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2012 Spring Break by Mind Map: 2012 Spring Break
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2012 Spring Break

Shotgun DNA Maping

Things to do

Tons of Richard Suggestions (OWW / Private wiki), Biggest thing is to make simulated data from random (or special) sequences and see how well SDM works. Probably like 4 more graphs

Kinesin Modeling Paper

LANL Proposal (Steve)

Image analysis growth rate

Modify Haiqing software

Image analysis Europe

Probably not do-able this week

Exactly synergistic with UC-Santa Cruz (Saxton)

Images are better (fly egg cytoplasm)

Tenure benefits

Accepted paper (can't see a route to this this week)

Submitted revisions

Kinesin modeling paper, Requires lots of reading, Not too much programming, but re-running simulations, making graphs, Middle author for Anthony

Submitted first drafts

Andy Isotope Paper, A bit of work for Steve

SDM, Requires some more programming, If lots of new programming and graphs (maybe some of our data), then first author for Anthony), New node

Crumley, Notebook / Figshare


Find Richard's SDM comments

Make list of figures/experiments to make

Find code for Haiqing

Get code running

Find Larry / Anthony SDM code

Get code running


Continue with Richard comments

Collaborate on SDM software

Find important sequences, These are probably in Anthony OWW notebook, Once found, SJK put into github repository as sensible text files (best way I can see to do it quickly)

SJK: Contemplate switching languages

This is probably not a good idea. The advantage is using fully-open-source (such as R). The disadvantage, of course, is it would take extra time. Must...resist...urge


After lunch, Find "old" simulation of pCP681 or pBR322, make sure "new" simulation provides same numbers, Add sequences and "development distribution" and EXE file to same directory; start github project(s)


find yeast genome, download, note location and details

find alternative sequences for hiding in yeast genomic data, human, fungi similar to yeast, drosophila, koch repetitive unzipping data, other plasmids, puc19, pbluescript, pals, lambda dna, e coli

finish experiments mindmap, read original paper



Find or create XhoI finding software

Get "automatic" simulator working

Find / get match scoring stuff working


Find yeast genome, Worth checking Larry's notebook private wiki to see if you can see where he got it, His notebook on private wiki has "all pages" view, But there may be a better source

Questions for Thursday

Will we have to rerun the simulation for the yeast genomic library?

If not where is data so I can throw up on FigShare

If so how long will this take? Can we make it faster? Is it worth it to make it faster?

XhoI software

Can we use other genomes on the XhoI software?, I'd like to at least do the other yeast species and simulate some random fragments to try and match., And also lambda DNA, and pALS

How long will it take to simulate gaussian noise (by this I mean to run the software)? Can we just do something simple like 1pN, 5pN, and 10pN of noise? Or maybe, 1, 2, 3?

I guess we want some probability that each data point will be adjusted and there is some spread of noise that each point can be adjusted up to the max value?, Does this make sense?

What about thermal noise? ie some factor of kT?

Is there anything better than just adding like 1pN noise?

Do we need to do anything to the matching algorithm?