ISTeC
Welcome to the Computer Science Department at Colorado State University

The ISTeC & Department of Computer Science
Workshop on Engineering Software for Scientific Applications

July 17, 2008
Rockwell Hall, Room 165
9:00 AM to 4:30 PM

Workshop Overview

This 1-day workshop will focus on the challenges of developing software to support scientific research. The targeted participants are CSU scientists who need to develop relatively complex software either as a research product or as a tool to support research. The software can range from web applications built to access and visualize large data sets, to complex modeling and simulation software that run on distributed computing platforms. Discussions and presentations at the workshop will cover at least the following topics:

About ISTeC

CSU's ISTeC (Information Science & Technology Center) is a university-wide organization for promoting, facilitating, and enhancing CSU's research, education, and outreach activities pertaining to the design and innovative application of computer, communication, and information systems. For more information please see istec.colostate.edu.

Workshop Aims and Outcomes

The following are the aims of the workshop:

The following are some of the outcomes we anticipate:

Workshop Structure

The workshop will be structured into four sessions. In the first three sessions, presenters from the CSU community outside of Computer Science will present ongoing and planned software development work. Each presenter will have a maximum of 15 minutes to present their work. Each session will end with a least a 30 minute discussion on the work presented in the session. In the fourth session, we will present a brief summary of the challenges and problems identified during the workshop. Computer Science faculty members will also present some of their experience with tackling the challenges and problems, and propose some specific areas of collaboration. This will be followed by an open discussion.

Contact Information

If you would like to make a presentation at the workshop or have questions about the workshop, please contact Robert France:
Email: france AT cs.colostate.edu
Tel: 970-491-6356

Venue

Search for Rockwell Hall on the CSU campus map.

Registration

There is no registration cost. Lunch, morning and afternoon snacks will be provided courtesy of ISTeC. If you plan to attend the workshop please register with Sharon VanGorder before July 8, 2008:
Email: vangord AT cs.colostate.edu
Tel: 970-491-5862
Fax: 970-491-2466
Please provide Sharon with the following registration information:

Workshop Program

9:00-9:15AM Opening Remarks (Robert France)

 

9:15-10:00AM Session 1 (Moderator: Jim Bieman)

Presenters

Mark van der Woerd, Biochemistry & Molecular Biology (SAXS project)

Chris Wilcox, Department of Computer Science (SAXS project)

Saul Lozano, Department of Microbiology, Immunology, and Pathology (Dengue DSS project)

 

10:00-10:30AM Open Discussion

 

10:30-11:00AM Morning Coffee/Tea Break

 

11:00-11:30AM Session 2 (Moderator: Sudipto Ghosh)

Presenters

Olaf David, Dept. of Civil Engineering (OMS)

Peter Clarke, Florida International University (Computer-Based Communication)

 

11:30-NOON Open Discussion

 

NOON-1:00PM Lunch (box lunches provided)

If weather permits, we’ll eat out in the College of Business courtyard, else we will eat in the Rockwell Hall Conference Room – Room 119.

 

1:00-2:00PM Session 3 (Moderator: Chuck Anderson)

Presenters

Jim Graham, Natural Resource Ecology Laboratory (Spatial analysis)

Anton Betten, Department of Mathematics (Large scale computations)

Crystal Redman, Department of Computer Science (Simulation tool)

 

2:00-2:30PM Open Discussion

 

2:30-3:00PM Afternoon Coffee/Tea Break

 

3:00-4:00PM Session 4 Presentations by Computer Science Faculty (Moderator: Robert France)

Presenters

Asa Ben-Hur

Sanjay Rajopadyhe

Kathy Kwinn/Debra Bartlett

SE group

 

4:00-4:30PM Open Discussion and closing remarks

Below are the presentations that we have information on thus far:

Topic: SAXS (Small Angle X-ray Scattering) Project
Presenter: Mark van der Woerd, Biochemistry & Molecular Biology

Title: Software Engineering on the SAXS Project
Abstract: The SAXS software project is a collaboration between the Biochemistry and Molecular Biology, Mathematics, Statistics, and Computer Science departments at Colorado State University. The project purpose is to develop software to help identify and refine the structure and function of proteins. An experimental technique called Small Angle X-Ray Scattering (SAXS) is used in the investigation. We are currently developing a software framework and several programs related to the SAXS investigation. We have completed a 'Scatter' program to compute the theoretical intensity curve from a rigid molecular model, and a preliminary 'Topology' program that models flexible molecular structure. The programs are run from a simple user interface which we distribute along with the programs under an open source license. Significant performance gains have been made from the inception of the project in early 2008. The computer science research areas associated with the project are software engineering and parallel computing.
Presenter: Chris Wilcox, Dept. of Computer Science

