we will go back to fundamentals to go over all the main features of Perl with several sets of hands-on examples. We will cover topics such as the Perl runtime environment, Perl data types and structures, file I/O, regular expressions (pattern matching), as well as some advanced features, such as subroutines, packages and modules, the POD system, and the Perl debugger.

Perl with Pipeline Example, Part Two (Hands-on)

Instructor: Yun Shen (yshen16@bu.edu)

Wednesday, September 19, 2:00pm – 4:00pm, BUMC L1110

This tutorial is a continuation of Perl with Pipeline Example, Part One and will continue introducing Perl’s more advanced features. Please make sure to sign up for Part One as well. We will come back to the pipeline example introduced at the beginning of Part One, take a detailed look at its design and code implementation, and give a code walk-through. During the tutorial, I will also share some of my experiences regarding the pipeline design and implementation techniques.

Version Control and Collaboration with Git and GitHub, Part One (Hands-on)

Instructor: Shuai Wei (shwei@bu.edu)

Tuesday, September 18, 2:30pm – 4:30pm
Thursday, February 15, 3:30pm – 5:30pm, BUMC L1110

Whether you are writing source code or a manuscript, keeping track of changes is a critical part of a successful project. Version control software, like Git, automates the process of backing up and annotating previous versions of your evolving projects. In conjunction with online hosting services like GitHub, it also greatly simplifies the logistical difficulties of working in parallel with collaborators. This “hands-on” tutorial will cover basic usage of the popular version control software Git and the online hosting service GitHub. This is a two-part tutorial so make sure to also sign up for Version Control and Collaboration with Git and GitHub, Part Two.

Basic knowledge of the Linux command line is assumed.

Version Control and Collaboration with Git and GitHub, Part Two (Hands-on)

Instructor: Shuai Wei (shwei@bu.edu)

Thursday, September 20, 2:30pm – 4:30pm
Thursday, February 15, 3:30pm – 5:30pm, BUMC L1110

This tutorial is a continuation of Version Control and Collaboration with Git and GitHub, Part One. We strongly recommend that if you are interested in this tutorial, you also register for Part One.

In this session, we will work on a practical example showing a typical workflow with multiple developers collaborating on a large project. We will use Gitk to visualize diverging and merging branches between versions.

Building Software from Source Code on Linux (Hands‐on)

Instructor: Shaohao Chen (shaohao@bu.edu)

Monday, September 24, 10:00am – 12:00pm

Compiling a working executable from C or Fortran source code can be a frustrating experience for new programmers. This “hands-on” tutorial will introduce the basic steps for compiling small- to medium-sized projects. Topics include working with multiple source files, header files, and external libraries, and automation using Make and Autotools (configure). For simplicity, we will only cover the build process for systems with a Linux operating system (such as the BU Shared Computing Cluster).

Familiarity with the Linux command line is assumed. Familiarity with C or Fortran will be helpful, but is not required.

Introduction to Perl, Part One

Instructor: Tim Kohl (tkohl@bu.edu)

Monday, September 24, 12:15pm – 2:15pm

Perl is a powerful and versatile programming language that can be used for a wide variety of programming tasks, including, but not limited to, text/data processing, system administration, and Web applications. Combing elements of C, Unix shell scripting languages, as well as text-processing utilities such as sed and awk, Perl can be used for both large scale projects and for small applications. Some experience in a command line environment (e.g. Unix) is helpful, but the basics of Perl are simpler than those of other languages making it accessible to a new programmer. Attending our Introduction to Linux tutorial or equivalent background is recommended. Please remember to sign up for all four sessions to complete the tutorial.

Introduction to Perl, Part Two

Instructor: Tim Kohl (tkohl@bu.edu)

Wednesday, September 26, 12:15pm – 2:15pm

This tutorial is a continuation of Introduction to Perl, Part One. We strongly recommend that if you are interested in this tutorial, you register for Parts One, Three, and Four as well.

Introduction to Perl, Part Three

Instructor: Tim Kohl (tkohl@bu.edu)

Friday, September 28, 12:15pm – 2:15pm

This tutorial is a continuation of Introduction to Perl, Part Two. We strongly recommend that if you are interested in this tutorial, you register for Parts One, Two, and Four as well.

