supporting scientific collaboration online scope workshop at san diego supercomputer center march...
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Supporting Scientific Collaboration Online
SCOPE Workshop at
San Diego Supercomputer CenterMarch 19-22, 2008
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Problem Spaces as an
Open Participatory Learning Infrastructure
E-Science
Web 2.0
Open Educational Resources
Engaged Science
Learning
Scholarship of
Teaching
A community model for teaching and learning science which integrates and acts on the role of technology in education.
Existing Technological
Resources
Building a Community of Teaching and
Learning
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Workshop Structure Overview• Introductions to working with:
– a Problem Space– an Investigative Case– OERCommons– Visualization tools– CaseIT– Planting Science
• 2 small group projects w/ presentations– Integrate OER, E-science, and/or Web 2.0 resources into a
teaching project of your choice.– Describe ways you will build and/or teach with
collaborative tools and resources.
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Investigations of HIV-1 Env Evolution
Evolutionary Bioinformatics:
Microbial analyses from sequence to structure to function to ecology
SCOPE Workshop at SDSCMarch 19-22, 2008
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1. Virus docks with receptors on host cell (CD4 + co-receptor)
2. Reverse transcription: viral RNA DNA
3. Viral DNA inserts into host’s DNA
4. Viral RNA transcribed & proteins assembled
5. New virions bud from host cell, killing it
Life Cycle of HIV
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HIV Virus
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The HIV Genome
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HIV env Gene
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gp120 V3 region sequence
Nucleic Acid Sequence
CTAGCAGAAGAAGAGGTAGTAATTAGATCTGCCAATTTCACAGACAATGCTAAAATCATAATAGTACAGCTGAATGCATCTGTAGAAATTAATTGTACAAGGCCCAACAACAATACAAGAAAAGGTATACATATAGGACCAGGGAGAGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCACATTGTAACATTAGTAGAGAAAAATGGAATAATACTTTAAACCAGGTAGTTACAGAATTAAGGGAACAATTTGGGAATAAAACAATAACCTTTAATCACTCCTCAGGAGGGGACCCAGAAATTGTAATGCACAGTTTTAATTGTGGAGGGGAATTTTTCTATTGTAAT
------------------------------------------------------------------------
Amino Acid Sequence
LAEEEVVIRSANFTDNAKIIIVQLNASVEINCTRPNNNTRKGIHIGPGRAFYATGEIIGDIRQAHCNISREKWNNTLNQVVTELREQFGNKTITFNHSSGGDPEIVMHSFNCGGEFFYCN
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gp 120 Structure
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The Markham et al.HIV-1 env Sequence Dataset
• Longitudinal study of 15 HIV+ patients from Baltimore
• Patients came in at 6-month intervals (“visits”) over 4-year period
• Focused on the 3rd variable loop of the env gene (285 bp)
• Each visit: sampled ~10 viral sequences and measured CD4 levels
Rich data set for analyzing patterns of HIV evolution and their correlation
with rates of T-cell decline
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Summary of the data set
• Subjects: 15
• Number of visits: 3-9
• Number of clones per visit: 2-18
• Total number of sequences available: 666
• CD4 cell counts for each visit
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Possible Investigations
• What is the pattern of HIV evolution within an individual? – Do the number of clones over time change in
any regular way?– Do certain clones appear to survive (leave
descendents) over time while other disappear (go extinct)?
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Possible Investigations
• What is the pattern of HIV evolution within the env sequence? – Are there particular positions in the sequence
that are more or less likely to mutate? – Are there different rates of synonymous (silent)
and non-synonymous mutations?
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User Web BrowserOutput to User
User Input
Format Translator, Query Engine and Program Driver
Workbench Server
Results to User
User Instructions and queries
Application Programs
(May have varyinginterfaces and be written in different
languages)Results
Instructions
Information Sources(May be of
varying formats)
Information
Queries
NCSA Computational Biology Group
The NCSA Information Workbench - An Architecture for Web-Based Computing