Dear Group,
cc. Anna.
5 and 6, (amongst others) might be useful to you.
Alan
Alán Aspuru-Guzik | Assistant Professor
Harvard University | Department of Chemistry and Chemical Biology
12 Oxford Street, Room M113 | Cambridge, MA 02138
(617)-384-8188 |
http://aspuru.chem.harvard.edu
---------- Forwarded message ----------
From: FAS research computing users group <
hptc-users-list(a)lists.fas.harvard.edu>
Date: Thu, Jun 10, 2010 at 9:24 AM
Subject: [Hptc-users-list] Summer workshop series
To: FAS research computing users group <
hptc-users-list(a)lists.fas.harvard.edu>
Dear Research Computing Users,
We are very happy to announce a series of workshops over the summer. This
series is being presented jointly by the SEAS Instructional and Research
Computing, FAS Sciences Division Research Computing and departmental
affiliates. All the workshops are going to be held at the room number B09 in
the basement of Science Center. The first workshop will be on June 16th
10am. Subsequent workshops will be held every Wednesday following the 16th.
1) Basic Guide to Unix and the Command Line Interface
Date: Wednesday, Jun 16, 2010
Time: 10 AM - 12:30 PM
Location: Science Center Room B-09
Sign-up: <http://isites.harvard.edu/icb/icb.do?keyword=k60502>
Instructor: Anne Marie-Countie
<http://zenkaku.huh.harvard.edu/people/index.php?personid=167&area=Info%20te
chnology>
This workshop will introduce how to use Unix-style operating systems and
command line programs. It will cover managing files and directories, running
processes, basic shell programming, etc. Most of the material will apply to
all Unix variants, including GNU/Linux as used on the Odyssey cluster and
Mac OS X.
2) Basic Guide to the SDRC HPC Resources
Date: Wednesday, Jun 16, 2010
Time: 1 PM - 4 PM
Location: Science Center Room B-09
Sign-up: Please sign-up here
<http://isites.harvard.edu/icb/icb.do?keyword=k60502>
Instructor: John Brunelle
<http://rc.fas.harvard.edu/about/leadership/staff#john>
This workshop will introduce the tools used to interact with the Odyssey
cluster. It will cover the basic aspects of a typical workflow: connecting
to the cluster, transferring files, setting up your environment to use the
software of your choice, submitting jobs to the batch system, etc. We will
suggest best practices for getting the most out of the cluster and for
writing help tickets when difficulties arise. This assumes basic knowledge
of running programs from the command line in a GNU/Linux environment.
3) R, Matlab, Mathematica on FAS HPC Resources
Date: Wednesday, June 23, 2010
Time: 10:00 AM - 12:30 PM
Location: Science Center Room B-09
Sign-up: <http://isites.harvard.edu/icb/icb.do?keyword=k60504>
Instructor: Steve Finch
Topics include programming, functions, graphs, symbolics & numerics, data
analysis and simulations. No background in scientific or statistical
computing is assumed. R, Matlab & Mathematica will each be thoroughly
introduced on lab PCs; batch jobs on the Odyssey cluster will be
demonstrated briefly as well.
4) Debugging and Profiling
Date: Wednesday, July 7, 2010
Time: 10 AM - 12:30 PM
Location: Science Center Room B-09
Sign-up: Please email ircshelp(a)seas.harvard.edu
Instructor: Seppo Sahrakorpi
<http://ircs.seas.harvard.edu/USERDOCS/IRCS+Bios>
In this workshop we will focus on debugging serial and parallel programs
using TotalView parallel debugger. The topics will cover e.g. preparation of
your code for debugging, executing your code under the debugger's control,
variable queries, data visualization, MPI message debugging, heap memory
management, and data manipulation. In the second part we will focus on
profiling the execution time of a sample code using Sun Studio Profiler. For
more information, and workshop slides, please see here:
<http://ircs.seas.harvard.edu/USERDOCS/IRCS+Workshops>
5) Introduction to SQL databases and Structured Query Language (SQL)
Date: Wednesday, Jul 7, 2010
Time: 1 PM - 4 PM
Location: Science Center Room B-09
Sign-up: Please email rchelp(a)fas.harvard.edu
Instructor: Brendan Haley
<http://rc.fas.harvard.edu/about/leadership/staff#brendan>
This workshop will introduce attendees to SQL databases, and basic database
design and normalization, as well as provide an introduction to Structured
Query Language, with a focus on data retrieval, analysis and reporting. This
workshop will be relevant to relational database systems such as Oracle,
MySQL and PostGRES. Desktop database applications such as Filemaker and
Microsoft Access will NOT be covered. It is assumed that participants have
no previous database experience.
6) Introduction to Scientific Computing with Python
Date: Wednesday, July 14, 2010
Time: 1 - 3:30 PM
Location: Science Center Room B-09
Sign-up: <http://isites.harvard.edu/icb/icb.do?keyword=k70678>
Instructors: John Brunelle
<http://rc.fas.harvard.edu/about/leadership/staff#john> , Raman Prasad
<http://rc.fas.harvard.edu/about/leadership/staff#raman>
SciPy, NumPy, and matplotlib are popular tools for doing scientific
computing in Python. This workshop will introduce these tools, plus other
uses of Python in a high performance cluster environment, such as shared
memory parallelism with the multiprocessing module and distributed memory
parallelism with MPI (mpi4py). Attendees should have a basic knowledge of
computer programming and the Python language.
7) Introduction to Perl and Bioperl
Wednesday, July 21, 10 am to 4 pm
Science Center Room B-09
Signup: Please email rchelp(a)fas.harvard.edu
Instructor: Amir Karger <http://rc.fas.harvard.edu/about/leadership/staff>
This workshop gives an overview of Perl, with a quick introduction to
Bioperl. Participants will learn to read and modify Perl scripts, as well as
write small scripts of their own. Special focus is given to reading,
filtering, and reformatting scientific data. Because the workshop lasts only
one day, we do not have time to introduce the basic concepts of programming,
such as loops, conditions, and variables. Anyone who has programmed even a
small amount in any programming language should be comfortable, but others
are encouraged to take a more extensive class.
8) Next Generation Sequencing and Microarray analysis
Date: Wednesday, July 28, 2010
Time: 10-12:30PM, 1PM- 4 PM
Location: Science Center Room B-09
Sign-up: <https://isites.harvard.edu/icb/icb.do?keyword=k60505>
Instructor: Jiangwen Zhang
<http://rc.fas.harvard.edu/about/leadership/staff#jiangwen>
This workshop will introduce various applications useful in analyzing high
throughput sequence datasets from Next Generation Sequencing (NGS). Learn
what to know before starting NGS project, and how to efficiently and
correctly process large datasets from high throughput sequencing like Solexa
in a statistical framework.This workshop will also introduce general
programming skills for the statistical programming language R, and
application of Bioconductor packages in microarray computation. Computation
workflow for microarray study, such as Affymetrix, Agilent, and custom
array, will also be covered as well as related statistical considerations.
We look forward to your participation in these workshops.
Please do not hesitate to contact rchelp(a)fas.harvard.edu with questions
about this or other research computing matters.
Thank you.
Sciences Division Research Computing
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