Introduction to Perl, Part Four

Instructor: Tim Kohl (tkohl@bu.edu)

Monday, October 1, 12:15pm – 2:15pm

This tutorial is a continuation of Introduction to Perl, Part Three. We strongly recommend that if you are interested in this tutorial, you register for Parts One, Two, and Three as well.

Introduction to C Programming, Part One (Hands‐on)

Instructor: Brian Gregor (bgregor@bu.edu)

Tuesday, September 25 12:15pm – 2:15pm

This tutorial is primarily aimed at those who have some experience programming in another language, such as MATLAB, and want to learn to read, write, and modify C codes in a Unix environment. Although previous programming experience would be helpful, it is not mandatory. In this tutorial we will cover basic syntax, and write, compile, and run some simple codes. Please remember to sign up for both parts of this tutorial.

Introduction to C Programming, Part Two (Hands‐on)

Instructor: Brian Gregor (bgregor@bu.edu)

Thursday, September 27, 12:15pm – 2:15pm

This tutorial is a continuation of Introduction to C Programming, Part One (Hands‐on) described above. We strongly recommend that if you are interested in this tutorial, you also register for Part One.

Introduction to C++ Programming, Part One (Hands‐on)

Instructor: Brian Gregor (bgregor@bu.edu)

Friday, September 28, 10:00am – 12:00pm

This tutorial is aimed at those who want to learn to read, write, and modify C++ code. Previous programming experience in languages such as C, MATLAB, or Python is strongly recommended but it is not mandatory. In this tutorial series we will cover basic C++ syntax, object-oriented programming concepts including classes and inheritance, and parts of the C++ standard library. This is a hands-on tutorial and we will write, compile, and run some simple codes using the NetBeans integrated development environment. Please remember to sign up for all four sessions to complete the tutorial.

Introduction to C++ Programming, Part Two (Hands‐on)

Instructor: Brian Gregor (bgregor@bu.edu)

Monday, October 1, 10:00am – 12:00pm

This tutorial is a continuation of Introduction to C++ Programming, Part One. We strongly recommend that if you are interested in this tutorial, you also register for Parts One, Three, and Four.

Introduction to C++ Programming, Part Three (Hands‐on)

Instructor: Brian Gregor (bgregor@bu.edu)

Wednesday, October 3, 10:00am – 12:00pm

This tutorial is a continuation of Introduction to C++ Programming, Part Two. We strongly recommend that if you are interested in this tutorial, you also register for Parts One, Two, and Four.

Introduction to C++ Programming, Part Four (Hands‐on)

Instructor: Brian Gregor (bgregor@bu.edu)

Friday, October 5, 10:00am – 12:00pm

This tutorial is a continuation of Introduction to C++ Programming, Part Three. We strongly recommend that if you are interested in this tutorial, you also register for Parts One, Two, and Three.

Register

Data Analysis Tutorials

Introduction to SAS (Hands‐on)

Instructor: Jack Chan (jack@bu.edu)

Friday, September 7, 2:30pm – 3:30pm

SAS (Statistical Analysis System) is one of the most powerful statistical packages available on any computer platform. This tutorial will introduce you to SAS on the desktop.

After completing this tutorial, you will be able to:
  • access SAS on Windows
  • create, edit, and save program files containing SAS commands
  • obtain printed output
  • create, run, and modify your own programs

Introduction to SPSS (Hands‐on)

Instructor: Jack Chan (jack@bu.edu)

Friday, September 7, 3:30pm – 4:30pm

SPSS (Statistical Package for the Social Sciences) is a widely used program for analyzing data. SPSS uses windows and dialog boxes to manipulate data and perform statistical analyses. This hands-on tutorial will introduce you to the basics of SPSS and will give you one hours’ practice using SPSS on Microsoft Windows.

