April 2015
*************
Anthony:
	setup ssh keys for self and use to monitor 
		disk
		iperf
		uptimes
		put these in /home/tmbshare/admin/hw-status/
	start to manage /home/tmbshare/public_html
		00contact needs updating
		and other files needs students moved around 
		add anik, ran and sandeep
	update tmblab calendar w/ your info
	contact James aboua april 15 High School demo (jli01???@latech.edu)

Anik/Ran:
	must put times in tmblab calendar 
	update ~tmbshare/public_html data in contacts and your personal web pageetc..
	will not attend lasigma technical april 20
	review 1kx5/2cv5 molecs:
		what's wrong w/ 1kx5/frog...
		any other problems

	
Sandeep	
	safty training
	group getting started manual
	set up svn (see me or rtfm)  /home/tmbshare/svn
	fill in tmblab calendar
	

Bishop:
DONE	set "lab" link for dna.engr.latech in ~wwwrun/htdocs/index.html to point to tmbshare not bishop	
	check eclipse
	check svn for ICM++

	

April 14
***********
EandS day april 15 see /autotmb/home/bishop/public_html/LASIGMA2015/EandS-at-Tech
	CTH rm 156 (basement south side)
	9-12 
		

April 21-29
***************
50ns completed for 1kx5/2cv5 (hu,mo,fr) on loni
and transferred to RNA: /simulations/mononucs/[1kx5,2cv5]
 TODO: 
	a) strip water (not ions) : see ~bishop/bin/stripwat.vmd or nowat.vmd
	b) rms analysis of histones and DNA in each
		dcd2rmsd.vmd should do this but what to fit is question
		SHOULD IDENTIFY HISTONE CORE SEQUENCE AND USE THIS
	c) calc DNA helical params 
		dcd2par.vmd or dcd2pardat.dcd should extract
		50,000 helix parm values from the trajectory
	d) hbonding for the amino acids that distinguish frog,mouse,human
	e) radial distributions for Cl-Cl, K-K, Cl-K as well as
		Cl-DNA and K-DNA and Cl-protein K-protein
TODO: 
	start multiple replica runs of 1kx5/2cv5 
	but which system?  see email on this
TODO: anik and ran got accepted for blue waters internship progam
	NEED to have them put together proposal for bluewaters time
	based on bishop'/s LONI propposal
	figures needed:  
		1) rscb "map" of histones for 1kx5,2cv5 (ran is doing this)
		2) above will also include diff btwn frog,mouse, human
		3) Graphic showing how generated FR,MO, HUM from 1kx5,2cv5
	OTHER:
	PLAN for the BWIP proposal:
		threading 12A12 (subset of 54A54) onto 
		HUMAN (1kx5) ... anik  21runs of 100=500ns = 2100-10500ns
		MOUSE (1kx5) ... ran   21 runs of 100-500ns =2100-10500ns
		expect each run to be ~200CORE 
		can bundle 21*200 = 4200 core /run and expect 
			2-3hrs run/ns -> means 500ns will take > 200hrs
			or about 10 days of 4200core runnign 24*7

		cost  100ns *21runs * 200core * 3 hrs = 1,260,000SU
		times 2x = 2,500,000 SU for both of these studies
		assuming 100ns  is enough for each system