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Latest News

New On-Site and On-Line Courses at Bioinformatics.Org
Posted by Ken Farmer, Saturday December 09 2006 @ 05:07PM EST

Bioinformatics.Org will be running an on-line version of the well-received, "Introduction to Bioinformatics Programming: Perl & R for Biologists, Level 1" (Open Source Bioinformatics for Researchers), and we're also pleased to introduce an advanced and extended version of the course. Please see the course descriptions below.

ON-LINE COURSE: Introduction to Bioinformatics Programming: Perl & R for Biologists, Level 1

Note that this is not a static tutorial but live instruction using interactive "webinar" software and voice conferencing that will closely replicate the on-site version of the course.

LOCALE: On-line (instructions will be given)

DATES: January 8-12, 2007


This is an on-line course on the fundamentals of open-source programming. It will help biologists understand how and when to use standard programming methods to solve computational biology problems, whether sequence analysis, gene expression, mass spectrometry, or systems biology.


The first part of the course will cover the basics of Perl, including installing and running simple Perl scripts; variables (scalars, arrays); variable interpolation; printing; string operations; mathematical, conditional and logical operators; file input/output; loops (if-then-else, for, while); list operations; regular expressions; and functions. BioPerl will also be introduced. Afterward, students will be assigned a Perl project.

The second part of the course will cover the basics of R, including installing and running R; understanding the R interactive environment; creating, storing and manipulating R data objects; reading data from files; applying built-in functions on data; for-loops; if-then-else statements; scripts; functions; and packages. Bioconductor will also be introduced. Afterward, students will be assigned an R project.


The course will run during the week of January 8 with about 3 hours of instruction starting at 16:30 UTC each day.


To find out more information on the course, including the registration process, please see the course schedule page: http://edu.bioinformatics.org/AB

ON-SITE COURSE: Advanced Bioinformatics Programming: Perl & R for Biologists, Level 2

LOCALE: Cambridge, Massachusetts
DATES: January 16-19, 2007


This a *30+ hour* intensive course that will help biologists learn how to use Perl as a scripting language to automate certain tasks in their research, and how to use R as a statistical scripting language for data analysis. It includes an introduction to Perl and R, so it may be taken instead of "Introduction to Bioinformatics Programming: Perl and R for Biologists, Level 1," or as a refresher course on the basics. The course also covers advanced topics and projects, all in the context of biological research.


Students will learn how to write Perl and R scripts using various data structures, loops and file I/O constructs. They will also learn scripting with the Perl DBI and how to write multi-function scripts and convert them into Perl modules and packages. Examples will include high-throughput BLAST output, BioPerl, MySQL database packages for Perl, Bioconductor packages for R, and Affymetrix CEL files.


This course will run January 16-19 and will be divided into 8 sessions of approximately 3.5 hours each. Instruction and exercises will begin at 8:30 AM and end at 5:00 PM.


To find out more information on the course, including the registration process, please see the course schedule page: http://edu.bioinformatics.org/AC

< Lightweight Linux for High-Performance Computing | Researchers Map the Route of DNA Unfolding Sequence >




Cluster Monkey

Golden Eggs
(HP Visual Diagram and Config Guides)
CP4000 32x DL145G2 GigE Opteron, Dual Core
CP4000 64x DL145 GigE Opteron
CP4000 102x DL145 GigE Opteron
CP4000 32x DL145 Myri Opteron
Rocks Cluster 16-22 DL145 Opteron
Rocks Cluster 30-46 DL145 Opteron
Rocks Cluster 64-84 DL145 Opteron
LC3000 GigaE 24-36 DL145 Opteron
LC3000 Myri 16-32x DL145 Opteron
LC3000 GigaE 16-22x DL145 Opteron
LC2000 GigaE 16-22x DL360G3 Xeon
DL365 System 2600Mhz 2P 1U Opteron Dual Core
DL360 G5 System 3000Mhz 2P 1U EM64T Dual/Quad Core
DL385 G2 2600Mhz 2P Opteron Dual Core
DL380 G5 3000Mhz 2P EM64T Dual/Quad Core
DL140 3060MHz 2P IA32
DL140 G2 3600MHz 2P EM64T
DL145 2600MHz 2P Opteron
DL145 G2 2600MHz 2P Opteron Dual Core
DL360 G4 3400MHz 2P EM64T
DL360 G4p 3800MHz 2P EM64T
DL380 G4 3800MHz 2P EM64T
DL385 2800MHz 2P Opteron Dual Core
DL560 3000MHz 4P IA32
DL580 G3 3330MHz 4P EM64T
DL585 2800MHz 4P Opteron Dual Core
Montecito 2P-16P, rx2660-rx8640 (multi-system diagram)
rx2660 1600MHz 2P 2U Montecito Systems and Cluster
rx6600 1600MHz 4P 7U Single & Cluster
rx3600 1600MHz 2P 4U Single & Cluster
rx2620 1600MHz 2P 2U Single & Cluster
Superdome 64P base configuration
Integrity Family Portrait (rx1620 thru rx8620), IA64
rx1620 1600MHz 2P MSA1000 Cluster IA64
rx2620 1600MHz 2P MSA1000 Cluster IA64
rx4640 1600MHz 4P MSA1000 Cluster IA64
rx7620 1600MHz 8P 10U Systems and MSA1000 Cluster
rx8620 1600MHz 16P 17U Systems and MSA1000 Cluster
MSA30-MI Dual SCSI Cluster, rx3600, rx6600 and rx2660
MSA30-MI Dual SCSI Cluster, rx1620...rx4640
MSA1500 48TB, SCSI and SATA
Dual Core AMD64 and EM64T systems with MSA1500

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