After completing this tutorial, you will be able to:
  • enter data into SPSS
  • use SPSS to transform data
  • use SPSS to perform basic statistical analyses

Introduction to R (Hands‐on)

Instructor: Katia Oleinik (koleinik@bu.edu)

Monday, September 10, 2:30pm – 4:30pm
Monday, September 17, 12:15pm – 2:15pm
Tuesday, September 25, 2:00pm – 4:00pm, BUMC L1110

R is the most powerful, rapidly developing, highly reliable, open source statistical language. It is widely used among statisticians for the development of statistical software and for data analysis. New features appear every few months.

This tutorial introduces the R environment for statistical computing and will cover the following topics:
  • operators and arithmetic operations
  • atomic types, variable rules and built-in constants
  • scalar and vector function overview
  • working with data (workspace setup as well as reading, creating, exploring, and saving data)
  • working with R data types (vectors, matrices, lists, data frames)
  • working with script files
  • installing and loading R extension packages and getting help
  • overview of functions for data analysis
After completing this tutorial you will:
  • know the basics of the R environment.
  • get a solid understanding of various data types and objects used in R.
  • be able to create, load and analyze data.
  • find appropriate functions and get necessary help and examples for these functions.

Data Wrangling in R (Hands‐on)

Instructor: Katia Oleinik (koleinik@bu.edu)

Tuesday, September 11, 2:30pm – 4:30pm
Tuesday, September 18, 12:15pm – 2:15pm
Thursday, September 27, 2:00pm – 4:00pm, BUMC L1110

“Tidy data” is a term that describes a standardized approach to structuring datasets to make statistical analyses and visualizations easier. In this tutorial you will learn how to modify, filter, arrange, and summarize your data with dplyr and other tidyverse packages. We will go over operations like merging two or more datasets, reshaping your data into the layout that works the best, and summarizing the data to explore hidden levels of information.

Recommended prerequisite: If you are new to the R environment we strongly recommend that you also register for the “Introduction to R” tutorial.

Graphics in R (Hands‐on)

Instructor: Katia Oleinik (koleinik@bu.edu)

Wednesday, September 12, 2:30pm – 4:30pm
Wednesday, September 19, 12:15pm – 2:15pm
Tuesday, October 2, 2:00pm – 4:00pm, BUMC L1110

R provides extensive and powerful graphics options that allow for the production of publication-ready, high quality diagrams, and plots. This tutorial introduces R graphics libraries and functions.

After completing this tutorial you will:
  • understand what to expect from R’s graphics capabilities.
  • be able to create, modify, and customize graphs and plots used in statistical analysis.
  • find appropriate libraries, download, and use them for your visualization needs.

Prerequisite: If you are new to the R environment we strongly recommend that you also register for the “Introduction to R” tutorial.

Programming in R (Hands‐on)

Instructor: Katia Oleinik (koleinik@bu.edu)

Thursday, September 13, 2:30pm – 4:30pm
Thursday, September 20, 12:15pm – 2:15pm
Thursday, October 4, 2:00pm – 4:00pm, BUMC L1110

This tutorial is the third in a series of R tutorials. It introduces basic R programming, debugging and optimization techniques and develops practices of proper and efficient R coding. It covers the following topics:

  • if-else and switch statements
  • types of loops (for, while, repeat) and loop control statements (next, break)
  • user functions and argument definitions
  • local and global variables
  • apply function family
  • sourcing, timing, compilation and debugging
  • code profiling and optimization

Prerequisite: We strongly recommend that you also register for the “Introduction to R” tutorial if you are new to the R environment.

R Code Optimization

Instructor: Katia Oleinik (koleinik@bu.edu)

Friday, September 21, 12:15pm – 2:15pm
Friday, October 5, 2:00pm – 4:00pm, BUMC L1110

This tutorial is primarily aimed at those who have some experience working in a Linux environment and programming in R. The topics covered in this tutorial:

  • debugging and profiling R code
  • choosing the right functions to speed-up your code
  • parallelization techniques
  • tuning your code for faster performance on the SCC cluster

Introduction to MATLAB (Hands‐on)

Instructor: Shaohao Chen (shaohao@bu.edu)

Tuesday, September 11, 12:15pm – 2:15pm

MATLAB (MATrix LABoratory) is a numerical computing environment developed by MathWorks, Inc. In short, MATLAB is a highly optimized interpreted programming language designed for intuitive and fast development of scientific computing software. This “hands-on” tutorial will introduce the MATLAB programming environment and the basic tools you will need to write your own MATLAB programs. Topics include matrix variables and operations, reading/writing data, plotting, loops, conditional statements, scripts, and functions.

