From FreeBio

Contents 1 Personalized medicine 1.1 What is Personalized Medicine? 1.2 Technology Development present & future 1.3 Implementation 1.4 Personal Genome Project 1.4.1 Library API ideas 1.4.2 Relevant Bioperl modules 2 New energy sources 2.1 Global energy demand and supply: now and in the future 2.2 Natural biofuel sources 2.3 Biomass-oil Needs and Recommendations 2.4 Obtain the critical parameters for each biofuel source 2.5 Other challenges/problems 2.6 Metabolic engineering: optimize biofuel production 2.7 Environmental Models 2.8 Economic Incentives 3 Biocomplexity and Randomness

Personalized medicine

What is Personalized Medicine?

Medical diagnosis and treatment, informed by the use of genetic and epigenetic characteristics unique to the patient being treated. This may include single nucleotide polymorphisms (SNPs), detailed patient and family histories, gene expression & protein abundance levels; other biomarkers.

• A quantitative approach to how personalized a treatment is?

Technology Development present & future

• genome sequencing & resequencing
  • Review of "Deeper into the genome commentary on HapMap milestone and where to go next"-Some information to begin with
• genome-based assessment
  • functional & comparative genomics
• diagnostic tools
• medical informatics
• drugs (Imatinib)

Implementation

• Past Lessons
• Economic analysis
  • Cost of Medical Misdiagnosis-This can serve to explain the economic motive behind personalized medicines (ie. even though sequencing individual genomes may be expensive, imagine how much money could be saved from preventable misdiagnosis)--Cgupta 01:53, 8 November 2005 (EST)
  • Preventive vs Curative Medicine
• Access to care
• Data collection
  • Great potential for longitudinal studies
• Privacy concerns

Personal Genome Project

Library API ideas

The code and Documentation for this Library can be found in the Biophysics 101 Software page in Personal Genome API

Relevant Bioperl modules

Full details of the discussion can be found on the Biophysics 101 Software page at Relevant Bioperl modules. --JeremyZucker 18:43, 12 January 2006 (EST)

New energy sources

Global energy demand and supply: now and in the future

• Establish upper and lower boundaries for global energy consumption over the next 100 years. (Thoughts on energy supply and demand.) --MatthewMeisel
• Current total energy use (ex.: how much is used in combustion engines for transport, how much is for electric appliances etc.) --MatthewMeisel
• Determine composition of current energy supply (ex.: oil x %, nuclear y %...) --MatthewMeisel
• 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.
• Some information on Global Demand for Oil: http://www.eia.doe.gov/pub/oil_gas/petroleum/analysis_publications/oil_market_basics/Demand_text.htm --Mark 13:34, 23 October 2005 (EDT)

Natural biofuel sources

Natural biofuel sources:

• crops,
• algae,
• methanogens
• and closed-loop microorganism production systems

Biomass-oil Needs and Recommendations

See the dedicated page for this.

Obtain the critical parameters for each biofuel source

• Metrics for Biofuels
• land use
• input - output
• energy density
• energy cost - oil vs. algae comparison
• etc.

Other challenges/problems

See Jason's section on other challenges/problems

Metabolic engineering: optimize biofuel production

• Jeremy's Metabolic Engineering Tutorial
• Which biofuel producing organisms are most suitable for metabolic flux analysis Overview of existing metabolic network data--Msommer 17:35, 20 October 2005 (EDT)
• 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
• 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)

Biocomplexity and Randomness

• Jeremy's Definitions of complexity & randomness
• Jason's definitions of complexity & randomness
• Chiki's definitions of complexity & randomness
• Matthew's definitions of complexity & randomness
• Morten's definitions of complexity & randomness
• Jeffrey's Pseudo-random thoughts

---