 

Title: Dengue Decision Support System
Presenters: Lars Eisen, Saul Lozano, Department of Microbiology, Immunology, and Pathology

Title: Collaborative scientific simulation model development using the Object Modeling System (OMS)
Abstract: The Object Modeling System (OMS) is a component based modeling framework that uses an open-source software approach to enable the scientific community to collaboratively address the many complex issues associated with the design, development, and application of distributed hydrological and environmental models. The modular modeling framework concept 1) facilitates using the resources of a larger science community to work collaboratively on development and application of a variety of modeling approaches to multi-disciplinary problems; 2) provides a framework in which to objectively compare alternative modeling approaches; and 3) provides a means of sharing the latest modeling advances.
Presenter: Olaf David, Dept. of Civil Engineering, CSU

Title: Computer-Based Communication in Distributed Collaborative Environments
Abstract: The advances and pervasiveness in the technology to support electronic communication has resulted in the need for a new approach to model and rapidly realize user-centric communication-intensive applications. One approach to solving this problem is using an executable domain specific modeling language (DSML) that supports the easy creation of communication models and the rapid realization of these models. Such a DSML and the supporting execution environment would be extremely beneficial in today's collaborative scientific environment since the number of geographically distributed research teams that need to collaborate in several domains continues to increase. I will present a technology we are developing at Florida International University that uses a DSML - Communication Modeling Language (CML), which supports the creation and rapid realization of models for communication-intensive applications. We are currently developing a prototype of the Communication Virtual Machine (CVM) platform to model and realize communication-intensive applications.
Presenter: Peter Clarke, School of Computing and Information Sciences, College of Engineering and Computing, Florida International University, Miami, Florida

Title: Building a web-based system for spatial analysis of species potential distributions
Abstract: With the latest technology it is possible to provide an online system that allows users to perform complex scientific analysis with little training and is easy to use. Traditionally performing spatial analysis requires collecting field data, purchasing remotely sensed data, purchasing and learning statistical packages, and setting up high-performance computers to provide the required performance. This process can take years and cost tens of thousands of dollars in software and hardware. Today's technology provides the opportunity to make spatial analysis available to virtually anyone with an Internet connection. This makes scientific data and analysis available to a wider audience including research scientists without the specific resources required.
Presenter: Jim Graham, Natural Resource Ecology Laboratory

Title: Large Scale Computations in Discrete Mathematics

Abstract: The speaker is concerned with investigating and analyzing discrete
mathematical objects like optimal linear codes and incidence structures.
The talk will be centered around the following three questions:
What are we trying to compute and how?
What are the issues with developing software?
What are the issues with doing the actual computation?
Presenter: Anton Betten, Department of Mathematics


Title: MASON: A Multi-Purpose Simulation Framework
Abstract: Since 2002, the Evolutionary Computation Lab and the Center for Social Complexity at George Mason University has been developing and expanding MASON, a simulation framework written in Java that is used for theMulti-Agent Simulation of Neighborhoods (or Networks). MASON has been leveraged to create simulators beyond intelligent agent research. A few of the domains modeled using MASON have ranged from Cooperative Observation, Keep-Away Soccer, and Traffic Control to 3D Models of the Solar System. MASON provides a mech- anism for discrete event simulation. Domain specifics like the actors and environment in the simulator are easy to create and customize making MASON a simple starting point for basic simulations. We will provide a tutorial that outlines the basic knowledge needed to begin creating simulators with MASON.
Presenter: Crystal Redman, Dept. of Computer Science

Title: Machine learning with PyML
Abstract: PyML is an open-source machine learning environment which has been available on sourceforge for around 6 years (see http://pyml.sf.net). In this talk I will share my rationale and experiences in sharing software which was developed for research purposes.
Presenters: Asa Ben-Hur, Department of Computer Science

Title: Software version control
Abstract: A version control system is a great asset to the development and maintenance of complex software. This talk will outline advantages of using version control and also some of the associated costs. It will mention some heavily used tools, discuss criteria for picking a tool, and look at how version control can be integrated with other tools commonly used in software development.
Presenters: Kathy Kwinn, Debra Bartlett, Department of Computer Science