Biophysics 101 Schedule
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Contents |
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Schedule
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September
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Week 1 : class organization
20-Sep-2005 & 22-Sep-2005 lectures
- George Church -
- Shawn Douglas - investigate mediawiki upgrade
- Chiki Gupta - started user page
- Lakshmanan Iyer - move class to Harvard square
- Mark Kaganovich -
- Jason Leith - started user page; definitions of complexity and randomness
- Matthew Meisel - started user page; definitions of complexity and randomness
- Morten Sommer - started user page; understanding of 101
- Alexander Wait - wiki curating
- Jeffrey Yip - started user page; links
- Jeremy Zucker -
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Week 2 : choose projects; exercise - a quantitative definition of life
27-Sep-2005 & 29-Sep-2005 lectures
- George Church - away 29-Sep.
- Shawn Douglas - personalized medicine.
- Chiki Gupta - personalized medicine.
- Lakshmanan Iyer - new papers to review in 101 Tasks.
- Mark Kaganovich - personalized medicine.
- Jason Leith - new energy sources.
- Matthew Meisel - new energy sources.
- Morten Sommer - new energy sources.
- Alexander Wait - meta definition of "life".
- Jeffrey Yip - personalized medicine; 27-Sep audio recording.
- Jeremy Zucker - new energy sources; "Toward a mathematical definition of "life" by Gregory Chaitin.
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October
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Week 3 : new energy sources and personalized medicine
- George Church -
- Shawn Douglas - personalized medicine definition, background.
- Mark Kaganovich - personalized medicine
- Chiki Gupta - Issues Facing Personalized Medicines & Stem Cell Basics
- Lakshmanan Iyer - tools for computational biology
- Jason Leith - biodiesel problems and challenges; problems with non-algal sources
- Matthew Meisel - historical aspects of changing energy sources Away 4-Oct
- Morten Sommer - sustainable environmental economics
- Alexander Wait - wiki curation.
- Jeffrey Yip - economics pharma and environment; energy policy
- Jeremy Zucker - reviews metabolic engineering, textbooks etc. Away 4-Oct
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Week 4 : biosphere facts
11-Oct-2005 & 13-Oct-2005 lectures
- George Church -
- Shawn Douglas -
- Chiki Gupta - Review of “Systems Biology, Proteomics, and the Future of Health Care: Toward Predictive, Preventative, and Personalized Medicine�?
- Lakshmanan Iyer - Away 13-Oct
- Mark Kaganovich - Away 13-Oct Review Systems Biology, Proteomics, etc. article
- Jason Leith - PQ for personalized medicine scale; a few metrics for various fuels
- Matthew Meisel - Personalized Medicine Scale - Away 13-Oct
- Morten Sommer - Metrics for various fuels
- Alexander Wait -
- Jeffrey Yip - Away 11-Oct
- Jeremy Zucker - Reviews Genome-scale models of microbial cells: evaluating the consequences of constraints; Away 13-Oct
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Week 5 : project literature review
18-Oct-2005 & 20-Oct-2005 lectures
- George Church - Away 18-Oct
- Shawn Douglas - Away 20-Oct
- Chiki Gupta - PM Project Ideas and review Jeremy's metabolic engineering tutorial
- Lakshmanan Iyer -
- Mark Kaganovich - Project Page, scribe for Oct. 20
- Jason Leith - Comments on D. Lovely bioremediation paper and how it relates to biomass-oil production.
- Matthew Meisel - Energy usage
- Morten Sommer - review Jeremy's metabolic eng. tuturial and the Palsson paper and biodiesel outline
- Alexander Wait -
- Jeffrey Yip - Please add contributions to group projects here
- Jeremy Zucker -
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Week 6 : metabolic networks and learning perl
25-Oct-2005 & 27-Oct-2005 lectures
- George Church -
- Shawn Douglas -
- Chiki Gupta - [[Biophysics_101_Lectures#Week_6 Scribe for Oct. 25]]; Install and play around with Bioperl; Medical Misdiagnosis Data
- Lakshmanan Iyer -
- Mark Kaganovich - start outline of project
- Jason Leith - May be late Oct. 25; Updated 101_Background
- Matthew Meisel - Speculation on the long, long-term effects of carbon sequestration
- Morten Sommer - Looking at metabolic data for bilevel optimization - scribe Oct. 27
- Alexander Wait - improve wiki back-end.
