PICASso Tutorials & Mini-Courses

Fall 2006 - Spring 2007

All PICASso tutorials and mini-courses are practice-oriented, so participants get hands-on experience

  Spring 2007

Scientific and Technical Writing Workshops” (May 7, 8, 9, and 10, 2007)

These 4 PICASso mini-courses will be led by Dr. Judith Swan, Assistant Director for Scientific and Technical Writing for the Princeton Writing Program who leads similar workshops at scientific institutions both nationally and internationally.

All classes will be from 1:30 - 3:30.

May 7 Workshop 1: Form and Function: The Elements of a Scientific/Technical Research Article

May 8 Workshop 2: The Theory and Practice of Writing an Effective Abstract

May 9 Workshop 3: Making Sense of the Science: Cohesion and Coherence in Scientific and Technical Writing

May 10 Workshop 4: Designing Graphics that Make Your Point

Space is limited.

Please register by emailing your Name, Phone, Email, Department and Position / Class year to ccolvin@cs.princeton.edu


Introduction to Perl/Matlab for Biologists

Have you ever sat at a computer for an hour, repeating the same task over and over? Have you ever had a list of hundreds of protein sequences and wanted to count the amino acid content? How about analyzing the intensity in a large set of microscopy images? For many experiments, data analysis can be a time-consuming affair. Perl and MATLAB are tools for automated data processing and analysis that can dramatically simplify these and other related tasks. This course is all about sitting back and learning to let the computer do the work for you...

The course will cover simple but practical applications of Perl and MATLAB to data analysis and image processing. We would like to stress that all classes will begin with a discussion of the relevant basic programming concepts, so no experience in Perl, MATLAB, or general programming is necessary.

The course is currently scheduled for April 3rd-26th, Tuesday, Wednesday, and Thursday afternoons in Schultz 107 from 3:30-5pm. The course will be taught by KC Huang, Chad Myers and Greg Reeves.

Please register at http://genomics.princeton.edu/~clmyers/PerlMatlab/survey_07.htm


Pathway-Centric Research: Data Analysis, Pathway Discovery, and Simulation in BioPathwise

Registration is limited. To register, email ccolvin@cs.princeton.edu

Date:  March 28, 2007

Time:  2:30 - 6:30 pm
Instructor: Ned Haubein


It is becoming increasingly common for biological systems and data to be analyzed in the context of a pathway.  RNA interference, for example, is based on the ability to interrupt a functional pathway, and the results of these experiments are analyzed by looking at the effect of this interference on the rest of the pathway.  Systems biology approaches aim to integrate multiple data types.  One of the most intuitive, informative and visual ways to understand data is in the context of a pathway.  This course will provide examples that show how to visualize data and extract the most information from a dataset by interpreting it within the context of a pathway.  In addition, the predictive capabilities of simulatable pathways will be highlighted.  Finally, it will be shown how separate, known pathways can be combined to form new systems in a novel way.  These examples will be highlighted using BioPathwise, a system developed and supported by The BioAnalytics Group.

Registration is limited. To register, email ccolvin@cs.princeton.edu


Computational Biology with Simulink March 6, 2007 12:30 - 2:30 pm

***Come learn from a MathWorks Engineer the aspects of using Simulink (and MATLAB) within Computational Biology. Topics will include the new toolbox SimBiology.

Space is limited.

Please register by emailing ccolvin@cs.princeton.edu.


Computational Biology with MATLAB March 6, 2007 4:30 - 6:30 pm

***Come learn from a MathWorks Engineer the aspects of using MATLAB within Computational Biology. Topics will include the use of the Bioinformatics Toolbox.

Space is limited.

Please register by emailing ccolvin@cs.princeton.edu.


