September 2017
*******************

ANNOUNCE:
	physics party tomorrow at 4pm

HW:
	GUA up (required rewritting boot sector but Raid5 is out)
	printers: ADE only
	sound: works on ADE but very quiet
	AV on ade and tmb5 work tmb4 and others not checked


RSU: 
	fixing ibiomes to include href for 
	yeast/nfr being checked
	checking ibiomes-publish -depth option
			

TODO:
	check w/ Julien and see if ibiomes works now
	install kyocera printers on TMB4,TMB4,cyt and tmb1
	remove boxes from lab... dump in BIomed garbage
	configure sound
	configure skype 
	configure google hangout

	

TODO: 
	zli pick up HDs from ifm
	printers: 
	cabling of main table


*********************
Thursday Sept 14
**********8
-stnd group meeting time Thursdays 9a-10a

NOTE: 
	gua: doing backup of rna:/simulations 
	things may be slow for next 2-3 days

	ade: /raid5 is full
		cannot remove /raid5/scratch THIS IS ONLY COPY OF SOME TRAJECTORY DATA and has bout 9TB
			not enough room on  RNA for all of this...
		cannot remove /raid5/ibiomes... but can it be cleaned? ZLI says no... it's clean
		could move /raid5/home somewhere else... 
	rna: has 7TB on it... 

	SOME THOUGHTS on how to restructure:
		replace HDs on DNA w/ bigger ones or get one biggerr for tmb4/tmb5 whatever
	
TcB:
	zli and rsu have appointments confirmed
		zli@COES/wick and rsu@CIMM/ramu
	Biomed Industry Day abstracts due tomorrow:  Meeting Friday Oct 20
		registration and attendance is free
		http://shvcardiovascularc.wixsite.com/id2017 
	today is physics seminar
	other upcoming events
	Bishop:
	Enhancement for LABoR due in NOvember... HPC group @ Tech => C^3 sumeet's name
	NIH Oct 5 R01...
	NSF/NIH? proposal November...? Tamar over the summer to October 5
	NSF LoI Sept. 24 ..?

ZLI:
	status of web and paper?
	/autotmb/home/tmbshare/Public/Papers/2017/ICM-GB/ICM-GB.v22.odt
	and images-v16.odp
	
	
RSU:	status of ibiomes and paper?
	ibiomes git-hub ..
	  modify the src s.t. data is not copy but a link to the sim directory 
		and modify xml to include a href to ../data for each item
	PROBLEM is getting mvn to work for ibiomes w/ our own updated version of ibiomes-lite


Thursday 9/21/
***************************
HW/SW: 
	Java/JDK 1.7 vsd 1.8... was 1.7 only for ibiomes
	
GUA: backups .. working... 
	gua: /dev/md127       22T   12T   11T  53% /raid5
		??? RNA~70TB (incld full trajecoctyry so maybe 7Tb w/out water + other stuff = 12T?)

	ade: /dev/md127       20T   19T  140G 100% /raid5
		what's here?	
		8TB of ibiomes 
		9TB of simulation 
		2TB of  home backup
ade:/raid5/scratch # du -chs *
1.6T    601-177
*3.0G    601anneal-wt
2.7T    601-nt
3.0T    601-wt
*181M    AMDruns
1.7T    MMTV-NucA-177
8.9T    total


TcB: 
	S'port Industry Day abstracts? 
		I received no notice
	the BPS poster left in France?

	tonight there is an IEEE_cluter meeting at Latech

	NOTE: removed dvd files from  rna:/simulations/dna/home/rmukhe1/floer-sims-Na

RSU: ibiomes and julien
	you can take code form ~thiabualt (see his ibiomes)
	Jmol w/ multtiple snapshots

	PoS: plan ofd study

ZLI:
	tamar schlick and biophkysicsl journal section on chromatin biology
	status paper;
		section on molec. viz in web interface 
			OLD: imd w/ vmd and rosette antibody/proteinfolding w/ Folding@home and modeller
			in between are Gateways for MD NWchem, and several other..(joyhuun kim @lsu/cct)
			MORE recent: charmm-gui and amber pytraj and even barcelona's SC tools
	see work w/ Amber in python pytraj and ngl for online/real time MD
	http://ambermd.org/tutorials/analysis/#pytraj
	find the original papers on Amber, pytraj and ngl

	http://www.charmm-gui.org/  also see the original apaper on this
	een VMD for long has done interactive molecular dynamics w/ imd.

	rosette antibody.. structure prediction.

	history:ref: imd w/ vmd, rosette server/modeller for protein folding, NWchem gateways, amber pytrj and charmm-gui
	and BSC's online trajc analysis
	ref/review: Schlicks' and  Korole'v f.f. for chromatin modeling
	refs/review of molec. browswers (ngl, etc..) from Toms proposal
	refs/review of genome browswer (dalliance, jbrowse, ucsc) 	
	COMBINE them for chrxomatin modeling and/or all atom modeling



Group Meeting 9/28
*******************
HW Status:
	GUA: doing backups... but they are not changing
	ADE: 140G free?  not enough for ibiomes and not changes since last time
	skype:?
	cabling?

RSU: PoS?
	TIMES IN LAB?
	Paper: no figures not changes, no data..
	ADE and ibiomes?
	CHANGES SINCE LAST MEETING?
		paper?
		web? pdb works using old ibiomes version
			julien's 

ZLI:
	Paper:  last mod 9/20?
	CHANGES SINCE LAST MEETING?
		paper? 9/20
		web?: now does clusters of DNA molecs
TODO: 
	fill in group calendar and double check
	send email w/ plan for rest of 1/4
		include a) industry day
			b) meetings and adbstracts (BPS? ACS?)
			c) papers and timeline for them
			d) other lab responsibilities