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Sequence data

Life Sciences Knowledge. Sequence data. Proteins. Non-protein. Enzymes. Non-enzymatic. Structural. Regulatory. Predictions (pathways, regulatory network….etc) Generating Hypothesis. Testing Hypothesis -- Generating new knowledge. Life Sciences Knowledge. Sequence data. Proteins.

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Sequence data

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  1. Life Sciences Knowledge Sequence data Proteins Non-protein Enzymes Non-enzymatic Structural Regulatory Predictions (pathways, regulatory network….etc) Generating Hypothesis Testing Hypothesis -- Generating new knowledge

  2. Life Sciences Knowledge Sequence data Proteins Non-protein Enzymes Non-enzymatic Structural Regulatory Cell Biology Virology Molecular Biology Anatomy Microbiology Biochemistry Predictions (pathways, regulatory network….etc) Generating Hypothesis Neuroscience Anthropology Physiology Genetics Botany Zoology Testing Hypothesis -- Generating new knowledge

  3. Life Sciences Knowledge Cell Biology Virology Ecology Anatomy Molecular Biology Biochemistry Anthropology Microbiology Predictions (Functional, pathways, regulatory network) Generating Hypothesis Genetics Neuroscience Physiology Botany Biotechnology Zoology Testing Hypothesis -- Generating new knowledge

  4. Generating an Indexed Gene library of “predicted” proteins in Bacteria with Established Genetic System Sequence Data Orphan Genes Unknowns/Hypotheticals Predicted functional ORF Bioinformatics Pipeline: BLAST(S), GO, COG, SCOPE, PSORT, TMHMM … Developing Testable Hypothesis No Results • Clonning • Expression • Deletion • Clone into E. coli • Expression Protein isolation Protein Crystallization

  5. Generating an Indexed Gene library of “predicted” proteins in Bacteria with Established Genetic System Orphan Genes Unknowns/Hypotheticals Predicted functional ORF BLASTP/y COG No Results Developing Testable Hypothesis KEGG GO PSORT PROSPECT • Clonning • Expression • Deletion • Clonning • Expression Protein isolation Protein Crystallization

  6. Preliminary Flowchart for Functional Genomics ORF Bioinformatics pipeline Are there biological predictions? Yes No Is the gene lethal ? • PCR • Clone in E. coli. Yes Generate Hypothesis Store Data Are there orthologesin genetically-established bacterium? No No Yes • Express • Purify • Crystallize Other tests? Generate Deletion mutation

  7. Dynamics of system biology’s family Student / Professor Generating Hypothesis Student / Professor / Postdocs and research scientists Experimental approach Student / Professor(s) / Postdocs and research scientists / Technicians

  8. Student / Professor(s) / Postdocs and research scientists / Technicians Student / Professor / Postdocs and research scientists Student / Professor

  9. Dynamics of system biology’s family

  10. Nature (vol. 444, p. 985)

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