Optimization Techniques in Linux Development

Dates: February 20, 21, 22, 2007

Instructor: Federico Lucifredi, Harvard University

Linux Performance measurement and optimization is a black art: to achieve results, knowledge of a varied set of tools and insight into the system's internals are required to successfully conclude the investigation with clear, irrefutable evidence of the responsible bottleneck. The speaker will take the audience through a marathon demonstration of the primary benchmarking tools, highlighting their features, pitfalls and limits, while at the same time describing the underlying system mechanisms interrelating with what is being measured. Initially focusing on the performance of the whole system, the discussion will then shift to performance measurement and optimization of a specific process, covering the approaches available to benchmark and tune programs running natively on the system or inside a virtual machine.

Three sessions will cover the necessary theory and introductory hands-on practice, as we cover both System and Network performance problems.

Registration is limited. To register, email ccolvin@cs.princeton.edu


  Fall 2006

Good Programming Practices in Scientific Computing

Instructor: Dr. Brian Kernighan

Dates: November 15-16, 2006 4:30- 6:00 p.m.

Programming is more than just writing code. Programmers must also assess tradeoffs among languages and systems, choose among design alternatives, debug and test, improve performance, and maintain software written by themselves and others. This pair of lectures will cover some of these issues.The first lecture will focus on design. Design of interfaces and representation of information within a program is very important but hard to get right, and different programming languages offer different mechanisms. This lecture will talk about some of the important ideas and give some advice on doing the job well, with examples from C, C++, Java and Fortran. I will also talk about design patterns, an attempt to classify design elements in an orderly way so they can be re-used.The second lecture will focus on systematic testing and debugging, with the emphasis on mechanization of testing and using tools. There will also be some discussion of performance, including some perhaps surprising experimental results in various languages.

To register please send an email to Chrissy Colvin [ccolvin@cs.princeton.edu].


Introduction to Scientific Visualization

Instructor: Dr. Adam Finklestein

Date: November 9, 2006 4:30-6:30 p.m.

Scientific inquiry produces data sets arising from theory, simulation, and experiment. Key to understanding these data is the ability to visualize them. This workshop provides an introduction to methods for visualizing data of various types. We will explore principles for effective graphical display of 2D and 3D (volumetric) data as well as higher-dimensional data sets. We will also offer a brief introduction to some widely available software packages for visualization.

Space is limited. Register by sending email to Chrissy Colvin at ccolvin@cs.princeton.edu.


Introduction to Parallel Programming with MPI

Instructor: Stephane Ethier (PPPL)

Dates: Wednesday & Thursday, October 25-26, 2006 4:30 – 6:30pm

PICASso is pleased to announce a hands-on introduction to parallel programming with MPI taught by Stephane Ethier (PPPL). Over two practice-oriented sessions participants will learn to exploit the power of parallel computing using the freely available Message Passing Interface (MPI, http://www-unix.mcs.anl.gov/mpi/mpich/). No previous experience with parallel programming is assumed, but participants are expected to be familiar with either C or Fortran.

This course was run by PICASso in the past, and was oversubscribed. To ensure your spot please register early by sending email to Chrissy Colvin [ccolvin@cs.princeton.edu].



An Introduction to Princeton’s New Computing Resources: IBM Blue Gene, SGI Altix and Dell BeoWulf Cluster

Instructor: Curt Hillegas

Date: Wednesday, October 18, 2006

Tour begins at 4:00 pm

Mini-course is from 4:30 - 6:30pm

Princeton University has greatly expanded their centrally available High Performance Computing resources in the past year with the acquisition of an SGI Altix, an IBM Blue Gene, and a Dell BeoWulf cluster.  These systems complement each other to form a well balanced facility designed to address a broad range of problems.  This new facility named the TIGRESS High Performance Computing Center (Terascale Infrastructure for Groundbreaking Research in Engineering and Science) elevates Princeton University to the forefront of academic computational research.  We will introduce the strengths of each of these systems as well as the programming paradigms and communication protocols they support.  To provide a practical perspective of the TIGRESS HPC Center, its dimensions, and its facilities requirements, the workshop will begin with a tour of the 87 Prospect Avenue data center.

Register by sending email to Chrissy Colvin [ccolvin@cs.princeton.edu] --- Please state whether you will be attending the tour, the mini-course, or both.