IGEM:UIUC/Software/2010/2010/03/10

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(Autocreate 2010/03/10 Entry for IGEM:UIUC/Software/2010)
Current revision (18:35, 29 May 2010) (view source)
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==Entry title==
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==March 10, 2010==
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===First Entry===
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* Information about Dijkstras -- searches network to get from one network to another
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<br/>
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* Many metabolic pathways
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** FBA - flux balance analysis
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** COBRA - (matlab) -- links things
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** KEGG - pathway maths
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** Environmental strains? - secondary enzymes
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** Crossing over pathways -- KEGG map -- galactose metabolism pathway -- enzymes, collecting compounds - group the enzymes to compounds
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*** Things can cross over and can be done in a different way
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*** They highlighted (competing people) -- intermediate pathways
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** Metabolic
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* Continue code -  pathway - nodes = products , lines = reactions (IMP)
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** Fewest constraints -- tried
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** Problems -- compounds are isolated -- some only connected in one way
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** Shortest path algorithm -- defined edge of dot product numbers we know and numbers we give it -- weights you define and facts (number of things)  = a number == length of the edge  (bad facts) --
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** Number of connectivity -- about 100 -- how many different compounds is each connected too -- each on its own scale -- dot matrices don't line up .. [0  1] . [~1  100]
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<br/>
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** How pathway effects cell (host)
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*** Host = hypothetical host
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* '''TO BE IMPRESSIVE AT IGEM'''
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** Gotta be impressive! -- tweak  a lot
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** Add massive new feature -- say how pathway would effect overall system
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** Many metabolic -- gotta really do something with it
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* Biobrick -
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** Freiburg
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* Look at previous iGEM -- iGEM website  -- Francis does this
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** Do use biobricks in some way
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* Google group -- check
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* Completely Different:
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** Working with the wetlab -
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*** model their current project?
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**** Cellular logic design - takes substance and fluoresces colors depending on two different things - working toward cellular computation -- (0s and 1s) -- more analog -- end goal: computation of things within a cell -- direct diseases
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***** Don't fluoresce, next step: release -- outputs and inputs produce things -- and, or gates
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***** Designer tool -- EC majors -- lay out-- coverts to biobricks
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***** See IBE person
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** Analyzing wetlab team -- give them a helping hand -- make smoother process
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*** Different interference sequence in wire diagram -- and: promoter promotes certain region which upreglates something else which gives you a specfic fluorescence
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**** Do a small model -- help our team by simulating
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**** OR as just a side project
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<br/>
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* Must come up with a way to keep track of all journals read -- for citing.
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'''Homework''' - look at all the old projects (software projects) -- and look up biobricks - go onto iGEM websites and check the schedule post -- color coated by category. Go through judging requirements
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** Modeling, safety, biobricks -- force your really cool idea into iGEM judging
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** Split up stuff to collect research -- Anna -- metabolic pathways,
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** Look up research from previous years
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[[category:OWWLabNotebookV1]]
[[category:OWWLabNotebookV1]]

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