BioNanoPlanning17-18Apr2008
From SC Education
Contents |
SC08 High Performance Computing in Nano and Bio Sciences Research and Education
Heredia Costa Rica Planning Meeting
Attendees
- Alvaro de la Ossa - CNCA, CeNAT
- Alejandro Cruz - CeNAT
- María del Rosario Sibaja - POLIUNA, UNA
- Jose Vega - LANOTEC, CeNAT
- Pedro León - Peace with Nature
- Santiago Núñez Corrales - CNCA, CeNAT
- Kevin Franklin - I-CHASS, NCSA, UIUC
- Fernando Hernández - CSULA
- Arun Datta - NUCRI, NU
- Gloria Rendón - NCSA, UIUC
- Eric Jakobsson - NCSA, UIUC
- Oswald Crasta - VTech
- Tom Murphy - SC
- Keilor Rojas - INBio
- Carlos Murillo - EARTH
Topics of discussion
- objectives/goals
- audience
- content
- format
- logistics
Background
The BioNano Workshop will take place in Costa Rica in two months; late June or early July 2008. Costa Rica focuses in the following areas in nano/bio-sciences:
- Nano:
- Multiscale, multiphysics simulation
- Advanced nanomaterials
- Surface modification
- Organic waste transformation
- NEMs & MEMs
- Molecular design for pharmacology
- Nanostructured materials
- Bio:
- Biochemistry
- Biophysics
- Metagenomics
- Virology
- Biodiversity informatics
- Bioprospection
In essence, SC education has a philosophy of creating a critical mass of replicators of knowledge in the areas of education using supercomputing resources. Another goal is to create a local community of users that support newcomers in the field and provide information on how to access and develop materials The term workshop means:
- Work: an audience that knows what it wants and goes for it in the workshop
- Shop: an audience that wants to get acquainted with technology and materials but does not have a specific target
Workshops are a mixture of lectures with hands-on activities, but heavily loaded toward practice. Normally the workshop requires access to some form of supercomputer or cluster (TeraGrid, SC, EDUGrid, local) and a cluster can be easily set up with the Bootable Cluster CD. Students benefit from group interactions in different forms (e.g. shoulder surfing) and they can help create the contents of courses that can be deployed after the workshop.
Wednesday afternoon and evening are used to let people explore what they have learned and they are polled to know if the conference goals/methods have to be reoriented. A project-driven approach lets people discover pitfalls, common misunderstandings and best practices while working with software and methods, and a cross-disciplinary approach immerses the student into the environment scientist are involved worldwide.
Objectives
- Create a local community of users of supercomputing resources in Bio/Nano Science
- Demonstrate the experience in the SC08 Education Program, Austin TX
- Use the workshop as a step in the process of defining the profile of the {bio, nano}-scientists of the XXI century
- Foster an adequate environment for multi-cultural scientific exchange
- Create a space where new applications, localizations and modules are a product of this and similar future workshops
- Use the Costa Rica experience in the workshop as a case of study for HASS
- Use the Costa Rica experience in the workshop to create a regional model of collaboration in supercomputing education
- Involve different audiences in order to maximize impact of results
- Scientists and researchers
- Science and technology policy makers
- Undergraduate and graduate students
- Faculty professors
q: focus on education-only or could it also include developing research-related and dissemination contacts
- They can be included to extent they foster undergraduate education. Note that the undergraduate internships possible could easily warrant research-related contacts
- The research and dissemination contacts should be part of process to help define the current direction to e incorporated in undergraduate education. We just have to remember the focus.
Audience
- q: educators only, students too? politicians too? scientists?
- Fundamentaly for undergrauate educators
- Easy to include students, in fact encouraged to have them be part of faculty/student team attending
- Easy for politicians and scientists to attend if they are alos presenters, since the ones presenting are encouraged to be there whole week.
- Also easy for politicians and scientists to attend if they are part of the process enabling undergraduate education
- q: if students then which level?
- Mainly undergraduate/graduate, we have woven HS students in (with extra planning)
- q: if Latin America, then reaching out to bilingual or Spanish-only
- At planning meeting, we agreed to have a bilingual workshop to the greatest extent possible
Content
At the conference we spoke of
- Training in use of TeraGrid and Open Science grid
- Training in use of nanoHub
- Training in use of Webmo
- Training in use of the Molecular Science Portal
- Training in use of CSERD
- Training in use of the Biology Student Workbench
- Training in use of ChemSketch
- q: Webmo front ends many applications, what are the ones needed for conference
- q: How do we provide Webmo if Internet goes down, local server?
Possible keynote speakers (with hands-on activities after their presentation):
- Pedro León (Biology)
- Alenjandro Cruz (Science and Technology Vision)
- Eric Jakobsson (Metagenomis)
- Gloria Rendón (Bioinformatics)
- Chris Barak (Health informatics)
- Narayana Aluru (MEMs, NEMs and multi-scale simulation)
- Leroy Hood (Systems Biology)
The Skeletal Workshop Structure from Santiago is a good framework to flesh out
- Monday (core: introduction)
- Keynote speakers
- Introduction to Computational Sciences
- Introduction to TeraGrid resources
- Tuesday (core: simulation and modeling)
- Introduction to mathematical modeling for engineering
- Simulation tools for (nanotechnology/bioinformatics)
- Wednesday (core: parallel and grid computing)
- Introduction to parallel computing
- Grid computing and cyberinfrastructure
- Introduction to Job submission systems
- Thursday (domain-specific activities)
- Research in (nanotech/bioinformatics): tools and methods, I part
- Dinner at Pueblo Antiguo
- Friday (visit)
- Research in nanotechnology/bioinformatics: tools and methods, II part (half day)
- Visit to INBio Biological Park (half day)
- Formal dinner
Format
like NCSI?
Logistics
q: a cluster can be configure 'on the fly'... would it be needed?
- I spoke with Paul and Charlie about the possibility of shipping a Little-FeAR cluster with pre-configured software. We need to talk more about this
q: What is the cost of running the materials on local machines and what logistics are needed?
- Access to resources and location must be revised
q: What staffing can be available for pre-training?
- CeNAT can provide current lab assitants (CNCA, LANOTEC) for preparation on the tools and methods prior to the workshop and the universities can provide computer science people
- Integrate recorded simultaneous translation into the workshop results
- Bilingual content as much as possible
- Two projection units with mirror content on both languages
- SC08 budget for translation
Other
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