Biophysics 101 Project

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Outline
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Kaganov (Talk | contribs)
'''Personalized medicine''' (e.g. stem-cells)
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** Transnational scale - what are the incentitives for organizations like UN to promote biofuels ** Transnational scale - what are the incentitives for organizations like UN to promote biofuels
-=='''Personalized medicine''' (e.g. stem-cells)==+=='''Personalized medicine''' (e.g. diagnostic tools)==
-* Let's start building the project from here... --[[User:Jeffrey|Jeffrey]] 12:51, 18 October 2005 (EDT)+ 
 +I like the idea that we discussed in class -- diagnostic software assuming that individualized genomic, proteomic, etc. data is soon going to be readily available and accessible. I think that something that would be really cool and feasibly is to build a platform that could incorporate all the different kinds of data that could be used for diagnostics (like biomarkers, biological networks, proteome "signatures", etc.). For example, there are thousands of SNPs out there that are known and are currently being discovered that could serve as valuable biomarkers for disease. Obviously many are probably trade-secrets, but those that are patented and available publicly can be uploaded to our databases of items that are searched by patients and physicians. Once it is possible to obtain data on individual genetic network dynamics this information can be compared to the healthy versions that researchers decipher. Same thing for things like proteome "signatures" and really any ways of characterizing cellular activity. So maybe we can think of a way to do that, and then start researching all the markers that are currently available, generate some random genomes, and test our tools. --[[User:Kaganov|Kaganov]] 03:07, 20 October 2005 (EDT)
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I've summarized [[User:Cgupta#Personalized Medicine Project Ideas | my thoughts]] on the PM project. Before I make an outline however, I'd appreciate it if people could read over the my thoughts and comment on them to make sure that the idea is reasonable. Thanks!--[[User:Cgupta|Cgupta]] 17:03, 19 October 2005 (EDT) I've summarized [[User:Cgupta#Personalized Medicine Project Ideas | my thoughts]] on the PM project. Before I make an outline however, I'd appreciate it if people could read over the my thoughts and comment on them to make sure that the idea is reasonable. Thanks!--[[User:Cgupta|Cgupta]] 17:03, 19 October 2005 (EDT)

Revision as of 07:07, 20 October 2005

Contents

Biodiesel: New energy sources

  • We need to start looking at environmental policy and economics. The KSG should be a good launching pad for this. --Jeffrey 11:27, 18 October 2005 (EDT)

Outline

--Msommer 16:16, 19 October 2005 (EDT)
  • Global energy demand and supply: now and in the future
    • Establish upper and lower boundaries for global energy consumption over the next 100 years.
    • Determine size of each segment of the total energy use (ex.: how much is used in combustion engines for trnasport, how much is for electric appliances etc.)
    • Determine composition of current energy supply (ex.: oil x %, nuclear y %...)
    • Explore viability of alternative energy sources (wind, sea-wave, solarcells, biofuels) for each segment of the energy use. I would expect that we will find that wind, wave and solar may be a better alternative for producing electricity, whereas biofuels are good for transportation.
  • Metabolic engineering: optimize biofuel production Jeremy's Metabolic Engineering Tutorial:User:JeremyZucker#Metabolic_Engineering_tutorial
    • Which biofuel producing organisms are most suitable for metabolic flux analysis
    • Which organisms are most suitable for metabolic engineering
    • Develop quantitative model for biodiesel production in most suitable organism
  • Environmental Models
    • What is the input for biofuel production
    • What are the waste output of production and utilization
    • What are the effects of these on the ecosystem
    • Can this be related to existing climatic models (global warming etc.)
  • Economic Incentives
    • Small scale - what are the incentitives for individuals to produce their own biofuel
    • Commercial scale - what are the incentitives for companies like BP and Shell to introduce biofuels
    • National scale - what are the incentitives for goverments to promote/produce biofuels
    • Transnational scale - what are the incentitives for organizations like UN to promote biofuels

Personalized medicine (e.g. diagnostic tools)

I like the idea that we discussed in class -- diagnostic software assuming that individualized genomic, proteomic, etc. data is soon going to be readily available and accessible. I think that something that would be really cool and feasibly is to build a platform that could incorporate all the different kinds of data that could be used for diagnostics (like biomarkers, biological networks, proteome "signatures", etc.). For example, there are thousands of SNPs out there that are known and are currently being discovered that could serve as valuable biomarkers for disease. Obviously many are probably trade-secrets, but those that are patented and available publicly can be uploaded to our databases of items that are searched by patients and physicians. Once it is possible to obtain data on individual genetic network dynamics this information can be compared to the healthy versions that researchers decipher. Same thing for things like proteome "signatures" and really any ways of characterizing cellular activity. So maybe we can think of a way to do that, and then start researching all the markers that are currently available, generate some random genomes, and test our tools. --Kaganov 03:07, 20 October 2005 (EDT)



I've summarized my thoughts on the PM project. Before I make an outline however, I'd appreciate it if people could read over the my thoughts and comment on them to make sure that the idea is reasonable. Thanks!--Cgupta 17:03, 19 October 2005 (EDT)

Wikipedia entry: Personalized Medicine

Refers to the use of detailed diagnostic information to guide medical therapy. For example, information such as a patient's genotype or level of gene expression is used to select a medication or therapy that specifically matches that genotype or gene expression level. Since different patients have different genotypes and gene expression levels, each patient can receive a therapy that is personalized rather than all patients receiving the same generic therapy. The term, personalized medicine, emerged in the late 1990's with progress in the Human Genome Project. Some of the earliest personalized medicines were Herceptin and Gleevec.

From Wikipedia:personalized medicine We can do better than this! --ASW 13:39, 18 October 2005 (EDT)

Preliminary Outlines

Outline (S. Douglas)

More details please ... --ASW 05:30, 6 Oct 2005 (EDT)
  • Background
  • Definition of the problem/situation
  • Specific aims of our project/proposal
    • tools required
  • Technical Challenges
    • metabolic engineering
  • Economic analysis
    • impact
    • funding
  • Social & Political Impact
    • laws, regulations
    • public health & distribution



Outline of Potential Project (G. Church)

More details please... --ASW 05:30, 6 Oct 2005 (EDT)

Working Title: Prove, Predict, prioritize, practice Breaking barriers & building bridges

Prove, predict: Connect problems, technologies, modeling options Example: Evolution - replicating &/or intelligent machines stem cells, abortion Model: Quantitatively define life.

Prioritize, practice: Metabolic networks Example: Carbon & Energy Model: Multilevel from molecular to global.

Prioritize: Privacy vs openess Example: Personal genomics Model: Evolutionary conservation, etc.

Prioritize, practice: Synthetic Biology & chemistry Examples: biosecurity, bioterrorism, GMOs Withholding experimental drugs (e.g. HIV & Cancer) Substance abuse, Vioxx Models: Risk & benefit, systems models