Synthetic Biology and Data-Driven Synthetic Biology for Personalized Medicine and Clean Energy at O\'Reilly\'s OSCON Data in Portland, OR
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A talk I gave at OSCON Data 2011 on how personalized medicine, data analysis, and open source synthetic biology can work together.
Synthetic Biology and Data-Driven Synthetic Biology for Personalized Medicine and Clean Energy at O\'Reilly\'s OSCON Data in Portland, OR
- 1. SYNTHETIC BIOLOGY AND DATA-DRIVEN SYNTHETIC D BIOLOGY FOR PERSONALIZED MEDICINE AND CLEAN ENERGY Russell Hanson OSCON D t J l 25 27 2011 Data July 25-27, Portland, OR Russell Hanson Dec 27, 2004 TheCureIsNow.org
- 2. Outline What is synthetic biology? y gy How does synthetic biology relate to genomic science/personalized medicine Open source tools in science and bioengineering/synbio Bio-Computer aided design (AutoCAD, etc.) Mesoscopic Physics p y Diff Eqs and parameter optimizations OSCON Data Portland, OR
- 3. Outline, cont. IP Issues in personalized medicine Pink Army and co-op, open-source biopharma Non-profit clinical research organizations Non profit (CROs) Disease-management companies, broken Disease management business model Big Data in electronic medical records, personal genomics, biostatistics, hospitals, community health centers OSCON Data Portland, OR
- 4. OSCON Data: This may not be a talk about a social web app and the pp database technologies used for that app, but truly, what would a social web, pp, y, , etc. app be without the life or biology on that social graph g p OSCON Data Portland, OR
- 5. What is life? What is artificial life? And, incidentally, what is consciousness? Igor Aleksander (1995) Bernard Baars (1988) Brain as state machine Definition and context setting Inner neuron partitioning Adaptation and learning Conscious and unconscious states Editing Perceptual learning and memory Flagging and debugging Prediction Recruiting and control Self-Awareness Decision-making (executive function) Representation and meaning Analogy forming-function Learning utterances Metacognitive and self monitoring self-monitoring Learning language function Will Autoprogramming and self-maintenance Instinct function Emotion Definitional and context-setting context setting function OSCON Data Portland, OR from When The Turing Test Is Not Enough, by George Dvorsky
- 6. We are open source Life is open source We should have excellent tools to manage our source (code) OSCON Data Portland, OR
- 7. OpenWetWare.org OSCON Data Portland, OR
- 8. BioBricks Foundation OSCON Data Portland, OR
- 9. iGEM OSCON Data Portland OR
- 10. NextGen sequencing OSCON Data Portland, OR
- 11. SNP Chips Affymetrix 500K probe chip ~$450USD OSCON Data Portland, OR
- 12. Single nucleotide polymorphism (SNP) and gene expression arrays CCopy number profile b fil Gene expression/over expression levels in a tissue Major copy proportion j py p p Machine learning on SNPs, SVM, Bayesian networks, Markov chains Biomarker identification, verification, and development. development Biomarker for autism lack autism, lack of empathy OSCON Data Portland, OR
- 13. Where are we? How much do we know about cellular processes, regulation, oncogenes, l ti protein-protein interactions, microbiome interactions? i t ti ? How much do we know about brain structure-function relationships, gene activation in neurons, memory, eletrophysiology, neuronal cognition, brainmaps from C. elegans, to Mus musculus, to Homo sapiens? OSCON Data Portland, OR
- 14. How to Access the Human Genome (and other seque ced genomes) sequenced ge o es) ftp://ftp.ncbi.nih.gov hs_phs0.fna.gz Survey sequence (appr hs_phs1.fna.gz Unordered contigs (ea hs_phs2.fna.gz Ordered contigs (each hs_phs3.fna.gz Finished sequence 21C3 Berlin
- 15. The second wave of synthetic biology: from modules to systems systems The second wave of synthetic biology: from y gy modules to systems, Purnick PEM, Weiss R, Nature Reviews Molecular Cell Biology, Vol 10 OSCON Data Portland, OR Iss 6 P410-422 Jun 2009
- 16. Using increasing abstraction, performance characteristics, datasheets -- like integrated circuits (ICs) OSCON Data Portland, OR
- 17. Graphical layout, design and programming, CellDesigner programming tutorial at: http://celldesigner.org/~funa/CellDesignerTutorial2007.pdf
- 18. Graphical layout, design and programming, CellDesigner 2 programming
- 19. Nanobots to treat NK leukemia cells DNA scaffolds and cell-surface receptors Software, etc. for DNA origami, scaffold design OSCON Data Portland OR
- 20. 23andMe, NextGen sequencing and SynBio get together 23andMe version 3 uses Illumina HumanOmniExpress BeadChip SNP chips ($250/sample) Genome Wide Association Studies --> At $250/sample, genomic personalization is very realizable OSCON DATA Portland, OR
- 21. More new CAD/BioCAD software tools Matter compiler Thingiverse, cheap 3d printers, laser g , p p , cutters, Shapeways, personal fab technology, makerbot, etc. gy, , AutoDesk, EugeneCAD, ClothoCAD RepRap exponentially scalable matter compiler / /extruding 3D p g printer OSCON Data Portland, OR
- 22. Movie at: p // / http://www.molecularmovies.com/movi es/berry_apoptosis.html Apoptosis Maya Animation by Drew Berry OSCON Data Portland, OR
- 23. Biological simulators simulators NAMD and other molecular dynamics, etc. Mixed Quantum Mechanics/Molecular Mechanics (QM/MM/) (QM/MM/ ) Biological pathway/chemical reaction simulators/optimizers Many projects on gene network analysis, stochastic simulation, etc. h i i l i OSCON Data Portland, OR
