November 2016
*******************

Wed Nov 9
*************
aaa,zli, ran

SW:  nov 18 all will get updated to opensuse leap stable 42.2
	will do by just updating
	checks:  vbox, movies, VMD/cuda, should all work

APACHE not running on ade
nvidia-smi and nvidia-settings to monitor/control fan speeds

HW:

Science

TODO's
AAA; please send list of HW/quotes to Bisop again we need to act on these before the break s.t. can do them dring break
RSU: will start the M-nuca-177/1kx5 sims on queenbee.. use 
	/home/tmbshare/bin/quenamd-qb.tcsh*  and  /home/tmbshare/bin/runnamd-qb.tcsh* as templates
	
	needs to make progress on ibiomes on ade

ZLI:  python version ICm runs and gives correct energies and can handle tet/oct/hex...
	recommended that ZLI do following
	a) benchmark ICM++ vs. ICM.py and see if easy to run ICM.py from within VMD .. these effect direction forward
	b) update ICM-GB to use ICM.py  (or run ICM-GB from w/in VMD if can easily be done)
	c) add the LAMMPs minimizer to the ICM.py/GB interace
	a-c will be sufficient for poublictiaon for the Biopyhysical meeting in Feb	
	
ALL:  todo:
	see about running a hub w/in a virtual environment
	and spend time learning how to make a hub run/work

November 16
***********
Zilong and Ran

TODO
	AAA's updates
	funding and TA
	trip to CA
		funding 
		poster

SimS:
	Ran/BGR and QB2	
	ER-ERE Sims from Randy

Break Plans
	Thurs Nove 17: grading
		make ER-ERE sims for Ran
	Friday nove 18: computer,sims and prep
	MTW: chromatin meeting in Sport/ class prep
		M cc meeting Li would need ridadfkajssdf
	Th Thanksgiving
	Friday
	M-W: get rredy again 

TODO: check w/ gergana and others about S'port on Monday
Thursday and friay are work days
TA: 
	ENGR492 conflicts w/ Math415/CSC470 conflicts



Nov  30 
*******************
AAA, ZLI, RSU,... BGR???

DONE:  send Ran class info


Business:
0) TcB: 
	SHI poster and web
	firefox
	http://dna.engr.latech.edu/~zli007/ICM-GB/ICM-GB/icmgb-dna.html

	support for RSU and ZLI 
	RSU(CIMM) and ZLI( supported )`

1) AAA:  report on HW and other
	all workstations updated to 42.2
	one error: filesystem package

	alt F1 -console not graphics	
	zypper update
	reboot -> goes into console mode b/c not nvidia drivers
	reinstall nvidia  
	/autotmb/home/aaa029/Downloads/NVIDIA-Linux-x86_64-367.44.run
	reboot once more and all is good

	cuda not fully working (no VMD)
	matlab works on all but TMB5d
	vlc and youtube work

TODO: make hangout, CUDA, audio-on-ade, stereo on ADE need to work 
	quotes for stuff
	data,data, AND SPACE
	web running on  ade

2) Ran Sun
overview/summary of IBIOMES application and IBIOME-descrption papers.
overview of Panchenko's trajectory publication paper
outline of Ran's Papers on IBIOMES data base of Nucleosome Sims:
    TABLE of SIMS
    How they are all arranged
    methods used
    RMSD in cc results
    MAX/min/avg/simple stats of DNA helical parameters
    Global Sequence alignment
TIMELINE for Getting it DONE
Outlne of BPS poster

3) ZIlong LI
    plans for the BPS

TIMELINE of todos btweeen now and BPS meeting
  
Outline of BPS poster
outline of ICM++ manuscript based on Model off of ICM by Stolz
    new features:
        chromatin model...  see  antony's RICE manuscript (ask anthony
for this)
        diff. types of nucleosomes
        integration w/ Dalliance 
        timing results?