- Jeffrey Yip - Note: We need to get a good omnidirectional microphone for conferencing on Google Talk with Jeremy when he is away. A decent set of speakers would be helpful as well.
- Jeremy Zucker -
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November
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Week 7 : midterm evaluation
1-Nov-2005 & 3-Nov-2005 lectures
- George Church - Away
- Shawn Douglas -
- Chiki Gupta - Review of “Systematic Survey Reveals General Applicability of ‘Guilt-by-Association�? within Gene Coexpression Networks�?
- Lakshmanan Iyer -
- Mark Kaganovich - Away 3-Nov
- Jason Leith - Scribe for 1 Nov.; Investigation of costs of producting energy from algae vs. oil.
- Matthew Meisel - "Hello DNA" program
- Morten Sommer - Learn some basic perl and pathway tools
- Alexander Wait - set-up personal genomics cluster
- Jeffrey Yip -
- Jeremy Zucker - Away
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Week 8
8-Nov-2005 & 10-Nov-2005 lectures
- George Church -
- Shawn Douglas -
- Chiki Gupta - Scribe for Nov. 8, Ran Ubuntu Live CD, Reviewed "Deeper into the genome commentary on HapMap milestone and where to go next"
- Lakshmanan Iyer - Away
- Mark Kaganovich - will review both HapMap papers; 10-Nov Away.
- Jason Leith - Added papers to look at re: Personalized Medicine, link to DOE's Chromosome Viewer.
- Matthew Meisel - a crack at a compression algorithm for a DNA sequence
- Morten Sommer - Things to do with a 1000 Human Genomes?
- Alexander Wait -
- Jeffrey Yip -
- Jeremy Zucker - Away
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Week 9
15-Nov-2005 & 17-Nov-2005 lectures
- George Church - Away 15th
- Shawn Douglas -
- Chiki Gupta -
- Lakshmanan Iyer -
- Mark Kaganovich -
- Jason Leith - May be late 15th. Made and ran Ubuntu live CD.
- Matthew Meisel - Continued work on 2-bit encoding, preparation for presentation on exact match searching (pdf)
- Morten Sommer -
- Alexander Wait -
- Jeffrey Yip -
- Jeremy Zucker - Away 15th and 17th
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Week 10
- Lakshmanan Iyer -
- Mark Kaganovich -
- Jason Leith -
- Matthew Meisel -
- Morten Sommer -
- Alexander Wait - Away
- Jeffrey Yip - (Most Likely) Away
- Jeremy Zucker - Away
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Week 11
29-Nov-2005 & 1-Dec-2005 lectures
- George Church -
- Shawn Douglas -
- Chiki Gupta - Aligned Genomes and Statistically Significant Mutations
- Lakshmanan Iyer -
- Mark Kaganovich -
- Jason Leith -
- Matthew Meisel -
- Morten Sommer -
- Alexander Wait - Away 29-Nov.
- Jeffrey Yip -
- Jeremy Zucker -
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December
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Week 12
6-Dec-2005 & 8-Dec-2005 lectures
- George Church -
- Shawn Douglas -
- Chiki Gupta -
- Lakshmanan Iyer -
- Mark Kaganovich -
- Jason Leith -
- Matthew Meisel -
- Morten Sommer - away dec 8
- Alexander Wait -
- Jeffrey Yip - LWP - The World-Wide Web library for Perl
- Jeremy Zucker -
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Week 13 : presentations
13-Dec-2005 & 15-Dec-2005 lectures
- George Church - away Dec 13 & 15
- Shawn Douglas -
- Chiki Gupta -
- Lakshmanan Iyer -
- Mark Kaganovich -
- Jason Leith - Discussion of criteria for a system to encode insertions and deletions, and a proposed system.
- Matthew Meisel -
- Morten Sommer - Away Dec 15
- Alexander Wait -
- Jeffrey Yip -
- Jeremy Zucker -
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Week 14 : pre-winter-break wrap-up
- George Church -
- Shawn Douglas - Away 20-Dec
- Chiki Gupta -
- Lakshmanan Iyer -
- Mark Kaganovich -
- Jason Leith - Away 20-Dec
- Matthew Meisel -
- Morten Sommer - Away 20-Dec
- Alexander Wait -
- Jeffrey Yip -
- Jeremy Zucker -
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January
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Week 15 : Final reports and plans for follow-up
(Fall reading and exam periods: Jan 3-14 & 14-24)