- 24. Design of bio/chemical devices from (1) first principles and functional fi t i i l df ti l abstractions and (2) from data Data Bio/chem/phys first principles and functional abstractions OSCON DATA Portland, OR
- 25. How and where these data are used, used or made usable Randomized clinical trials Biomarker development, genomic tests in CLIA certified labs Licensing to other companies for marketing and development OSCON Data Portland, OR
- 26. Tools that are used to analyze these data R (!), BioConductor Biostatistics, Matlab Python Chi-square tests, permutation tests, Monte Carlo resampling Parametric statistics, nonparametric statistics, generative statistics Statistical learning theory, online learning theory OSCON Data Portland, OR
- 27. Approval of processes for cellular therapies/treatments FDA approval for process, not f lf t for drug/biologic/device progress on the development of a new experimental MCL treatment called immunotherapy, in which a patients own immune cells are collected from the bloodstream before ASCT, treated in the laboratory to have antitumor activity, and reintroduced into the body after ASCT. The goal of this immunotherapy is to reduce the likelihood of relapse after transplantation. A major challenge of immunotherapy is getting the transferred immune cells to persist in the body after the transfer. In preclinical studies, Dr. Jensen and his colleagues found ft th t f I li i l t di D J d hi ll f d that using a certain subset of immune cells called central memory T-cells in- creased the likelihood that the transferred T-cells will persist. Report from the Lymphoma Research Foundation, Spring 2010, Volume 8, Number 1 OSCON Data Portland, OR
- 28. Pink Army a biopharma co-op bi h You own your own cells, therapies based off your own cells should be yours in the co-op. If a biopharma company cures your disease, they lose a customer, who is cured. 2 weeks and $1000 in lab resources OSCON Data Portland OR
- 29. Cancer 5-year survival rates, US OSCON Data Portland, OR Division of Cancer Control and Population Sciences, 2008
- 30. Non-profit clinical research organizations ( (CROs) ) Randomized trials A melanoma trial with 1,000 patients 1 000 costs $60M in CRO expenses A 10,000 patient chronic obstructive 10 000 pulmonary disease (COPD) costs $240- $250M in CRO expenses OSCON Data Portland, OR
- 31. More medical foci of SynBio y Oncolytic viruses y RNAi for HER2 in breast cancer (also an iGEM team project) Designed, logic, and programmed Not comp tational devices b t use logic computational de ices but se and/or procedures OSCON Data Portland OR
- 32. Using data to engineer therapies or cures for genetic diseases IF ( RNA AND RNA AND RNA AND RNA AND RNA ) THEN RELEASE PROTEIN INITIATING APOPTOSIS IN THE TUMOR CELL OSCON Data Portland OR
- 33. More biological nanobots T t h d l robots, made from biological or organic Tetrahedral b t d f bi l i l i substrate: 12Tet Tetrahedral Rover Robot http://www.youtube.com/watch?v txZMLS7YD6Q http://www.youtube.com/watch?v=txZMLS7YD6Q OSCON Data Portland, OR
- 34. More biological nanobots, 2 DNA O i Origami i OSCON Data Portland, OR
- 35. Energy, biofules Energy biofules, and bioreactors The oil multinational, despised by green activists for its support of , p yg f pp f scientists skeptical of climate change, plans to invest $600 million (贈370 million) in a joint venture with Mr Venters company, Synthetic Genomics. The thinking is that algae is a more efficient source of fuel than conventional biofuels, such as ethanol made from corn or sugar cane and biodiesel made from wheat or palm oil. Algae can be processed into fuels similar to petrol and diesel and it consumes carbon dioxide as it grows. According to Exxon, the yield of biofuel from algae is 2,000 gallons per A di E h i ld f bi f l f l i 2 000 ll acre, more than three times that of biodiesel from palm oil and eight times the ethanol yield from corn. It is also believed to have the edge over other biofuels because of its suitability for use as a jet fuel. The real challenge to fuel The creating a viable, next-generation biofuel is the ability to produce it in large volumes, Mr Venter said. via http://www.timesonline.co.uk/tol/news/environment/article6710846.ece OSCON Data Portland OR
- 36. Biological light sources E.glowli: a bioluminescent future U Cambridge, iGEM 2010 team OSCON Data Portland, OR
- 37. Biological memory CUHK, iGEM 2010 team OSCON Data Portland OR
- 38. OSCON Data Portland, OR
- 39. Microbiome Engineering Use the microbiome to produce therapies for existing diseases in controlled, continuous ways: insulin for diabetics, interleukin 10 for Crohns disease, etc. Highly competitive environment: microbe needs orthogonal edge to survive g g OSCON Data Portland, OR
- 40. And so forth and biology PolySilicon and biology SynBio in chemicals industry cleaning cleaning, refinement, scalability, sensors, etc. OSCON Data Portland, OR
- 41. Conclusions Wide ranging implications to existing problems in health, engineering, energy, manufacture P ti l l for human healthcare, genomic research Particularly f h h lth i h on diseases, data-aided design and testing New manufacture processes for new biologically- biologically designed constructs http://www.linkedin.com/in/russellhanson http://twitter.com/russell_hanson http://www.russellhanson.com/ http://www russellhanson com/ OSCON Data Portland OR