No prior programming experience in any language is required to attend this course.

Python for Data Analysis (Hands‐on)

Instructor: Shuai Wei (shwei@bu.edu)

Friday, September 14, 12:15pm – 2:15pm
Monday, September 17, 10:00am – 12:00pm, BUMC L1110
Friday, September 21, 10:00am – 12:00pm

This tutorial will introduce the basics of Data Analysis with Python and its powerful libraries such as Pandas and Matplotlib.

What you will learn:
  • Importing and Exporting the data
  • Basic data processing, cleaning, and manipulation
  • Basic inferential statistical analysis
  • Data Visualization techniques

Prerequisite: basic familiarity with the Python environment or our Introduction to Python tutorial.

Register

High Performance Computing Tutorials

Introduction to High-Performance Computing

Instructor: Shaohao Chen (shaohao@bu.edu)

Thursday, September 6, 2:30pm – 3:30pm

High-performance computing (HPC) or supercomputing (SC) refers to the practice of aggregating computing power in order to solve large problems in science, engineering, or business. In this tutorial, the following questions will be discussed: Why a computer cluster is necessary? What is the basic structure of a computer cluster? What resources does an HPC system provide? How to measure computer performance? What are the most powerful computers in the world? What scientific disciplines benefit from HPC? What is parallel computing? In particular, the nation-wide HPC resource XSEDE (eXtreme Science and Engineering Discovery Environment) will be introduced. This tutorial will also guide you to other RCS tutorials being offered this semester that might be helpful to your particular study or research work.

Note that this tutorial has no hands-on exercises

MATLAB for High-Performance Computing (Hands-on)

Instructor: Shaohao Chen (shaohao@bu.edu)

Thursday, September 13, 10:00am – 12:00pm

MATLAB programs can be exceptionally fast if they are well-designed, and painfully slow if not. Fortunately, it does not take a professional programmer to write an efficient MATLAB program or to take advantage of multi-core processors and computer clusters. This tutorial will introduce (1) using MATLAB on the BU SCC, and (2) optimizing MATLAB codes. The first part will cover how to use the MATLAB platform remotely and how submitting batch jobs for MATLAB works. In the second part, some useful skills for removing unnecessary computation and optimizing memory usage will be introduced. The skills you learn should enable you to solve bigger problems faster using MATLAB.

MATLAB Parallel Computing Toolbox (Hands‐on)

Instructor: Shaohao Chen (shaohao@bu.edu)

Friday, September 14, 2:30pm – 4:30pm

The MATLAB Parallel Computing Toolbox allows you to write programs that leverage multi-core processors, GPUs, and computer clusters by dividing up work between independent cores. Converting serial MATLAB applications to parallel MATLAB applications usually requires few code modifications and no programming in a low-level language. This tutorial will introduce MATLAB parallel processing tools, such as parfor, spmd, and distributed array types. The skills you learn should enable you to solve bigger problems faster using MATLAB.

Basic knowledge of MATLAB is assumed.

Introduction to MPI, Part One (Hands-on)

Instructor: Shaohao Chen (shaohao@bu.edu)

Monday, September 17, 2:30pm – 4:30pm

On contemporary computers, speeding up computations is most often achieved by employing multiprocessors concurrently on shared.memory multi.cored nodes or multiprocessor distributed.memory clusters. MPI is a library of communication functions to enable and enhance multiprocessing on these computer architectures. This tutorial introduces many of the basic MPI functions through practical examples. Working knowledge of C or Fortran is required to attend the course. Basic knowledge of Unix/Linux will be helpful.

Introduction to MPI, Part Two (Hands-on)

Instructor: Shaohao Chen (shaohao@bu.edu)

Wednesday, September 19, 2:30pm – 4:30pm

This tutorial is a continuation of Introduction to MPI, Part One. We recommend that, if you are interested in this tutorial, you also register for Part One.

