December 2014 Group Meeting
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DECEMBER  5
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1) pick a regular lab meeint time

	a) coarse-grained folks   Friday: 1:00
		cam
		priya
		gaynadeep

	
	b) MD folks  : 
		anik
		ahmed
		ran
	
	c) data/workflow folks
		pardhu
	
	d) systems stuff
		anthony


2) Goals:
	need to organize goals and objectives both as teams and individuals
	I would like to use google drive for this so please assist

	google-groups as well



3) TODO
	Dec 7: sunday ... loni proposal for time allocatoins are due
	LATER: NSF and NIH proposals


4) HW and SW
	tmb4 had IP conflict w/ another machine it's solved
	RNA had a HD die/rebuild I think it's solved.
	pay attention to RNA when you walk by the machine room
		if it's beeping definitely let me know
		if it's flasing that means RNA is checking itself
	
	SW all upated to Opensuse 13.2 
		dig around in 
		http://software.opensuse.org/find
		or download.opensuse.org
	and look for things you might like

	kdevelop is KDE version eclipse
	eclipse still missing on most all machines
	others?

	tmb4 not working

	svn
	

	LITTLESUE

PRINTER configurations

	


	
December 9 MD GROUP MEETING
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1) solve the data/file management problem
2) TODO this by Dec 16:
	a) login/setup LONI account on QB2
		note all files on other system removed may be able to copy some
	
		 using loni_start_2014
			aka029 and sstewart are members /

		set up secure shell keys s.t. login w/out password.. .see vsp004's web page in the group
	b) setup /download the proper version namd executable
	c) run benchmarks using  the files found in /autotmb/simulations/bench2.9/stampede-2014/sin-bench.tar.z
	BUT USE THE NAMD CONFIG FILE /simulations/bench2.9/bench.conf
	NOT THE ONE IN THE sin-bench.tar.z file
		should run w/ similar processor count as in  Bishop's proposal see
		/home/tmbshare/Proposals/2014/Bishop-LONI-NucA-MTV.pdf

	d) setup your own nucleosome simulation using the sequence from MMTV or HMTV assigned to you.
		EXTEND THE SEQUENCE +/- 10 BP s.t. the total sequence is 167bp long
		CHECK with bishop once you have this system setup
		THIS IS NOT EASY! but see the tools in 
		/autotmb/simulations/Example/utils/01-make-any.tcsh.org
		AND look at  http://ambermd.org/tutorials/