January 2016

Group Meeting 1/08/2016
**********************
3:30: anthony and dilip
ran and anik excused

TODO: 
	bishop double check  to make sure denis is on emails

HW: tmb3 still dead
  /home/ still way full/overfull 4.8 TB left 94% full  
	trajectory decision for achiving
SW: anthony will do updates on all 

Hub: 
	138.47.29.74 enter in local /etc/hosts of DNA as 
		tmbhub.coes.latech.edu
	running w/ debian (wheezy 7.9) and hubzero2.0
	TODOs:
	document HOWTO:	 
	 /home/tmbshare/docman/Hub-HowTo
		install and config of the OS
		install and config of the hub
		
		make the above at very simple formatted html READmE like documents
	
		development plan?
			?rwhat triggeers a reinstall and how much time for that
			?hardware? dvd vs cd vs old opeteron boxes	

SOS: bishop will be doing a SOS talk in S'port and need the Little Fe	

1/15/2016
**********************
HW: rna still out of space 
	backups need to be checked on gua and ade
	tmb3 getting restored (???) by anthony maybe

SW: 
tmb1 115% vlc 16-yeast-positions.mpg 
VLC media player 2.2.1 Terry Pratchett (Weatherwax) (revision 2.2.1-0-ga425c42)
[0000000001a73eb8] core demux error: corrupt module: /usr/lib64/vlc/plugins/access/libdvdnav_plugin.so
[00000000019a00b8] core libvlc: Running vlc with the default interface. Use 'cvlc' to use vlc without interface.
[00007f8600000e88] core demux error: corrupt module: /usr/lib64/vlc/plugins/access/libdvdnav_plugin.so
setNativeLocks failed: Resource temporarily unavailable
[00007f8600c03cd8] avcodec decoder: Using NVIDIA VDPAU Driver Shared Library  340.96  Sun Nov  8 22:09:55 PST 2015 for hardware decoding.
[00007f8600c15ab8] core demux error: corrupt module: /usr/lib64/vlc/plugins/access/libdvdnav_plugin.so
setNativeLocks failed: Resource temporarily unavailable
[00007f8600c03f48] avcodec decoder: Using NVIDIA VDPAU Driver Shared Library  340.96  Sun Nov  8 22:09:55 PST 2015 for hardware decoding.
[00007f8600c02dd8] core demux error: corrupt module: /usr/lib64/vlc/plugins/access/libdvdnav_plugin.so

but the image still looks good!

JabRef works and now so does jabref 

Science
*********
Hub: /home/tmbshare/docman/HubHowTo/
	is still empty.. anthony has volunteered to do this.
	still no notes form dilip on hub install
	status report from dilip 	
	apparently no "history" dump exits for install command but rather handnotes
	check w/ dilip

RAN: 
	dsdna ; has issues 
		send "instruction set" to group
		and put it in the svn repo
	pyton modules being updated  
		s.t. run anywhere
	  look at the ibiomes PAPERS 
		see tom cheatham's website and or pubmed or the google ibiomes provides the refs
	
Anik: models w/ nucA

	
	
	

1/22/16
************
RAN: organize a short lit. review of nucleosome dynamics
	JBSD paper reviewed by bishop
	NAR paper under review by bishop
	earlier review for BJ by bishop
	review the manuscript by Suma and Bishop that's in works still

Anik: reports on running dsdna using ran's instructions
	bishop confirms
	
	make and review nucA models

AAA: post open suse install notes	
	look for a site on bishop's web
	http://dna.engr.latech.edu/~aaa029/Guide%20for%20PXE%20Boot%20by%20Anthony%20Agee.html
	forward this littlefe folks listserve

DISCUSSION: 
	necessary and sufficient set of analysis for nucleosomes

	how to make namd run an arbitrary TCL/shell script in background

	


	
1/29/16
*********
discuss a benchmarks for bluewaters
	3DNA, vmd, 

hub:
	progress on hiub configuration
		openldap
		rappture
		pegasus
		submit
	configuration of hub menus  
	fqdn from danny configured
	update the howto/docman in tmbshare