Introduction to GPU Programming

Instructor: Brian Gregor (bgregor@bu.edu)

Monday, September 24, 2:30pm – 4:30pm

Originally designed to render computer graphics, GPUs now provide the ability to accelerate scientific applications traditionally handled by CPUs. This tutorial is an introduction to general programming using GPUs. We will explore the applications that would benefit the most from GPU acceleration, go over different languages and software tools available on our Linux cluster, and discuss their benefits for different types of applications.

Introduction to CUDA (Hands-on)

Instructor: Brian Gregor (bgregor@bu.edu)

Wednesday, September 26, 2:30pm – 4:30pm

This tutorial will show you how to do calculations with CUDA C/C++, an API for programming massively parallel GPUs.
In this tutorial you will learn to do the following tasks in CUDA:

  • Write a basic “Hello, World!” program
  • Write and launch CUDA C kernels
  • Manage GPU memory
  • Run parallel kernels in CUDA C
  • Parallel communication and synchronization
  • Race conditions and atomic operations

C/C++ programming experience is required for this tutorial. You do not need prior parallel programming or graphics experience.

Introduction to OpenMP

Instructor: Shaohao Chen (shaohao@bu.edu)

Thursday, September 27, 2:30pm – 4:30pm

The OpenMP application program interface (API) provides simple and flexible tools to develop parallel software for shared-memory multiprocessor systems. The basic approach to parallelizing with OpenMP is to insert special comments (directives) into the code that assist the compiler in mapping computation onto the CPUs. The beauty of this approach is that it is often possible to create efficient parallel code with only minor modifications to a serial code. This tutorial covers the major features of OpenMP through discussion and examples in C and Fotran.

Some experience in C or Fortran programming is assumed. Understanding of parallel programming in general is helpful, but not required.

Register

Visualization Tutorials

Introduction to ImageJ (Hands‐on)

Instructor: Brian Gregor (bgregor@bu.edu)

Thursday, September 20, 2:00pm – 4:00pm, BUMC L1110
Friday, September 21, 2:30pm – 4:30pm

ImageJ is a popular open source tool for image analysis and processing. In this tutorial we will cover the use of ImageJ for basic image manipulation, writing ImageJ macros, and quantitative measurements of a fluorescent image. The details of different image file formats and using ImageJ in preparing and formatting images for publication will also be covered.

Neuroimaging on the SCC (Hands‐on)

Instructor: Dustin Clark (clarkdc@bu.edu)

Tuesday, September 25, 10:00am – 12:00pm
Wednesday, September 26, 2:00pm – 4:00pm, BUMC L1110

This tutorial will introduce Boston University’s Shared Computing Cluster (SCC) for use with Magnetic Resonance (MR) neuroimaging methods. It will address basic concepts in MR neuroimaging and give investigators the background required to start or optimize their research. We will work hands-on with the SCC to highlight the wide variety of neuroimaging tools available on the SCC and how to effectively utilize them for high-performance computing. Software covered includes FreeSurfer, FSL, AFNI, MRIcron, Nipype, MATLAB, SPM, and CONN. Topics covered include loading data onto the SCC, project management (directory structure/permissions), unpacking DICOMs, batch processing, and interactive environments (VNC & VirtualGL/OpenGL). It is recommended that you attend the “Introduction to BU’s SCC” tutorial if you are not a regular user of the SCC.

Introduction to FreeSurfer (Hands‐on)

Instructor: Dustin Clark (clarkdc@bu.edu)

Thursday, September 27, 10:00am – 12:00pm
Friday, September 28, 2:00pm – 4:00pm, BUMC L1110

This tutorial is a guided walkthrough of FreeSurfer’s Workshop on Boston University’s Shared Computing Cluster (SCC). FreeSurfer is a neuroimaging tool that reconstructs a 2D surface representation of the cortex, as opposed to the traditional 3D voxel representation in other neuroimaging software suites. It is recommended that you attend either the “Neuroimaging on the SCC” or “Introduction to BU’s SCC” tutorial if you are not a regular user of the SCC. Topics will include recon-all, brain editing, structural analysis, and functional resting state analysis.

Register